Daily Papers

Single-cell RNA-seq representation learning is fundamentally label-free: cell identities, states, and contexts are not fixed training targets, so what constitutes signal or nuisance is analysis-dependent. A single representation must therefore preserve biological identity and state, remain robust to nuisance context, and retain the gene-level variation needed for expression analysis, three demands we call the representation trilemma. To tackle this problem, we introduce scTrilemma, a latent-bottleneck VAE that routes expression-derived variation to the embedding, the decoder, or the prior rather than forcing all of it through one embedding. It gates gene tokens by expression, routes the cell representation through the decoder, and conditions the prior on unlabeled pseudo-bulk context, under a single reconstruction objective and without target annotations or auxiliary representation losses. In release-based zero-shot evaluation on successive CZ CELLxGENE Census releases, scTrilemma leads all three demands at once and preserves biological-state, differential-expression, and pathway structure across multiple disease settings. Latent interventions further show that context can be removed at almost no cost to the other demands, leaving identity against fidelity as the remaining tension. Code is publicly available at https://github.com/yunhak0/scTrilemma.

Histopathology whole-slide images (WSIs) are routinely acquired in clinical practice and contain rich tissue morphology but lack direct molecular architecture and functional programs defining pathological states, whereas RNA sequencing (RNA-seq) provides genome-wide transcriptional profiles at substantial cost, thereby motivating WSI-based genome-wide transcriptomic prediction. Existing approaches for predicting gene expression from WSIs predominantly rely on deterministic regression with one-to-one mapping, limiting their ability to capture biological heterogeneity and predictive uncertainty. We propose RNA-FM, a flow-matching generative framework for genome-wide bulk RNA-seq prediction from WSIs. RNA-FM formulates transcriptomic prediction as a continuous-time conditional transport problem, learning a velocity field that maps a simple prior to the target gene expression distribution conditioned on morphologies. By integrating pathway-level structure, RNA-FM enables scalable and biologically interpretable genome-wide gene expression imputation. Extensive experiments demonstrate that RNA-FM consistently outperforms state-of-the-art approaches while maintaining biological meaningfulness. Code is available at https://github.com/YXSong000/RNA-FM.

Quantum optimization holds promise for addressing classically intractable combinatorial problems, yet a standardized framework for benchmarking its performance, particularly in terms of solution quality, computational speed, and scalability is still lacking. In this work, we introduce a comprehensive benchmarking framework designed to systematically evaluate a range of quantum optimization techniques against well-established NP-hard combinatorial problems. Our framework focuses on key problem classes, including the Multi-Dimensional Knapsack Problem (MDKP), Maximum Independent Set (MIS), Quadratic Assignment Problem (QAP), and Market Share Problem (MSP). Our study evaluates gate-based quantum approaches, including the Variational Quantum Eigensolver (VQE) and its CVaR-enhanced variant, alongside advanced quantum algorithms such as the Quantum Approximate Optimization Algorithm (QAOA) and its extensions. To address resource constraints, we incorporate qubit compression techniques like Pauli Correlation Encoding (PCE) and Quantum Random Access Optimization (QRAO). Experimental results, obtained from simulated quantum environments and classical solvers, provide key insights into feasibility, optimality gaps, and scalability. Our findings highlight both the promise and current limitations of quantum optimization, offering a structured pathway for future research and practical applications in quantum-enhanced decision-making.

Latent Action Models (LAMs) enable the learning of world models from unlabeled video by inferring abstract actions between consecutive frames. However, LAMs face a fundamental trade-off between action abstraction and generation fidelity. Existing methods typically circumvent this issue by using two-stage training with pre-trained world models or by limiting predictions to optical flow. In this paper, we introduce DiLA, a novel Disentangled Latent Action world model that aims to resolve this trade-off via content-structure disentanglement. Our key insight is that disentanglement and latent action learning are co-evolving: the predictive bottleneck inherent in latent action learning serves as a driving force for disentanglement, compelling the model to distill spatial layouts into the structure pathway while offloading visual details to a separate content pathway for generation. This synergy yields a continuous, semantically structured latent action space without compromising generative quality. DiLA achieves superior results in video generation quality, action transfer, visual planning, and manifold interpretability. These findings establish DiLA as a unified framework that simultaneously achieves high-level action abstraction and high-fidelity generation, advancing the frontier of self-supervised world model learning.

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

Recent research has made substantial progress on video reasoning, with many models leveraging spatio-temporal evidence chains to strengthen their inference capabilities. At the same time, a growing set of datasets and benchmarks now provides structured annotations designed to support and evaluate such reasoning. However, little attention has been paid to reasoning about how objects move between observations: no prior work has articulated the motion patterns by connecting successive observations, leaving trajectory understanding implicit and difficult to verify. We formalize this missing capability as Spatial-Temporal-Trajectory (STT) reasoning and introduce Motion-o, a motion-centric video understanding extension to visual language models that makes trajectories explicit and verifiable. To enable motion reasoning, we also introduce a trajectory-grounding dataset artifact that expands sparse keyframe supervision via augmentation to yield denser bounding box tracks and a stronger trajectory-level training signal. Finally, we introduce Motion Chain of Thought (MCoT), a structured reasoning pathway that makes object trajectories through discrete <motion/> tag summarizing per-object direction, speed, and scale (of velocity) change to explicitly connect grounded observations into trajectories. To train Motion-o, we design a reward function that compels the model to reason directly over visual evidence, all while requiring no architectural modifications. Empirical results demonstrate that Motion-o improves spatial-temporal grounding and trajectory prediction while remaining fully compatible with existing frameworks, establishing motion reasoning as a critical extension for evidence-based video understanding. Code is available at https://github.com/ostadabbas/Motion-o.

Multimodal image fusion aims to integrate complementary information from different modalities into a fused image that preserves rich local details while maintaining globally consistent appearance. Existing approaches build shared representations on 2D feature grids, which excel at modeling local structures but offer limited leverage over image-level global appearance factors. To balance these objectives, we introduce a compact 1D token interface based on a frozen pretrained image tokenizer for modeling non-local appearance/base factors. Rather than using the tokenizer as a reconstruction backbone, our design uses the 1D token space as a global carrier while retaining the 2D spatial pathway for local structure restoration. Specifically, we introduce Selective Token Editing (STE), which sparsely updates/replaces a small set of critical tokens, providing a lightweight mechanism to steer global appearance coherence while keeping the fusion backbone unchanged and avoiding extra losses. Experiments on four commonly used benchmarks show that our method achieves the best overall performance, with consistent, multi-metric improvements in both global coherence and local fidelity. Project page: https://zju-xyc.github.io/1D-Fusion-Project-Page/

Spatial understanding of the physical world from 2D visual inputs hinges on two complementary forms of geometric knowledge: holistic 3D structural perception and fine-grained metric scale estimation. Existing multimodal large language models (MLLMs) typically address only one facet, ingesting either depth maps or point clouds as additional model inputs, which incurs substantial computational overhead and inherits the generalization limitations of upstream prediction models. We propose GAMSI, a dual-pathway Geometry-Aware MLLM for Spatial Intelligence that takes only RGB images as input while internalizing both forms of geometric prior within a unified autoregressive backbone. Specifically, we introduce Metric-Structure Decoupled Queries (MSDQ) which employ two groups of learnable queries to respectively extract dense metric signals and sparse structural cues from the shared visual context, with a task-decoupled attention mask further preventing the two pathways from contaminating each other. Building on this, an Expert-Guided Visual Grounding (EVG) module projects the aggregated cues back to frame-level visual features and aligns them with vision foundation models, which serve purely as training-time supervision, rather than as model inputs. We further build a multi-task spatial instruction-tuning dataset (MTS) comprising 152{,}776 samples spanning 13 task types and three visual modalities, consolidated from six public datasets. Trained with a two-stage curriculum, GAMSI achieves state-of-the-art performance on seven spatial intelligence benchmarks.

Large Language Models (LLMs) excel in complex reasoning tasks but struggle with consistent rule application, exception handling, and explainability, particularly in domains like legal analysis that require both natural language understanding and precise logical inference. This paper introduces a structured prompting framework that decomposes reasoning into three verifiable steps: entity identification, property extraction, and symbolic rule application. By integrating neural and symbolic approaches, our method leverages LLMs' interpretive flexibility while ensuring logical consistency through formal verification. The framework externalizes task definitions, enabling domain experts to refine logical structures without altering the architecture. Evaluated on the LegalBench hearsay determination task, our approach significantly outperformed baselines, with OpenAI o-family models showing substantial improvements - o1 achieving an F1 score of 0.929 and o3-mini reaching 0.867 using structured decomposition with complementary predicates, compared to their few-shot baselines of 0.714 and 0.74 respectively. This hybrid neural-symbolic system offers a promising pathway for transparent and consistent rule-based reasoning, suggesting potential for explainable AI applications in structured legal reasoning tasks.

This report details the creation of Bielik-Minitron-7B, a compressed 7.35B parameter version of the Bielik-11B-v3.0 model, specifically optimized for European languages. By leveraging a two-stage compression methodology inspired by the NVIDIA Minitron approach, we combined structured hybrid pruning and knowledge distillation to reduce the model's parameter count by 33.4%, from 11.04B to 7.35B. We utilized the NVIDIA Model Optimizer for structural pruning and the NVIDIA NeMo Framework for logit-based distillation for quality recovery. Following distillation, the model underwent a rigorous alignment pipeline consisting of Supervised Fine-Tuning (SFT), Direct Preference Optimization (DPO-P), and Reinforcement Learning (GRPO). Our final model successfully recovered approximately 90% of the baseline model's performance while providing up to 50% inference speedup. This approach demonstrates an efficient pathway to create language models for less-represented languages, preserving the original model quality while reducing inference deployment costs.

Complex tables with multi-level headers, merged cells and heterogeneous layouts pose persistent challenges for LLMs in both understanding and reasoning. Existing approaches typically rely on table linearization or normalized grid modeling. However, these representations struggle to explicitly capture hierarchical structures and cross-dimensional dependencies, which can lead to misalignment between structural semantics and textual representations for non-standard tables. To address this issue, we propose an Orthogonal Hierarchical Decomposition (OHD) framework that constructs structure-preserving input representations of complex tables for LLMs. OHD introduces an Orthogonal Tree Induction (OTI) method based on spatial--semantic co-constraints, which decomposes irregular tables into a column tree and a row tree to capture vertical and horizontal hierarchical dependencies, respectively. Building on this representation, we design a dual-pathway association protocol to symmetrically reconstruct semantic lineage of each cell, and incorporate an LLM as a semantic arbitrator to align multi-level semantic information. We evaluate OHD framework on two complex table question answering benchmarks, AITQA and HiTab. Experimental results show that OHD consistently outperforms existing representation paradigms across multiple evaluation metrics.

Video world models trained with Joint Embedding Predictive Architectures (JEPA) acquire rich spatiotemporal representations by predicting masked regions in latent space rather than reconstructing pixels. This removes the visual verification pathway of generative models, creating a structural interpretability gap: the encoder has learned physical structure inaccessible in any inspectable form. Existing probing methods either operate in continuous space without a structured intermediate layer, or attach generative components whose parameters confound attribution of behavior to the encoder. We propose the AI Mother Tongue (AIM) framework as a passive quantization probe: a lightweight, vocabulary-free probe that converts V-JEPA 2 continuous latent vectors into discrete symbol sequences without task-specific supervision or modifying the encoder. Because the encoder is kept completely frozen, any symbolic structure in the AIM codebook is attributable entirely to V-JEPA 2 pre-trained representations -- not to the probe. We evaluate through category-contrast experiments on Kinetics-mini along three physical dimensions: grasp angle, object geometry, and motion temporal structure. AIM symbol distributions differ significantly across all three experiments (chi^2 p < 10^{-4}; MI 0.036--0.117 bits, NMI 1.2--3.9% of the 3-bit maximum; JSD up to 0.342; codebook active ratio 62.5%). The experiments reveal that V-JEPA 2 latent space is markedly compact: diverse action categories share a common representational core, with semantic differences encoded as graded distributional variations rather than categorical boundaries. These results establish Stage 1 of a four-stage roadmap toward an action-conditioned symbolic world model, demonstrating that structured symbolic manifolds are discoverable properties of frozen JEPA latent spaces.

Training reliable tool-augmented agents remains a significant challenge, largely due to the difficulty of credit assignment in multi-step reasoning. While process-level reward models offer a promising direction, existing LLM-based judges often produce noisy and inconsistent signals because they lack fine-grained, task-specific rubrics to distinguish high-level planning from low-level execution. In this work, we introduce SCRIBE (Skill-Conditioned Reward with Intermediate Behavioral Evaluation), a reinforcement learning framework that intervenes at a novel mid-level abstraction. SCRIBE grounds reward modeling in a curated library of skill prototypes, transforming open-ended LLM evaluation into a constrained verification problem. By routing each subgoal to a corresponding prototype, the reward model is equipped with precise, structured rubrics that substantially reduce reward variance. Experimental results show that SCRIBE achieves state-of-the-art performance across a range of reasoning and tool-use benchmarks. In particular, it improves the AIME25 accuracy of a Qwen3-4B model from 43.3% to 63.3%, and significantly increases success rates in complex multi-turn tool interactions. Further analysis of training dynamics reveals a co-evolution across abstraction levels, where mastery of mid-level skills consistently precedes the emergence of effective high-level planning behaviors. Finally, we demonstrate that SCRIBE is additive to low-level tool optimizations, providing a scalable and complementary pathway toward more autonomous and reliable tool-using agents.

Vision-Language-Action (VLA) models have recently been proposed as a pathway toward generalist robotic policies capable of interpreting natural language and visual inputs to generate manipulation actions. However, their effectiveness and efficiency on structured, long-horizon manipulation tasks remain unclear. In this work, we present a head-to-head empirical comparison between a fine-tuned open-weight VLA model π0 and a neuro-symbolic architecture that combines PDDL-based symbolic planning with learned low-level control. We evaluate both approaches on structured variants of the Towers of Hanoi manipulation task in simulation while measuring both task performance and energy consumption during training and execution. On the 3-block task, the neuro-symbolic model achieves 95% success compared to 34% for the best-performing VLA. The neuro-symbolic model also generalizes to an unseen 4-block variant (78% success), whereas both VLAs fail to complete the task. During training, VLA fine-tuning consumes nearly two orders of magnitude more energy than the neuro-symbolic approach. These results highlight important trade-offs between end-to-end foundation-model approaches and structured reasoning architectures for long-horizon robotic manipulation, emphasizing the role of explicit symbolic structure in improving reliability, data efficiency, and energy efficiency. Code and models are available at https://price-is-not-right.github.io

Action supervision in vision-language-action (VLA) models is often treated as a downstream objective for learning action prediction. In this paper, we study it instead as a force that shapes inherited multimodal representations. We show that this shaping has a dual effect: it is necessary for forming action-compatible representations, but when action supervision is applied too directly to the inherited multimodal pathway, it can also destabilize representations that support language-side processing and object grounding. To address this tension, we introduce Action QFormer, a query-based action-facing interface that uses instruction-conditioned queries to reorganize inherited multimodal information into action-facing representations before downstream action generation. In zero-shot sim-to-real navigation, Action QFormer improves average closed-loop task success from 18.8% to 56.3%, raises fixed-instruction action-generation correctness from 22.5% to 75.5%, and nearly eliminates out-of-distribution instruction generations. Further analyses show that Action QFormer changes how action supervision shapes inherited multimodal representations, reducing broad upstream rewriting while preserving targeted and sometimes constructive action-supervised adaptation. These results suggest that improving VLA performance requires not only stronger pretrained backbones, but also better ways of selecting and organizing inherited multimodal information while controlling how it is shaped under action supervision.

Artificial General Intelligence (AGI) Agents and Robots must be able to cope with everchanging environments and tasks. They must be able to actively construct new internal causal models of their interactions with the environment when new structural changes take place in the environment. Thus, we claim that active causal structure learning with latent variables (ACSLWL) is a necessary component to build AGI agents and robots. This paper describes how a complex planning and expectation-based detour behavior can be learned by ACSLWL when, unexpectedly, and for the first time, the simulated robot encounters a sort of transparent barrier in its pathway towards its target. ACSWL consists of acting in the environment, discovering new causal relations, constructing new causal models, exploiting the causal models to maximize its expected utility, detecting possible latent variables when unexpected observations occur, and constructing new structures-internal causal models and optimal estimation of the associated parameters, to be able to cope efficiently with the new encountered situations. That is, the agent must be able to construct new causal internal models that transform a previously unexpected and inefficient (sub-optimal) situation, into a predictable situation with an optimal operating plan.

Accurately predicting gene expression from histopathology images offers a scalable and non-invasive approach to molecular profiling, with significant implications for precision medicine and computational pathology. However, existing methods often underutilize the cross-modal representation alignment between histopathology images and gene expression profiles across multiple representational levels, thereby limiting their prediction performance. To address this, we propose Gene-DML, a unified framework that structures latent space through Dual-pathway Multi-Level discrimination to enhance correspondence between morphological and transcriptional modalities. The multi-scale instance-level discrimination pathway aligns hierarchical histopathology representations extracted at local, neighbor, and global levels with gene expression profiles, capturing scale-aware morphological-transcriptional relationships. In parallel, the cross-level instance-group discrimination pathway enforces structural consistency between individual (image/gene) instances and modality-crossed (gene/image, respectively) groups, strengthening the alignment across modalities. By jointly modelling fine-grained and structural-level discrimination, Gene-DML is able to learn robust cross-modal representations, enhancing both predictive accuracy and generalization across diverse biological contexts. Extensive experiments on public spatial transcriptomics datasets demonstrate that Gene-DML achieves state-of-the-art performance in gene expression prediction. The code and checkpoints will be released soon.

Structured shape completion recovers missing geometry as primitives rather than as unstructured points, which enables primitive-based surface reconstruction. Instead of following the prevailing cascade, we rethink how primitives and points should interact, and find it more effective to decode primitives in a dedicated pathway that attends to shared shape features. Following this principle, we present UniCo, which in a single feed-forward pass predicts a set of primitives with complete geometry, semantics, and inlier membership. To drive this unified representation, we introduce primitive proxies, learnable queries that are contextualized to produce assembly-ready outputs. To ensure consistent optimization, our training strategy couples primitives and points with online target updates. Across synthetic and real-world benchmarks with four independent assembly solvers, UniCo consistently outperforms recent baselines, lowering Chamfer distance by up to 50% and improving normal consistency by up to 7%. These results establish an attractive recipe for structured 3D understanding from incomplete data. Project page: https://unico-completion.github.io.

Electron-beam (e-beam) manipulation of single dopant atoms in an aberration-corrected scanning transmission electron microscope is emerging as a method for directed atomic motion and atom-by-atom assembly. Until now, the dopant species have been limited to atoms closely matched to carbon in terms of ionic radius and capable of strong covalent bonding with carbon atoms in the graphene lattice. In situ dopant insertion into a graphene lattice has thus far been demonstrated only for Si, which is ubiquitously present as a contaminant in this material. Here, we achieve in situ manipulation of Pt atoms and their insertion into the graphene host matrix using the e-beam deposited Pt on graphene as a host system. We further demonstrate a mechanism for stabilization of the Pt atom, enabled through the formation of Si-stabilized Pt heteroatomic clusters attached to the graphene surface. This study provides evidence toward the universality of the e-beam assembly approach, opening a pathway for exploring cluster chemistry through direct assembly.

Accurate survival prediction is essential for personalized treatment planning in head and neck cancer, yet remains challenging due to the heterogeneous and high-dimensional nature of multimodal clinical data. While deep survival models have improved predictive performance over classical statistical approaches, existing methods typically rely on static fusion strategies or temporally agnostic modeling, limiting their ability to capture structured clinical workflows. In this work, we propose ChronoSurv, a heterogeneous hierarchical directed graph framework for multimodal survival analysis. ChronoSurv represents patient care as a progression-aware clinical trajectory using directed graphs aligned with key diagnostic steps. A hierarchical topology incorporates fine-grained, coarse, and global representations, further supporting flexible adaptation to missing modalities, while heterogeneous message passing models complex and asymmetric relationships across modalities and clinical steps. Experimental results on two public datasets demonstrate that ChronoSurv achieves state-of-the-art discriminative performance while maintaining statistically reliable calibration. Comprehensive ablation studies further confirm the contribution of each architectural component, highlighting the potential of trajectory-aware graph modeling for multimodal survival prediction.

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.

Egocentric video understanding is inherently complex due to the dynamic 4D nature of the environment, where camera motion and object displacements necessitate a continuous re-evaluation of spatial relations. In this work, we target a suite of under-explored egocentric 4D reasoning tasks, including fixture interaction counting, viewpoint-relative fixture location, object movement itinerary tracking, and stationary object localization, that require fundamentally different cognitive operations: spatial anchoring, temporal tracking, and duration reasoning. We observe that these structural differences make task-agnostic approaches insufficient: generic Chain-of-Thought methods lack task-appropriate reasoning primitives, and uniform reinforcement learning actively destabilizes performance on spatial tasks. To address this, we propose EgoReasoner, a two-stage framework that aligns both the reasoning scaffold and the reward signal to each task's cognitive structure. In the first stage, Task-Adaptive Thinking Templates guide the synthesis of structured CoT traces that teach the model to reason adaptively across task types via supervised fine-tuning. In the second stage, task-aware reward functions verify entity grounding, temporal alignment, and task-adaptive logical consistency, selectively strengthening each reasoning pathway via reinforcement fine-tuning with GRPO. Our 3B-parameter model, trained on only 16K samples, achieves 37.5% average accuracy on the challenging HD-EPIC benchmark, surpassing Qwen2.5-VL-7B (25.7%) by over 10 points.

The lack of sufficiently diverse data, coupled with limited data efficiency, remains a major bottleneck for generalist robotic models, yet systematic strategies for collecting and curating such data are not fully explored. Task diversity arises from implicit factors that are sparsely distributed across multiple dimensions and are difficult to define explicitly. To address this challenge, we propose F-ACIL, a heuristic factor-aware compositional iterative learning framework that enables structured data factorization and promotes compositional generalization. F-ACIL decomposes the data distribution into structured factor spaces such as object, action, and environment. Based on the factorized formulation, we develop a factor-wise data collection and an iterative training paradigm that promotes compositional generalization over the high-dimensional factor space, leading to more effective utilization of real-world robotic demonstrations. With extensive real-world experiments, we show that F-ACIL can achieve more than 45% performance gains with 5-10times fewer demonstrations comparing to that of which without the strategy. The results suggest that structured factorization offers a practical pathway toward efficient compositional generalization in real-world robotic learning. We believe F-ACIL can inspire more systematic research on building generalizable robotic data flywheel strategies. More demonstrations can be found at: https://f-acil.github.io/

Adapting pre-trained image models to video modality has proven to be an effective strategy for robust few-shot action recognition. In this work, we explore the potential of adapter tuning in image-to-video model adaptation and propose a novel video adapter tuning framework, called Disentangled-and-Deformable Spatio-Temporal Adapter (D^2ST-Adapter). It features a lightweight design, low adaptation overhead and powerful spatio-temporal feature adaptation capabilities. D^2ST-Adapter is structured with an internal dual-pathway architecture that enables built-in disentangled encoding of spatial and temporal features within the adapter, seamlessly integrating into the single-stream feature learning framework of pre-trained image models. In particular, we develop an efficient yet effective implementation of the D^2ST-Adapter, incorporating the specially devised anisotropic Deformable Spatio-Temporal Attention as its pivotal operation. This mechanism can be individually tailored for two pathways with anisotropic sampling densities along the spatial and temporal domains in 3D spatio-temporal space, enabling disentangled encoding of spatial and temporal features while maintaining a lightweight design. Extensive experiments by instantiating our method on both pre-trained ResNet and ViT demonstrate the superiority of our method over state-of-the-art methods. Our method is particularly well-suited to challenging scenarios where temporal dynamics are critical for action recognition. Code is available at https://github.com/qizhongtan/D2ST-Adapter.

Massively multilingual automatic speech recognition (ASR) models covering hundreds of languages must maintain robust performance across diverse linguistic and acoustic conditions. However, these models often encounter the curse of multilinguality, where model capacity is diluted across languages. To address this challenge, we propose Mixture of Language Group Experts (MoLGE), built upon speech self-supervised models (S3Ms). MoLGE assigns dedicated expert modules to clusters of similar languages, reducing the number of required submodules compared to conventional language-specific Mixture-of-Experts (MoE) schemes. It further integrates a hierarchical Low-Rank Adaptation (LoRA) strategy into the disentangled acoustic and linguistic components of the S3M architecture, enabling efficient modeling of language-specific characteristics while maintaining parameter efficiency. Further, we investigate the impact of language grouping strategies based on both linguistic and data-driven criteria on overall performance, providing an interpretable perspective on how language structure influences scalability in multilingual speech systems. In experiments, we evaluate MoLGE on a multilingual benchmark encompassing 495 languages. Results demonstrate that MoLGE consistently outperforms dense multilingual baselines with a minimal increase in trainable parameters. Notably, these language grouping strategies yield substantial improvements for both phonetic and orthographic aspects of ASR modeling. Our findings suggest that structured language specialization provides an effective pathway for massively scaling language coverage of multilingual ASR.

Current genomic foundation models (GFMs) rely on extensive neural computation to implicitly approximate conserved biological motifs from single-nucleotide inputs. We propose Gengram, a conditional memory module that introduces an explicit and highly efficient lookup primitive for multi-base motifs via a genomic-specific hashing scheme, establishing genomic "syntax". Integrated into the backbone of state-of-the-art GFMs, Gengram achieves substantial gains (up to 14%) across several functional genomics tasks. The module demonstrates robust architectural generalization, while further inspection of Gengram's latent space reveals the emergence of meaningful representations that align closely with fundamental biological knowledge. By establishing structured motif memory as a modeling primitive, Gengram simultaneously boosts empirical performance and mechanistic interpretability, providing a scalable and biology-aligned pathway for the next generation of GFMs. The code is available at https://github.com/zhejianglab/Genos, and the model checkpoint is available at https://huggingface.co/ZhejiangLab/Gengram.

Recent advancements have endowed Large Language Models (LLMs) with impressive general reasoning capabilities, yet they often struggle with personalization reasoning - the crucial ability to analyze user history, infer unique preferences, and generate tailored responses. To address this limitation, we introduce TagPR, a novel training framework that significantly enhances an LLM's intrinsic capacity for personalization reasoning through a tagging the thought approach. Our method first develops a data-driven pipeline to automatically generate and semantically label reasoning chains, creating a structured dataset that fosters interpretable reasoning. We then propose a synergistic training strategy that begins with Supervised Fine-Tuning (SFT) on this tagged data to establish foundational reasoning patterns, followed by a multi-stage reinforcement learning (RL) process. This RL phase is guided by a unique composite reward signal, which integrates tag-based constraints and a novel Personalization Reward Model with User Embeddings (PRMU) to achieve fine-grained alignment with user-specific logic. Extensive experiments on the public LaMP benchmark and a self-constructed dataset demonstrate that our approach achieves state-of-the-art results, delivering an average improvement of 32.65% over the base model across all tasks. Our work validates that structured, interpretable reasoning is a highly effective pathway to unlocking genuine personalization capabilities in LLMs.

Scientific diagrams are vital tools for communicating structured knowledge across disciplines. However, they are often published as static raster images, losing symbolic semantics and limiting reuse. While Multimodal Large Language Models (MLLMs) offer a pathway to bridging vision and structure, existing methods lack semantic control and structural interpretability, especially on complex diagrams. We propose Draw with Thought (DwT), a training-free framework that guides MLLMs to reconstruct diagrams into editable mxGraph XML code through cognitively-grounded Chain-of-Thought reasoning. DwT enables interpretable and controllable outputs without model fine-tuning by dividing the task into two stages: Coarse-to-Fine Planning, which handles perceptual structuring and semantic specification, and Structure-Aware Code Generation, enhanced by format-guided refinement. To support evaluation, we release Plot2XML, a benchmark of 247 real-world scientific diagrams with gold-standard XML annotations. Extensive experiments across eight MLLMs show that our approach yields high-fidelity, semantically aligned, and structurally valid reconstructions, with human evaluations confirming strong alignment in both accuracy and visual aesthetics, offering a scalable solution for converting static visuals into executable representations and advancing machine understanding of scientific graphics.

Photorealistic frontal view synthesis from a single face image has a wide range of applications in the field of face recognition. Although data-driven deep learning methods have been proposed to address this problem by seeking solutions from ample face data, this problem is still challenging because it is intrinsically ill-posed. This paper proposes a Two-Pathway Generative Adversarial Network (TP-GAN) for photorealistic frontal view synthesis by simultaneously perceiving global structures and local details. Four landmark located patch networks are proposed to attend to local textures in addition to the commonly used global encoder-decoder network. Except for the novel architecture, we make this ill-posed problem well constrained by introducing a combination of adversarial loss, symmetry loss and identity preserving loss. The combined loss function leverages both frontal face distribution and pre-trained discriminative deep face models to guide an identity preserving inference of frontal views from profiles. Different from previous deep learning methods that mainly rely on intermediate features for recognition, our method directly leverages the synthesized identity preserving image for downstream tasks like face recognition and attribution estimation. Experimental results demonstrate that our method not only presents compelling perceptual results but also outperforms state-of-the-art results on large pose face recognition.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Current text-to-image models struggle to provide precise camera control using natural language alone. In this work, we present a framework for precise camera control with global scene understanding in text-to-image generation by learning parametric camera tokens. We fine-tune image generation models for viewpoint-conditioned text-to-image generation on a curated dataset that combines 3D-rendered images for geometric supervision and photorealistic augmentations for appearance and background diversity. Qualitative and quantitative experiments demonstrate that our method achieves state-of-the-art accuracy while preserving image quality and prompt fidelity. Unlike prior methods that overfit to object-specific appearance correlations, our viewpoint tokens learn factorized geometric representations that transfer to unseen object categories. Our work shows that text-vision latent spaces can be endowed with explicit 3D camera structure, offering a pathway toward geometrically-aware prompts for text-to-image generation. Project page: https://randdl.github.io/viewtoken_control/

Large and demographically balanced datasets are essential for reliable neuroimaging biomarkers. Full-resolution 3D brain MRI synthesis can support data augmentation in this setting, but existing approaches either incur prohibitive computational cost at volumetric scale or rely on lossy latent compression that may compromise anatomical detail. As a result, practical 3D generative augmentation often requires specialized compute infrastructure. We propose WaveDiT, a conditional flow matching framework operating in the coefficient space of a 3D Haar Discrete Wavelet Transform. The model combines factorized spatio-depth attention with band-wise heteroscedastic uncertainty modeling derived from higher-order wavelet statistics. Predicted log-variance is integrated directly into both the flow objective and conditioning pathway, enabling adaptive precision consistent with the heavy-tailed and input-dependent variance structure of anatomical detail. This formulation supports full-resolution 3D synthesis under practical memory and time constraints on a single modern GPU. Evaluation on a multi-site cohort demonstrates improved alignment between generated and real MRI distributions, together with enhanced downstream brain age prediction and region-level anatomical agreement relative to diffusion, latent, and wavelet-based baselines. Code is available at https://github.com/sisinflab/WaveDiT

The manufacturing sector is increasingly adopting Multimodal Large Language Models (MLLMs) to transition from simple perception to autonomous execution, yet current evaluations fail to reflect the rigorous demands of real-world manufacturing environments. Progress is hindered by data scarcity and a lack of fine-grained domain semantics in existing datasets. To bridge this gap, we introduce FORGE. Wefirst construct a high-quality multimodal dataset that combines real-world 2D images and 3D point clouds, annotated with fine-grained domain semantics (e.g., exact model numbers). We then evaluate 18 state-of-the-art MLLMs across three manufacturing tasks, namely workpiece verification, structural surface inspection, and assembly verification, revealing significant performance gaps. Counter to conventional understanding, the bottleneck analysis shows that visual grounding is not the primary limiting factor. Instead, insufficient domain-specific knowledge is the key bottleneck, setting a clear direction for future research. Beyond evaluation, we show that our structured annotations can serve as an actionable training resource: supervised fine-tuning of a compact 3B-parameter model on our data yields up to 90.8% relative improvement in accuracy on held-out manufacturing scenarios, providing preliminary evidence for a practical pathway toward domain-adapted manufacturing MLLMs. The code and datasets are available at https://ai4manufacturing.github.io/forge-web.

Vision-Language Models (VLMs) in remote sensing often fail at complex analytical tasks, a limitation stemming from their end-to-end training paradigm that bypasses crucial reasoning steps and leads to unverifiable outputs. To address this limitation, we introduce the Perceptually-Grounded Geospatial Chain-of-Thought (Geo-CoT), a framework that models remote sensing analysis as a verifiable, multi-step process. We instill this analytical process through a two-stage alignment strategy, leveraging Geo-CoT380k, the first large-scale dataset of structured Geo-CoT rationales. This strategy first employs supervised fine-tuning (SFT) to instill the foundational cognitive architecture, then leverages Group Reward Policy Optimization (GRPO) to refine the model's reasoning policy towards factual correctness. The resulting model, RSThinker, outputs both a final answer and its justifying, verifiable analytical trace. This capability yields dominant performance, significantly outperforming state-of-the-art models across a comprehensive range of tasks. The public release of our Geo-CoT380k dataset and RSThinker model upon publication serves as a concrete pathway from opaque perception towards structured, verifiable reasoning for Earth Observation.

Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited knowledge retention, and large cloud-based language models plagued by privacy risks and high inference costs. To bridge this gap, we introduce ChemCRAFT, a novel framework leveraging agentic reinforcement learning to decouple chemical reasoning from knowledge storage. Instead of forcing the model to memorize vast chemical data, our approach empowers the language model to interact with a sandbox for precise information retrieval. This externalization of knowledge allows a locally deployable small model to achieve superior performance with minimal inference costs. To enable small language models for agent-calling ability, we build an agentic trajectory construction pipeline and a comprehensive chemical-agent sandbox. Based on sandbox interactions, we constructed ChemToolDataset, the first large-scale chemical tool trajectory dataset. Simultaneously, we propose SMILES-GRPO to build a dense chemical reward function, promoting the model's ability to call chemical agents. Evaluations across diverse aspects of drug design show that ChemCRAFT outperforms current cloud-based LLMs in molecular structure analysis, molecular optimization, and synthesis pathway prediction, demonstrating that scientific reasoning is not solely an emergent ability of model scale, but a learnable policy of tool orchestration. This work establishes a cost-effective and privacy-preserving paradigm for AI-aided chemistry, opening new avenues for accelerating molecular discovery with locally deployable agents. Code available at https://github.com/HowardLi1984/ChemCraft.

Large language models (LLMs) increasingly interact with external environments and accumulate substantial behavioral experience, yet existing agent benchmarks largely evaluate them as fixed policies. It therefore remains unclear whether an agent can actively test its behavior, judge the resulting experience, and use that experience to improve future decisions. We introduce S\textsuperscript{3Gym}, an interactive benchmark for evaluating LLM self-improvement through three coupled capabilities: Self-Testing, Self-Judging, and Self-Improvement. S^3Gym separates permissive exploration from strict held-out evaluation and instantiates this protocol in seven text-based games with executable environment verifiers. We evaluate three pathways for incorporating interaction experience: direct History ICL, score-conditioned Summary Memory, and parameter Training. Our experiments reveal that self-improvement is neither automatic nor uniform. Context-level experience improves performance for several model--game pairs, but the most effective pathway depends strongly on the task structure: summaries are beneficial when experience can be compressed into reusable strategic rules, yet often underperform raw history when success depends on precise, state-contingent information. Parameter training produces substantial gains on some tasks, but also exhibits unstable improvement and severe negative transfer on others. These findings show that recognizing successful actions is insufficient; agents must also transform feedback into executable and transferable policies. S^3Gym provides a unified framework for diagnosing this process and identifying the bottlenecks that prevent agents from translating interaction experience into reliable self-improvement.

Layer interventions are widely used to probe the internal organization of language models, yet most analyses examine a single training checkpoint even though model representations and computations evolve throughout pretraining. This leaves open which depth-dependent intervention responses reflect persistent organization and which are transient consequences of training. We study this question using single-block identity bypass on fixed teacher-forced contexts across five released trajectories and 11 model-domain combinations. We find that block-bypass responses retain recognizable depth ordering while their magnitudes redistribute: nearby checkpoints preserve stronger rank correspondence than distant ones, and large changes concentrate at positions that recur across text samples and transfer across evaluation domains. Controlled experiments further show that changes in the natural bypass effect cannot be reduced to a single downstream sensitivity: in replicated Pythia runs, local missing-update magnitude grows while the pooled matched downstream response decreases, whereas OLMo-2 7B exhibits a different balance. These matched responses also depend on perturbation strength and direction, without identifying targeted compensation. Together, our results show that longitudinal layer sensitivity is structured but not static, and that single-checkpoint intervention responses should be interpreted in the context of how the underlying perturbation pathway evolves during training.

Radiologists routinely compare current and prior chest X-rays to track disease progression, producing follow-up reports that describe multiple findings, each localised to an anatomical region and annotated with a temporal change status. Existing automated methods either generate reports from a single image without modelling temporal context, or incorporate temporal information but do not ground their outputs spatially. The few approaches that combine temporal reasoning with spatial grounding are restricted to single-finding descriptions, leaving multi-finding reports with mixed change directions unaddressed. We present GRCD, a framework for grounded report generation from chest X-ray pairs in the multi-finding setting. We first construct a rigorously cleaned dataset of temporal chest X-ray pairs by identifying and correcting two systematic labelling errors in the source annotations. We then introduce a Region-Guided Change Token module that encodes per-region temporal change across anatomical structures and injects this signal into a language model through a dual-pathway strategy combining prepended spatial tokens with gated cross-attention. On a multi-finding test set, GRCD outperforms existing baselines on text generation and clinical accuracy metrics, with gains in change detection. Ablation studies confirm that the dual-pathway design outperforms either integration strategy in isolation on text and clinical metrics, and that region-level change encoding is necessary for multi-finding generation. Code is available at https://github.com/UTSA-VIRLab/GRCD

Image degradation from blur, noise, compression, and poor illumination severely undermines multimodal understanding in real-world settings. Unified multimodal models that combine understanding and generation within a single architecture are a natural fit for this challenge, as their generative pathway can model the fine-grained visual structure that degradation destroys. Yet these models fail to leverage their own generative capacity on degraded inputs. We trace this disconnect to two compounding factors: existing training regimes never ask the model to invoke generation during reasoning, and the standard decode-reencode pathway does not support effective joint optimization. We present CLEAR, a framework that connects the two capabilities through three progressive steps: (1) supervised fine-tuning on a degradation-aware dataset to establish the generate-then-answer reasoning pattern; (2) a Latent Representation Bridge that replaces the decode-reencode detour with a direct, optimizable connection between generation and reasoning; (3) Interleaved GRPO, a reinforcement learning method that jointly optimizes text reasoning and visual generation under answer-correctness rewards. We construct MMD-Bench, covering three degradation severity levels across six standard multimodal benchmarks. Experiments show that CLEAR substantially improves robustness on degraded inputs while preserving clean-image performance. Our analysis further reveals that removing pixel-level reconstruction supervision leads to intermediate visual states with higher perceptual quality, suggesting that task-driven optimization and visual quality are naturally aligned.

Despite achieving high accuracy on medical benchmarks, LLMs exhibit the Einstellung Effect in clinical diagnosis--relying on statistical shortcuts rather than patient-specific evidence, causing misdiagnosis in atypical cases. Existing benchmarks fail to detect this critical failure mode. We introduce MedEinst, a counterfactual benchmark with 5,383 paired clinical cases across 49 diseases. Each pair contains a control case and a "trap" case with altered discriminative evidence that flips the diagnosis. We measure susceptibility via Bias Trap Rate--probability of misdiagnosing traps despite correctly diagnosing controls. Extensive Evaluation of 17 LLMs shows frontier models achieve high baseline accuracy but severe bias trap rates. Thus, we propose ECR-Agent, aligning LLM reasoning with Evidence-Based Medicine standard via two components: (1) Dynamic Causal Inference (DCI) performs structured reasoning through dual-pathway perception, dynamic causal graph reasoning across three levels (association, intervention, counterfactual), and evidence audit for final diagnosis; (2) Critic-Driven Graph and Memory Evolution (CGME) iteratively refines the system by storing validated reasoning paths in an exemplar base and consolidating disease-specific knowledge into evolving illness graphs. Source code is to be released.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Vision-Language Models (VLMs) have shown remarkable capabilities in joint vision-language understanding, but their large scale poses significant challenges for deployment in resource-constrained scenarios. Knowledge Distillation (KD) offers a viable way to improve model capabilities without increasing model size or data requirements, making deployment more efficient. However, applying KD to VLMs is challenged by modality-specific supervision: although multimodal knowledge in VLMs is fused within the language space, current methods supervise each modality separately without explicitly addressing multimodal alignment, leading to inconsistent multimodal knowledge transfer. To address this, we propose Switch-KD, a visual-switch distillation framework that unifies vision-language knowledge transfer within a shared text-probability space. Switch-KD comprises two key components: (1) Visual-Switch Distillation, which switches the student's visual outputs into the teacher's language pathway to construct cross-modal probabilistic references for implicit visual knowledge transfer; and (2) Dynamic Bi-directional Logits Difference (DBiLD) loss, which adaptively aligns informative probability regions while preserving the distributional structures of teacher and student through bidirectional supervision. Guided by Switch-KD, a 0.5B TinyLLaVA effectively distills rich multimodal knowledge from its 3B teacher, yielding an average improvement of 3.6 points across 10 multimodal benchmarks without any architectural modification.

Given a 3-dimensional (para-)CR structure, its family of chains define a 3-dimensional path geometry. We provide necessary and sufficient conditions that determine whether a path geometry in dimension three arises from chains of a CR or para-CR 3-manifold. We demonstrate how our characterization can be verified computationally for a given 3-dimensional path geometry and discuss a few examples.

Contrastive Language-Image Pre-training (CLIP) has accomplished extraordinary success for semantic understanding but inherently struggles to perceive geometric structure. Existing methods attempt to bridge this gap by querying CLIP with textual prompts, a process that is often indirect and inefficient. This paper introduces a fundamentally different approach using a dual-pathway decoder. We present SPACE-CLIP, an architecture that unlocks and interprets latent geometric knowledge directly from a frozen CLIP vision encoder, completely bypassing the text encoder and its associated textual prompts. A semantic pathway interprets high-level features, dynamically conditioned on global context using feature-wise linear modulation (FiLM). In addition, a structural pathway extracts fine-grained spatial details from early layers. These complementary streams are hierarchically fused, enabling a robust synthesis of semantic context and precise geometry. Extensive experiments on the KITTI benchmark show that SPACE-CLIP dramatically outperforms previous CLIP-based methods. Our ablation studies validate that the synergistic fusion of our dual pathways is critical to this success. SPACE-CLIP offers a new, efficient, and architecturally elegant blueprint for repurposing large-scale vision models. The proposed method is not just a standalone depth estimator, but a readily integrable spatial perception module for the next generation of embodied AI systems, such as vision-language-action (VLA) models. Our model is available at https://github.com/taewan2002/space-clip

Grokking, i.e., test performance keeps improving long after training loss converged, has been recently witnessed in neural network training, making the mechanism of generalization and other emerging capabilities such as reasoning mysterious. While prior studies usually train small models on a few toy or highly-specific tasks for thousands of epochs, we conduct the first study of grokking on checkpoints during one-pass pretraining of a 7B large language model (LLM), i.e., OLMoE. We compute the training loss and evaluate generalization on diverse benchmark tasks, including math reasoning, code generation, and commonsense/domain-specific knowledge retrieval tasks. Our study, for the first time, verifies that grokking still happens in the pretraining of large-scale foundation models, though different data may enter grokking stages asynchronously. We further demystify grokking's "emergence of generalization" by investigating LLM internal dynamics. Specifically, we find that training samples' pathways (i.e., expert choices across layers) evolve from random, instance-specific to more structured and shareable between samples during grokking. Also, the complexity of a sample's pathway reduces despite the converged loss. These indicate a memorization-to-generalization conversion, providing a mechanistic explanation of delayed generalization. In the study, we develop two novel metrics to quantify pathway distance and the complexity of a single pathway. We show their ability to predict the generalization improvement on diverse downstream tasks. They are efficient, simple to compute and solely dependent on training data. Hence, they have practical value for pretraining, enabling us to monitor the generalization performance without finetuning and test. Theoretically, we show that more structured pathways reduce model complexity and improve the generalization bound.

Heterogeneous high--performance computing architectures expose numerical algorithms to perturbations arising from the non--associativity of floating--point arithmetic. In Large--Eddy Simulation (LES), similar numerical effects may become relevant when they affect the filter--width entering the subgrid scale (SGS) model. This work investigates this mechanism for the least--squares (LSQ) based filter--width formulation, focusing on how floating--point effects are generated, transmitted, and coupled with the resolved flow. We show that, for fixed resolved kinematics, the LSQ filter--width is logarithmically non-expansive but not strictly contractive with respect to perturbations of the mesh metrics. Consequently, small disturbances may be transmitted with little attenuation through strongly directional filter-width responses. To mitigate this sensitivity, we introduce a scalar max--min compression of the directional mesh scales together with a bounded modulation based on the resolved velocity gradient. The resulting formulation reroutes floating--point perturbations through the filter-width operator, improving robustness while preserving the flow--dependent character of the original LSQ construction. The framework is assessed on heterogeneous CPU and GPU architectures for flow past a circular cylinder at Re=3900 and the Taylor--Green vortex at Re=1600. In the former, nearly one--to--one transmission of relative metric disturbances can become relevant when the transmitted perturbations interact with shear-layer transition. By contrast, on orthogonal Taylor--Green vortex grids, the accumulation pathway is structurally absent and no comparable macroscopic response develops. These results suggest floating--point sensitivity matters for LES filter--width formulations in heterogeneous computing environments.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Retrieval-augmented generation systems increasingly rely on document-structure treatments: structure-aligned chunking, LLM-generated chunk contexts, heading-path metadata, and hierarchical two-stage retrieval. Separate studies support each on different corpora, embedders, and metrics, and none control for a shared confound: any text prepended to a chunk perturbs its embedding. We present a mechanism-isolating ablation testing all four treatments under one protocol, matching chunk sizes across conditions and adding a semantically null placebo---heading paths that are structurally valid but shuffled across documents. We score retrieval with a coverage-aware nDCG and test four pre-registered contrasts via document-clustered bootstrap with Holm correction, on two distant corpora: 200 Wikipedia Featured Articles (951 queries) and 1,585 QASPER papers (4,303 questions). Organization helps, and the cause is content, not tokens: structure-aligned chunks with real heading paths beat contextualized fixed windows (+0.022 / +0.012 cov-nDCG@10) and the placebo (+0.010 / +0.016). Naive two-stage hierarchical retrieval hurts (-0.033 / -0.015), traceable to first-stage section recall. Gold structure beats LLM-induced structure on Wikipedia but not on QASPER. Effects are small (dz 0.06-0.11) but Holm-significant and consistent across corpora.

Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but rather from the sparsity it introduces. We conducted a comprehensive analysis of all relevant pathway-based neural network models for predictive tasks, critically evaluating each study's contributions. From this review, we curated a subset of methods for which the source code was publicly available. The comparison of the biologically informed state-of-the-art deep learning models and their randomized counterparts showed that models based on randomized information performed equally well as biologically informed ones across different metrics and datasets. Notably, in 3 out of the 15 analyzed models, the randomized versions even outperformed their biologically informed counterparts. Moreover, pathway-informed models did not show any clear advantage in interpretability, as randomized models were still able to identify relevant disease biomarkers despite lacking explicit pathway information. Our findings suggest that pathway annotations may be too noisy or inadequately explored by current methods. Therefore, we propose a methodology that can be applied to different domains and can serve as a robust benchmark for systematically comparing novel pathway-informed models against their randomized counterparts. This approach enables researchers to rigorously determine whether observed performance improvements can be attributed to biological insights.

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

We present the design of a new large scale orchestration layer for accelerators. Our system, Pathways, is explicitly designed to enable exploration of new systems and ML research ideas, while retaining state of the art performance for current models. Pathways uses a sharded dataflow graph of asynchronous operators that consume and produce futures, and efficiently gang-schedules heterogeneous parallel computations on thousands of accelerators while coordinating data transfers over their dedicated interconnects. Pathways makes use of a novel asynchronous distributed dataflow design that lets the control plane execute in parallel despite dependencies in the data plane. This design, with careful engineering, allows Pathways to adopt a single-controller model that makes it easier to express complex new parallelism patterns. We demonstrate that Pathways can achieve performance parity (~100% accelerator utilization) with state-of-the-art systems when running SPMD computations over 2048 TPUs, while also delivering throughput comparable to the SPMD case for Transformer models that are pipelined across 16 stages, or sharded across two islands of accelerators connected over a data center network.

Trajectories in complex systems often contain structure that is not captured by the population-averaged, scalar statistics traditionally used to describe them. Here we reconstruct, through independent numerical re-simulation rather than literature review, a systematic search across representational forms - from single scalar statistics, through two independent discrete multi-feature classification attempts, to a trajectory-level structural representation and a diagnostic surrogate test, to a continuous low-dimensional compression - applied to the same underlying trajectory ensemble in a critical complex system. Predictive failure is not explained by insufficient correlation: one discrete representation's own strongest individual feature correlates with the target more strongly (r=0.588) than the eventual successful representation's own headline statistic (r=0.540), yet fails to separate the ensemble's two most consequential cases - while the continuous representation succeeds, robustly, across eight independent scale-removal folds (r=0.677-0.717, all p<0.001). The determining factor was not correlation strength but whether the representation preserved the structure relevant to prediction. These results indicate that the choice of representation determines whether predictive structure in complex systems becomes accessible - a scientific variable in its own right, not a downstream analysis choice.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Large reasoning models (LRMs) produce reasoning traces with non-linear structures, such as backtracking and self-correction, that complicate the evaluation and monitoring of the reasoning process. We introduce ReasoningFlow, a framework that captures the discourse structures of LRM reasoning traces into fine-grained directed acyclic graphs (DAGs). We develop and validate our annotation schema through careful manual annotation of 31 traces (2.1k steps), achieving high inter-annotator agreement, then scale to automatic annotation of 1,260 traces (247.7k steps) spanning three tasks (math, science, argumentation) and five models (Qwen2.5-32B-Inst, QwQ-32B, DeepSeek-V3, DeepSeek-R1, GPT-oss-120B). By analyzing ReasoningFlow graphs, we find: (1) LRMs exhibit structurally similar traces, despite being trained from different base models and potentially non-overlapping post-training data. (2) ReasoningFlow reveals diverse fine-grained reasoning behaviors (e.g., local verification, self-reflection, and assumptions) that can be used for better reasoning trace monitorability. (3) In LRMs, most of the erroneous steps are not used to derive final answers. (4) Mechanistic causal dependencies between steps do not reflect the language-level discourse structure. We release the dataset and code in: https://github.com/jinulee-v/reasoningflow.

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

We propose to improve transformers of a specific modality with irrelevant data from other modalities, e.g., improve an ImageNet model with audio or point cloud datasets. We would like to highlight that the data samples of the target modality are irrelevant to the other modalities, which distinguishes our method from other works utilizing paired (e.g., CLIP) or interleaved data of different modalities. We propose a methodology named Multimodal Pathway - given a target modality and a transformer designed for it, we use an auxiliary transformer trained with data of another modality and construct pathways to connect components of the two models so that data of the target modality can be processed by both models. In this way, we utilize the universal sequence-to-sequence modeling abilities of transformers obtained from two modalities. As a concrete implementation, we use a modality-specific tokenizer and task-specific head as usual but utilize the transformer blocks of the auxiliary model via a proposed method named Cross-Modal Re-parameterization, which exploits the auxiliary weights without any inference costs. On the image, point cloud, video, and audio recognition tasks, we observe significant and consistent performance improvements with irrelevant data from other modalities. The code and models are available at https://github.com/AILab-CVC/M2PT.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

Adaptive hierarchical systems accumulate routing state as they learn which components to select. We show that this state already defines a coherent attribution over the hierarchy. A leaf receives the product of the local routing weights on its path, while an internal node receives the corresponding prefix product. The same learned state can therefore be read consistently at group and component levels, and every finer readout sums exactly to its coarser counterpart. This attribution describes the preferences learned by the deployed router rather than an intrinsic or counterfactual value of a component. Across LLM, Census, agentic, and telecom-network hierarchies, the learned state contains meaningful structure at several levels, and the clearest organisation need not occur at the leaves. In the telecom study, Site- or Region-level readouts usually reveal clearer structure than Cell-level readouts. Comparison with Shapley attribution can then show whether the preferences learned in deployment match capabilities revealed by counterfactual coalitions. The result is a hierarchical explanation that requires no separate attribution model: the same routing state supports consistent explanations at several levels of the system.

Schema-guided reasoning pipelines ask LLMs to produce explicit intermediate structures -- rubrics, checklists, verification queries -- before committing to a final decision. But do these structures causally determine the output, or merely accompany it? We introduce a causal evaluation protocol that makes this directly measurable: by selecting tasks where a deterministic function maps intermediate structures to decisions, every controlled edit implies a unique correct output. Across eight models and three benchmarks, models appear self-consistent with their own intermediate structures but fail to update predictions after intervention in up to 60% of cases -- revealing that apparent faithfulness is fragile once the intermediate structure changes. When derivation of the final decision from the structure is delegated to an external tool, this fragility largely disappears; however, prompts which ask to prioritize the intermediate structure over the original input do not materially close the gap. Overall, intermediate structures in schema-guided pipelines function as influential context rather than stable causal mediators.

Cross-entropy pretraining and preference alignment update the same transformer weights, but leave geometrically distinct traces. We characterise this asymmetry with a relative-subspace-fraction probe that tracks how weight deltas align with residual-stream activation subspaces and with the prediction subspace defined by the unembedding. Alignment deltas concentrate in the read pathway (W_Q, W_K), along principal directions of attention-input activations, while remaining near-isotropic in the write pathway (W_O, W_2) relative to the prediction subspace. We explain this pattern through anisotropic gradient accumulation: updates to a matrix W are sums of outer products δ_t a_t^top, and inherit directional structure from whichever side has concentrated covariance. For read-pathway matrices, this side is the input activation a_t, whose covariance is spiked in trained transformers and therefore produces objective-agnostic concentration. For write-pathway matrices, the relevant side is the upstream gradient δ_t, whose anisotropy depends on the loss. Cross-entropy supplies the canonical sharp per-sample signal, inducing write-pathway prediction geometry during pretraining; alignment objectives typically add little further write-side concentration. We support this explanation with a within-checkpoint trajectory, a graded contrastive-objective control, and a closed-form rank-1 intervention with matched direction controls, providing causal evidence for the proposed weight-space geometry.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at https://github.com/Jun-Hyeong-Kim/AdaPath.

In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storms), and their implications for cancer are discussed. Genomic alterations spur cancer genome evolution. Thus, the relationship between cancer clonal evolution and cancer stems cells is commented. The key question in cancer biology concerns how these genomic alterations support cancer development and metastasis in the context of biological functioning. Thus far, efforts such as pathway analysis have improved the understanding of the functional contributions of genetic mutations and DNA copy number variations to cancer development, progression and metastasis. However, the known pathways correspond to a small fraction, plausibly 5-10%, of somatic mutations and genes with an altered copy number. To develop a comprehensive understanding of the function of these genomic alterations in cancer, an integrative network framework is proposed and discussed. Finally, the challenges and the directions of studying cancer omic data using an integrative network approach are commented.

Graphs provide a natural representation of relational structure that arises across diverse domains. Despite this ubiquity, graph structure is typically learned in a modality- and task-isolated manner, where graph representations are constructed within individual task contexts and discarded thereafter. As a result, structural regularities across modalities and tasks are repeatedly reconstructed rather than accumulated at the level of intermediate graph representations. This motivates a representation-learning question: how should graph structure be organized so that it can persist and accumulate across heterogeneous modalities and tasks? We adopt a representation-centric perspective in which graph structure is treated as a structural substrate that persists across learning contexts. To instantiate this perspective, we propose G-Substrate, a graph substrate framework that organizes learning around shared graph structures. G-Substrate comprises two complementary mechanisms: a unified structural schema that ensures compatibility among graph representations across heterogeneous modalities and tasks, and an interleaved role-based training strategy that exposes the same graph structure to multiple functional roles during learning. Experiments across multiple domains, modalities, and tasks show that G-Substrate outperforms task-isolated and naive multi-task learning methods. The codebase, model, and datasets are available at https://github.com/zmli6/G-Substrate.

There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant transformation is a two-phase process, where an initial increase of system plasticity is followed by a decrease of plasticity at late stages of carcinogenesis as a model of cellular learning. We describe the hallmarks of increased system plasticity of early, tumor initiating cells, such as increased noise, entropy, conformational and phenotypic plasticity, physical deformability, cell heterogeneity and network rearrangements. Finally, we argue that the large structural changes of molecular networks during cancer development necessitate a rather different targeting strategy in early and late phase of carcinogenesis. Plastic networks of early phase cancer development need a central hit, while rigid networks of late stage primary tumors or established metastases should be attacked by the network influence strategy, such as by edgetic, multi-target, or allo-network drugs. Cancer stem cells need special diagnosis and targeting, since their dormant and rapidly proliferating forms may have more rigid, or more plastic networks, respectively. The extremely high ability to change their rigidity/plasticity may be a key differentiating hallmark of cancer stem cells. The application of early stage-optimized anti-cancer drugs to late-stage patients may be a reason of many failures in anti-cancer therapies. Our hypotheses presented here underlie the need for patient-specific multi-target therapies applying the correct ratio of central hits and network influences -- in an optimized sequence.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

The presence of linear paths in parameter space between two different network solutions in certain cases, i.e., linear mode connectivity (LMC), has garnered interest from both theoretical and practical fronts. There has been significant research that either practically designs algorithms catered for connecting networks by adjusting for the permutation symmetries as well as some others that more theoretically construct paths through which networks can be connected. Yet, the core reasons for the occurrence of LMC, when in fact it does occur, in the highly non-convex loss landscapes of neural networks are far from clear. In this work, we take a step towards understanding it by providing a model of how the loss landscape needs to behave topographically for LMC (or the lack thereof) to manifest. Concretely, we present a `mountainside and ridge' perspective that helps to neatly tie together different geometric features that can be spotted in the loss landscape along the training runs. We also complement this perspective by providing a theoretical analysis of the barrier height, for which we provide empirical support, and which additionally extends as a faithful predictor of layer-wise LMC. We close with a toy example that provides further intuition on how barriers arise in the first place, all in all, showcasing the larger aim of the work -- to provide a working model of the landscape and its topography for the occurrence of LMC.

Inference-time steering enables pretrained diffusion/flow models to be adapted to new tasks without retraining. A widely used approach is the ratio-of-densities method, which defines a time-indexed target path by reweighting probability-density trajectories from multiple models with positive, or in some cases, negative exponents. This construction, however, harbors a critical and previously unformalized failure mode: Marginal Path Collapse, where intermediate densities become non-normalizable even though endpoints remain valid. Collapse arises systematically when composing heterogeneous models trained on different noise schedules or datasets, including a common setting in molecular design where de-novo, conformer, and pocket-conditioned models must be combined for tasks such as flexible-pose scaffold decoration. We provide a novel and complete solution for the problem. First, we derive a simple path existence criterion that predicts exactly when collapse occurs from noise schedules and exponents alone. Second, we introduce Adaptive path Correction with Exponents (ACE), which extends Feynman-Kac steering to time-varying exponents and guarantees a valid probability path. On a synthetic 2D benchmark and on flexible-pose scaffold decoration, ACE eliminates collapse and enables high-guidance compositional generation, improving distributional and docking metrics over constant-exponent baselines and even specialized task-specific scaffold decoration models. Our work turns ratio-of-densities steering with heterogeneous experts from an unstable heuristic into a reliable tool for controllable generation.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

Cancer progression arises from interactions across multiple biological layers, especially beyond morphological and across molecular layers that remain invisible to image-only models. To capture this broader biological landscape, we present EXAONE Path 2.5, a pathology foundation model that jointly models histologic, genomic, epigenetic and transcriptomic modalities, producing an integrated patient representation that reflects tumor biology more comprehensively. Our approach incorporates three key components: (1) multimodal SigLIP loss enabling all-pairwise contrastive learning across heterogeneous modalities, (2) a fragment-aware rotary positional encoding (F-RoPE) module that preserves spatial structure and tissue-fragment topology in WSI, and (3) domain-specialized internal foundation models for both WSI and RNA-seq to provide biologically grounded embeddings for robust multimodal alignment. We evaluate EXAONE Path 2.5 against six leading pathology foundation models across two complementary benchmarks: an internal real-world clinical dataset and the Patho-Bench benchmark covering 80 tasks. Our framework demonstrates high data and parameter efficiency, achieving on-par performance with state-of-the-art foundation models on Patho-Bench while exhibiting the highest adaptability in the internal clinical setting. These results highlight the value of biologically informed multimodal design and underscore the potential of integrated genotype-to-phenotype modeling for next-generation precision oncology.

Large Language Models (LLMs) have shown potential in reasoning over structured environments, e.g., knowledge graph and table. Such tasks typically require multi-hop reasoning, i.e., match natural language utterance with instances in the environment. Previous methods leverage LLMs to incrementally build a reasoning path, where the LLMs either invoke tools or pick up schemas by step-by-step interacting with the environment. We propose Reasoning-Path-Editing (Readi), a novel framework where LLMs can efficiently and faithfully reason over structured environments. In Readi, LLMs initially generate a reasoning path given a query, and edit the path only when necessary. We instantiate the path on structured environments and provide feedback to edit the path if anything goes wrong. Experimental results on three KGQA and two TableQA datasets show the effectiveness of Readi, significantly surpassing previous LLM-based methods (by 9.1% Hit@1 on WebQSP, 12.4% on MQA-3H and 9.5% on WTQ), comparable with state-of-the-art fine-tuned methods (67% on CWQ and 74.7% on WebQSP) and substantially boosting the vanilla LLMs (by 14.9% on CWQ). Our code will be available on https://aka.ms/readi.

With the development of large language models (LLMs), particularly with the introduction of the long reasoning chain technique, the reasoning ability of LLMs in complex problem-solving has been significantly enhanced. While acknowledging the power of long reasoning chains, we cannot help but wonder: Why do different reasoning chains perform differently in reasoning? What components of the reasoning chains play a key role? Existing studies mainly focus on evaluating reasoning chains from a functional perspective, with little attention paid to their structural mechanisms. To address this gap, this work is the first to analyze and evaluate the quality of the reasoning chain from a structural perspective. We apply persistent homology from Topological Data Analysis (TDA) to map reasoning steps into semantic space, extract topological features, and analyze structural changes. These changes reveal semantic coherence, logical redundancy, and identify logical breaks and gaps. By calculating homology groups, we assess connectivity and redundancy at various scales, using barcode and persistence diagrams to quantify stability and consistency. Our results show that the topological structural complexity of reasoning chains correlates positively with accuracy. More complex chains identify correct answers sooner, while successful reasoning exhibits simpler topologies, reducing redundancy and cycles, enhancing efficiency and interpretability. This work provides a new perspective on reasoning chain quality assessment and offers guidance for future optimization.

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development of all-atom foundation models for molecular modeling and generation, existing approaches face challenges in generalization due to the multi-modal nature of atomic data and the lack of comprehensive analysis of training and sampling strategies. To address these limitations, we propose PharMolixFM, a unified framework for constructing all-atom foundation models based on multi-modal generative techniques. Our framework includes three variants using state-of-the-art multi-modal generative models. By formulating molecular tasks as a generalized denoising process with task-specific priors, PharMolixFM achieves robust performance across various structural biology applications. Experimental results demonstrate that PharMolixFM-Diff achieves competitive prediction accuracy in protein-small-molecule docking (83.9% vs. 90.2% RMSD < 2Å, given pocket) with significantly improved inference speed. Moreover, we explore the empirical inference scaling law by introducing more sampling repeats or steps. Our code and model are available at https://github.com/PharMolix/OpenBioMed.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

Large reasoning models (LRMs) spend substantial test-time compute on long chain-of-thought (CoT) traces, but what *characterizes* an effective CoT remains unclear. While prior work reports gains from lengthening CoTs and increasing review (revisiting earlier steps) via appended *wait* tokens, recent studies suggest that shorter thinking can outperform longer traces. We therefore conduct a systematic evaluation across ten LRMs on math and scientific reasoning. Contrary to the "longer-is-better" narrative, we find that both naive CoT lengthening and increased review are associated with *lower* accuracy. As CoT unfolds step by step, token-level metrics can conflate verbosity with process quality. We introduce a graph view of CoT to extract structure and identify a single statistic-the *Failed-Step Fraction (FSF)*, the fraction of steps in abandoned branches-that consistently outpredicts length and review ratio for correctness across models. To probe causality, we design two interventions. First, we rank candidate CoTs by each metric at test time, where FSF yields the largest pass@1 gains; second, we edit CoTs to remove failed branches, which significantly improves accuracy, indicating that failed branches bias subsequent reasoning. Taken together, these results characterize effective CoTs as those that *fail less* and support *structure-aware* test-time scaling over indiscriminately generating long CoT.

Scientific progress depends on sequences of enabling contributions, yet existing AI4Science benchmarks largely focus on citation prediction, literature retrieval, or idea generation rather than the dependencies that make progress possible. In this paper, we introduce discovery pathway forecasting: given a target scientific contribution and the prior literature available at a specified time, the task is to (1) identify the enabling contributions required to realize it and (2) ground each in prior work when such prior work exists. We present SciPaths, a benchmark of 262 expert-annotated gold pathways and 2,444 silver pathways constructed from machine learning and natural language processing papers, where each pathway records enabling contributions, roles, rationales, and prior-work groundings or unmapped decisions. Evaluating frontier and open-weight language models, we find that the best model reaches only 0.189 F1 under strict semantic matching, with core methodological dependencies hardest to recover. Prior-work grounding improves substantially when gold enabling contributions are provided, showing that decomposition quality is a major bottleneck for end-to-end pathway recovery. SciPaths therefore shifts evaluation toward a missing capability in scientific forecasting: reasoning backward from a target contribution to the enabling scientific building blocks and prior-work dependencies that make it feasible.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

Clinical case formulation organizes patient symptoms and psychosocial factors into causal models, often using the 5P framework. However, constructing such graphs from therapy transcripts is time consuming and varies across clinicians. We present InsightFlow, an LLM based approach that automatically generates 5P aligned causal graphs from patient-therapist dialogues. Using 46 psychotherapy intake transcripts annotated by clinical experts, we evaluate LLM generated graphs against human formulations using structural (NetSimile), semantic (embedding similarity), and expert rated clinical criteria. The generated graphs show structural similarity comparable to inter annotator agreement and high semantic alignment with human graphs. Expert evaluations rate the outputs as moderately complete, consistent, and clinically useful. While LLM graphs tend to form more interconnected structures compared to the chain like patterns of human graphs, overall complexity and content coverage are similar. These results suggest that LLMs can produce clinically meaningful case formulation graphs within the natural variability of expert practice. InsightFlow highlights the potential of automated causal modeling to augment clinical workflows, with future work needed to improve temporal reasoning and reduce redundancy.

Large Language Model (LLM) agentic systems are software systems powered by LLMs that autonomously reason, plan, and execute multi-step workflows to achieve human goals, rather than merely executing predefined steps. During execution, these workflows frequently encounter exceptions. Existing exception handling solutions often treat exceptions superficially, failing to trace execution-phase exceptions to their reasoning-phase root causes. Furthermore, their recovery logic is brittle, lacking structured escalation pathways when initial attempts fail. To tackle these challenges, we first present a comprehensive taxonomy of 36 exception types across 12 agent artifacts. Building on this, we propose SHIELDA (Structured Handling of Exceptions in LLM-Driven Agentic Workflows), a modular runtime exception handling framework for LLM agentic workflows. SHIELDA uses an exception classifier to select a predefined exception handling pattern from a handling pattern registry. These patterns are then executed via a structured handling executor, comprising local handling, flow control, and state recovery, to enable phase-aware recovery by linking exceptions to their root causes and facilitating composable strategies. We validate SHIELDA's effectiveness through a case study on the AutoPR agent, demonstrating effective, cross-phase recovery from a reasoning-induced exception.

Diffusion Transformers (DiTs) have established themselves as a scalable backbone for high-fidelity image synthesis. However, unlike U-Net based diffusion models that rely on rigid, hand-crafted skip connections, DiTs predominantly use a uniform residual stream that integrates all preceding layers as a monolithic state. In this work, we rethink residual connections in diffusion transformers and propose to transform them from passive summation into an active retrieval mechanism optimized for image denoising. First, we conduct a systematic analysis of DiT's internal representation, revealing a latent preference for early-layer feature reuse and symmetric layer guidance. Motivated by this, we introduce a structured connectivity design that explicitly integrates local residual connections with long-range pathways. Instead of static skip connections or dense all-layer routing, our method enables each transformer block to selectively ``attend'' to critical earlier representations, dynamically retrieving spatial and semantic cues through direct, differentiable cross-depth paths. Experiments show that our adaptive connectivity leads to faster convergence, with up to 1.73times fewer training iterations, and significant gains in FID and visual quality with less than 0.1% additional parameters, further improving a strong REPA-XL/2 model from 5.9 to 4.34 FID without guidance and reaching 1.39 FID with classifier-free guidance. Our findings suggest that adaptive cross-layer connectivity is a critical yet underexplored factor in diffusion transformers, and that incorporating structured information pathways provides a simple and effective direction for improving scalable generative models.

Organizing a large-scale knowledge graph into a typed property graph requires structural decisions -- which entities become nodes, which properties become edges, and what schema governs these choices. Existing approaches embed these decisions in pipeline code or extract relations ad hoc, producing schemas that are tightly coupled to their construction process and difficult to reuse for downstream ontology-level tasks. We present an ontology-oriented approach in which the schema is designed from the outset for ontology analysis, entity disambiguation, domain customization, and LLM-guided extraction -- not merely as a byproduct of graph building. The core mechanism is intrinsic-relational routing, which classifies every property as either intrinsic or relational and routes it to the corresponding schema module. This routing produces a declarative schema that is portable across storage backends and independently reusable. We instantiate the approach on the January 2026 Wikidata dump. A rule-based cleaning stage identifies a 34.6M-entity core set from the full dump, followed by iterative intrinsic-relational routing that assigns each property to one of 94 modules organized into 8 categories. With tool-augmented LLM support and human review, the schema reaches 93.3% category coverage and 98.0% module assignment among classified entities. Exporting this schema yields a property graph with 34.0M nodes and 61.2M edges across 38 relationship types. We validate the ontology-oriented claim through five applications that consume the schema independently of the construction pipeline: ontology structure analysis, benchmark annotation auditing, entity disambiguation, domain customization, and LLM-guided extraction.

We reveal that feedforward network (FFN) layers, rather than attention layers, are the primary contributors to Vision Transformer (ViT) inference latency, with their impact signifying as model size increases. This finding highlights a critical opportunity for optimizing the efficiency of large-scale ViTs by focusing on FFN layers. In this work, we propose a novel channel idle mechanism that facilitates post-training structural reparameterization for efficient FFN layers during testing. Specifically, a set of feature channels remains idle and bypasses the nonlinear activation function in each FFN layer, thereby forming a linear pathway that enables structural reparameterization during inference. This mechanism results in a family of ReParameterizable Vision Transformers (RePaViTs), which achieve remarkable latency reductions with acceptable sacrifices (sometimes gains) in accuracy across various ViTs. The benefits of our method scale consistently with model sizes, demonstrating greater speed improvements and progressively narrowing accuracy gaps or even higher accuracies on larger models. In particular, RePa-ViT-Large and RePa-ViT-Huge enjoy 66.8% and 68.7% speed-ups with +1.7% and +1.1% higher top-1 accuracies under the same training strategy, respectively. RePaViT is the first to employ structural reparameterization on FFN layers to expedite ViTs to our best knowledge, and we believe that it represents an auspicious direction for efficient ViTs. Source code is available at https://github.com/Ackesnal/RePaViT.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

We introduce directional routing, a lightweight mechanism that gives each transformer attention head learned suppression directions controlled by a shared router, at 3.9% parameter cost. We train a 433M-parameter model alongside an identical baseline in a single run, then trace the resulting circuits through mechanistic interpretability. Routing becomes the model's dominant computational pathway. Disabling it collapses factual recall to near-zero probability across all 8 test prompts and drops induction accuracy from 93.4% to 0.0%. Knocking out individual attention heads has negligible effect: the primary mover head's removal actually increases target probability, and induction heads retain 98.6% accuracy without their strongest member. The coordination mechanism is irreplaceable; the components it coordinates are not. The model also self-organizes, without explicit pressure, into two regimes: domain-adaptive routing in early layers and fixed syntactic pruning in late layers, where the least-varying layer is the most critical (+42.6 PPL when disabled). Routing reduces perplexity 31-56% relative to the baseline, though downstream multiple-choice benchmarks do not yet reflect these gains.

Modern training on a new task often starts from a previously trained model rather than from scratch, raising the question of how this initialization affects the subsequent training trajectory. Classical implicit-bias results characterize the direction selected by prolonged training, but this direction alone does not provide information regarding the intermediate behavior. We address this question through a geometric approximation of full-batch logistic gradient descent (GD) trajectories on strictly linearly separable data, with large initialization of scale R motivated by prior training. From any limiting normalized initial position, we use minimum-norm projection rules to construct a unique continuous ideal path consisting of finitely many linear segments. The path has two stages: negative-margin correction followed by minimum-margin growth. We prove that, after an explicit two-stage time reparameterization, the fixed-step GD trajectory divided by R converges uniformly to this path on every fixed parameter interval as Rtoinfty. Further, our quantitative error bounds account for initialization perturbations and the transition between stages. This approximation provides asymptotic formulas for peak evaluation loss and cumulative training loss. In particular, peak evaluation loss can grow linearly in R even when both endpoint losses tend to zero. The cumulative losses in the correction and margin-growth stages, normalized by R^2 and R, respectively, converge to explicit limits. Experiments on controlled geometries and fixed image features complement our theoretical results.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Claims made by individuals or entities are oftentimes nuanced and cannot be clearly labeled as entirely "true" or "false" -- as is frequently the case with scientific and political claims. However, a claim (e.g., "vaccine A is better than vaccine B") can be dissected into its integral aspects and sub-aspects (e.g., efficacy, safety, distribution), which are individually easier to validate. This enables a more comprehensive, structured response that provides a well-rounded perspective on a given problem while also allowing the reader to prioritize specific angles of interest within the claim (e.g., safety towards children). Thus, we propose ClaimSpect, a retrieval-augmented generation-based framework for automatically constructing a hierarchy of aspects typically considered when addressing a claim and enriching them with corpus-specific perspectives. This structure hierarchically partitions an input corpus to retrieve relevant segments, which assist in discovering new sub-aspects. Moreover, these segments enable the discovery of varying perspectives towards an aspect of the claim (e.g., support, neutral, or oppose) and their respective prevalence (e.g., "how many biomedical papers believe vaccine A is more transportable than B?"). We apply ClaimSpect to a wide variety of real-world scientific and political claims featured in our constructed dataset, showcasing its robustness and accuracy in deconstructing a nuanced claim and representing perspectives within a corpus. Through real-world case studies and human evaluation, we validate its effectiveness over multiple baselines.

In this paper, we present the findings of our Project ALPINE which stands for ``Autoregressive Learning for Planning In NEtworks." Project ALPINE initiates a theoretical investigation into the development of planning capabilities in Transformer-based language models through their autoregressive learning mechanisms, aiming to identify any potential limitations in their planning abilities. We abstract planning as a network path-finding task where the objective is to generate a valid path from a specified source node to a designated target node. In terms of expressiveness, we show that the Transformer is capable of executing path-finding by embedding the adjacency and reachability matrices within its weights. Our theoretical analysis of the gradient-based learning dynamic of the Transformer reveals that the Transformer is capable of learning both the adjacency matrix and a limited form of the reachability matrix. These theoretical insights are then validated through experiments, which demonstrate that the Transformer indeed learns the adjacency matrix and an incomplete reachability matrix, which aligns with the predictions made in our theoretical analysis. Additionally, when applying our methodology to a real-world planning benchmark, called Blocksworld, our observations remain consistent. Our theoretical and empirical analyses further unveil a potential limitation of Transformer in path-finding: it cannot identify reachability relationships through transitivity, and thus would fail when path concatenation is needed to generate a path. In summary, our findings shed new light on how the internal mechanisms of autoregressive learning enable planning in networks. This study may contribute to our understanding of the general planning capabilities in other related domains.

Large Language Models (LLMs) are prone to hallucination, the generation of plausible yet factually incorrect statements. This work investigates the intrinsic, architectural origins of this failure mode through three primary contributions.First, to enable the reliable tracing of internal semantic failures, we propose Distributional Semantics Tracing (DST), a unified framework that integrates established interpretability techniques to produce a causal map of a model's reasoning, treating meaning as a function of context (distributional semantics). Second, we pinpoint the model's layer at which a hallucination becomes inevitable, identifying a specific commitment layer where a model's internal representations irreversibly diverge from factuality. Third, we identify the underlying mechanism for these failures. We observe a conflict between distinct computational pathways, which we interpret using the lens of dual-process theory: a fast, heuristic associative pathway (akin to System 1) and a slow, deliberate contextual pathway (akin to System 2), leading to predictable failure modes such as Reasoning Shortcut Hijacks. Our framework's ability to quantify the coherence of the contextual pathway reveals a strong negative correlation (rho = -0.863) with hallucination rates, implying that these failures are predictable consequences of internal semantic weakness. The result is a mechanistic account of how, when, and why hallucinations occur within the Transformer architecture.

Multimodal large language models (MLLMs) excel at high-level reasoning yet fail on OCR tasks where fine-grained visual details are compromised or misaligned. We identify an overlooked optimization issue in multi-layer feature fusion. Skip pathways introduce direct back-propagation paths from high-level semantic objectives to early visual layers. This mechanism overwrites low-level signals and destabilizes training. To mitigate this gradient interference, we propose Detached Skip-Links, a minimal modification that reuses shallow features in the forward pass while stopping gradients through the skip branch during joint training. This asymmetric design reduces gradient interference, improving stability and convergence without adding learnable parameters. To diagnose whether fine-grained information is preserved and usable by an LLM, we introduce R-Probe, which measures pixel-level reconstructability of projected visual tokens using a shallow decoder initialized from the first quarter of the LLM layers. Across multiple ViT backbones and multimodal benchmarks, and at scales up to 7M training samples, our approach consistently improves OCR-centric benchmarks and delivers clear gains on general multimodal tasks.

Recent advances in psychotherapy have focused on treatment personalization, such as by selecting treatment modules based on personalized networks. However, estimating personalized networks typically requires intensive longitudinal data, which is not always feasible. A solution to facilitate scalability of network-driven treatment personalization is leveraging LLMs. In this study, we present an end-to-end pipeline for automatically generating client networks from 77 therapy transcripts to support case conceptualization and treatment planning. We annotated 3364 psychological processes and their corresponding dimensions in therapy transcripts. Using these data, we applied in-context learning to jointly identify psychological processes and their dimensions. The method achieved high performance even with a few training examples. To organize the processes into networks, we introduced a two-step method that grouped them into clinically meaningful clusters. We then generated explanation-augmented relationships between clusters. Experts found that networks produced by our multi-step approach outperformed those built with direct prompting for clinical utility and interpretability, with up to 90% preferring our approach. In addition, the networks were rated favorably by experts, with scores for clinical relevance, novelty, and usefulness ranging from 72-75%. Our findings provide a proof of concept for using LLMs to create clinically relevant networks from therapy transcripts. Advantages of our approach include bottom-up case conceptualization from client utterances in therapy sessions and identification of latent themes. Networks generated from our pipeline may be used in clinical settings and supervision and training. Future research should examine whether these networks improve treatment outcomes relative to other methods of treatment personalization, including statistically estimated networks.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have ignited investigation into important aspects of molecular diffusion in 3D cellular architectures. This paper describes fundamental mechanics of diffusion with equations for modeling these dynamic processes under a variety of scenarios in 3D cellular tissue constructs. The effects of these diffusion processes and resultant concentration gradients are described in the context of the major molecular signaling pathways in stem cells that both mediate and are influenced by gas and nutrient concentrations, including how diffusion phenomena can affect stem cell state, cell differentiation, and metabolic states of the cell. The application of these diffusion models and pathways is of vital importance for future studies of developmental processes, disease modeling, and tissue regeneration.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

Cross-domain scientific synthesis requires connecting mechanistic explanations across fragmented literature, a capability that remains challenging for both retrieval-based systems and unconstrained language models. While recent work has applied large language models to scientific summarization and question answering, these approaches provide limited control over reasoning depth and structural grounding. We frame mechanistic synthesis as a graph-constrained multi-hop reasoning problem over literature-derived concept graphs. Given a scientific query and a compact, query-local corpus, SciNets constructs a directed concept graph and synthesizes mechanistic explanations by identifying multi-hop reasoning paths that connect concepts that rarely co-occur within individual papers. We systematically compare shortest-path reasoning, k-shortest paths with diversity constraints, stochastic random walks, and a retrieval-augmented language model baseline. Rather than evaluating correctness, which is often indeterminate when synthesizing connections across distributed sources, we introduce a behavioral framework that measures symbolic reasoning depth, mechanistic diversity, and grounding stability. Across machine learning, biology, and climate science tasks, explicit graph constraints enable controllable multi-hop reasoning while revealing a consistent trade-off: deeper and more diverse symbolic reasoning increases grounding instability, whereas shortest-path reasoning remains highly stable but structurally conservative. These findings provide a systematic behavioral characterization of the limits and capabilities of current graph-LLM integration for scientific synthesis.

Answering complex questions over long documents frequently requires integrating evidence that the source itself disperses naturally across distant passages. In an incident report, the operating condition, design flaw, and missed safety check that jointly explain a disaster may appear dozens of sections apart; in a novel, a character's true motive may surface only through scenes far removed from the moment it becomes relevant. This source-internal evidence integration is central to real-world long-document analysis, yet existing benchmarks largely sidestep it. Needle probes, planted facts, and reverse-engineered multi-hop chains embed evidence that may differ from the host text in distribution, placement, or register, making it unclear whether strong performance reflects genuine source reasoning or distributional artifacts. We introduce WILDTRACE, a benchmark of 481 tasks over 214 naturally occurring long-form sources such as technical incident reports and lesser-known literary narratives, where all evidence trails arise from the document's own causal, temporal, and narrative logic. Drawing on Pearl's causal hierarchy and prior multi-hop reasoning typologies, we define seven source-internal evidence geometries that characterize the distinct relational demands of analytical reading in long documents. A source-first construction pipeline mines candidate trails from document structure before writing questions; each item then undergoes multi-stage validation covering clue necessity, answer groundedness, rubric fidelity, contamination resistance and answerability. As models are increasingly entrusted with real-world high-stakes analytical tasks, this gap between accessing information and reasoning over naturally dispersed evidence emerges as a defining challenge for the next stage of long-context research.

Large language models place structured concepts on geometrically faithful manifolds: weekdays lie on a circle, months on another, usually taken to be a fixed world-model the network stores and looks up. We show that context is king: the structure a model actually uses is set by the in-context specification. A declarative rule fixes not only which relations the geometry encodes but its topology type: the same tokens form a cycle or a branching tree on command, built even on arbitrary, meaning-free tokens with no prior to inherit, which a relabeled stored shape cannot do. When the specification conflicts with a strong pretrained prior, the context-set geometry dominates it in capable models, read from the same activations (representational similarity 0.6--0.9 to the imposed structure versus near-zero to the prior), across the priors we test and both families we study (Gemma, Qwen). Activation patching shows the map is causally used, not a probe correlate: swapping one entity's activation for another's makes the model answer with the other entity's successor under the imposed order. A rough map forms readily, present even in small and base models; what scale gates is using it cleanly: clean dominance and the causal crossover emerge only in the larger models (up to Gemma-31B and Qwen-27B) and weaken or reverse below, so a mechanism present in a large model can be absent in a smaller one of the same family. Whether the model builds this geometry anew or reconfigures a stored one we leave open; operationally, the geometry it uses is the one the context specifies.

Think about how human handles complex reading tasks: marking key points, inferring their relationships, and structuring information to guide understanding and responses. Likewise, can a large language model benefit from text structure to enhance text-processing performance? To explore it, in this work, we first introduce Structure of Thought (SoT), a prompting technique that explicitly guides models to construct intermediate text structures, consistently boosting performance across eight tasks and three model families. Building upon this insight, we present T2S-Bench, the first benchmark designed to evaluate and improve text-to-structure capabilities of models. T2S-Bench includes 1.8K samples across 6 scientific domains and 32 structural types, rigorously constructed to ensure accuracy, fairness, and quality. Evaluation on 45 mainstream models reveals substantial improvement potential: the average accuracy on the multi-hop reasoning task is only 52.1%, and even the most advanced model achieves 58.1% node accuracy in end-to-end extraction. Furthermore, on Qwen2.5-7B-Instruct, SoT alone yields an average +5.7% improvement across eight diverse text-processing tasks, and fine-tuning on T2S-Bench further increases this gain to +8.6%. These results highlight the value of explicit text structuring and the complementary contributions of SoT and T2S-Bench. Dataset and eval code have been released at https://t2s-bench.github.io/T2S-Bench-Page/.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

Synthesis planning aiming to find pathways of reactions for a target molecule is one of the most important and challenging tasks in drug discovery. Recent progress has produced both specialized deep-learning retrosynthesis systems and general-purpose large language models, but objective comparison remains difficult due to the lack of flexible, chemically interpretable benchmarking protocols. In the current study, we are introducing the URSA (Utilitarian RetroSynthesis Assessment) evaluation framework that provides the opportunity to benchmark the synthetic routes not only from a formal perspective, such as convergence to commercially available starting materials, but also from a chemical plausibility perspective, mimicking the way expert chemists evaluate the reactions and routes. The study covers a comprehensive evaluation of both conventional end-to-end retrosynthesis solutions and LLMs for the synthesis planning task on a set of novel, diverse target molecules with undisclosed synthetic routes, which represent realistic tasks in the daily drug design routine. We find that while LLMs can support high-level strategic planning, they currently underperform specialized retrosynthesis models in reliably solving synthesis planning tasks.

We present a fast algorithm for the design of smooth paths (or trajectories) that are constrained to lie in a collection of axis-aligned boxes. We consider the case where the number of these safe boxes is large, and basic preprocessing of them (such as finding their intersections) can be done offline. At runtime we quickly generate a smooth path between given initial and terminal positions. Our algorithm designs trajectories that are guaranteed to be safe at all times, and detects infeasibility whenever such a trajectory does not exist. Our algorithm is based on two subproblems that we can solve very efficiently: finding a shortest path in a weighted graph, and solving (multiple) convex optimal-control problems. We demonstrate the proposed path planner on large-scale numerical examples, and we provide an efficient open-source software implementation, fastpathplanning.

In this paper, we introduce agentic unlearning which removes specified information from both model parameters and persistent memory in agents with closed-loop interaction. Existing unlearning methods target parameters alone, leaving two critical gaps: (i) parameter-memory backflow, where retrieval reactivates parametric remnants or memory artifacts reintroduce sensitive content, and (ii) the absence of a unified strategy that covers both parameter and memory pathways. We present Synchronized Backflow Unlearning (SBU), a framework that unlearns jointly across parameter and memory pathways. The memory pathway performs dependency closure-based unlearning that prunes isolated entities while logically invalidating shared artifacts. The parameter pathway employs stochastic reference alignment to guide model outputs toward a high-entropy prior. These pathways are integrated via a synchronized dual-update protocol, forming a closed-loop mechanism where memory unlearning and parametric suppression reinforce each other to prevent cross-pathway recontamination. Experiments on medical QA benchmarks show that SBU reduces traces of targeted private information across both pathways with limited degradation on retained data.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.