Daily Papers

Automatic operator design (AOD) has increasingly adopted large language models (LLMs) to generate problem-specific search and variation operators for multi-objective combinatorial optimization (MOCO). Yet most methods evolve the operators while leaving the process that discovers them fixed. This limits adaptation as new Pareto trade-offs and operator interactions change where and how the search should proceed. We introduce HEMO, which makes the AOD harness itself a self-evolving optimization target. HEMO maintains a persistent harness state and updates one module at a time, revising the logic that determines which experience to retrieve, which operators to improve, which parents to select, and how to formulate the orchestration of search steps. Downstream solution quality and runtime guide these updates, while a discounted UCB scheduler directs adaptation toward promising modules as their utility changes. A persistent memory filesystem preserves candidate outcomes and diagnostic feedback across harness states, enabling successive states to build on accumulated optimization experience. Experiments across eight MOCO tasks and two structurally distinct evolutionary backbones demonstrate strong performance against conventional evolutionary, neural, and LLM-based AOD baselines, together with effective transfer to related tasks. HEMO extends automatic operator design beyond evolving individual operators to improving the search process that discovers them.

Large Language Models (LLMs) have made significant progress in handling complex programming tasks. However, current methods rely on manual model selection and fixed workflows, which limit their ability to adapt to changing task complexities. To address this, we propose SEMAG, a Self-Evolutionary Multi-Agent code Generation framework that mimics human coding practices. It decomposes programming tasks into stages, including planning, coding, debugging, and discussion, while adapting workflows to task difficulty. Its self-evolutionary agents can access the latest models in real time and automatically upgrade the backbone model. SEMAG sets new state-of-the-art Pass@1 accuracy across benchmarks. Using identical backbone models, SEMAG outperforms prior methods by 3.3% on CodeContests. When augmented with self-evolutionary model selection that automatically identifies optimal backbones, SEMAG reaches 52.6%, showcasing both framework effectiveness and adaptability to evolving LLM capabilities.

Since late 2022, Large Language Models (LLMs) have become very prominent with LLMs like ChatGPT and Bard receiving millions of users. Hundreds of new LLMs are announced each week, many of which are deposited to Hugging Face, a repository of machine learning models and datasets. To date, nearly 16,000 Text Generation models have been uploaded to the site. Given the huge influx of LLMs, it is of interest to know which LLM backbones, settings, training methods, and families are popular or trending. However, there is no comprehensive index of LLMs available. We take advantage of the relatively systematic nomenclature of Hugging Face LLMs to perform hierarchical clustering and identify communities amongst LLMs using n-grams and term frequency-inverse document frequency. Our methods successfully identify families of LLMs and accurately cluster LLMs into meaningful subgroups. We present a public web application to navigate and explore Constellation, our atlas of 15,821 LLMs. Constellation rapidly generates a variety of visualizations, namely dendrograms, graphs, word clouds, and scatter plots. Constellation is available at the following link: https://constellation.sites.stanford.edu/.

Automated heuristic design (AHD) with large language models (LLMs) has produced strong heuristics for combinatorial optimization problems (COPs). Yet existing frameworks optimize for average performance on a small fixed dataset and steer the search with "verbal gradients" distilled from scalar better/worse feedback. No single heuristic dominates across instance distributions, and scalar feedback tells the LLM whether a heuristic improved, but not where in the instance space or why. We propose MOSAIC, a grid-based framework that adversarially co-evolves problem instances and specialist heuristics inside a Quality-Diversity (QD) archive indexed by structural instance features. Instances evolve to expose weaknesses of the current heuristics, and heuristics evolve to eliminate them by specializing to the newly exposed regions. Each archive cell keeps a specialist heuristic, representative instances, and insights explaining what works in its region, forming a persistent memory that accumulates over the evolutionary search. For each heuristic pair sampled from distant grid regions, an LLM-guided evolutionary loop generates discriminative instances, and a decision tree identifies the feature-space regions where each heuristic wins. A reflection LLM then contrasts the two heuristics to produce multi-directional insights that persist in those regions and guide crossover and mutation. The archive is simultaneously a co-evolved benchmark of discriminative instances and a pool of region specialist heuristics, from which greedy selection extracts a compact complementary portfolio. Across COPs, test sizes, and LLM backbones, the portfolio consistently outperforms state-of-the-art LLM-based AHD methods, and the co-evolved instances attain higher feature-space coverage and stronger heuristic discrimination than evolutionary instance-generation baselines.

Advances in self-supervised learning (SSL) for machine vision have improved representation robustness and model performance, giving rise to pre-trained backbones like ResNet and ViT models tuned with SSL methods such as SimCLR. Due to the computational and data demands of pre-training, the utilization of such backbones becomes a strenuous necessity. However, employing these backbones may inherit vulnerabilities to adversarial attacks. While adversarial robustness has been studied under white-box and black-box settings, the robustness of models tuned on pre-trained backbones remains largely unexplored. Additionally, the role of tuning meta-information in mitigating exploitation risks is unclear. This work systematically evaluates the adversarial robustness of such models across 20,000 combinations of tuning meta-information, including fine-tuning techniques, backbone families, datasets, and attack types. We propose using proxy models to transfer attacks, simulating varying levels of target knowledge by fine-tuning these proxies with diverse configurations. Our findings reveal that proxy-based attacks approach the effectiveness of white-box methods, even with minimal tuning knowledge. We also introduce a naive "backbone attack," leveraging only the backbone to generate adversarial samples, which outperforms black-box attacks and rivals white-box methods, highlighting critical risks in model-sharing practices. Finally, our ablations reveal how increasing tuning meta-information impacts attack transferability, measuring each meta-information combination.

Visual backbones have evolved from Convolutional Neural Networks (CNNs) with local aggregation to Vision Transformers (ViTs) with global interactions, State-Space Models (SSMs) with input-dependent state transitions, and Test-Time Training (TTT) layers that adapt an inner learner while processing an image. Across this progression, visual computation has become increasingly adaptive to each input, yet the rules governing that adaptation remain largely prescribed by the trained backbone. We introduce VisionHOPE, the first generic visual backbone formulated as a self-modifying learning system, in which what the model remembers and how it learns co-evolve within an image. Building on the self-referential construction of Nested Learning (NL), VisionHOPE realizes this co-evolution through five coupled memories that store content, generate key and value representations, and govern learning rate and retention. These memories evolve jointly as visual context accumulates along each scan. However, directly applying the unconstrained self-referential update to a visual backbone leads to instability. We therefore derive a stability-matched step-size control scheme that combines a soft cap on self-referential injection with a spectral clamp on the retained memory transition, and prove that the resulting memory dynamics are non-expansive along each scan. For two-dimensional feature maps, we adapt NL's chunk formulation by aligning chunks with image rows and columns across four directional scans. The proposed VisionHOPE achieves competitive results on ImageNet-1K, COCO, and ADE20K, establishing self-modifying learning systems as a practical foundation for general-purpose visual backbones. The code is available at https://github.com/PSRben/VisionHOPE.

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

Modern machine learning is still largely organized around a single recipe: choose a parameterized model family and optimize its weights. Although highly successful, this paradigm is too narrow for many structured prediction problems, where the main bottleneck is not parameter fitting but discovering what should be computed from the data. Success often depends on identifying the right transformations, statistics, invariances, interaction structures, temporal summaries, gates, or nonlinear compositions, especially when objectives are non-differentiable, evaluation is cross-validation-based, interpretability matters, or continual adaptation is required. We present EvoForest, a hybrid neuro-symbolic system for end-to-end open-ended evolution of computation. Rather than merely generating features, EvoForest jointly evolves reusable computational structure, callable function families, and trainable low-dimensional continuous components inside a shared directed acyclic graph. Intermediate nodes store alternative implementations, callable nodes encode reusable transformation families such as projections, gates, and activations, output nodes define candidate predictive computations, and persistent global parameters can be refined by gradient descent. For each graph configuration, EvoForest evaluates the discovered computation and uses a lightweight Ridge-based readout to score the resulting representation against a non-differentiable cross-validation target. The evaluator also produces structured feedback that guides future LLM-driven mutations. In the 2025 ADIA Lab Structural Break Challenge, EvoForest reached 94.13% ROC-AUC after 600 evolution steps, exceeding the publicly reported winning score of 90.14% under the same evaluation protocol.

Neural network based computer vision systems are typically built on a backbone, a pretrained or randomly initialized feature extractor. Several years ago, the default option was an ImageNet-trained convolutional neural network. However, the recent past has seen the emergence of countless backbones pretrained using various algorithms and datasets. While this abundance of choice has led to performance increases for a range of systems, it is difficult for practitioners to make informed decisions about which backbone to choose. Battle of the Backbones (BoB) makes this choice easier by benchmarking a diverse suite of pretrained models, including vision-language models, those trained via self-supervised learning, and the Stable Diffusion backbone, across a diverse set of computer vision tasks ranging from classification to object detection to OOD generalization and more. Furthermore, BoB sheds light on promising directions for the research community to advance computer vision by illuminating strengths and weakness of existing approaches through a comprehensive analysis conducted on more than 1500 training runs. While vision transformers (ViTs) and self-supervised learning (SSL) are increasingly popular, we find that convolutional neural networks pretrained in a supervised fashion on large training sets still perform best on most tasks among the models we consider. Moreover, in apples-to-apples comparisons on the same architectures and similarly sized pretraining datasets, we find that SSL backbones are highly competitive, indicating that future works should perform SSL pretraining with advanced architectures and larger pretraining datasets. We release the raw results of our experiments along with code that allows researchers to put their own backbones through the gauntlet here: https://github.com/hsouri/Battle-of-the-Backbones

Recent advances in large multimodal models (LMMs) have enabled impressive reasoning and perception abilities, yet most existing training pipelines still depend on human-curated data or externally verified reward models, limiting their autonomy and scalability. In this work, we strive to improve LMM reasoning capabilities in a purely unsupervised fashion (without any annotated data or reward distillation). To this end, we propose a self-evolving framework, named EvoLMM, that instantiates two cooperative agents from a single backbone model: a Proposer, which generates diverse, image-grounded questions, and a Solver, which solves them through internal consistency, where learning proceeds through a continuous self-rewarding process. This dynamic feedback encourages both the generation of informative queries and the refinement of structured reasoning without relying on ground-truth or human judgments. When using the popular Qwen2.5-VL as the base model, our EvoLMM yields consistent gains upto sim3\% on multimodal math-reasoning benchmarks, including ChartQA, MathVista, and MathVision, using only raw training images. We hope our simple yet effective approach will serve as a solid baseline easing future research in self-improving LMMs in a fully-unsupervised fashion. Our code and models are available at https://github.com/mbzuai-oryx/EvoLMM.

Accurate estimation of pasture biomass from agricultural imagery is critical for sustainable livestock management, yet existing methods are limited by the small, imbalanced, and sparsely annotated datasets typical of real world monitoring. In this study, adaptation of vision foundation models to agricultural regression is systematically evaluated on the CSIRO Pasture Biomass benchmark, a 357 image dual view dataset with laboratory validated, component wise ground truth for five biomass targets, through 17 configurations spanning four backbones (EfficientNet-B3 to DINOv3-ViT-L), five cross view fusion mechanisms, and a 4x2 metadata factorial. A counterintuitive principle, termed "fusion complexity inversion", is uncovered: on scarce agricultural data, a two layer gated depthwise convolution (R^2 = 0.903) outperforms cross view attention transformers (0.833), bidirectional SSMs (0.819), and full Mamba (0.793, below the no fusion baseline). Backbone pretraining scale is found to monotonically dominate all architectural choices, with the DINOv2 -> DINOv3 upgrade alone yielding +5.0 R^2 points. Training only metadata (species, state, and NDVI) is shown to create a universal ceiling at R^2 ~ 0.829, collapsing an 8.4 point fusion spread to 0.1 points. Actionable guidelines for sparse agricultural benchmarks are established: backbone quality should be prioritized over fusion complexity, local modules preferred over global alternatives, and features unavailable at inference excluded.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Self-evolving language models train on tasks they generate, so every round must decide which updated model the next round inherits. Current loops such as R-Zero, Agent0, and Skill Self-Play make this decision through the task, admitting tasks that look learnable and inheriting every resulting update. We identify a selection-to-update gap in these loops, where a task that looks learnable need not produce a useful update. Most updates on verified tasks fail to make correct answers more likely, yet these loops inherit them all. HeirCommit freezes the updated model and uses fresh evaluation questions to decide whether to inherit it or retain the current model. EvoHeir separates parameter inheritance from experience inheritance, using current and archived experience to repair failures and preserve successes before final confirmation. Our analysis characterizes selection-induced optimism and decomposes regret into selection, absorption, and confirmation errors. HeirCommit cuts the harmful share of accepted updates by 68-83% relative to random inheritance at the same acceptance rate. Across four backbones, EvoHeir achieves the best mathematics and general-reasoning averages, raising the math average by 5.3% relative to the strongest baseline, Agent0. The framework lets useful experience persist even when the model that produced it is not inherited.

Predicting the fitness impact of mutations is central to protein engineering but constrained by limited assays relative to the size of sequence space. Protein language models (pLMs) trained with masked language modeling (MLM) exhibit strong zero-shot fitness prediction; we provide a unifying view by interpreting natural evolution as implicit reward maximization and MLM as inverse reinforcement learning (IRL), in which extant sequences act as expert demonstrations and pLM log-odds serve as fitness estimates. Building on this perspective, we introduce EvoIF, a lightweight model that integrates two complementary sources of evolutionary signal: (i) within-family profiles from retrieved homologs and (ii) cross-family structural-evolutionary constraints distilled from inverse folding logits. EvoIF fuses sequence-structure representations with these profiles via a compact transition block, yielding calibrated probabilities for log-odds scoring. On ProteinGym (217 mutational assays; >2.5M mutants), EvoIF and its MSA-enabled variant achieve state-of-the-art or competitive performance while using only 0.15% of the training data and fewer parameters than recent large models. Ablations confirm that within-family and cross-family profiles are complementary, improving robustness across function types, MSA depths, taxa, and mutation depths. The codes will be made publicly available.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

Modern LLM agents are often improved by modifying prompts, tools, or workflows manually, while the executable scaffold surrounding the model---the harness---is typically treated as a fixed artifact after deployment. This work studies an alternative where the harness is task-specific and continuously evolvable: each task family maintains its own harness, which is hot-swapped across iterations through a fixed task-injection seam and rewritten using environment feedback. We introduce Hierarchical Self-Improvement (HSI), a framework in which a single frozen LLM M operates across three hierarchical scopes: a task harness H that executes tasks, an evolver that rewrites H, and a meta-evolver that rewrites the evolver's strategy code under a frozen outer anchor. A thinking-on/off design isolates the contribution of harness evolution by disabling reasoning during task execution while enabling it during self-modification. HSI is bounded by two factors: a feedback-fidelity bound, since evolution requires informative reward signals to guide selection, and a backbone capability bound, since harness redesign cannot overcome limitations of the frozen model. On BALROG with DeepSeek-V4-Flash-Preview as the frozen backbone, HSI achieves consistent gains over the initial harness on moderate-difficulty tasks (+39.3 on BabyAI, +33.0 on Crafter, +25.0 on TextWorld, and +15.0 on MiniHack, all in raw \% Progress), while obtaining strong held-out generalization on BabaIsAI sub-suites (0.98 best-test on BreakStop and 1.00 on GoTo from a 20% unseen split). On tasks beyond the backbone's capability (NLE), harness evolution provides no improvement. These results demonstrate task-specific harness evolution as a viable axis for improving frozen LLM agents under clear empirical limits. Code is available at https://github.com/TailinZhou/hsi.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

Advances in Large Language Models (LLMs) have enabled a new class of self-evolving agents that autonomously improve through interaction with the environment, demonstrating strong capabilities. However, self-evolution also introduces novel risks overlooked by current safety research. In this work, we study the case where an agent's self-evolution deviates in unintended ways, leading to undesirable or even harmful outcomes. We refer to this as Misevolution. To provide a systematic investigation, we evaluate misevolution along four key evolutionary pathways: model, memory, tool, and workflow. Our empirical findings reveal that misevolution is a widespread risk, affecting agents built even on top-tier LLMs (e.g., Gemini-2.5-Pro). Different emergent risks are observed in the self-evolutionary process, such as the degradation of safety alignment after memory accumulation, or the unintended introduction of vulnerabilities in tool creation and reuse. To our knowledge, this is the first study to systematically conceptualize misevolution and provide empirical evidence of its occurrence, highlighting an urgent need for new safety paradigms for self-evolving agents. Finally, we discuss potential mitigation strategies to inspire further research on building safer and more trustworthy self-evolving agents. Our code and data are available at https://github.com/ShaoShuai0605/Misevolution . Warning: this paper includes examples that may be offensive or harmful in nature.

Scientific discovery is increasingly shifting from isolated disciplines to multi-domain reasoning, and AI for science faces a similar transition. Existing systems are either specialised for individual domains or unify scientific data mainly through text tokenisation and prompt-based interfaces, limiting their ability to handle diverse scientific inputs, produce modality-native outputs, and support joint understanding, reasoning, and generation across scientific domains. We introduce MKB, a unified scientific multimodal model for both understanding and generation, built around a shared Transformer backbone and modality-tailored encoders, adapters, and decoders. MKB covers six scientific branches, including DNA, RNA, proteins, small molecules, earth science, and medical images, and supports native outputs such as biological sequences, molecular strings, meteorological fields, and segmentation masks. Training follows a two-stage modality-then-language curriculum: Stage 1 aligns modality-specific components with the frozen backbone, and Stage 2 consolidates them with the language backbone using mixed scientific and general corpora. Experiments show that MKB achieves competitive scientific understanding across biological and molecular benchmarks, produces high-fidelity native outputs for weather forecasting, biological generation, and medical-image segmentation, and largely retains the general capabilities of its Qwen3-VL backbone. These results demonstrate the feasibility of the proposed paradigm, suggesting that shared-backbone models with modality-tailored components can provide a promising foundation for future cross-domain scientific multimodal exploration. The model and code are publicly available at https://github.com/Shanghai-Academy-of-AI-For-Science/MKB and https://huggingface.co/sais-org/MKB.

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce THE-Tree (Technology History Evolution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

Agents based on Large Language Models (LLMs) are increasingly permeating various domains of human production and life, highlighting the importance of aligning them with human values. The current alignment of AI systems primarily focuses on passively aligning LLMs through human intervention. However, agents possess characteristics like receiving environmental feedback and self-evolution, rendering the LLM alignment methods inadequate. In response, we propose an evolutionary framework for agent evolution and alignment, named EvolutionaryAgent, which transforms agent alignment into a process of evolution and selection under the principle of survival of the fittest. In an environment where social norms continuously evolve, agents better adapted to the current social norms will have a higher probability of survival and proliferation, while those inadequately aligned dwindle over time. Experimental results assessing the agents from multiple perspectives in aligning with social norms demonstrate that EvolutionaryAgent can align progressively better with the evolving social norms while maintaining its proficiency in general tasks. Effectiveness tests conducted on various open and closed-source LLMs as the foundation for agents also prove the applicability of our approach.

Automated red teaming frameworks for Large Language Models (LLMs) have become increasingly sophisticated, yet they share a fundamental limitation: their jailbreak logic is confined to selecting, combining, or refining pre-existing attack strategies. This binds their creativity and leaves them unable to autonomously invent entirely new attack mechanisms. To overcome this gap, we introduce EvoSynth, an autonomous framework that shifts the paradigm from attack planning to the evolutionary synthesis of jailbreak methods. Instead of refining prompts, EvoSynth employs a multi-agent system to autonomously engineer, evolve, and execute novel, code-based attack algorithms. Crucially, it features a code-level self-correction loop, allowing it to iteratively rewrite its own attack logic in response to failure. Through extensive experiments, we demonstrate that EvoSynth not only establishes a new state-of-the-art by achieving an 85.5\% Attack Success Rate (ASR) against highly robust models like Claude-Sonnet-4.5, but also generates attacks that are significantly more diverse than those from existing methods. We release our framework to facilitate future research in this new direction of evolutionary synthesis of jailbreak methods. Code is available at: https://github.com/dongdongunique/EvoSynth.

Continued pretraining offers a promising solution for adapting foundation models to a new target domain. However, in specialized domains, available datasets are often very small, limiting the applicability of SSL methods developed for large-scale pretraining and making hyperparameter search infeasible. In addition, pretrained models are usually released as backbone-weights only, lacking important information to continue pretraining. We propose to bridge this gap with DIET-CP, a simple continued pretraining strategy, where any strong foundation model can be steered towards the new data distribution of interest. DIET-CP relies on a very simple objective, requires no labels, and introduces no more hyperparameters than supervised finetuning. It is stable across data modalities and backbone choices, while providing a significant performance boost for state-of-the-art models such as DINOv3 using only 1000 images.

We present Darwin Family, a framework for training-free evolutionary merging of large language models via gradient-free weight-space recombination. We ask whether frontier-level reasoning performance can be improved without additional training, by reorganizing latent capabilities already encoded in existing checkpoints. Darwin introduces three key ideas: (i) a 14-dimensional adaptive merge genome enabling fine-grained component- and block-level recombination; (ii) MRI-Trust Fusion, which adaptively balances diagnostic layer-importance signals with evolutionary search through a learnable trust parameter; and (iii) an Architecture Mapper that enables cross-architecture breeding between heterogeneous model families. Empirically, the flagship Darwin-27B-Opus achieves 86.9% on GPQA Diamond, ranking #6 among 1,252 evaluated models, and outperforming its fully trained foundation model without any gradient-based training. Across scales from 4B to 35B parameters, Darwin models consistently improve over their parents, support recursive multi-generation evolution, and enable a training-free evolutionary merge that combines Transformer- and Mamba-based components. Together, the Darwin Family demonstrates that diagnostic-guided evolutionary merging is a practical and reproducible alternative to costly post-training pipelines for reasoning-centric language models.

Recent work such as AlphaEvolve has shown that combining LLM-driven optimization with evolutionary search can effectively improve programs, prompts, and algorithms across domains. In this paradigm, previously evaluated solutions are reused to guide the model toward new candidate solutions. Crucially, the effectiveness of this evolution process depends on the search strategy: how prior solutions are selected and varied to generate new candidates. However, most existing methods rely on fixed search strategies with predefined knobs (e.g., explore-exploit ratios) that remain static throughout execution. While effective in some settings, these approaches often fail to adapt across tasks, or even within the same task as the search space changes over time. We introduce EvoX, an adaptive evolution method that optimizes its own evolution process. EvoX jointly evolves candidate solutions and the search strategies used to generate them, continuously updating how prior solutions are selected and varied based on progress. This enables the system to dynamically shift between different search strategies during the optimization process. Across nearly 200 real-world optimization tasks, EvoX outperforms existing AI-driven evolutionary methods including AlphaEvolve, OpenEvolve, GEPA, and ShinkaEvolve on the majority of tasks.

Recent advancements in generation models have showcased remarkable capabilities in generating fantastic content. However, most of them are trained on proprietary high-quality data, and some models withhold their parameters and only provide accessible application programming interfaces (APIs), limiting their benefits for downstream tasks. To explore the feasibility of training a text-to-image generation model comparable to advanced models using publicly available resources, we introduce EvolveDirector. This framework interacts with advanced models through their public APIs to obtain text-image data pairs to train a base model. Our experiments with extensive data indicate that the model trained on generated data of the advanced model can approximate its generation capability. However, it requires large-scale samples of 10 million or more. This incurs significant expenses in time, computational resources, and especially the costs associated with calling fee-based APIs. To address this problem, we leverage pre-trained large vision-language models (VLMs) to guide the evolution of the base model. VLM continuously evaluates the base model during training and dynamically updates and refines the training dataset by the discrimination, expansion, deletion, and mutation operations. Experimental results show that this paradigm significantly reduces the required data volume. Furthermore, when approaching multiple advanced models, EvolveDirector can select the best samples generated by them to learn powerful and balanced abilities. The final trained model Edgen is demonstrated to outperform these advanced models. The code and model weights are available at https://github.com/showlab/EvolveDirector.

We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and refining structural details over scales. To achieve this, PAR consists of three key components: (i) multi-scale downsampling operations that represent protein structures across multiple scales during training; (ii) an autoregressive transformer that encodes multi-scale information and produces conditional embeddings to guide structure generation; (iii) a flow-based backbone decoder that generates backbone atoms conditioned on these embeddings. Moreover, autoregressive models suffer from exposure bias, caused by the training and the generation procedure mismatch, and substantially degrades structure generation quality. We effectively alleviate this issue by adopting noisy context learning and scheduled sampling, enabling robust backbone generation. Notably, PAR exhibits strong zero-shot generalization, supporting flexible human-prompted conditional generation and motif scaffolding without requiring fine-tuning. On the unconditional generation benchmark, PAR effectively learns protein distributions and produces backbones of high design quality, and exhibits favorable scaling behavior. Together, these properties establish PAR as a promising framework for protein structure generation.

Modern text-to-image (T2I) systems can be improved without modifying generator parameters by adapting the external system around frozen generators. However, existing approaches typically optimize a predefined dimension, such as prompts, routing, or workflows, restricting the space in which generation failures can be corrected. Allowing multiple generator-external responsibilities to evolve provides a broader adaptation space, but introduces a new challenge: visual feedback reveals what failed, but not where persistent evolution should occur or how this space should be explored efficiently. We introduce EvoGen-Harness, a generator-agnostic framework for multi-responsibility image-generation harness evolution, together with Trace (Trajectory-Relative Attribution and Coordinated Evolution). Trace aggregates evidence across stochastic executions, uses failure attribution as a search prior to focus candidate updates, and progressively re-attributes residual failures to coordinate evolution across responsibilities, while No-Patch and held-out validation prevent unnecessary or harmful updates. Across GenEval2, T2I-CompBench++, and WISE, EvoGen-Harness improves over the strongest evaluated baselines by +0.2633, +0.0720, and +0.0752, respectively, while achieving 87.9-91.4% attribution recall, 94.8% No-Patch accuracy, and only 1.9% regression. These results demonstrate that attribution-guided multi-responsibility evolution can substantially enhance frozen T2I systems beyond single-dimension adaptation.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

We test whether artificial intelligence architectural evolution obeys the same statistical laws as biological evolution. Compiling 935 ablation experiments from 161 publications, we show that the distribution of fitness effects (DFE) of architectural modifications follows a heavy-tailed Student's t-distribution with proportions (68% deleterious, 19% neutral, 13% beneficial for major ablations, n=568) that place AI between compact viral genomes and simple eukaryotes. The DFE shape matches D. melanogaster (normalized KS=0.07) and S. cerevisiae (KS=0.09); the elevated beneficial fraction (13% vs. 1-6% in biology) quantifies the advantage of directed over blind search while preserving the distributional form. Architectural origination follows logistic dynamics (R^2=0.994) with punctuated equilibria and adaptive radiation into domain niches. Fourteen architectural traits were independently invented 3-5 times, paralleling biological convergences. These results demonstrate that the statistical structure of evolution is substrate-independent, determined by fitness landscape topology rather than the mechanism of selection.

Complex agentic AI systems, powered by a coordinated ensemble of Large Language Models (LLMs), tool and memory modules, have demonstrated remarkable capabilities on intricate, multi-turn tasks. However, this success is shadowed by prohibitive economic costs and severe latency, exposing a critical, yet underexplored, trade-off. We formalize this challenge as the Agent System Trilemma: the inherent tension among achieving state-of-the-art performance, minimizing monetary cost, and ensuring rapid task completion. To dismantle this trilemma, we introduce EvoRoute, a self-evolving model routing paradigm that transcends static, pre-defined model assignments. Leveraging an ever-expanding knowledge base of prior experience, EvoRoute dynamically selects Pareto-optimal LLM backbones at each step, balancing accuracy, efficiency, and resource use, while continually refining its own selection policy through environment feedback. Experiments on challenging agentic benchmarks such as GAIA and BrowseComp+ demonstrate that EvoRoute, when integrated into off-the-shelf agentic systems, not only sustains or enhances system performance but also reduces execution cost by up to 80% and latency by over 70%.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Data Darwinism (Part I) established a ten-level hierarchy for data processing, showing that stronger processing can unlock greater data value. However, that work relied on manually designed strategies for a single category. Modern pretraining corpora comprise hundreds of heterogeneous categories spanning domains and content types, each demanding specialized treatment. At this scale, manual strategy design becomes prohibitive. This raises a key question: can strategies evolve in an automated way? We introduce DataEvolve, a framework that enables strategies to evolve through iterative optimization rather than manual design. For each data category, DataEvolve operates in a closed evolutionary loop: it identifies quality issues, generates candidate strategies, executes them on sampled data, evaluates results, and refines approaches across generations. The process accumulates knowledge through an experience pool of discovered issues and a strategy pool tracking performance across iterations. Applied to 8 categories spanning 672B tokens from Nemotron-CC, DataEvolve produces Darwin-CC, a 504B-token dataset with strategies evolved through 30 iterations per category. Training 3B models on 500B tokens, Darwin-CC outperforms raw data (+3.96 points) and achieves a 44.13 average score across 18 benchmarks, surpassing DCLM, Ultra-FineWeb, and FineWeb-Edu, with strong gains on knowledge-intensive tasks such as MMLU. Analysis shows evolved strategies converge on cleaning-focused approaches: targeted noise removal and format normalization with domain-aware preservation, echoing the L4 (Generative Refinement) principles from Part I. Ablation studies confirm iterative evolution is essential: optimized strategies outperform suboptimal ones by 2.93 points, establishing evolutionary strategy design as feasible and necessary for pretraining-scale data curation.

Pre-trained models have become the preferred backbone due to the expansion of model parameters, with techniques like Parameter-Efficient Fine-Tuning (PEFTs) typically fixing the parameters of these models. However, pre-trained models may not always be optimal, especially when there are discrepancies between training tasks and target tasks, potentially resulting in negative transfer. To address this, we introduce KIND, which performs Knowledge INtegration and Diversion in diffusion models. KIND first integrates knowledge by decomposing parameter matrices of models using U, Sigma, and V matrices, formally inspired by singular value decomposition (SVD). Then it explicitly partitions the components of these matrices into learngenes and tailors to condense common and class-specific knowledge, respectively, through a class gate. In this way, KIND redefines traditional pre-training methods by adjusting training objectives from maximizing model performance on current tasks to condensing transferable common knowledge, leveraging the Learngene framework. We conduct experiments on ImageNet-1K and compare KIND with PEFT and other learngene methods. Results indicate that KIND achieves state-of-the-art performance compared to other PEFT and learngene methods. Specifically, the images generated by KIND achieves more than 6.54 and 1.07 decrease in FID and sFID on DiT-L/2, utilizing only 45.4M trainable parameters and saving at least 35.4G FLOPs in computational cost.

Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these methods overlook affinity maturation as a rich and largely untapped source of information about the evolutionary process by which antibodies explore the underlying fitness landscape. In contrast, classical phylogenetic models explicitly represent evolutionary dynamics but lack the expressivity to capture complex epistatic interactions. We bridge this gap with CoSiNE, a continuous-time Markov chain parameterized by a deep neural network. Mathematically, we prove that CoSiNE provides a first-order approximation to the intractable sequential point mutation process, capturing epistatic effects with an error bound that is quadratic in branch length. Empirically, CoSiNE outperforms state-of-the-art language models in zero-shot variant effect prediction by explicitly disentangling selection from context-dependent somatic hypermutation. Finally, we introduce Guided Gillespie, a classifier-guided sampling scheme that steers CoSiNE at inference time, enabling efficient optimization of antibody binding affinity toward specific antigens.

Large language models (LLMs) are increasingly used to evolve programs and multi-agent systems, yet most existing approaches rely on overwrite-based mutations that maintain only a single candidate at a time. Such methods discard useful variants, suffer from destructive edits, and explore a brittle search space prone to structural failure. We introduce EvoLattice, a framework that represents an entire population of candidate programs or agent behaviors within a single directed acyclic graph. Each node stores multiple persistent alternatives, and every valid path through the graph defines a distinct executable candidate, yielding a large combinatorial search space without duplicating structure. EvoLattice enables fine-grained alternative-level evaluation by scoring each alternative across all paths in which it appears, producing statistics that reveal how local design choices affect global performance. These statistics provide a dense, data-driven feedback signal for LLM-guided mutation, recombination, and pruning, while preserving successful components. Structural correctness is guaranteed by a deterministic self-repair mechanism that enforces acyclicity and dependency consistency independently of the LLM. EvoLattice naturally extends to agent evolution by interpreting alternatives as prompt fragments or sub-agent behaviors. Across program synthesis (proxy and optimizer meta-learning), EvoLattice yields more stable evolution, greater expressivity, and stronger improvement trajectories than prior LLM-guided methods. The resulting dynamics resemble quality-diversity optimization, emerging implicitly from EvoLattice's internal multi-alternative representation rather than an explicit external archive.

An LLM agent's capability depends not only on model weights but on its harness: prompts, tools, skills, and control flow. Self-improvement loops already edit harnesses, yet single-lineage search is path-dependent and local wins often regress other tasks. We introduce DarwinX, which treats self-evolution as selection over a population of harnesses with the model frozen: a preserve-and-extend contract admits only variants that extend coverage without regressing, an archive keeps alternative lineages for recombination, and failure-, teacher-, and self-derived evidence share one edit interface. Fitness comes from each benchmark's own verifier: no gold solutions, no hand-picked winners. Across four benchmarks that progressively separate the evolution signal from the test, one loop adds about 17 points on average: Terminal-Bench 2.1 rises +7.7 to 83.2% on a matched base and to the verified frontier at 84.7% on a stronger one; TerminalWorld's held-out split reaches 68.3%, ahead of every off-the-shelf agent; WebArena-Infinity real-task pass@1 rises from 43.5% to 93.0% audit-clean; and a Terminal-Bench 2.1 harness transfers unchanged to SWE-bench Verified. What evolves is general agent competence, not benchmark-specific patches, so it survives changes of task, verifier, and base model. A frozen model need not be a fixed agent: harness selection turns evaluation compute into durable capability.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Open source code: https://github.com/chaitjo/geometric-rna-design

Evolutionary program synthesis systems such as AlphaEvolve, OpenEvolve, and ShinkaEvolve offer a new approach to AI-assisted mathematical discovery. These systems utilize teams of large language models (LLMs) to generate candidate solutions to a problem as human readable code. These candidate solutions are then 'evolved' with the goal of improving them beyond what an LLM can produce in a single shot. While existing mathematical applications have mostly focused on problems of establishing bounds (e.g., sphere packing), the program synthesis approach is well suited to any problem where the solution takes the form of an explicit construction. With this in mind, in this paper we explore the use of OpenEvolve for combinatorial bijection discovery. We describe the results of applying OpenEvolve to three bijection construction problems involving Dyck paths, two of which are known and one of which is open. We find that while systems like OpenEvolve show promise as a valuable tool for combinatorialists, the problem of finding novel, research-level bijections remains a challenging task for current frontier systems, reinforcing the need for human mathematicians in the loop. We describe some lessons learned for others in the field interested in exploring the use of these systems.

In here presented in silico study we suggest a way how to implement the evolutionary principles into anti-cancer therapy design. We hypothesize that instead of its ongoing supervised adaptation, the therapy may be constructed as a self-sustaining evolutionary process in a dynamic fitness landscape established implicitly by evolving cancer cells, microenvironment and the therapy itself. For these purposes, we replace a unified therapy with the `therapy species', which is a population of heterogeneous elementary therapies, and propose a way how to turn the toxicity of the elementary therapy into its fitness in a way conforming to evolutionary causation. As a result, not only the therapies govern the evolution of different cell phenotypes, but the cells' resistances govern the evolution of the therapies as well. We illustrate the approach by the minimalistic ad hoc evolutionary model. Its results indicate that the resistant cells could bias the evolution towards more toxic elementary therapies by inhibiting the less toxic ones. As the evolutionary causation of cancer drug resistance has been intensively studied for a few decades, we refer to cancer as a special case to illustrate purely theoretical analysis.

Network Architecture Search and specifically Regularized Evolution is a common way to refine the structure of a deep learning model.However, little is known about how models empirically evolve over time which has design implications for designing caching policies, refining the search algorithm for particular applications, and other important use cases.In this work, we algorithmically analyze and quantitatively characterize the patterns of model evolution for a set of models from the Candle project and the Nasbench-201 search space.We show how the evolution of the model structure is influenced by the regularized evolution algorithm. We describe how evolutionary patterns appear in distributed settings and opportunities for caching and improved scheduling. Lastly, we describe the conditions that affect when particular model architectures rise and fall in popularity based on their frequency of acting as a donor in a sliding window.

LLM-guided evolutionary methods such as AlphaEvolve have proven effective in domains like math, systems research, and algorithmic discovery, but their reliance on frontier models makes each run expensive. We argue this is largely an artifact of how existing frameworks allocate search: archives that fail to preserve solution diversity force compensation through stronger mutation models; blind model use spends frontier dollars on local edits a smaller model could handle; and full-set evaluation wastes rollouts on redundant examples. We introduce LEVI, a harness-first evolutionary framework built on the bet that stronger search architectures can substitute for or even outperform larger LLMs in evolutionary search. LEVI improves on three core components of evolutionary search: a solution database that establishes diversity from the beginning, and then maintains it throughout the run; a smarter mutation router that plays into the strengths of large and small LLMs; and a rank-preserving proxy benchmark for rollout-heavy settings. Across systems-research benchmarks LEVI attains the highest score on a budget 3.3-6.7x smaller than the published frontier-model runs of existing frameworks like ShinkaEvolve, GEPA, and AdaEvolve; on one problem, LEVI matches the existing best at a 35x lower cost. On prompt optimization, LEVI matches or exceeds GEPA at less than half of its rollout budget on four different benchmarks. LEVI is available as an open-source framework at https://github.com/ttanv/levi.

Evolution-based protein structure prediction models have achieved breakthrough success in recent years. However, they struggle to generalize beyond evolutionary priors and on sequences lacking rich homologous data. Here we present a novel, out-of-domain benchmark based on sactipeptides, a rare class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by sulfur-to-alpha-carbon thioether bridges creating cross-links between cysteine residues and backbone. We evaluate recent models on predicting conformations compatible with these cross-links bridges for the 10 known sactipeptides with elucidated post-translational modifications. Crucially, the structures of 5 of them have not yet been experimentally resolved. This makes the task a challenging problem for evolution-based models, which we find exhibit limited performance (0.0% to 19.2% GDT-TS on sulfur-to-alpha-carbon distance). Our results point at the need for physics-informed models to sustain progress in biomolecular structure prediction.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Protein backbone generation plays a central role in de novo protein design and is significant for many biological and medical applications. Although diffusion and flow-based generative models provide potential solutions to this challenging task, they often generate proteins with undesired designability and suffer computational inefficiency. In this study, we propose a novel rectified quaternion flow (ReQFlow) matching method for fast and high-quality protein backbone generation. In particular, our method generates a local translation and a 3D rotation from random noise for each residue in a protein chain, which represents each 3D rotation as a unit quaternion and constructs its flow by spherical linear interpolation (SLERP) in an exponential format. We train the model by quaternion flow (QFlow) matching with guaranteed numerical stability and rectify the QFlow model to accelerate its inference and improve the designability of generated protein backbones, leading to the proposed ReQFlow model. Experiments show that ReQFlow achieves state-of-the-art performance in protein backbone generation while requiring much fewer sampling steps and significantly less inference time (e.g., being 37x faster than RFDiffusion and 62x faster than Genie2 when generating a backbone of length 300), demonstrating its effectiveness and efficiency. The code is available at https://github.com/AngxiaoYue/ReQFlow.

LLM-powered tool-calling agents fulfill user requests by interacting with environments, querying data, and invoking tools in a multi-turn process. Yet, most existing benchmarks evaluate these systems under static environment interfaces, with fixed schemas and toolsets, making it difficult to assess how agents behave as environments evolves -- when capabilities are added, reorganized, or deprecated across successive environment versions. In this paper, we study structured environment evolution as a benchmark-construction problem for tool-calling agents. We propose ProEvolve, a graph-based framework that makes environment evolution programmable. At its core, a typed relational graph provides a unified, explicit representation of the environment - data, tools, and schema. Under this formalism, adding, removing, or modifying capabilities are expressed as graph transformations that coherently propagate updates across tools, schemas, and data access. Building on this, ProEvolve supports (1) automatic generation of evolved executable environments through explicit graph transformations, and (2) graph-grounded construction of task sandboxes via subgraph sampling and instantiation. We validate ProEvolve in two tool-calling domains, e-commerce and airline booking, in terms of quality, implementation validity, and failure modes. Finally, we use the generated benchmark as a downstream diagnostic to study how representative agents behave under structured environment evolution.

Large Language Models (LLMs) for formal theorem proving have shown significant promise, yet they often lack generalizability and are fragile to even minor transformations of problem statements. To address this limitation, we introduce a novel data augmentation pipeline designed to enhance model robustness from two perspectives: symmetry and difficulty. From the symmetry perspective, we propose two complementary methods: EvolAST, an Abstract Syntax Tree (AST) based approach that targets syntactic symmetry to generate semantically equivalent problem variants, and EvolDomain, which leverages LLMs to address semantic symmetry by translating theorems across mathematical domains. From the difficulty perspective, we propose EvolDifficulty, which uses carefully designed evolutionary instructions to guide LLMs in generating new theorems with a wider range of difficulty. We then use the evolved data to train EvolProver, a 7B-parameter non-reasoning theorem prover. EvolProver establishes a new state-of-the-art (SOTA) on FormalMATH-Lite with a 53.8% pass@32 rate, surpassing all models of comparable size, including reasoning-based models. It also sets new SOTA records for non-reasoning models on MiniF2F-Test (69.8% pass@32), Ineq-Comp-Seed (52.2% pass@32), and Ineq-Comp-Transformed (34.0% pass@32). Ablation studies further confirm our data augmentation pipeline's effectiveness across multiple benchmarks.

Recent advances in large language models (LLMs) have enabled breakthroughs in mathematical discovery, exemplified by AlphaEvolve, a closed-source system that evolves programs to improve bounds on open problems. However, it relies on ensembles of frontier LLMs to achieve new bounds and is a pure inference system that models cannot internalize the evolving strategies. We introduce ThetaEvolve, an open-source framework that simplifies and extends AlphaEvolve to efficiently scale both in-context learning and Reinforcement Learning (RL) at test time, allowing models to continually learn from their experiences in improving open optimization problems. ThetaEvolve features a single LLM, a large program database for enhanced exploration, batch sampling for higher throughput, lazy penalties to discourage stagnant outputs, and optional reward shaping for stable training signals, etc. ThetaEvolve is the first evolving framework that enable a small open-source model, like DeepSeek-R1-0528-Qwen3-8B, to achieve new best-known bounds on open problems (circle packing and first auto-correlation inequality) mentioned in AlphaEvolve. Besides, across two models and four open tasks, we find that ThetaEvolve with RL at test-time consistently outperforms inference-only baselines, and the model indeed learns evolving capabilities, as the RL-trained checkpoints demonstrate faster progress and better final performance on both trained target task and other unseen tasks. We release our code publicly: https://github.com/ypwang61/ThetaEvolve

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

Most existing LLM safety evaluation and defense methods follow a static formulation: jailbreak vulnerabilities are evaluated with fixed attack methods, and guardrails are trained on fixed malicious prompt datasets. However, real-world adversaries continuously evolve their capabilities and expand the attack space. To address this challenge, we propose DARWIN, an evolutionary attack-defense framework that formulates jailbreaking as an open-ended evolution process and continuously updates guardrails through an evolving attack-defense loop. DARWIN-Attack is an evolutionary adversary that expands its capabilities through strategy discovery, mutation, selection, and feedback-driven composition. It collects strategies from broad external sources, generates new variants through self-reflection and genetic evolution, and retains effective strategies based on their performance against aligned LLMs. During attack execution, DARWIN-Attack adaptively selects and combines evolved strategies according to feedback from target LLMs and guardrails. Across frontier models and guardrails, it achieves state-of-the-art attack success rates, including nearly 100% on DeepSeek-V4-Pro and YuFeng-XGuard and over 90% on GPT-5.5. On the defense side, we introduce DARWIN-Guard, an online adversarial training paradigm that iteratively learns from emerging adversarial samples generated by DARWIN-Attack. To improve robustness without sacrificing utility, DARWIN-Guard jointly trains on malicious and benign disguised queries, encouraging the model to identify underlying intent rather than superficial attack patterns. DARWIN-Guard achieves an average unsafe recall of 91.6% across 12 safety benchmarks, outperforming strong guardrails such as YuFeng-XGuard and Nemotron Guard, while maintaining a nearly 100% pass rate on standard benign datasets.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

Post-training via Supervised Fine-Tuning (SFT) and Reinforcement Learning (RL) is crucial for enhancing reasoning in Multimodal Large Language Models (MLLMs), yet existing paradigms often reach a performance bottleneck due to the limitations of static data. While current methods leverage self-reflection or self-evolution to push these boundaries, they still suffer from cognitive drift and hallucinated reasoning paths caused by low-quality synthetic data. To address these challenges, we propose Anchor Evolution (AnE), a new paradigm that integrates truth-anchored data curation and model evolution, achieving faithful and steady performance gains at the reasoning frontier. Specifically, we propose Truth Anchor Expansion, which pinpoints the model failing frontier via trajectory rollouts and leverages ground-truth databases to retrieve high-fidelity anchors for faithful data curation. Subsequently, we introduce the Scaffold-Stripping Mechanism to internalize reasoning capabilities. This mechanism first anchors reasoning paths via scaffold-augmented supervision to mitigate the learning complexity and distribution drift of direct SFT on raw data, then leverages RL to strip the scaffold template, thereby effectively transitioning the reasoning paths into intrinsic model capabilities. Experimental results on multimodal reasoning benchmarks show that our method substantially advances the model performance frontier, improving the base model by 10.3\% across eight multimodal benchmarks and achieving state-of-the-art results. The code will be made publicly available.

Evolutionary agentic systems intensify the trade-off between computational efficiency and reasoning capability by repeatedly invoking large language models (LLMs) during inference. This setting raises a central question: how can an agent dynamically select an LLM that is sufficiently capable for the current generation step while remaining computationally efficient? While model cascades offer a practical mechanism for balancing this trade-off, existing routing strategies typically rely on static heuristics or external controllers and do not explicitly account for model uncertainty. We introduce AdaptEvolve: Adaptive LLM Selection for Multi-LLM Evolutionary Refinement within an evolutionary sequential refinement framework that leverages intrinsic generation confidence to estimate real-time solvability. Empirical results show that confidence-driven selection yields a favourable Pareto frontier, reducing total inference cost by an average of 37.9% across benchmarks while retaining 97.5% of the upper-bound accuracy of static large-model baselines. Our code is available at https://github.com/raypretam/adaptive_llm_selection.

The effort devoted to hand-crafting neural network image classifiers has motivated the use of architecture search to discover them automatically. Although evolutionary algorithms have been repeatedly applied to neural network topologies, the image classifiers thus discovered have remained inferior to human-crafted ones. Here, we evolve an image classifier---AmoebaNet-A---that surpasses hand-designs for the first time. To do this, we modify the tournament selection evolutionary algorithm by introducing an age property to favor the younger genotypes. Matching size, AmoebaNet-A has comparable accuracy to current state-of-the-art ImageNet models discovered with more complex architecture-search methods. Scaled to larger size, AmoebaNet-A sets a new state-of-the-art 83.9% / 96.6% top-5 ImageNet accuracy. In a controlled comparison against a well known reinforcement learning algorithm, we give evidence that evolution can obtain results faster with the same hardware, especially at the earlier stages of the search. This is relevant when fewer compute resources are available. Evolution is, thus, a simple method to effectively discover high-quality architectures.

Large Language Models (LLMs) have demonstrated strong capabilities but remain fundamentally static, unable to adapt their internal parameters to novel tasks, evolving knowledge domains, or dynamic interaction contexts. As LLMs are increasingly deployed in open-ended, interactive environments, this static nature has become a critical bottleneck, necessitating agents that can adaptively reason, act, and evolve in real time. This paradigm shift -- from scaling static models to developing self-evolving agents -- has sparked growing interest in architectures and methods enabling continual learning and adaptation from data, interactions, and experiences. This survey provides the first systematic and comprehensive review of self-evolving agents, organized around three foundational dimensions -- what to evolve, when to evolve, and how to evolve. We examine evolutionary mechanisms across agent components (e.g., models, memory, tools, architecture), categorize adaptation methods by stages (e.g., intra-test-time, inter-test-time), and analyze the algorithmic and architectural designs that guide evolutionary adaptation (e.g., scalar rewards, textual feedback, single-agent and multi-agent systems). Additionally, we analyze evaluation metrics and benchmarks tailored for self-evolving agents, highlight applications in domains such as coding, education, and healthcare, and identify critical challenges and research directions in safety, scalability, and co-evolutionary dynamics. By providing a structured framework for understanding and designing self-evolving agents, this survey establishes a roadmap for advancing adaptive agentic systems in both research and real-world deployments, ultimately shedding lights to pave the way for the realization of Artificial Super Intelligence (ASI), where agents evolve autonomously, performing at or beyond human-level intelligence across a wide array of tasks.

Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture with up to 5x as many parameters as previous models. To meaningfully quantify performance, we introduce a new set of metrics that directly measure the distributional similarity of generated proteins with reference sets, complementing existing metrics. We further explore scaling training data to millions of synthetic protein structures and explore improved training and sampling recipes adapted to protein backbone generation. This includes fine-tuning strategies like LoRA for protein backbones, new guidance methods like classifier-free guidance and autoguidance for protein backbones, and new adjusted training objectives. Proteina achieves state-of-the-art performance on de novo protein backbone design and produces diverse and designable proteins at unprecedented length, up to 800 residues. The hierarchical conditioning offers novel control, enabling high-level secondary-structure guidance as well as low-level fold-specific generation.

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

Modern top-performing object detectors depend heavily on backbone networks, whose advances bring consistent performance gains through exploring more effective network structures. In this paper, we propose a novel and flexible backbone framework, namely CBNetV2, to construct high-performance detectors using existing open-sourced pre-trained backbones under the pre-training fine-tuning paradigm. In particular, CBNetV2 architecture groups multiple identical backbones, which are connected through composite connections. Specifically, it integrates the high- and low-level features of multiple backbone networks and gradually expands the receptive field to more efficiently perform object detection. We also propose a better training strategy with assistant supervision for CBNet-based detectors. Without additional pre-training of the composite backbone, CBNetV2 can be adapted to various backbones (CNN-based vs. Transformer-based) and head designs of most mainstream detectors (one-stage vs. two-stage, anchor-based vs. anchor-free-based). Experiments provide strong evidence that, compared with simply increasing the depth and width of the network, CBNetV2 introduces a more efficient, effective, and resource-friendly way to build high-performance backbone networks. Particularly, our Dual-Swin-L achieves 59.4% box AP and 51.6% mask AP on COCO test-dev under the single-model and single-scale testing protocol, which is significantly better than the state-of-the-art result (57.7% box AP and 50.2% mask AP) achieved by Swin-L, while the training schedule is reduced by 6times. With multi-scale testing, we push the current best single model result to a new record of 60.1% box AP and 52.3% mask AP without using extra training data. Code is available at https://github.com/VDIGPKU/CBNetV2.

In this work, we introduce CodeEvolve, an open-source evolutionary coding agent that unites Large Language Models (LLMs) with genetic algorithms to solve complex computational problems. Our framework adapts powerful evolutionary concepts to the LLM domain, building upon recent methods for generalized scientific discovery. CodeEvolve employs an island-based genetic algorithm to maintain population diversity and increase throughput, introduces a novel inspiration-based crossover mechanism that leverages the LLMs context window to combine features from successful solutions, and implements meta-prompting strategies for dynamic exploration of the solution space. We conduct a rigorous evaluation of CodeEvolve on a subset of the mathematical benchmarks used to evaluate Google DeepMind's closed-source AlphaEvolve. Our findings show that our method surpasses AlphaEvolve's performance on several challenging problems. To foster collaboration and accelerate progress, we release our complete framework as an open-source repository.

Large vision--language models (VLMs) often use a frozen vision backbone, whose image features are mapped into a large language model through a lightweight connector. While transformer-based encoders are the standard visual backbone, we ask whether state space model (SSM) vision backbones can be a strong alternative. We systematically evaluate SSM vision backbones for VLMs in a controlled setting. Under matched ImageNet-1K initialization, the SSM backbone achieves the strongest overall performance across both VQA and grounding/localization. We further adapt both SSM and ViT-family backbones with detection or segmentation training and find that dense-task tuning generally improves performance across families; after this adaptation, the SSM backbone remains competitive while operating at a substantially smaller model scale. We further observe that (i) higher ImageNet accuracy or larger backbones do not reliably translate into better VLM performance, and (ii) some visual backbones are unstable in localization. Based on these findings, we propose stabilization strategies that improve robustness for both backbone families and highlight SSM backbones as a strong alternative to transformer-based vision encoders in VLMs.

Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formally defines a newly emerging problem -- the population-based evolution of large language models (LLMs) -- and introduces a novel framework. Starting with a population of parent LLMs, our framework enables the population to evolve through four key operations: (i) crossover, merging the weights of different parents to create offspring LLMs, (ii) mutation, introducing small, random changes to model weights to foster diversity, (iii) selection, prioritizing high-performing models, and (iv) succession, transferring the learned experience from parent to offspring LLMs. With only 200 samples per new task, the LLM population evolves rapidly to adapt to the task at hand, without any gradients. Experiments on 12 datasets show that our framework consistently outperforms existing multi-LLM merging and adaptation methods, achieving accuracy gains of up to 54.8% over the best LLM in the initial population. Moreover, our framework allows for the evolution of LLMs across multiple new tasks simultaneously, scaling effectively with populations of up to 40 LLMs, and even zero-shot generalization to unseen held-out tasks. We have open-sourced the code on GitHub and released the weights of 10 parent LLMs, fine-tuned from gemma-2-2b-it, on HuggingFace$, enabling reproduction of our proposed framework using just a single 4090 GPU with 24GB memory, without any performance degradation.

Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for analysis and design. Here we propose a custom generative large-language model to enable design of novel spider silk protein sequences to meet complex combinations of target mechanical properties. The model, pretrained on a large set of protein sequences, is fine-tuned on ~1,000 major ampullate spidroin (MaSp) sequences for which associated fiber-level mechanical properties exist, to yield an end-to-end forward and inverse generative strategy. Performance is assessed through: (1), a novelty analysis and protein type classification for generated spidroin sequences through BLAST searches, (2) property evaluation and comparison with similar sequences, (3) comparison of molecular structures, as well as, and (4) a detailed sequence motif analyses. We generate silk sequences with property combinations that do not exist in nature, and develop a deep understanding the mechanistic roles of sequence patterns in achieving overarching key mechanical properties (elastic modulus, strength, toughness, failure strain). The model provides an efficient approach to expand the silkome dataset, facilitating further sequence-structure analyses of silks, and establishes a foundation for synthetic silk design and optimization.

AlphaEvolve is a generic evolutionary coding agent that combines the generative capabilities of LLMs with automated evaluation in an iterative evolutionary framework that proposes, tests, and refines algorithmic solutions to challenging scientific and practical problems. In this paper we showcase AlphaEvolve as a tool for autonomously discovering novel mathematical constructions and advancing our understanding of long-standing open problems. To demonstrate its breadth, we considered a list of 67 problems spanning mathematical analysis, combinatorics, geometry, and number theory. The system rediscovered the best known solutions in most of the cases and discovered improved solutions in several. In some instances, AlphaEvolve is also able to generalize results for a finite number of input values into a formula valid for all input values. Furthermore, we are able to combine this methodology with Deep Think and AlphaProof in a broader framework where the additional proof-assistants and reasoning systems provide automated proof generation and further mathematical insights. These results demonstrate that large language model-guided evolutionary search can autonomously discover mathematical constructions that complement human intuition, at times matching or even improving the best known results, highlighting the potential for significant new ways of interaction between mathematicians and AI systems. We present AlphaEvolve as a powerful new tool for mathematical discovery, capable of exploring vast search spaces to solve complex optimization problems at scale, often with significantly reduced requirements on preparation and computation time.

In medical imaging, it is common to use learned perceptual image patch similarity (LPIPS) to compare images semantically in feature space. Although backbones pretrained on natural images are widely used for LPIPS computation, B-mode ultrasound images possess distinct speckle patterns and acoustic-specific image statistics that are fundamentally different from natural images and even from other images in radiology. Consequently, we propose that domain-specific models are needed to measure perceptual similarity in ultrasound data, a finding which is not necessarily the case for other imaging modalities. We compare LPIPS metrics across downstream tasks like classification, segmentation and reconstruction using natural image, medical generalist and ultrasound backbone models and show that selection of LPIPS backbone is a non-trivial design choice. In particular, the ultrasound backbone models were more correlated with downstream performance of supervised models than classical and natural image models, and optimization of the LPIPS loss with an ultrasound backbone achieved a strong balance between reconstruction quality and realism. Our code is available at https://github.com/talg2324/UltraPIPS and introduces the UltraPIPS library, a set of LPIPS metrics based on the open-source foundation models analyzed in this paper.

Diffusion-based text-to-image models have demonstrated impressive achievements in diversity and aesthetics but struggle to generate images with legible visual texts. Existing backbone models have limitations such as misspelling, failing to generate texts, and lack of support for Chinese text, but their development shows promising potential. In this paper, we propose a series of methods, aiming to empower backbone models to generate visual texts in English and Chinese. We first conduct a preliminary study revealing that Byte Pair Encoding (BPE) tokenization and the insufficient learning of cross-attention modules restrict the performance of the backbone models. Based on these observations, we make the following improvements: (1) We design a mixed granularity input strategy to provide more suitable text representations; (2) We propose to augment the conventional training objective with three glyph-aware training losses, which enhance the learning of cross-attention modules and encourage the model to focus on visual texts. Through experiments, we demonstrate that our methods can effectively empower backbone models to generate semantic relevant, aesthetically appealing, and accurate visual text images, while maintaining their fundamental image generation quality.

Choosing the right large language model (LLM) backbone is the most consequential decision when building a vision-language model (VLM), yet it remains fundamentally unprincipled: compute-based scaling laws fail to generalize across model families, and no framework exists for directly predicting VLM performance before training begins. We propose the Capability-Driven Multimodal Scaling Law, the first cross-family framework that predicts VLM benchmark accuracy from directly observable textual capability. Given a low-dimensional capability score S extracted from LLM textual benchmarks via PCA, we model VLM performance as a function of S, with a per-backbone transfer rate and an absorption rate that quantifies data-scaling efficiency. To fit and validate the framework, we train over 150 VLMs on 34 LLMs spanning 7 model families under a strictly controlled recipe. Evaluations on more than 200 textual and 50 multimodal benchmarks show that the law accurately extrapolates transfer rate from models up to 8B parameters to 72B-scale backbones, predicts full VLM training trajectories with high fidelity, and generalizes to entirely held-out model families. Beyond the scaling law, our analysis surfaces actionable insights: certain textual benchmarks negatively correlate with multimodal performance, exposing latent benchmark-gaming behavior; base LLMs outperform instruction-tuned counterparts as VLM backbones due to higher absorption rates and lower data-scaling decay; and different model families occupy distinct positions in the transfer--absorption space. The framework turns backbone selection from costly empirical sweeps into a principled, quantitative decision. Code and data are available at https://github.com/wangq-dev/CDMScaling.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

We present a novel application of evolutionary algorithms to automate the creation of powerful foundation models. While model merging has emerged as a promising approach for LLM development due to its cost-effectiveness, it currently relies on human intuition and domain knowledge, limiting its potential. Here, we propose an evolutionary approach that overcomes this limitation by automatically discovering effective combinations of diverse open-source models, harnessing their collective intelligence without requiring extensive additional training data or compute. Our approach operates in both parameter space and data flow space, allowing for optimization beyond just the weights of the individual models. This approach even facilitates cross-domain merging, generating models like a Japanese LLM with Math reasoning capabilities. Surprisingly, our Japanese Math LLM achieved state-of-the-art performance on a variety of established Japanese LLM benchmarks, even surpassing models with significantly more parameters, despite not being explicitly trained for such tasks. Furthermore, a culturally-aware Japanese VLM generated through our approach demonstrates its effectiveness in describing Japanese culture-specific content, outperforming previous Japanese VLMs. This work not only contributes new state-of-the-art models back to the open-source community, but also introduces a new paradigm for automated model composition, paving the way for exploring alternative, efficient approaches to foundation model development.

Recent advances in large language models have sparked growing interest in AI agents capable of solving complex, real-world tasks. However, most existing agent systems rely on manually crafted configurations that remain static after deployment, limiting their ability to adapt to dynamic and evolving environments. To this end, recent research has explored agent evolution techniques that aim to automatically enhance agent systems based on interaction data and environmental feedback. This emerging direction lays the foundation for self-evolving AI agents, which bridge the static capabilities of foundation models with the continuous adaptability required by lifelong agentic systems. In this survey, we provide a comprehensive review of existing techniques for self-evolving agentic systems. Specifically, we first introduce a unified conceptual framework that abstracts the feedback loop underlying the design of self-evolving agentic systems. The framework highlights four key components: System Inputs, Agent System, Environment, and Optimisers, serving as a foundation for understanding and comparing different strategies. Based on this framework, we systematically review a wide range of self-evolving techniques that target different components of the agent system. We also investigate domain-specific evolution strategies developed for specialised fields such as biomedicine, programming, and finance, where optimisation objectives are tightly coupled with domain constraints. In addition, we provide a dedicated discussion on the evaluation, safety, and ethical considerations for self-evolving agentic systems, which are critical to ensuring their effectiveness and reliability. This survey aims to provide researchers and practitioners with a systematic understanding of self-evolving AI agents, laying the foundation for the development of more adaptive, autonomous, and lifelong agentic systems.

Scientific agents must learn not only how to reason, but also what to believe. However, existing LLM agents typically express scientific hypotheses in free-form text, leaving their beliefs implicit and difficult to test or revise. We introduce EvoSCM, which equips scientific agents with explicit structural causal models that evolve as new experimental evidence is collected. EvoSCM maintains a population of competing SCM hypotheses, each encoding a candidate causal explanation of the environment, and evolves them through a closed discovery loop. In each round, the agent abduces latent mechanisms from accumulated evidence, designs discriminative interventions, and commits to falsifiable predictions that it tests through experimentation. Discrepancies between prediction and observation are inductively distilled into correction rules that revise the causal structures and mechanisms of each hypothesis, and the agent then deductively validates the revised population against accumulated evidence and structural consistency to guide the next round. We evaluate EvoSCM on DiscoverPhysics, a benchmark requiring agents to uncover the hidden dynamics of noncanonical physical worlds through experimentation. EvoSCM consistently improves scientific discovery over baselines, yielding more accurate explanations and predictions while making more effective use of experimental interactions.

Recent advances in self-improving LLM agents have demonstrated the potential of AI systems that drive their own intelligence. However, many domain-specific applications rely on specialized foundation models that possess strong domain expertise but remain dependent on human-designed improvements. Extending recursive self-improvement to these models presents a key challenge: as a specialist improves, the strategies used to advance it must also adapt. To address this challenge, we propose Heterogeneous Agentic CoEvolution (HACE), a framework that jointly evolves specialized foundation models and LLM agents through reciprocal learning. HACE improves the specialist through supervised learning while training the agent with on-policy reinforced self-training, guided by verified performance gains on the current specialist. The agent's exploration, in turn, informs subsequent specialist training, enabling both models to adapt to each other's progress. To sustain this reciprocal learning, HACE further employs evolutionary search to optimize their interaction harness, adapting how the models exchange information and select training experiences as their capabilities evolve. We evaluate HACE across three challenging domains: recommendation systems, protein function prediction in biology, and crystal stability prediction in material discovery. We show that HACE outperforms the evaluated self-improving methods on the primary task metrics across all three domains. These results shed light on heterogeneous coevolution as a universal approach to improving specialized foundation models through reciprocal interaction with a learning agent.

It is well known that anti-malware scanners depend on malware signatures to identify malware. However, even minor modifications to malware code structure results in a change in the malware signature thus enabling the variant to evade detection by scanners. Therefore, there exists the need for a proactively generated malware variant dataset to aid detection of such diverse variants by automated antivirus scanners. This paper proposes and demonstrates a generic assembly source code based framework that facilitates any evolutionary algorithm to generate diverse and potential variants of an input malware, while retaining its maliciousness, yet capable of evading antivirus scanners. Generic code transformation functions and a novelty search supported quality metric have been proposed as components of the framework to be used respectively as variation operators and fitness function, for evolutionary algorithms. The results demonstrate the effectiveness of the framework in generating diverse variants and the generated variants have been shown to evade over 98% of popular antivirus scanners. The malware variants evolved by the framework can serve as antigens to assist malware analysis engines to improve their malware detection algorithms.

In conventional object detection frameworks, a backbone body inherited from image recognition models extracts deep latent features and then a neck module fuses these latent features to capture information at different scales. As the resolution in object detection is much larger than in image recognition, the computational cost of the backbone often dominates the total inference cost. This heavy-backbone design paradigm is mostly due to the historical legacy when transferring image recognition models to object detection rather than an end-to-end optimized design for object detection. In this work, we show that such paradigm indeed leads to sub-optimal object detection models. To this end, we propose a novel heavy-neck paradigm, GiraffeDet, a giraffe-like network for efficient object detection. The GiraffeDet uses an extremely lightweight backbone and a very deep and large neck module which encourages dense information exchange among different spatial scales as well as different levels of latent semantics simultaneously. This design paradigm allows detectors to process the high-level semantic information and low-level spatial information at the same priority even in the early stage of the network, making it more effective in detection tasks. Numerical evaluations on multiple popular object detection benchmarks show that GiraffeDet consistently outperforms previous SOTA models across a wide spectrum of resource constraints. The source code is available at https://github.com/jyqi/GiraffeDet.

Large Language Model (LLM) Agents, often trained with Reinforcement Learning (RL), are constrained by a dependency on human-curated data, limiting scalability and tethering AI to human knowledge. Existing self-evolution frameworks offer an alternative but are typically restricted by the model's inherent capabilities and single-round interactions, hindering the development of complex curricula involving tool use or dynamic reasoning. We introduce Agent0, a fully autonomous framework that evolves high-performing agents without external data through multi-step co-evolution and seamless tool integration. Agent0 establishes a symbiotic competition between two agents initialized from the same base LLM: a curriculum agent that proposes increasingly challenging frontier tasks, and an executor agent that learns to solve them. We integrate external tools to enhance the executor's problem-solving capacity; this improvement, in turn, pressures the curriculum agent to construct more complex, tool-aware tasks. Through this iterative process, Agent0 establishes a self-reinforcing cycle that continuously produces high-quality curricula. Empirically, Agent0 substantially boosts reasoning capabilities, improving the Qwen3-8B-Base model by 18% on mathematical reasoning and 24% on general reasoning benchmarks. Code is available at https://github.com/aiming-lab/Agent0.

We introduce **EvoGraph**, a framework that enables software systems to evolve their own source code, build pipelines, documentation, and tickets. EvoGraph represents every artefact in a typed directed graph, applies learned mutation operators driven by specialized small language models (SLMs), and selects survivors with a multi-objective fitness. On three benchmarks, EvoGraph fixes 83% of known security vulnerabilities, translates COBOL to Java with 93% functional equivalence (test verified), and maintains documentation freshness within two minutes. Experiments show a 40% latency reduction and a sevenfold drop in feature lead time compared with strong baselines. We extend our approach to **evoGraph**, leveraging language-specific SLMs for modernizing .NET, Lisp, CGI, ColdFusion, legacy Python, and C codebases, achieving 82-96% semantic equivalence across languages while reducing computational costs by 90% compared to large language models. EvoGraph's design responds to empirical failure modes in legacy modernization, such as implicit contracts, performance preservation, and integration evolution. Our results suggest a practical path toward Software 3.0, where systems adapt continuously yet remain under measurable control.

Agentic systems are increasingly expected to improve after deployment, yet single-entity self-evolution is often bounded by a static learning context, such as fixed tasks and feedback. This survey focuses on co-evolution in agentic systems, a multi-component form of self-evolution in which multiple agents and their environment impose adaptive pressure on one another. To organize existing papers, we propose a progressive three-stage taxonomy that traces how the system gradually sheds human-engineered constraints. Agent--Agent Co-Evolution studies how agents adapt through dynamic peers, including adversarial, collaborative, and organizational adaptation. Agent--Environment Co-Evolution extends this loop to adaptive tasks, feedback, and interaction spaces that change with the agents. Meta Co-Evolution further explores the possibility of making the evolution mechanism itself evolvable. We also discuss open challenges in evaluating such systems, scaling them across multiple components, and keeping increasingly autonomous evolutionary processes safe and controllable. This survey provides a unified foundation for building robust and open-ended agentic systems that can improve beyond fixed human-designed paths.

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a phylogenetic distance metrics based on the similarity of LLMs' output. The resulting metric is then used to construct dendrograms, which satisfactorily capture known relationships across a set of 111 open-source and 45 closed models. Furthermore, our phylogenetic distance predicts performance in standard benchmarks, thus demonstrating its functional validity and paving the way for a time and cost-effective estimation of LLM capabilities. To sum up, by translating population genetic concepts to machine learning, we propose and validate a tool to evaluate LLM development, relationships and capabilities, even in the absence of transparent training information.

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

Graph neural networks have moved from a niche representation-learning technique to the default model class wherever data carry relational structure. The interesting question is no longer whether message passing helps on a given dataset, but where graph structure earns its computational cost and where it does not. This survey organises the field around a single design space, derives the spectral and spatial formulations from shared first principles, and connects expressive power to the Weisfeiler-Leman hierarchy with explicit statements of what current architectures can and cannot separate. Against that methodological backbone we examine twelve application domains, among them recommendation and social networks, knowledge graphs and language-model integration, drug discovery and molecular property learning, healthcare and neuroscience, computer vision, traffic and urban computing, power and renewable-energy systems, wireless and sixth-generation networks, fraud and cybersecurity, industrial prognostics, materials science, and climate modelling. For each domain we specify the graph-construction choices and their costs, identify which architecture families dominate and why, and separate reported gains from artefacts of weak baselines or favourable splits. A cross-domain comparison exposes recurring patterns: heterophily and scale undercut the same models almost everywhere, temporal graphs remain harder than their static counterparts, and the architectures that top public leaderboards are seldom the ones that reach deployment. We treat over-smoothing, over-squashing, robustness, distribution shift, fairness, and explainability not as a closing checklist but as the constraints that decide adoption.

Large Language Models (LLMs) have shown great promise in tool-making, yet existing frameworks often struggle to efficiently construct reliable toolsets and are limited to single-task settings. To address these challenges, we propose GATE (Graph-based Adaptive Tool Evolution), an adaptive framework that dynamically constructs and evolves a hierarchical graph of reusable tools across multiple scenarios. We evaluate GATE on open-ended tasks (Minecraft), agent-based tasks (TextCraft, DABench), and code generation tasks (MATH, Date, TabMWP). Our results show that GATE achieves up to 4.3x faster milestone completion in Minecraft compared to the previous SOTA, and provides an average improvement of 9.23% over existing tool-making methods in code generation tasks and 10.03% in agent tasks. GATE demonstrates the power of adaptive evolution, balancing tool quantity, complexity, and functionality while maintaining high efficiency. Code and data are available at https://github.com/ayanami2003/GATE.

Self-evolving agents are increasingly used to improve language model systems without human intervention through either weight updates or harness improvements. Existing approaches typically pursue these directions separately: some methods update model weights using self-generated experience, while others rewrite the harness that defines how an agent uses prompts, tools, context, and execution feedback. However, these approaches overlook the relationship between model weights and the agent harness. To connect these processes and ensure effective and smooth agent self-evolving, we propose Evo^2, a framework for weight-harness co-evolution. For harness updates, we design a unified dual-role pipeline that a single policy serves as both a Proposer, which writes harness edits, and a Reflector, which diagnoses their effects and guides revision. For weight updates, harness modifications and their execution outcomes guide the training of both the Proposer and the Reflector. We further develop EvoTIDE, a training pipeline that recovers usable trajectories through edit extraction and prefix continuation, then combines SFT with interleaved GRPO across the two roles. Extensive experiments across three coding benchmarks demonstrate that Evo^2 significantly outperforms existing self-evolution methods. It achieves 82.1% on Polyglot and 48.3% on SWE-bench Verified, compared with 62.6% and 41.0% for the strongest baseline, respectively. We also show that the evolved harnesses transfer to different tasks without further evolution and rank first in cross-benchmark evaluations. Our dual-role harness improvement framework is also able to extend to self-evolution with proprietary models, improving a GPT-5-mini agent's performance from 24.4% to 48.3%. These results demonstrate the applicability of the framework Evo^2 across domains and its broad transferability across models and tasks.

We analyze cumulative parameter trajectories of transformer training under AdamW and identify a dominant low-dimensional drift direction ("backbone") that captures 60--80% of long-horizon displacement from initialization. This direction is highly stable over rolling training windows yet reorients gradually across phases, particularly following objective reweighting. Per-batch gradients exhibit near-noise-floor alignment with the backbone, whereas optimizer-integrated updates align strongly with it, indicating that the structure emerges from accumulated optimizer dynamics rather than instantaneous gradient geometry. Replacing AdamW with SGD-family optimizers eliminates this structure, and reducing β_2 smoothly degrades backbone dominance and reheating recoverability. Reheating experiments show that transverse probe modes can be transiently re-excited without substantially altering accumulated backbone drift. These results provide a trajectory-level characterization of optimizer-induced geometric structure in transformer training and shift attention from instantaneous gradient properties to cumulative update dynamics.

Harness self-evolution revises an agent's software scaffolding, including prompts, memory, workflows, and executable components, while keeping model weights fixed. We formalize a feedback-driven process in which accepted revisions persist across runs. The framework separates update targets from proposal and admission mechanisms. It distinguishes changes to interpreted state from revisions to tools and code, repository-level control logic, and plugin composition. We characterize search through evolutionary optimization and examine its reliability through continual PAC-learning. Under explicit assumptions, the analysis yields an expected generalization bound, a retention bound conditional on historical regression budgets, and a high-probability admission rule using fresh, independent validation data. We examine how persistent harness revisions affect knowledge sharing and organizational workflows, with implications for scientific reliability, physical safety, and institutional accountability. Cases from prior work illustrate model--harness co-design, distributed execution, and plugin reuse. Reliable deployment requires continual validation as task distributions and evaluators change, with independent safeguards for learning, runtime privileges, and consequential actions. We provide a comprehensive 66-page discussion of related work, theory, algorithms, evaluation, applications, and the broader impact of Harness RSI, together with continuously updated code and supplementary materials, at https://github.com/zgcagi/Harness-RSI.

Recent LLM agents tackle increasingly long-horizon, open-ended tasks, and external skills, reusable procedural knowledge supplied to the agent, further extend this capability. However, a fixed, hand-authored skill is rarely optimal, and cannot adapt to the diversity of tasks an agent encounters. Self-improving agents address this by rewriting their own skill files from execution traces, yielding meaningful gains on challenging benchmarks. Yet such self-evolution remains non-recursive: it improves only the task skill (what the agent does) while the improvement procedure (how it improves) is authored once and held fixed. We introduce MetaSkill-Evolve, a two-timescale framework that makes agentic skill improvement recursive: every branch carries both a task skill s and a branch-local meta-skill m=(ψ,σ,α,π,varepsilon) whose five components parameterise the Analyzer, Retriever, Allocator, Proposer, and Evolver agents of the improvement pipeline. Task skills evolve on a fast loop while the meta-skill evolves on a slower one under the same pipeline applied to itself, with no additional model or objective. With all five pipeline agents sharing a single frozen backbone, MetaSkill-Evolve outperforms no-skill, static-skill, and single-level evolution baselines on three agentic benchmarks (OfficeQA, SealQA, ALFWorld), improving held-out test accuracy over the raw backbone by +23.54, +16.09, and +1.92 points respectively.

Click-based interactive image segmentation aims at extracting objects with a limited user clicking. A hierarchical backbone is the de-facto architecture for current methods. Recently, the plain, non-hierarchical Vision Transformer (ViT) has emerged as a competitive backbone for dense prediction tasks. This design allows the original ViT to be a foundation model that can be finetuned for downstream tasks without redesigning a hierarchical backbone for pretraining. Although this design is simple and has been proven effective, it has not yet been explored for interactive image segmentation. To fill this gap, we propose SimpleClick, the first interactive segmentation method that leverages a plain backbone. Based on the plain backbone, we introduce a symmetric patch embedding layer that encodes clicks into the backbone with minor modifications to the backbone itself. With the plain backbone pretrained as a masked autoencoder (MAE), SimpleClick achieves state-of-the-art performance. Remarkably, our method achieves 4.15 NoC@90 on SBD, improving 21.8% over the previous best result. Extensive evaluation on medical images demonstrates the generalizability of our method. We further develop an extremely tiny ViT backbone for SimpleClick and provide a detailed computational analysis, highlighting its suitability as a practical annotation tool.

Prosocial behaviors are encountered in the donation game, the prisoner's dilemma, relaxed social dilemmas, and public goods games. Many studies assume that the population structure is homogeneous, meaning all individuals have the same number of interaction partners, or that the social good is of one particular type. Here, we explore general evolutionary dynamics for arbitrary spatial structures and social goods. We find that heterogeneous networks, wherein some individuals have many more interaction partners than others, can enhance the evolution of prosocial behaviors. However, they often accumulate most of the benefits in the hands of a few highly-connected individuals, while many others receive low or negative payoff. Surprisingly, selection can favor producers of social goods even if the total costs exceed the total benefits. In summary, heterogeneous structures have the ability to strongly promote the emergence of prosocial behaviors, but they also create the possibility of generating large inequality.

The evolution of generative artificial intelligence (GenAI) constitutes a turning point in reshaping the future of technology in different aspects. Wireless networks in particular, with the blooming of self-evolving networks, represent a rich field for exploiting GenAI and reaping several benefits that can fundamentally change the way how wireless networks are designed and operated nowadays. To be specific, large language models (LLMs), a subfield of GenAI, are envisioned to open up a new era of autonomous wireless networks, in which a multimodal large model trained over various Telecom data, can be fine-tuned to perform several downstream tasks, eliminating the need for dedicated AI models for each task and paving the way for the realization of artificial general intelligence (AGI)-empowered wireless networks. In this article, we aim to unfold the opportunities that can be reaped from integrating LLMs into the Telecom domain. In particular, we aim to put a forward-looking vision on a new realm of possibilities and applications of LLMs in future wireless networks, defining directions for designing, training, testing, and deploying Telecom LLMs, and reveal insights on the associated theoretical and practical challenges.

The public model zoo containing enormous powerful pretrained model families (e.g., ResNet/DeiT) has reached an unprecedented scope than ever, which significantly contributes to the success of deep learning. As each model family consists of pretrained models with diverse scales (e.g., DeiT-Ti/S/B), it naturally arises a fundamental question of how to efficiently assemble these readily available models in a family for dynamic accuracy-efficiency trade-offs at runtime. To this end, we present Stitchable Neural Networks (SN-Net), a novel scalable and efficient framework for model deployment. It cheaply produces numerous networks with different complexity and performance trade-offs given a family of pretrained neural networks, which we call anchors. Specifically, SN-Net splits the anchors across the blocks/layers and then stitches them together with simple stitching layers to map the activations from one anchor to another. With only a few epochs of training, SN-Net effectively interpolates between the performance of anchors with varying scales. At runtime, SN-Net can instantly adapt to dynamic resource constraints by switching the stitching positions. Extensive experiments on ImageNet classification demonstrate that SN-Net can obtain on-par or even better performance than many individually trained networks while supporting diverse deployment scenarios. For example, by stitching Swin Transformers, we challenge hundreds of models in Timm model zoo with a single network. We believe this new elastic model framework can serve as a strong baseline for further research in wider communities.

Reasoning models have demonstrated remarkable capabilities in solving complex problems by leveraging long chains of thought. However, this more deliberate reasoning comes with substantial computational overhead at inference time. The Long-to-Short (L2S) reasoning problem seeks to maintain high accuracy using fewer tokens, but current training-free model merging approaches rely on scalarized, fixed-hyperparameter arithmetic methods that are highly brittle and force suboptimal compromises. To address this gap, we introduce Evo-L2S, a novel framework that formulates L2S reasoning as a multi-objective optimization challenge. By leveraging evolutionary model merging, Evo-L2S explicitly optimizes the trade-off between accuracy and output length to produce a robust Pareto front of merged models. To make this search computationally tractable for large language models, we propose an entropy-based subset sampling technique that drastically reduces the overhead of fitness estimation. Comprehensive experiments across 1.5B, 7B, and 14B parameter scales on six mathematical reasoning benchmarks demonstrate that Evo-L2S can reduce the length of generated reasoning traces by over 50% while preserving, or even improving, the problem-solving accuracy of the original reasoning models.

Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs, a binder that engages both active and inactive states provides no functional specificity regardless of how tightly it binds. We introduce AlloGen, a modular framework that decouples backbone generation from a learned state-selectivity scorer Q_θ, an SE(3)-invariant interface graph transformer trained via a two-phase curriculum that first learns interface geometry before imposing conformational discrimination. Because Q_θ is fully differentiable and generator-agnostic, it integrates with any backbone generator as a passive reranker or an active gradient-based guide without retraining. Across a diverse benchmark of proteins spanning multiple families and conformational mechanisms, AlloGen consistently identifies binders that preferentially recognize desired structural states while rejecting alternative conformations. Experimental validation on calmodulin further demonstrates that these computational selectivity signals translate to physical molecules, yielding de novo peptides that bind the desired holo conformation while exhibiting no detectable binding to the apo state. Together, these results establish conformational selectivity as a learnable property and provide a general framework for state-selective protein binder design.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

One of the biggest missing capabilities in current AI systems is the ability to learn continuously after deployment. Implementing such continually learning systems have several challenges, one of which is the large memory requirement of gradient-based algorithms that are used to train state-of-the-art LLMs. Evolutionary Strategies (ES) have recently re-emerged as a gradient-free alternative to traditional learning algorithms and have shown encouraging performance on specific tasks in LLMs. In this paper, we perform a comprehensive analysis of ES and specifically evaluate its forgetting curves when training for an increasing number of update steps. We first find that ES is able to reach performance numbers close to GRPO for math and reasoning tasks with a comparable compute budget. However, and most importantly for continual learning, the performance gains in ES is accompanied by significant forgetting of prior abilities, limiting its applicability for training models online. We also explore the reason behind this behavior and show that the updates made using ES are much less sparse and have orders of magnitude larger ell_2 norm compared to corresponding GRPO updates, explaining the contrasting forgetting curves between the two algorithms. With this study, we aim to highlight the issue of forgetting in gradient-free algorithms like ES and hope to inspire future work to mitigate these issues.

Current popular backbones in computer vision, such as Vision Transformers (ViT) and ResNets are trained to perceive the world from 2D images. However, to more effectively understand 3D structural priors in 2D backbones, we propose Mask3D to leverage existing large-scale RGB-D data in a self-supervised pre-training to embed these 3D priors into 2D learned feature representations. In contrast to traditional 3D contrastive learning paradigms requiring 3D reconstructions or multi-view correspondences, our approach is simple: we formulate a pre-text reconstruction task by masking RGB and depth patches in individual RGB-D frames. We demonstrate the Mask3D is particularly effective in embedding 3D priors into the powerful 2D ViT backbone, enabling improved representation learning for various scene understanding tasks, such as semantic segmentation, instance segmentation and object detection. Experiments show that Mask3D notably outperforms existing self-supervised 3D pre-training approaches on ScanNet, NYUv2, and Cityscapes image understanding tasks, with an improvement of +6.5% mIoU against the state-of-the-art Pri3D on ScanNet image semantic segmentation.

This paper delves into the interplay between vision backbones and optimizers, unvealing an inter-dependent phenomenon termed \textbf{backbone-optimizer coupling bias} (BOCB). We observe that canonical CNNs, such as VGG and ResNet, exhibit a marked co-dependency with SGD families, while recent architectures like ViTs and ConvNeXt share a tight coupling with the adaptive learning rate ones. We further show that BOCB can be introduced by both optimizers and certain backbone designs and may significantly impact the pre-training and downstream fine-tuning of vision models. Through in-depth empirical analysis, we summarize takeaways on recommended optimizers and insights into robust vision backbone architectures. We hope this work can inspire the community to question long-held assumptions on backbones and optimizers, stimulate further explorations, and thereby contribute to more robust vision systems. The source code and models are publicly available at https://bocb-ai.github.io/.

Research in efficient vision backbones is evolving into models that are a mixture of convolutions and transformer blocks. A smart combination of both, architecture-wise and component-wise is mandatory to excel in the speedaccuracy trade-off. Most publications focus on maximizing accuracy and utilize MACs (multiply accumulate operations) as an efficiency metric. The latter however often do not measure accurately how fast a model actually is due to factors like memory access cost and degree of parallelism. We analyzed common modules and architectural design choices for backbones not in terms of MACs, but rather in actual throughput and latency, as the combination of the latter two is a better representation of the efficiency of models in real applications. We applied the conclusions taken from that analysis to create a recipe for increasing hardware-efficiency in macro design. Additionally we introduce a simple slimmed-down version of MultiHead Self-Attention, that aligns with our analysis. We combine both macro and micro design to create a new family of hardware-efficient backbone networks called LowFormer. LowFormer achieves a remarkable speedup in terms of throughput and latency, while achieving similar or better accuracy than current state-of-the-art efficient backbones. In order to prove the generalizability of our hardware-efficient design, we evaluate our method on GPU, mobile GPU and ARM CPU. We further show that the downstream tasks object detection and semantic segmentation profit from our hardware-efficient architecture. Code and models are available at https://github.com/ altair199797/LowFormer.

Agent-evolution methods use execution feedback to improve prompts, skills, tools, and orchestration, but their implementations often rebuild the same experimental machinery. We present RSIHub, an open-source framework for building, comparing, and extending these methods on shared infrastructure. Recipes compose reusable operators and declare mutable resources; RSIHub supplies execution, evaluation, recovery, and lineage. Researchers can focus on evolution policy while evaluation stays outside the mutable surface and results remain tied to candidates and evaluation conditions. We instantiate AHE, Hyperagents, A-Evolve, and GEPA without modifying the framework core, keeping method-specific logic in recipes and operators. We evaluate them with MiniSWE and Codex on Terminal Bench 2 and τ^3 Banking under fixed model and evaluator configurations. The largest observed overall pass@1 gain is 13.5 percentage points, while method rankings vary across settings and optimization gains do not always transfer to held-out tasks. RSIHub provides a common protocol for comparing evolution policies, inspectable candidate histories, and reusable components for developing new methods.

Deploying language-model agents in production often requires substantial compute and human effort to tune prompts, parsers, validators, and other components of the agent pipeline. Self-evolution offers a promising alternative, but most existing frameworks assume access to frontier models that can reliably diagnose failures, propose revisions, and judge their own updates. We study whether frozen small language models (SLMs) can serve as effective self-evolving agents under resource constraints. We propose PACE (Prompt And Control Logic Evolution), a two-timescale framework that coordinates low-risk prompt refinement with higher-risk control-logic updates. PACE evolves prompts under fixed control logic until prompt-level gains saturate, then considers constrained control-logic updates that are accepted through held-out validation. Across three frozen SLM backbones ranging from 4B to 14B parameters and four controlled benchmarks, PACE achieves the best performance on all 12 backbone--benchmark combinations, improving over vanilla SLM agents by up to +9.2% relative improvement and over the stronger single-mode evolution baseline by up to +5.4% relative improvement. A tau-bench case study further shows that PACE improves multi-turn tool-use success over vanilla and prompt-only evolution. These results suggest that reliable SLM agent self-evolution is possible without updating model weights or relying on frontier-model teachers, and that the key benefit is not any single final solver pattern but autonomous, validated discovery of task-appropriate inference strategies.

Generative recommendation has emerged as a promising end-to-end paradigm for personalized recommendation. However, user preferences continuously evolve over time, making self-evolving an essential capability for generative recommender systems. Existing evolving strategies, such as continual retraining and distillation-based adaptation, directly update the shared model parameters using streaming interactions. Nevertheless, we find that directly applying such strategies to generative recommendation introduces a critical issue, termed evolution conflict. Specifically, heterogeneous preference shifts from different users are optimized within a fully shared autoregressive parameter space, causing dominant behavioral patterns to progressively dominate the model evolution process while underrepresented patterns become increasingly overlooked. To address this issue, we propose a self-evolving memory paradigm for generative recommendation, aiming to enable effective evolution across heterogeneous behavioral patterns. We further identify three key principles for effective self-evolving recommendation systems, including isolated memorization, reinforced evolution, and scalable application. Guided by these principles, we develop LION, a simple yet effective framework centered on a sparse Key-Value memory layer. Specifically, LION introduces sparse memory activation to isolate the evolution of different behavioral patterns, while a consolidation loss is designed to reinforce the learning of underrepresented preference dynamics during continual adaptation. Extensive experiments on diverse real-world datasets demonstrate the effectiveness of LION under various continual evolution settings (e.g., per-period evaluation, user/item group evaluation, and evolution convergence analysis). The codes are released at https://github.com/JazyJiang/Self-Evolving-Memory-for-Generative-Recommendation.

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

Autonomous discovery systems such as OpenEvolve and TTT-Discover are often used as general-purpose harnesses. However, in practice these are composite systems combining several design choices about archives, parent selection, exploration, and budget allocation into a single recipe. Because discovery runs are expensive and inherently stochastic, existing harnesses are often compared using too few independent trials to distinguish key methodological improvements from run-to-run variance. We systematically decompose OpenEvolve-style evolutionary search and the TTT-Discover search harness into its constituent components and systematically evaluate 30 budget-matched harnesses across 12 model-problem pairs using more than 3.1 million LLM rollouts and repeated-trial statistical analysis. Our results show that discovery harnesses have a generalization problem: No fixed harness is reliably superior across the evaluated model-problem pairs, and variants of OpenEvolve generally underperform simpler alternatives. Thus, harness choice is better viewed as a hyperparameter rather than as a universal recipe, and should be tailored to the specific problem and underlying model. We also find that early discovery progress predicts final performance, and use this property to present a budget-matched adaptive-allocation experiment that starts multiple harnesses, prunes weak partial runs, and reallocates compute to stronger survivors, outperforming both commitment to a randomly sampled fixed harness and a non-adaptive harness ensemble. Together, these results motivate shifting from fixed harness selection to online adaptation guided by early performance. We release all run pools including baseline null distributions for every model-problem pair as reusable statistical infrastructure against for future harness proposals.

Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in complex domains, while pure deep research proposes ideas without validation, resulting in unrealistic or unimplementable solutions. We present DeepEvolve, an agent that integrates deep research with algorithm evolution, uniting external knowledge retrieval, cross-file code editing, and systematic debugging under a feedback-driven iterative loop. Each iteration not only proposes new hypotheses but also refines, implements, and tests them, avoiding both shallow improvements and unproductive over-refinements. Across nine benchmarks in chemistry, mathematics, biology, materials, and patents, DeepEvolve consistently improves the initial algorithm, producing executable new algorithms with sustained gains. By bridging the gap between unguided evolution and research without grounding, DeepEvolve provides a reliable framework for advancing scientific algorithm discovery. Our code is available at https://github.com/liugangcode/deepevolve.

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model. Herein, we present ProteinGuide, a method for such "on-the-fly" conditioning, amenable to a broad class of protein generative models including Masked Language Models (e.g. ESM3), any-order auto-regressive models (e.g. ProteinMPNN) as well as diffusion and flow matching models (e.g. MultiFlow). ProteinGuide stems from our unifying view of these model classes under a single statistical framework. As proof of principle, we perform several in silico experiments. We first guide pre-trained generative models to design proteins with user-specified properties, such as higher stability or activity. Next, we design for optimizing two desired properties that are in tension with each other. Finally, we apply our method in the wet lab, using ProteinGuide to increase the editing activity of an adenine base editor in vivo with data from only a single pooled library of 2,000 variants. We find that a single round of ProteinGuide achieves a higher editing efficiency than was previously achieved using seven rounds of directed evolution.

Since its emergence, SARS-CoV-2 has demonstrated a rapid and unpredictable evolutionary trajectory, characterized by the continual emergence of immune-evasive variants. This poses persistent challenges to public health and vaccine development. While large-scale generative pre-trained transformers (GPTs) have revolutionized the modeling of sequential data, their direct applications to noisy viral genomic sequences are limited. In this paper, we introduce PETRA(Pretrained Evolutionary TRAnsformer), a novel transformer approach based on evolutionary trajectories derived from phylogenetic trees rather than raw RNA sequences. This method effectively mitigates sequencing noise and captures the hierarchical structure of viral evolution. With a weighted training framework to address substantial geographical and temporal imbalances in global sequence data, PETRA excels in predicting future SARS-CoV-2 mutations, achieving a weighted recall@1 of 9.45% for nucleotide mutations and 17.10\% for spike amino-acid mutations, compared to 0.49% and 6.64% respectively for the best baseline. PETRA also demonstrates its ability to aid in the real-time mutation prediction of major clades like 24F(XEC) and 25A(LP.8.1). The code is open sourced on https://github.com/xz-keg/PETra

Prototype-based neural networks aim to provide intrinsic interpretability by grounding predictions in a small set of part prototypes. However, modern vision backbones typically operate in normalized, directional embedding spaces where each semantic part exhibits substantial intra-class variability. As a result, point prototypes often become redundant or unstable, hurting both explanation quality and robustness. We propose vMFProto, a distributional part-prototype framework that models each class as a mixture of von Mises-Fisher components on the hypersphere. Each prototype learns its own concentration, capturing part-specific variability, and we use entropic optimal transport (OT) to obtain structured patch-to-prototype assignments. A two-stage training schedule performs OT-driven prototype discovery followed by end-to-end refinement with patch-level distillation and distribution-aware diversity regularization. Experiments with frozen DINO backbones show that vMFProto achieves leading consistency and distinctiveness on CUB-200-2011 and competitive classification accuracy across CUB, Stanford Dogs, and Stanford Cars. Qualitative results confirm that vMFProto yields localized, non-redundant part evidence.

Autonomous agents driven by Large Language Models (LLMs) have revolutionized reasoning and problem-solving but remain static after training, unable to grow with experience as intelligent beings do during deployment. We introduce Forward Learning with EXperience (FLEX), a gradient-free learning paradigm that enables LLM agents to continuously evolve through accumulated experience. Specifically, FLEX cultivates scalable and inheritable evolution by constructing a structured experience library through continual reflection on successes and failures during interaction with the environment. FLEX delivers substantial improvements on mathematical reasoning, chemical retrosynthesis, and protein fitness prediction (up to 23% on AIME25, 10% on USPTO50k, and 14% on ProteinGym). We further identify a clear scaling law of experiential growth and the phenomenon of experience inheritance across agents, marking a step toward scalable and inheritable continuous agent evolution. Project Page: https://flex-gensi-thuair.github.io.

We present RoboPhD, a system where AI agents autonomously conduct research to improve Text-to-SQL performance. RoboPhD implements a closed-loop evolution cycle with two coordinated components: a SQL Generation agent composed of a database analysis script and SQL generation instructions, and an Evolution agent that designs new versions based on performance feedback. Central to the framework is an ELO-based selection mechanism enabling survival-of-the-fittest dynamics while handling non-transitivity in performance. Starting from a naive 70-line baseline, RoboPhD evolves agents through iterative cross-pollination, discovering effective techniques without any external guidance on the Text-to-SQL domain. Our best agent, evolved to 1500 lines over 18 iterations, autonomously discovered strategies such as size-adaptive database analysis that adjusts depth based on schema complexity and SQL generation patterns for column selection, evidence interpretation, and aggregation. Evolution provides the largest gains on cheaper models: while we improve by 2.3 points over a strong Claude Opus 4.5 naive baseline, we show an improvement of 8.9 points over the weaker Claude Haiku model. This enables 'skip a tier' deployment: evolved Haiku exceeds naive Sonnet accuracy, and evolved Sonnet exceeds naive Opus, both at lower cost. The full system achieves 73.67% accuracy on the BIRD test set, demonstrating that AI can autonomously build a strong agentic system with only a trivial human-provided starting point.

Proteins change shape as they function, yet most inverse folding models predict amino acid sequences from a single, fixed backbone. A central challenge in protein engineering is to design proteins that undergo specific motions, which requires accounting for how their structures change over time. This motivates inverse protein folding conditioned on protein motion. We introduce SPINET, which predicts sequences from molecular dynamics trajectories. It uses cellular sheaves to represent residue interactions within each frame and recurrent units to integrate information across frames, then predicts all amino acids in a single pass. We evaluate SPINET on mdCATH and ATLAS, where it outperforms all evaluated static and ensemble baselines in sequence recovery. On mdCATH, it achieves 56.7% top-1 recovery, compared with 44.5% for the strongest static baseline and 40.7% for the strongest ensemble baseline. We also evaluate whether the predicted sequences are compatible with conformations sampled along the target trajectory. On mdCATH, they achieve a median TM-score of 0.760, and structural recovery favors target conformations over unrelated decoys for 99.5% of test domains.

Classical continual learning (CL) has primarily focused on enabling models to update and retain knowledge through parameter-centric mechanisms, e.g., training strategies, architectural designs, and weight adaptation. However, emerging paradigms are reshaping the scope of CL beyond this traditional model adaptation view. For instance, on-policy learning broadens the space of update mechanisms; test-time training extends CL from the training phase to inference; and external harness components such as memory, skill libraries, and interaction protocols extend the evolutionary boundaries of model capabilities far beyond the static parameter space. Collectively, these developments indicate a transition from parameter-centric learning toward system-level adaptation. To characterize this transition, we examine the evolution of continual learning through three dimensions: When, How, and Where learning occurs. The How dimension encompasses off-policy, on-policy, and beyond-gradient optimization mechanics. The When dimension captures evolution across pre-training, post-training, and inference-time stages. The Where dimension delineates updates occurring within internal parameters versus external structural constraints. Anchored by this tri-axial framework, we systematically survey representative methods, trace the ongoing transition of continual learning, and discuss the key challenges, broader implications, and future directions arising from this paradigm shift.

Language models (LMs) perform well on standardized coding benchmarks but struggle with real-world software engineering tasks such as resolving GitHub issues in SWE-Bench, especially when model parameters are less than 100B. While smaller models are preferable in practice due to their lower computational cost, improving their performance remains challenging. Existing approaches primarily rely on supervised fine-tuning (SFT) with high-quality data, which is expensive to curate at scale. An alternative is test-time scaling: generating multiple outputs, scoring them using a verifier, and selecting the best one. Although effective, this strategy often requires excessive sampling and costly scoring, limiting its practical application. We propose Evolutionary Test-Time Scaling (EvoScale), a sample-efficient method that treats generation as an evolutionary process. By iteratively refining outputs via selection and mutation, EvoScale shifts the output distribution toward higher-scoring regions, reducing the number of samples needed to find correct solutions. To reduce the overhead from repeatedly sampling and selection, we train the model to self-evolve using reinforcement learning (RL). Rather than relying on external verifiers at inference time, the model learns to self-improve the scores of its own generations across iterations. Evaluated on SWE-Bench-Verified, EvoScale enables our 32B model, Satori-SWE-32B, to match or exceed the performance of models with over 100B parameters while using a few samples. Code, data, and models will be fully open-sourced.

Self-supervised image backbones can be used to address complex 2D tasks (e.g., semantic segmentation, object discovery) very efficiently and with little or no downstream supervision. Ideally, 3D backbones for lidar should be able to inherit these properties after distillation of these powerful 2D features. The most recent methods for image-to-lidar distillation on autonomous driving data show promising results, obtained thanks to distillation methods that keep improving. Yet, we still notice a large performance gap when measuring the quality of distilled and fully supervised features by linear probing. In this work, instead of focusing only on the distillation method, we study the effect of three pillars for distillation: the 3D backbone, the pretrained 2D backbones, and the pretraining dataset. In particular, thanks to our scalable distillation method named ScaLR, we show that scaling the 2D and 3D backbones and pretraining on diverse datasets leads to a substantial improvement of the feature quality. This allows us to significantly reduce the gap between the quality of distilled and fully-supervised 3D features, and to improve the robustness of the pretrained backbones to domain gaps and perturbations.

In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.2 billion parameters, trained on over 280 million protein sequences belonging to the UniRef-100 database. Such generative models hold the promise of greatly accelerating protein design. We conduct the first systematic study of how capabilities evolve with model size for autoregressive transformers in the protein domain: we evaluate RITA models in next amino acid prediction, zero-shot fitness, and enzyme function prediction, showing benefits from increased scale. We release the RITA models openly, to the benefit of the research community.

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13\% in designability and 13\% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

3D content creation has achieved significant progress in terms of both quality and speed. Although current feed-forward models can produce 3D objects in seconds, their resolution is constrained by the intensive computation required during training. In this paper, we introduce Large Multi-View Gaussian Model (LGM), a novel framework designed to generate high-resolution 3D models from text prompts or single-view images. Our key insights are two-fold: 1) 3D Representation: We propose multi-view Gaussian features as an efficient yet powerful representation, which can then be fused together for differentiable rendering. 2) 3D Backbone: We present an asymmetric U-Net as a high-throughput backbone operating on multi-view images, which can be produced from text or single-view image input by leveraging multi-view diffusion models. Extensive experiments demonstrate the high fidelity and efficiency of our approach. Notably, we maintain the fast speed to generate 3D objects within 5 seconds while boosting the training resolution to 512, thereby achieving high-resolution 3D content generation.

Relational Databases (RDBs) are the backbone of modern business, yet they lack foundation models comparable to those in text or vision. A key obstacle is that high-quality RDBs are private, scarce and structurally heterogeneous, making internet-scale pre-training infeasible. To overcome this data scarcity, We introduce RDB-PFN, the first relational foundation model trained purely via synthetic data. Inspired by Prior-Data Fitted Networks (PFNs) where synthetic data generated from Structural Causal Models (SCMs) enables reasoning on single tables, we design a Relational Prior Generator to create an infinite stream of diverse RDBs from scratch. Pre-training on over 2 million synthetic single-table and relational tasks, RDB-PFN learns to adapt to any new database instantly via genuine in-context learning. Experiments verify RDB-PFN achieves strong few-shot performance on 19 real-world relational prediction tasks, outperforming graph-based and single-table foundation-model baselines (given the same DFS-linearized inputs), while using a lightweight architecture and fast inference. The code is available at https://github.com/MuLabPKU/RDBPFN

We propose a new concept, Evolution 6.0, which represents the evolution of robotics driven by Generative AI. When a robot lacks the necessary tools to accomplish a task requested by a human, it autonomously designs the required instruments and learns how to use them to achieve the goal. Evolution 6.0 is an autonomous robotic system powered by Vision-Language Models (VLMs), Vision-Language Action (VLA) models, and Text-to-3D generative models for tool design and task execution. The system comprises two key modules: the Tool Generation Module, which fabricates task-specific tools from visual and textual data, and the Action Generation Module, which converts natural language instructions into robotic actions. It integrates QwenVLM for environmental understanding, OpenVLA for task execution, and Llama-Mesh for 3D tool generation. Evaluation results demonstrate a 90% success rate for tool generation with a 10-second inference time, and action generation achieving 83.5% in physical and visual generalization, 70% in motion generalization, and 37% in semantic generalization. Future improvements will focus on bimanual manipulation, expanded task capabilities, and enhanced environmental interpretation to improve real-world adaptability.

An LLM agent's capability is largely magnified by its harness, namely the prompts, control flow, tooling, memory, and context management surrounding the frozen backbone model. Recent methods increasingly automate this process by iteratively proposing and selecting component-wise edits of an agent harness, practically establishing a form of recursive self-improvement (RSI) at the agent-system level. However, such recursive evolution may overfit by memorizing the training tasks, showing large in-distribution gains that shrink or even vanish on out-of-distribution benchmarks. We introduce Regularized Recursive Self-Improvement of Agent Harnesses (RRSI), which incorporates the principles of regularizations into harness self-improvement by constraining the evolution candidate proposal and selection. The proposer operates with a temporally annealed budget, limiting how many edits a candidate can bundle, and it encourages unexplored trajectories based on evolution history. The selector is equipped with a critic and a pruner: the critic screens benchmark-specific proposals, while the pruner, removes changes that are too small, too expensive, or no longer useful. Together these constraints favor reusable agent mechanisms over benchmark-specific ones or even noises. Across eight benchmarks spanning coding, agentic workspace and engineering design tasks, RRSI gains up to 14.1 points on the split it evolves against and up to 4.7 points on the five out-of-distribution benchmarks, while producing a harness that runs on 30% fewer policy tokens than the unregularized evolution. Code is available at https://github.com/google-research/rrsi and project page is https://regularized-rsi.com/.

We introduce MORAD, an online reinforcement learning framework for backbone-conditioned RNA diffusion models that trains a single shared policy across diverse target backbones. Structure-conditioned RNA inverse design seeks nucleotide sequences compatible with a target three-dimensional backbone, yet existing reinforcement learning approaches either optimize a separate policy for each target backbone or rely on offline preference optimization, leaving online post-training of a reusable backbone-conditioned model largely unexplored. MORAD combines backbone-conditioned group sampling, group-relative reward normalization, and a forward-process diffusion objective. Beyond existing RL rewards that primarily target tertiary structural quality, MORAD jointly optimizes six measurements spanning tertiary geometry, base pairing, ensemble behavior, and sequence composition. To aggregate these heterogeneous objectives despite differences in scale and optimization direction, MORAD maps each measurement to a bounded desirability score and combines them with a weighted geometric mean. Compared with a tertiary-structure-only reward, this multi-objective formulation improves 10 of the 11 evaluation metrics that have a preferred direction. Applied to pretrained RIDE, MORAD improves GDT-TS by 16.0% (from 0.3300 to 0.3827) and pairing MCC by 19.4% (from 0.6110 to 0.7295), while reducing normalized ensemble defect by 27.5% (from 0.3906 to 0.2830). On the test set, MORAD outperforms RiboDiffusion, gRNAde, and RDesign across tertiary structural accuracy, secondary-structure pairing, and thermodynamic quality, establishing a new state of the art in structure-conditioned RNA inverse design.

The increasing adoption of Large Language Models (LLMs) has enabled AI scientists to perform complex end-to-end scientific discovery tasks requiring coordination of specialized roles, including idea generation and experimental execution. However, most state-of-the-art AI scientist systems rely on static, hand-designed pipelines and fail to adapt based on accumulated interaction histories. As a result, these systems overlook promising research directions, repeat failed experiments, and pursue infeasible ideas. To address this, we introduce EvoScientist, an evolving multi-agent AI scientist framework that continuously improves research strategies through persistent memory and self-evolution. EvoScientist comprises three specialized agents: a Researcher Agent (RA) for scientific idea generation, an Engineer Agent (EA) for experiment implementation and execution, and an Evolution Manager Agent (EMA) that distills insights from prior interactions into reusable knowledge. EvoScientist contains two persistent memory modules: (i) an ideation memory, which summarizes feasible research directions from top-ranked ideas while recording previously unsuccessful directions; and (ii) an experimentation memory, which captures effective data processing and model training strategies derived from code search trajectories and best-performing implementations. These modules enable the RA and EA to retrieve relevant prior strategies, improving idea quality and code execution success rates over time. Experiments show that EvoScientist outperforms 7 open-source and commercial state-of-the-art systems in scientific idea generation, achieving higher novelty, feasibility, relevance, and clarity via automatic and human evaluation. EvoScientist also substantially improves code execution success rates through multi-agent evolution, demonstrating persistent memory's effectiveness for end-to-end scientific discovery.