Daily Papers

We study a class of optimization problems motivated by automating the design and update of AI systems like coding assistants, robots, and copilots. We propose an end-to-end optimization framework, Trace, which treats the computational workflow of an AI system as a graph akin to neural networks, based on a generalization of back-propagation. Optimization of computational workflows often involves rich feedback (e.g. console output or user's responses), heterogeneous parameters (e.g. prompts, hyper-parameters, codes), and intricate objectives (beyond maximizing a score). Moreover, its computation graph can change dynamically with the inputs and parameters. We frame a new mathematical setup of iterative optimization, Optimization with Trace Oracle (OPTO), to capture and abstract these properties so as to design optimizers that work across many domains. In OPTO, an optimizer receives an execution trace along with feedback on the computed output and updates parameters iteratively. Trace is the tool to implement OPTO in practice. Trace has a Python interface that efficiently converts a computational workflow into an OPTO instance using a PyTorch-like interface. Using Trace, we develop a general-purpose LLM-based optimizer called OptoPrime that can effectively solve OPTO problems. In empirical studies, we find that OptoPrime is capable of first-order numerical optimization, prompt optimization, hyper-parameter tuning, robot controller design, code debugging, etc., and is often competitive with specialized optimizers for each domain. We believe that Trace, OptoPrime and the OPTO framework will enable the next generation of interactive agents that automatically adapt using various kinds of feedback. Website: https://microsoft.github.io/Trace

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at two levels: First, using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks related to publications indexed in PubMed Central. We identified such notebooks by mining the articles full text, locating them on GitHub and re-running them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. Second, this study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over two years. Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles, 22578 notebooks were written in Python, including 15817 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 10388 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

Computational workloads composing traditional Transformer models are starkly bifurcated. Multi-Head Attention (MHA) is memory-bound, with low arithmetic intensity, while feedforward layers are compute-bound. This dichotomy has long motivated research into specialized hardware to mitigate the MHA bottleneck. This paper argues that recent architectural shifts, namely Multi-head Latent Attention (MLA) and Mixture-of-Experts (MoE), challenge the premise of specialized attention hardware. We make two key observations. First, the arithmetic intensity of MLA is over two orders of magnitude greater than that of MHA, shifting it close to a compute-bound regime well-suited for modern accelerators like GPUs. Second, by distributing MoE experts across a pool of accelerators, their arithmetic intensity can be tuned through batching to match that of the dense layers, creating a more balanced computational profile. These findings reveal a diminishing need for specialized attention hardware. The central challenge for next-generation Transformers is no longer accelerating a single memory-bound layer. Instead, the focus must shift to designing balanced systems with sufficient compute, memory capacity, memory bandwidth, and high-bandwidth interconnects to manage the diverse demands of large-scale models.

As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a `DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment.

Deep reinforcement learning (DRL) algorithms require substantial samples and computational resources to achieve higher performance, which restricts their practical application and poses challenges for further development. Given the constraint of limited resources, it is essential to leverage existing computational work (e.g., learned policies, samples) to enhance sample efficiency and reduce the computational resource consumption of DRL algorithms. Previous works to leverage existing computational work require intrusive modifications to existing algorithms and models, designed specifically for specific algorithms, lacking flexibility and universality. In this paper, we present the Snapshot Reinforcement Learning (SnapshotRL) framework, which enhances sample efficiency by simply altering environments, without making any modifications to algorithms and models. By allowing student agents to choose states in teacher trajectories as the initial state to sample, SnapshotRL can effectively utilize teacher trajectories to assist student agents in training, allowing student agents to explore a larger state space at the early training phase. We propose a simple and effective SnapshotRL baseline algorithm, S3RL, which integrates well with existing DRL algorithms. Our experiments demonstrate that integrating S3RL with TD3, SAC, and PPO algorithms on the MuJoCo benchmark significantly improves sample efficiency and average return, without extra samples and additional computational resources.

Large Language Models (LLMs) face significant computational bottlenecks during inference due to the quadratic complexity of self-attention mechanisms, particularly as context lengths increase. We introduce SpecAttn, a novel training-free approach that seamlessly integrates with existing speculative decoding techniques to enable efficient sparse attention in pre-trained transformers. Our key insight is to exploit the attention weights already computed by the draft model during speculative decoding to identify important tokens for the target model, eliminating redundant computation while maintaining output quality. SpecAttn employs three core techniques: KL divergence-based layer alignment between draft and target models, a GPU-optimized sorting-free algorithm for top-p token selection from draft attention patterns, and dynamic key-value cache pruning guided by these predictions. By leveraging the computational work already performed in standard speculative decoding pipelines, SpecAttn achieves over 75% reduction in key-value cache accesses with a mere 15.29% increase in perplexity on the PG-19 dataset, significantly outperforming existing sparse attention methods. Our approach demonstrates that speculative execution can be enhanced to provide approximate verification without significant performance degradation.

People are remarkably capable of generating their own goals, beginning with child's play and continuing into adulthood. Despite considerable empirical and computational work on goals and goal-oriented behavior, models are still far from capturing the richness of everyday human goals. Here, we bridge this gap by collecting a dataset of human-generated playful goals (in the form of scorable, single-player games), modeling them as reward-producing programs, and generating novel human-like goals through program synthesis. Reward-producing programs capture the rich semantics of goals through symbolic operations that compose, add temporal constraints, and allow for program execution on behavioral traces to evaluate progress. To build a generative model of goals, we learn a fitness function over the infinite set of possible goal programs and sample novel goals with a quality-diversity algorithm. Human evaluators found that model-generated goals, when sampled from partitions of program space occupied by human examples, were indistinguishable from human-created games. We also discovered that our model's internal fitness scores predict games that are evaluated as more fun to play and more human-like.

Historical encrypted manuscripts require both paleographic interpretation of cipher symbols and cryptanalytic recovery of plaintext. Most existing computational workflows rely on a transcription-first paradigm, in which handwritten symbols are transcribed prior to decipherment. This intermediate step is labor-intensive, error-prone, and not always aligned with the goal of direct plaintext recovery. We propose an end-to-end, transcription-free approach that directly maps handwritten cipher images to plaintext. Using the Copiale cipher as a case study, we introduce the first text-line-level dataset pairing cipher images with German plaintext. We show that pretraining on generic handwriting data followed by cipher-specific fine-tuning substantially improves decipherment accuracy. Our results demonstrate that transcription-free image-to-plaintext decipherment is both feasible and effective for historical substitution ciphers, offering a simplified and scalable alternative to traditional pipelines. https://github.com/leitro/Decipher-from-Pixels-Copiale

Reinforcement Learning from Human Feedback (RLHF) stands as a pivotal technique in empowering large language model (LLM) applications. Since RLHF involves diverse computational workloads and intricate dependencies among multiple LLMs, directly adopting parallelization techniques from supervised training can result in sub-optimal performance. To overcome this limitation, we propose a novel approach named parameter ReaLlocation, which dynamically redistributes LLM parameters in the cluster and adapts parallelization strategies during training. Building upon this idea, we introduce ReaLHF, a pioneering system capable of automatically discovering and running efficient execution plans for RLHF training given the desired algorithmic and hardware configurations. ReaLHF formulates the execution plan for RLHF as an augmented dataflow graph. Based on this formulation, ReaLHF employs a tailored search algorithm with a lightweight cost estimator to discover an efficient execution plan. Subsequently, the runtime engine deploys the selected plan by effectively parallelizing computations and redistributing parameters. We evaluate ReaLHF on the LLaMA-2 models with up to 4times70 billion parameters and 128 GPUs. The experiment results showcase ReaLHF's substantial speedups of 2.0-10.6times compared to baselines. Furthermore, the execution plans generated by ReaLHF exhibit an average of 26% performance improvement over heuristic approaches based on Megatron-LM. The source code of ReaLHF is publicly available at https://github.com/openpsi-project/ReaLHF .

Euphemisms are a form of figurative language relatively understudied in natural language processing. This research extends the current computational work on potentially euphemistic terms (PETs) to Turkish. We introduce the Turkish PET dataset, the first available of its kind in the field. By creating a list of euphemisms in Turkish, collecting example contexts, and annotating them, we provide both euphemistic and non-euphemistic examples of PETs in Turkish. We describe the dataset and methodologies, and also experiment with transformer-based models on Turkish euphemism detection by using our dataset for binary classification. We compare performances across models using F1, accuracy, and precision as evaluation metrics.

Sports competitions are widely researched in computer and social science, with the goal of understanding how players act under uncertainty. While there is an abundance of computational work on player metrics prediction based on past performance, very few attempts to incorporate out-of-game signals have been made. Specifically, it was previously unclear whether linguistic signals gathered from players' interviews can add information which does not appear in performance metrics. To bridge that gap, we define text classification tasks of predicting deviations from mean in NBA players' in-game actions, which are associated with strategic choices, player behavior and risk, using their choice of language prior to the game. We collected a dataset of transcripts from key NBA players' pre-game interviews and their in-game performance metrics, totalling in 5,226 interview-metric pairs. We design neural models for players' action prediction based on increasingly more complex aspects of the language signals in their open-ended interviews. Our models can make their predictions based on the textual signal alone, or on a combination with signals from past-performance metrics. Our text-based models outperform strong baselines trained on performance metrics only, demonstrating the importance of language usage for action prediction. Moreover, the models that employ both textual input and past-performance metrics produced the best results. Finally, as neural networks are notoriously difficult to interpret, we propose a method for gaining further insight into what our models have learned. Particularly, we present an LDA-based analysis, where we interpret model predictions in terms of correlated topics. We find that our best performing textual model is most associated with topics that are intuitively related to each prediction task and that better models yield higher correlation with more informative topics.

Soft context compression reduces the computational workload of processing long contexts in LLMs by encoding long context into a smaller number of latent tokens. However, existing frameworks apply uniform compression ratios, failing to account for the extreme variance in natural language information density. While adopting a density-aware dynamic compression ratio seems intuitive, empirical investigations reveal that models struggle intrinsically with operations parameterized by input dependent, continuous structural hyperparameters. To resolve this pitfall, we introduce Semi-Dynamic Context Compression framework. Our approach features a Discrete Ratio Selector, which predicts a compression target based on intrinsic information density and quantizes it to a predefined set of discrete compression ratios. It is efficiently jointly trained with the compressor on synthetic data, with the summary lengths as a proxy to create labels for compression ratio prediction. Extensive evaluations confirm that our density-aware framework, utilizing mean pooling as the backbone, consistently outperforms static baselines, establishing a robust Pareto frontier for context compression techniques. Our code, data and model weights are available at https://github.com/yuyijiong/semi-dynamic-context-compress

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30times speedup in data preparation.

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

As computational demands continue to rise, assessing the environmental footprint of AI requires moving beyond energy and water consumption to include the material demands of specialized hardware. This study quantifies the material footprint of AI training by linking computational workloads to physical hardware needs. The elemental composition of the Nvidia A100 SXM 40 GB graphics processing unit (GPU) was analyzed using inductively coupled plasma optical emission spectroscopy, which identified 32 elements. The results show that AI hardware consists of about 90% heavy metals and only trace amounts of precious metals. The elements copper, iron, tin, silicon, and nickel dominate the GPU composition by mass. In a multi-step methodology, we integrate these measurements with computational throughput per GPU across varying lifespans, accounting for the computational requirements of training specific AI models at different training efficiency regimes. Scenario-based analyses reveal that, depending on Model FLOPs Utilization (MFU) and hardware lifespan, training GPT-4 requires between 1,174 and 8,800 A100 GPUs, corresponding to the extraction and eventual disposal of up to 7 tons of toxic elements. Combined software and hardware optimization strategies can reduce material demands: increasing MFU from 20% to 60% lowers GPU requirements by 67%, while extending lifespan from 1 to 3 years yields comparable savings; implementing both measures together reduces GPU needs by up to 93%. Our findings highlight that incremental performance gains, such as those observed between GPT-3.5 and GPT-4, come at disproportionately high material costs. The study underscores the necessity of incorporating material resource considerations into discussions of AI scalability, emphasizing that future progress in AI must align with principles of resource efficiency and environmental responsibility.

Expert parallelism has been introduced as a strategy to distribute the computational workload of sparsely-gated mixture-of-experts (MoE) models across multiple computing devices, facilitating the execution of these increasingly large-scale models. However, the All-to-All communication intrinsic to expert parallelism constitutes a significant overhead, diminishing the MoE models' efficiency. Current optimization approaches offer some relief, yet they are constrained by the sequential interdependence of communication and computation operations. To address this limitation, we present a novel shortcut-connected MoE architecture with overlapping parallel strategy, designated as ScMoE, which effectively decouples communication from its conventional sequence, allowing for a substantial overlap of 70% to 100% with computation. When compared with the prevalent top-2 MoE architecture, ScMoE demonstrates training speed improvements of 30% and 11%, and inference improvements of 40% and 15%, in our PCIe and NVLink hardware environments, respectively, where communication constitutes 60% and 15% of the total MoE time consumption. On the other hand, extensive experiments and theoretical analyses indicate that ScMoE not only achieves comparable but in some instances surpasses the model quality of existing approaches in vision and language tasks.

Decentralized learning offers a promising approach to crowdsource data consumptions and computational workloads across geographically distributed compute interconnected through peer-to-peer networks, accommodating the exponentially increasing demands. However, proper incentives are still in absence, considerably discouraging participation. Our vision is that a fair incentive mechanism relies on fair attribution of contributions to participating nodes, which faces non-trivial challenges arising from the localized connections making influence ``cascade'' in a decentralized network. To overcome this, we design the first method to estimate Data Influence CascadE (DICE) in a decentralized environment. Theoretically, the framework derives tractable approximations of influence cascade over arbitrary neighbor hops, suggesting the influence cascade is determined by an interplay of data, communication topology, and the curvature of loss landscape. DICE also lays the foundations for applications including selecting suitable collaborators and identifying malicious behaviors. Project page is available at https://raiden-zhu.github.io/blog/2025/DICE/.

Transformers have emerged as the underpinning architecture for Large Language Models (LLMs). In generative language models, the inference process involves two primary phases: prompt processing and token generation. Token generation, which constitutes the majority of the computational workload, primarily entails vector-matrix multiplications and interactions with the Key-Value (KV) Cache. This phase is constrained by memory bandwidth due to the overhead of transferring weights and KV cache values from the memory system to the computing units. This memory bottleneck becomes particularly pronounced in applications that require long-context and extensive text generation, both of which are increasingly crucial for LLMs. This paper introduces "Keyformer", an innovative inference-time approach, to mitigate the challenges associated with KV cache size and memory bandwidth utilization. Keyformer leverages the observation that approximately 90% of the attention weight in generative inference focuses on a specific subset of tokens, referred to as "key" tokens. Keyformer retains only the key tokens in the KV cache by identifying these crucial tokens using a novel score function. This approach effectively reduces both the KV cache size and memory bandwidth usage without compromising model accuracy. We evaluate Keyformer's performance across three foundational models: GPT-J, Cerebras-GPT, and MPT, which employ various positional embedding algorithms. Our assessment encompasses a variety of tasks, with a particular emphasis on summarization and conversation tasks involving extended contexts. Keyformer's reduction of KV cache reduces inference latency by 2.1x and improves token generation throughput by 2.4x, while preserving the model's accuracy.

The development of materials science is undergoing a shift from empirical approaches to data-driven and algorithm-oriented research paradigm. The state-of-the-art platforms are confined to inorganic crystals, with limited chemical space, sparse experimental data and a lack of integrated online computation for rapid validation. Here, we introduce the Clean Energy Materials Platform (CEMP), an open-access platform that integrates high-throughput computing workflows, multi-scale machine learning (ML) models and a comprehensive materials database tailored for clean energy applications. A key feature of CEMP is the online calculation module, which enables fully automatic quantum and molecular dynamics simulations via structured table uploads. CEMP harmonizes heterogeneous data from experimental measurements, theoretical calculation and AI-based predictions for four material classes, including small molecules, polymers, ionic liquids, and crystals. The platform hosts ~ 376,000 entries, including ~6,000 experimental records, ~50,000 quantum-chemical calculations and ~320,000 AI-predicted properties. The database covers 12 critical properties and the corresponding ML models demonstrate robust predictive power with R2 ranging from 0.64 to 0.94, thus ensures rapid material screening, structure-property relationship analysis and multi-objective optimization for clean energy applications. CEMP aims to establish a digital ecosystem for clean energy materials, enabling a closed-loop workflow from data acquisition to material discovery and real-time online validation.

Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial bottlenecks, with CPU-based analytical pipelines requiring hours or days for routine processing steps like filtering, normalization, and clustering. These scalability limitations fundamentally restrict common interactive data exploration and iterative hypothesis testing. Here we introduce rapids-singlecell, a GPU-accelerated framework that integrates natively with the scverse ecosystem and operates directly on the AnnData data structure, which delivers orders-of-magnitude speedups for single-cell workflows. Built on CuPy arrays and the NVIDIA CUDA-X Data Science (RAPIDS) ecosystem, rapids-singlecell provides near drop-in GPU replacements for core scanpy-based analysis steps. Across standard single-cell workflows such as preprocessing, dimensionality reduction, neighborhood graph construction, clustering, and batch correction, rapids-singlecell achieves speedups of up to several hundred-fold compared to optimized CPU baselines. This reduces analysis time from hours to minutes on standard hardware, while maintaining consistent biological interpretations. These performance improvements make it possible to analyze large data sets in close to real time, without the need for data splitting. Together with real-time parameter tuning and iterative workflows, rapids-singlecell makes interactive large-scale single-cell analysis possible.

Enabling VLA models to predict environmental dynamics, known as world modeling, has been recognized as essential for improving robotic reasoning and generalization. However, current approaches face two main issues: 1. The training objective forces models to over-emphasize pixel-level reconstruction, which constrains semantic learning and generalization 2. Reliance on predicted future observations during inference often leads to error accumulation. To address these challenges, we introduce Future Representation Alignment via Parallel Progressive Expansion (FRAPPE). Our method adopts a two-stage fine-tuning strategy: In the mid-training phase, the model learns to predict the latent representations of future observations; In the post-training phase, we expand the computational workload in parallel and align the representation simultaneously with multiple different visual foundation models. By significantly improving fine-tuning efficiency and reducing dependence on action-annotated data, FRAPPE provides a scalable and data-efficient pathway to enhance world-awareness in generalist robotic policies. Experiments on the RoboTwin benchmark and real-world tasks demonstrate that FRAPPE outperforms state-of-the-art approaches and shows strong generalization in long-horizon and unseen scenarios.

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, Meta FAIR presents a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only ~50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to continue to build increasingly capable AI models.

Transformer-based Large Language Models (LLMs) have significantly advanced AI capabilities but pose considerable challenges for deployment on edge devices due to high computational demands, memory bandwidth constraints, and energy consumption. This paper addresses these challenges by presenting an efficient framework for deploying the Qwen2.5-0.5B model on the Xilinx Kria KV260 edge platform, a heterogeneous system integrating an ARM Cortex-A53 CPU with reconfigurable FPGA logic. Leveraging Activation-aware Weight Quantization (AWQ) with FPGA-accelerated execution pipelines, the proposed approach enhances both model compression rate and system throughput. Additionally, we propose a hybrid execution strategy that intelligently offloads compute-intensive operations to the FPGA while utilizing the CPU for lighter tasks, effectively balancing the computational workload and maximizing overall performance. Our framework achieves a model compression rate of 55.08% compared to the original model and produces output at a rate of 5.1 tokens per second, outperforming the baseline performance of 2.8 tokens per second.

PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows. The present paper explains the design and philosophy behind PYSCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PYSCF as a development environment. We then summarize the capabilities of PYSCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PYSCF across the domains of quantum chemistry, materials science, machine learning and quantum information science.

The convergence of artificial intelligence and materials science presents a transformative opportunity, but achieving true acceleration in discovery requires moving beyond task-isolated, fine-tuned models toward agentic systems that plan, act, and learn across the full discovery loop. This survey advances a unique pipeline-centric view that spans from corpus curation and pretraining, through domain adaptation and instruction tuning, to goal-conditioned agents interfacing with simulation and experimental platforms. Unlike prior reviews, we treat the entire process as an end-to-end system to be optimized for tangible discovery outcomes rather than proxy benchmarks. This perspective allows us to trace how upstream design choices-such as data curation and training objectives-can be aligned with downstream experimental success through effective credit assignment. To bridge communities and establish a shared frame of reference, we first present an integrated lens that aligns terminology, evaluation, and workflow stages across AI and materials science. We then analyze the field through two focused lenses: From the AI perspective, the survey details LLM strengths in pattern recognition, predictive analytics, and natural language processing for literature mining, materials characterization, and property prediction; from the materials science perspective, it highlights applications in materials design, process optimization, and the acceleration of computational workflows via integration with external tools (e.g., DFT, robotic labs). Finally, we contrast passive, reactive approaches with agentic design, cataloging current contributions while motivating systems that pursue long-horizon goals with autonomy, memory, and tool use. This survey charts a practical roadmap towards autonomous, safety-aware LLM agents aimed at discovering novel and useful materials.

Large language models are increasingly deployed as autonomous coding agents and have achieved remarkably strong performance on software engineering benchmarks. However, it is unclear whether such success transfers to computational scientific workflows, where tasks require not only strong coding ability, but also the ability to navigate complex, domain-specific procedures and to interpret results in the context of scientific claims. To address this question, we present AutoMat, a benchmark for evaluating LLM-based agents' ability to reproduce claims from computational materials science. AutoMat poses three interrelated challenges: recovering underspecified computational procedures, navigating specialized toolchains, and determining whether the resulting evidence supports a claim. By working closely with subject matter experts, we curate a set of claims from real materials science papers to test whether coding agents can recover and execute the end-to-end workflow needed to support (or undermine) such claims. We then evaluate multiple representative coding agent settings across several foundation models. Our results show that current LLM-based agents obtain low overall success rates on AutoMat, with the best-performing setting achieving a success rate of only 54.1%. Error analysis further reveals that agents perform worst when workflows must be reconstructed from paper text alone and that they fail primarily due to incomplete procedures, methodological deviations, and execution fragility. Taken together, these findings position AutoMat as both a benchmark for computational scientific reproducibility and a tool for diagnosing the current limitations of agentic systems in AI-for-science settings.

In recent years, a standard computational pathology workflow has emerged where whole slide images are cropped into tiles, these tiles are processed using a foundation model, and task-specific models are built using the resulting representations. At least 15 different foundation models have been proposed, and the vast majority are trained exclusively with tiles using the 20times magnification. However, it is well known that certain histologic features can only be discerned with larger context windows and requires a pathologist to zoom in and out when analyzing a whole slide image. Furthermore, creating 224times224 pixel crops at 20times leads to a large number of tiles per slide, which can be gigapixel in size. To more accurately capture multi-resolution features and investigate the possibility of reducing the number of representations per slide, we propose a region-level mixing encoder. Our approach jointly fuses image tile representations of a mixed magnification foundation model using a masked embedding modeling pretraining step. We explore a design space for pretraining the proposed mixed-magnification region aggregators and evaluate our models on transfer to biomarker prediction tasks representing various cancer types. Results demonstrate cancer dependent improvements in predictive performance, highlighting the importance of spatial context and understanding.

Whole-slide image (WSI) preprocessing, typically comprising tissue detection followed by patch extraction, is foundational to AI-driven computational pathology workflows. This remains a major computational bottleneck as existing tools either rely on inaccurate heuristic thresholding for tissue detection, or adopt AI-based approaches trained on limited-diversity data that operate at the patch level, incurring substantial computational complexity. We present AtlasPatch, an efficient and scalable slide preprocessing framework for accurate tissue detection and high-throughput patch extraction with minimal computational overhead. AtlasPatch's tissue detection module is trained on a heterogeneous and semi-manually annotated dataset of ~30,000 WSI thumbnails, using efficient fine-tuning of the Segment-Anything model. The tool extrapolates tissue masks from thumbnails to full-resolution slides to extract patch coordinates at user-specified magnifications, with options to stream patches directly into common image encoders for embedding or store patch images, all efficiently parallelized across CPUs and GPUs. We assess AtlasPatch across segmentation precision, computational complexity, and downstream multiple-instance learning, matching state-of-the-art performance while operating at a fraction of their computational cost. AtlasPatch is open-source and available at https://github.com/AtlasAnalyticsLab/AtlasPatch.

Work in Computational Affective Science and Computational Social Science explores a wide variety of research questions about people, emotions, behavior, and health. Such work often relies on language data that is first labeled with relevant information, such as the use of emotion words or the age of the speaker. Although many resources and algorithms exist to enable this type of labeling, discovering, accessing, and using them remains a substantial impediment, particularly for practitioners outside of computer science. Here, we present the ABCDE dataset (Affect, Body, Cognition, Demographics, and Emotion), a large-scale collection of over 400 million text utterances drawn from social media, blogs, books, and AI-generated sources. The dataset is annotated with a wide range of features relevant to computational affective and social science. ABCDE facilitates interdisciplinary research across numerous fields, including affective science, cognitive science, the digital humanities, sociology, political science, and computational linguistics.

We present a machine-checked formalization of structurally governed AI workflow architectures and prove that effect-level governance can be imposed without reducing internal computational expressivity. Using Interaction Trees in Rocq 8.19, we define a governance operator G that mediates all effectful directives, including memory access, external calls, and oracle (LLM) queries. Our development compiles with 0 admitted lemmas and consists of 36 modules, ~12,000 lines of Rocq, and 454 theorems. We establishseven properties: (P1) governed Turing completeness, (P2) governed oracle expressivity, (P3) a decidability boundary in which governance predicates are total and closed under Boolean composition while semantic program properties remain non-trivial and undecidable by governance, (P4) goal preservation for permitted executions, (P5) expressive minimality of primitive capabilities (compute, memory, reasoning, external call, observability), (P6) subsumption asymmetry showing structural governance strictly subsumes content-level filtering, and (P7) semantic transparency: on all executions where governance permits, the governed interpretation is observationally equivalent (modulo governance-only events) to the ungoverned interpretation. Together, these results show that governance and computational expressivity are orthogonal dimensions: governance constrains the effect boundary of programs while remaining semantically transparent to internal computation.

Large Language Models (LLMs) have demonstrated strong performance across general NLP tasks, but their utility in automating numerical experiments of complex physical system -- a critical and labor-intensive component -- remains underexplored. As the major workhorse of computational science over the past decades, Computational Fluid Dynamics (CFD) offers a uniquely challenging testbed for evaluating the scientific capabilities of LLMs. We introduce CFDLLMBench, a benchmark suite comprising three complementary components -- CFDQuery, CFDCodeBench, and FoamBench -- designed to holistically evaluate LLM performance across three key competencies: graduate-level CFD knowledge, numerical and physical reasoning of CFD, and context-dependent implementation of CFD workflows. Grounded in real-world CFD practices, our benchmark combines a detailed task taxonomy with a rigorous evaluation framework to deliver reproducible results and quantify LLM performance across code executability, solution accuracy, and numerical convergence behavior. CFDLLMBench establishes a solid foundation for the development and evaluation of LLM-driven automation of numerical experiments for complex physical systems. Code and data are available at https://github.com/NREL-Theseus/cfdllmbench/.

Offline paired preference optimization algorithms have become a popular approach for fine-tuning on preference data, outperforming traditional supervised fine-tuning in various tasks. However, traditional implementations often involve redundant computations, especially for tasks with long shared prompts. We introduce prefix sharing for preference tuning, a novel technique that processes chosen and rejected responses as one sequence with a shared prefix. To prevent cross-response contamination, we use a custom block-sparse attention mask. Our method achieves 1.1-1.5times improvement in training throughput on popular DPO datasets, without any effect on convergence. When combined with sequence packing, we observe consistent 1.3-1.6times speedups, benefiting even datasets with smaller sequence lengths. While we focus on Direct Preference Optimization (DPO), our approach is applicable to other paired preference tuning methods. By enhancing computational efficiency, our work contributes to making preference-based fine-tuning more accessible for a wider range of applications and model sizes. We open-source our code at https://github.com/frankxwang/dpo-prefix-sharing.

The proliferation of Large Language Models (LLMs) has catalyzed a shift towards autonomous agents capable of complex reasoning and tool use. However, current agent architectures are frequently constructed using imperative, ad hoc patterns. This results in brittle systems plagued by difficulties in state management, error handling, and concurrency. This paper introduces Monadic Context Engineering (MCE), a novel architectural paradigm leveraging the algebraic structures of Functors, Applicative Functors, and Monads to provide a formal foundation for agent design. MCE treats agent workflows as computational contexts where cross-cutting concerns, such as state propagation, short-circuiting error handling, and asynchronous execution, are managed intrinsically by the algebraic properties of the abstraction. We demonstrate how Monads enable robust sequential composition, how Applicatives provide a principled structure for parallel execution, and crucially, how Monad Transformers allow for the systematic composition of these capabilities. This layered approach enables developers to construct complex, resilient, and efficient AI agents from simple, independently verifiable components. We further extend this framework to describe Meta-Agents, which leverage MCE for generative orchestration, dynamically creating and managing sub-agent workflows through metaprogramming. Project Page: https://github.com/yifanzhang-pro/monadic-context-engineering.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Buildings are a central feature of human culture and are increasingly being analyzed with computational methods. However, recent works on computational building understanding have largely focused on natural imagery of buildings, neglecting the fundamental element defining a building's structure -- its floorplan. Conversely, existing works on floorplan understanding are extremely limited in scope, often focusing on floorplans of a single semantic category and region (e.g. floorplans of apartments from a single country). In this work, we introduce WAFFLE, a novel multimodal floorplan understanding dataset of nearly 20K floorplan images and metadata curated from Internet data spanning diverse building types, locations, and data formats. By using a large language model and multimodal foundation models, we curate and extract semantic information from these images and their accompanying noisy metadata. We show that WAFFLE enables progress on new building understanding tasks, both discriminative and generative, which were not feasible using prior datasets. We will publicly release WAFFLE along with our code and trained models, providing the research community with a new foundation for learning the semantics of buildings.

The dominant image-to-image translation methods are based on fully convolutional networks, which extract and translate an image's features and then reconstruct the image. However, they have unacceptable computational costs when working with high-resolution images. To this end, we present the Multi-Curve Translator (MCT), which not only predicts the translated pixels for the corresponding input pixels but also for their neighboring pixels. And if a high-resolution image is downsampled to its low-resolution version, the lost pixels are the remaining pixels' neighboring pixels. So MCT makes it possible to feed the network only the downsampled image to perform the mapping for the full-resolution image, which can dramatically lower the computational cost. Besides, MCT is a plug-in approach that utilizes existing base models and requires only replacing their output layers. Experiments demonstrate that the MCT variants can process 4K images in real-time and achieve comparable or even better performance than the base models on various photorealistic image-to-image translation tasks.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

Large Language Models (LLMs) have demonstrated strong capabilities in general-purpose code generation. However, generating the code which is deeply hardware-specific, architecture-aware, and performance-critical, especially for massively parallel GPUs, remains a complex challenge. In this work, we explore the use of LLMs for the automated generation and optimization of CUDA programs, with the goal of producing high-performance GPU kernels that fully exploit the underlying hardware. To address this challenge, we propose a novel framework called Feature Search and Reinforcement (FSR). FSR jointly optimizes compilation and functional correctness, as well as the runtime performance, which are validated through extensive and diverse test cases, and measured by actual kernel execution latency on the target GPU, respectively. This approach enables LLMs not only to generate syntactically and semantically correct CUDA code but also to iteratively refine it for efficiency, tailored to the characteristics of the GPU architecture. We evaluate FSR on representative CUDA kernels, covering AI workloads and computational intensive algorithms. Our results show that LLMs augmented with FSR consistently guarantee correctness rates. Meanwhile, the automatically generated kernels can outperform general human-written code by a factor of up to 179times in execution speeds. These findings highlight the potential of combining LLMs with performance reinforcement to automate GPU programming for hardware-specific, architecture-sensitive, and performance-critical applications.

TinyML is a novel area of machine learning that gained huge momentum in the last few years thanks to the ability to execute machine learning algorithms on tiny devices (such as Internet-of-Things or embedded systems). Interestingly, research in this area focused on the efficient execution of the inference phase of TinyML models on tiny devices, while very few solutions for on-device learning of TinyML models are available in the literature due to the relevant overhead introduced by the learning algorithms. The aim of this paper is to introduce a new type of adaptive TinyML solution that can be used in tasks, such as the presented Tiny Speaker Verification (TinySV), that require to be tackled with an on-device learning algorithm. Achieving this goal required (i) reducing the memory and computational demand of TinyML learning algorithms, and (ii) designing a TinyML learning algorithm operating with few and possibly unlabelled training data. The proposed TinySV solution relies on a two-layer hierarchical TinyML solution comprising Keyword Spotting and Adaptive Speaker Verification module. We evaluated the effectiveness and efficiency of the proposed TinySV solution on a dataset collected expressly for the task and tested the proposed solution on a real-world IoT device (Infineon PSoC 62S2 Wi-Fi BT Pioneer Kit).

Recent breakthroughs in the development of agents to solve challenging sequential decision making problems such as Go, StarCraft, or DOTA, have relied on both simulated environments and large-scale datasets. However, progress on this research has been hindered by the scarcity of open-sourced datasets and the prohibitive computational cost to work with them. Here we present the NetHack Learning Dataset (NLD), a large and highly-scalable dataset of trajectories from the popular game of NetHack, which is both extremely challenging for current methods and very fast to run. NLD consists of three parts: 10 billion state transitions from 1.5 million human trajectories collected on the NAO public NetHack server from 2009 to 2020; 3 billion state-action-score transitions from 100,000 trajectories collected from the symbolic bot winner of the NetHack Challenge 2021; and, accompanying code for users to record, load and stream any collection of such trajectories in a highly compressed form. We evaluate a wide range of existing algorithms including online and offline RL, as well as learning from demonstrations, showing that significant research advances are needed to fully leverage large-scale datasets for challenging sequential decision making tasks.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Protein design aims to compose amino-acid sequences that fold into stable three-dimensional structures while satisfying targeted functional properties. The field is increasingly shifting toward vibe protein design, where a single model is expected to generate novel sequences, engineer existing proteins, and reason about protein characteristics through flexible natural-language constraints. Large language models (LLMs) have emerged as a leading paradigm in this space. However, existing evaluation benchmarks often limit their scope to a partial aspect of protein design, while others restrict design objectives to structured input schemas, lacking an integrated framework that evaluates the broad spectrum of protein design competence under open-ended intents. To this end, we present Vibe Protein design Benchmark (VibeProteinBench), a language-interfaced benchmark that probes generalist capabilities through three complementary stages mirroring a computational protein design workflow: recognition, engineering, and generation. Each stage is grounded in expert-curated mechanistic rationales and multi-faceted in silico validation, to computationally verify whether model outputs are biologically plausible. Evaluations across diverse general-purpose and domain-specialized LLMs reveal that no model achieves strong performance across all three stages, suggesting that generalist protein design remains a substantial open challenge for current LLMs.

In this paper, we develop and implement an efficient asymptotic-preserving (AP) scheme to solve the gas mixture of Boltzmann equations under the disparate mass scaling relevant to the so-called "epochal relaxation" phenomenon. The disparity in molecular masses, ranging across several orders of magnitude, leads to significant challenges in both the evaluation of collision operators and the designing of time-stepping schemes to capture the multi-scale nature of the dynamics. A direct implementation of the spectral method faces prohibitive computational costs as the mass ratio increases due to the need to resolve vastly different thermal velocities. Unlike [I. M. Gamba, S. Jin, and L. Liu, Commun. Math. Sci., 17 (2019), pp. 1257-1289], we propose an alternative approach based on proper truncation of asymptotic expansions of the collision operators, which significantly reduces the computational complexity and works well for small varepsilon. By incorporating the separation of three time scales in the model's relaxation process [P. Degond and B. Lucquin-Desreux, Math. Models Methods Appl. Sci., 6 (1996), pp. 405-436], we design an AP scheme that captures the specific dynamics of the disparate mass model while maintaining computational efficiency. Numerical experiments demonstrate the effectiveness of the proposed scheme in handling large mass ratios of heavy and light species, as well as capturing the epochal relaxation phenomenon.

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

LLMs have shown promise in replicating human-like behavior in crowdsourcing tasks that were previously thought to be exclusive to human abilities. However, current efforts focus mainly on simple atomic tasks. We explore whether LLMs can replicate more complex crowdsourcing pipelines. We find that modern LLMs can simulate some of crowdworkers' abilities in these "human computation algorithms," but the level of success is variable and influenced by requesters' understanding of LLM capabilities, the specific skills required for sub-tasks, and the optimal interaction modality for performing these sub-tasks. We reflect on human and LLMs' different sensitivities to instructions, stress the importance of enabling human-facing safeguards for LLMs, and discuss the potential of training humans and LLMs with complementary skill sets. Crucially, we show that replicating crowdsourcing pipelines offers a valuable platform to investigate (1) the relative strengths of LLMs on different tasks (by cross-comparing their performances on sub-tasks) and (2) LLMs' potential in complex tasks, where they can complete part of the tasks while leaving others to humans.

This research presents a computational social science approach to preserving Telugu Chandassu, the metrical poetry tradition representing centuries of collective cultural intelligence. We develop the first comprehensive digital framework for analyzing Telugu prosodic patterns, bridging traditional community knowledge with modern computational methods. Our social computing approach involves collaborative dataset creation of 4,651 annotated padyams, expert-validated linguistic patterns, and culturally-informed algorithmic design. The framework includes AksharamTokenizer for prosody-aware tokenization, LaghuvuGuruvu Generator for classifying light and heavy syllables, and PadyaBhedam Checker for automated pattern recognition. Our algorithm achieves 91.73% accuracy on the proposed Chandassu Score, with evaluation metrics reflecting traditional literary standards. This work demonstrates how computational social science can preserve endangered cultural knowledge systems while enabling new forms of collective intelligence around literary heritage. The methodology offers insights for community-centered approaches to cultural preservation, supporting broader initiatives in digital humanities and socially-aware computing systems.

Recent breakthroughs in self-supervised learning have enabled the use of large unlabeled datasets to train visual foundation models that can generalize to a variety of downstream tasks. While this training paradigm is well suited for the medical domain where annotations are scarce, large-scale pre-training in the medical domain, and in particular pathology, has not been extensively studied. Previous work in self-supervised learning in pathology has leveraged smaller datasets for both pre-training and evaluating downstream performance. The aim of this project is to train the largest academic foundation model and benchmark the most prominent self-supervised learning algorithms by pre-training and evaluating downstream performance on large clinical pathology datasets. We collected the largest pathology dataset to date, consisting of over 3 billion images from over 423 thousand microscopy slides. We compared pre-training of visual transformer models using the masked autoencoder (MAE) and DINO algorithms. We evaluated performance on six clinically relevant tasks from three anatomic sites and two institutions: breast cancer detection, inflammatory bowel disease detection, breast cancer estrogen receptor prediction, lung adenocarcinoma EGFR mutation prediction, and lung cancer immunotherapy response prediction. Our results demonstrate that pre-training on pathology data is beneficial for downstream performance compared to pre-training on natural images. Additionally, the DINO algorithm achieved better generalization performance across all tasks tested. The presented results signify a phase change in computational pathology research, paving the way into a new era of more performant models based on large-scale, parallel pre-training at the billion-image scale.

Artificial neural networks have become a staple computing technique in many fields. Yet, they present fundamental differences with classical computing hardware in the way they process information. Photonic implementations of neural network architectures potentially offer fundamental advantages over their electronic counterparts in terms of speed, processing parallelism, scalability and energy efficiency. Scalable and high performance photonic neural networks (PNNs) have been demonstrated, yet they remain scarce. In this work, we study the performance of such a scalable, fully parallel and autonomous PNN based on a large area vertical-cavity surface-emitting laser (LA-VCSEL). We show how the performance varies with different physical parameters, namely, injection wavelength, injection power, and bias current. Furthermore, we link these physical parameters to the general computational measures of consistency and dimensionality. We present a general method of gauging dimensionality in high dimensional nonlinear systems subject to noise, which could be applied to many systems in the context of neuromorphic computing. Our work will inform future implementations of spatially multiplexed VCSEL PNNs.

Strategic coopetition in multi-stakeholder systems requires understanding how cooperation persists through time without binding contracts. This technical report extends computational foundations for strategic coopetition to sequential interaction dynamics, bridging conceptual modeling (i* framework) with game-theoretic reciprocity analysis. We develop: (1) bounded reciprocity response functions mapping partner deviations to finite conditional responses, (2) memory-windowed history tracking capturing cognitive limitations over k recent periods, (3) structural reciprocity sensitivity derived from interdependence matrices where behavioral responses are amplified by structural dependencies, and (4) trust-gated reciprocity where trust modulates reciprocity responses. The framework applies to both human stakeholder interactions and multi-agent computational systems. Comprehensive validation across 15,625 parameter configurations demonstrates robust reciprocity effects, with all six behavioral targets exceeding thresholds: cooperation emergence (97.5%), defection punishment (100%), forgiveness dynamics (87.9%), asymmetric differentiation (100%), trust-reciprocity interaction (100%), and bounded responses (100%). Empirical validation using the Apple iOS App Store ecosystem (2008-2024) achieves 43/51 applicable points (84.3%), reproducing documented cooperation patterns across five ecosystem phases. Statistical significance confirmed at p < 0.001 with Cohen's d = 1.57. This report concludes the Foundations Series (TR-1 through TR-4) adopting uniaxial treatment where agents choose cooperation levels along a single continuum. Companion work on interdependence (arXiv:2510.18802), trust (arXiv:2510.24909), and collective action (arXiv:2601.16237) has been prepublished. Extensions Series (TR-5 through TR-8) introduces biaxial treatment where cooperation and competition are independent dimensions.

Mixed-motive multi-agent settings are rife with persistent free-riding because individual effort benefits all members equally, yet each member bears the full cost of their own contribution. Classical work by Holmström established that under pure self-interest, Nash equilibrium is universal shirking. While i* represents teams as composite actors, it lacks scalable computational mechanisms for analyzing how collective action problems emerge and resolve in coopetitive settings. This technical report extends computational foundations for strategic coopetition to team-level dynamics, building on companion work formalizing interdependence/complementarity (arXiv:2510.18802) and trust dynamics (arXiv:2510.24909). We develop loyalty-moderated utility functions with two mechanisms: loyalty benefit (welfare internalization plus intrinsic contribution satisfaction) and cost tolerance (reduced effort burden for loyal members). We integrate i* structural dependencies through dependency-weighted team cohesion, connecting member incentives to team-level positioning. The framework applies to both human teams (loyalty as psychological identification) and multi-agent systems (alignment coefficients and adjusted cost functions). Experimental validation across 3,125 configurations demonstrates robust loyalty effects (15.04x median effort differentiation). All six behavioral targets achieve thresholds: free-riding baseline (96.5%), loyalty monotonicity (100%), effort differentiation (100%), team size effect (100%), mechanism synergy (99.5%), and bounded outcomes (100%). Empirical validation using published Apache HTTP Server (1995-2023) case study achieves 60/60 points, reproducing contribution patterns across formation, growth, maturation, and governance phases. Statistical significance confirmed at p<0.001, Cohen's d=0.71.

Recently, Visual Autoregressive (VAR) Models introduced a groundbreaking advancement in the field of image generation, offering a scalable approach through a coarse-to-fine "next-scale prediction" paradigm. However, the state-of-the-art algorithm of VAR models in [Tian, Jiang, Yuan, Peng and Wang, NeurIPS 2024] takes O(n^4) time, which is computationally inefficient. In this work, we analyze the computational limits and efficiency criteria of VAR Models through a fine-grained complexity lens. Our key contribution is identifying the conditions under which VAR computations can achieve sub-quadratic time complexity. Specifically, we establish a critical threshold for the norm of input matrices used in VAR attention mechanisms. Above this threshold, assuming the Strong Exponential Time Hypothesis (SETH) from fine-grained complexity theory, a sub-quartic time algorithm for VAR models is impossible. To substantiate our theoretical findings, we present efficient constructions leveraging low-rank approximations that align with the derived criteria. This work initiates the study of the computational efficiency of the VAR model from a theoretical perspective. Our technique will shed light on advancing scalable and efficient image generation in VAR frameworks.

Thermal imaging is crucial for night vision but fundamentally hampered by the ghosting effect, a loss of detailed texture in cluttered photon streams. While conventional ghosting mitigation has relied on data post-processing, the recent breakthrough in heat-assisted detection and ranging (HADAR) opens a promising frontier for hyperspectral computational thermal imaging that produces night vision with day-like visibility. However, universal anti-ghosting imaging remains elusive, as state-of-the-art HADAR applies only to limited scenes with uniform materials, whereas material non-uniformity is ubiquitous in the real world. Here, we propose a universal computational thermal imaging framework, TAG (thermal anti-ghosting), to address material non-uniformity and overcome ghosting for high-fidelity night vision. TAG takes hyperspectral photon streams for nonparametric texture recovery, enabling our experimental demonstration of unprecedented expression recovery in thus-far-elusive ghostly human faces -- the archetypal, long-recognized ghosting phenomenon. Strikingly, TAG not only universally outperforms HADAR across various scenes, but also reveals the influence of material non-uniformity, shedding light on HADAR's effectiveness boundary. We extensively test facial texture and expression recovery across day and night, and demonstrate, for the first time, thermal 3D topological alignment and mood detection. This work establishes a universal foundation for high-fidelity computational night vision, with potential applications in autonomous navigation, reconnaissance, healthcare, and wildlife monitoring.

Consider a market of competing model providers selling query access to models with varying costs and capabilities. Customers submit problem instances and are willing to pay up to a budget for a verifiable solution. An arbitrageur efficiently allocates inference budget across providers to undercut the market, thus creating a competitive offering with no model-development risk. In this work, we initiate the study of arbitrage in AI model markets, empirically demonstrating the viability of arbitrage and illustrating its economic consequences. We conduct an in-depth case study of SWE-bench GitHub issue resolution using two representative models, GPT-5 mini and DeepSeek v3.2. In this verifiable domain, simple arbitrage strategies generate net profit margins of up to 40%. Robust arbitrage strategies that generalize across different domains remain profitable. Distillation further creates strong arbitrage opportunities, potentially at the expense of the teacher model's revenue. Multiple competing arbitrageurs drive down consumer prices, reducing the marginal revenue of model providers. At the same time, arbitrage reduces market segmentation and facilitates market entry for smaller model providers by enabling earlier revenue capture. Our results suggest that arbitrage can be a powerful force in AI model markets with implications for model development, distillation, and deployment.

Simultaneous Localization and Mapping (SLAM) is pivotal in robotics, with photorealistic scene reconstruction emerging as a key challenge. To address this, we introduce Computational Alignment for Real-Time Gaussian Splatting SLAM (CaRtGS), a novel method enhancing the efficiency and quality of photorealistic scene reconstruction in real-time environments. Leveraging 3D Gaussian Splatting (3DGS), CaRtGS achieves superior rendering quality and processing speed, which is crucial for scene photorealistic reconstruction. Our approach tackles computational misalignment in Gaussian Splatting SLAM (GS-SLAM) through an adaptive strategy that optimizes training, addresses long-tail optimization, and refines densification. Experiments on Replica and TUM-RGBD datasets demonstrate CaRtGS's effectiveness in achieving high-fidelity rendering with fewer Gaussian primitives. This work propels SLAM towards real-time, photorealistic dense rendering, significantly advancing photorealistic scene representation. For the benefit of the research community, we release the code on our project website: https://dapengfeng.github.io/cartgs.

Content generation modeling has emerged as a promising direction in computational pathology, offering capabilities such as data-efficient learning, synthetic data augmentation, and task-oriented generation across diverse diagnostic tasks. This review provides a comprehensive synthesis of recent progress in the field, organized into four key domains: image generation, text generation, molecular profile-morphology generation, and other specialized generation applications. By analyzing over 150 representative studies, we trace the evolution of content generation architectures -- from early generative adversarial networks to recent advances in diffusion models and generative vision-language models. We further examine the datasets and evaluation protocols commonly used in this domain and highlight ongoing limitations, including challenges in generating high-fidelity whole slide images, clinical interpretability, and concerns related to the ethical and legal implications of synthetic data. The review concludes with a discussion of open challenges and prospective research directions, with an emphasis on developing integrated and clinically deployable generation systems. This work aims to provide a foundational reference for researchers and practitioners developing content generation models in computational pathology.

This work introduces a new computational theory of mind grounded in set theory and hyperdimensional computing. Whereas traditional neural networks rely on continuous weights and matrix multiplication, this framework works with sparse binary data. It represents information as discrete sets, directly modeling biological neural population codes. I demonstrate that associative memory emerges naturally from network topologies featuring a combinatorially expanded hidden layer. Learning is driven by topological plasticity rather than scalar weight adjustments. This architecture unifies auto-associative and hetero-associative learning under a single core algorithm: information retrieval via subset pattern matching and exact nearest-neighbor search. Operating with constant-time complexity, these mechanisms bridge perceptual data (sparse distributed representations) and symbols (sparse holographic representations) without continuous bottlenecks. Mapping this framework to neuroanatomy, I propose that both the cerebellum and the neocortex implement variants of this algorithm, making subset pattern matching the fundamental engine of cognition. Because it relies on discrete logic rather than matrix arithmetic, this algorithm translates directly into in-memory hardware. This opens a new route toward synthetic intelligence with human-level energy efficiency.

Modern socio-technical systems increasingly involve multi-stakeholder environments where actors simultaneously cooperate and compete. These coopetitive relationships exhibit dynamic trust evolution based on observed behavior over repeated interactions. While conceptual modeling languages like i* represent trust relationships qualitatively, they lack computational mechanisms for analyzing how trust changes with behavioral evidence. Conversely, computational trust models from multi-agent systems provide algorithmic updating but lack grounding in conceptual models that capture strategic dependencies covering mixed motives of actors. This technical report bridges this gap by developing a computational trust model that extends game-theoretic foundations for strategic coopetition with dynamic trust evolution. Building on companion work that achieved 58/60 validation (96.7%) for logarithmic specifications, we introduce trust as a two-layer system with immediate trust responding to current behavior and reputation tracking violation history. Trust evolves through asymmetric updating where cooperation builds trust gradually while violations erode it sharply, creating hysteresis effects and trust ceilings that constrain relationship recovery. We develop a structured translation framework enabling practitioners to instantiate computational trust models from i* dependency networks encompassing mixed motives of actors. Comprehensive experimental validation across 78,125 parameter configurations establishes robust emergence of negativity bias, hysteresis effects, and cumulative damage amplification. Empirical validation using the Renault-Nissan Alliance case study (1999-2025) achieves 49/60 validation points (81.7%), successfully reproducing documented trust evolution across five distinct relationship phases including crisis and recovery periods.

The brain has computational capabilities that surpass those of modern systems, being able to solve complex problems efficiently in a simple way. Neuromorphic engineering aims to mimic biology in order to develop new systems capable of incorporating such capabilities. Bio-inspired learning systems continue to be a challenge that must be solved, and much work needs to be done in this regard. Among all brain regions, the hippocampus stands out as an autoassociative short-term memory with the capacity to learn and recall memories from any fragment of them. These characteristics make the hippocampus an ideal candidate for developing bio-inspired learning systems that, in addition, resemble content-addressable memories. Therefore, in this work we propose a bio-inspired spiking content-addressable memory model based on the CA3 region of the hippocampus with the ability to learn, forget and recall memories, both orthogonal and non-orthogonal, from any fragment of them. The model was implemented on the SpiNNaker hardware platform using Spiking Neural Networks. A set of experiments based on functional, stress and applicability tests were performed to demonstrate its correct functioning. This work presents the first hardware implementation of a fully-functional bio-inspired spiking hippocampal content-addressable memory model, paving the way for the development of future more complex neuromorphic systems.

Current Chain-of-Thought (CoT) verification methods predict reasoning correctness based on outputs (black-box) or activations (gray-box), but offer limited insight into why a computation fails. We introduce a white-box method: Circuit-based Reasoning Verification (CRV). We hypothesize that attribution graphs of correct CoT steps, viewed as execution traces of the model's latent reasoning circuits, possess distinct structural fingerprints from those of incorrect steps. By training a classifier on structural features of these graphs, we show that these traces contain a powerful signal of reasoning errors. Our white-box approach yields novel scientific insights unattainable by other methods. (1) We demonstrate that structural signatures of error are highly predictive, establishing the viability of verifying reasoning directly via its computational graph. (2) We find these signatures to be highly domain-specific, revealing that failures in different reasoning tasks manifest as distinct computational patterns. (3) We provide evidence that these signatures are not merely correlational; by using our analysis to guide targeted interventions on individual transcoder features, we successfully correct the model's faulty reasoning. Our work shows that, by scrutinizing a model's computational process, we can move from simple error detection to a deeper, causal understanding of LLM reasoning.

Large Language Models (LLMs) like ChatGPT are capable of successfully performing many language processing tasks zero-shot (without the need for training data). If this capacity also applies to the coding of social phenomena like persuasiveness and political ideology, then LLMs could effectively transform Computational Social Science (CSS). This work provides a road map for using LLMs as CSS tools. Towards this end, we contribute a set of prompting best practices and an extensive evaluation pipeline to measure the zero-shot performance of 13 language models on 24 representative CSS benchmarks. On taxonomic labeling tasks (classification), LLMs fail to outperform the best fine-tuned models but still achieve fair levels of agreement with humans. On free-form coding tasks (generation), LLMs produce explanations that often exceed the quality of crowdworkers' gold references. We conclude that today's LLMs can radically augment the CSS research pipeline in two ways: (1) serving as zero-shot data annotators on human annotation teams, and (2) bootstrapping challenging creative generation tasks (e.g., explaining the hidden meaning behind text). In summary, LLMs can significantly reduce costs and increase efficiency of social science analysis in partnership with humans.

Surrogate models are necessary to optimize meaningful quantities in physical dynamics as their recursive numerical resolutions are often prohibitively expensive. It is mainly the case for fluid dynamics and the resolution of Navier-Stokes equations. However, despite the fast-growing field of data-driven models for physical systems, reference datasets representing real-world phenomena are lacking. In this work, we develop AirfRANS, a dataset for studying the two-dimensional incompressible steady-state Reynolds-Averaged Navier-Stokes equations over airfoils at a subsonic regime and for different angles of attacks. We also introduce metrics on the stress forces at the surface of geometries and visualization of boundary layers to assess the capabilities of models to accurately predict the meaningful information of the problem. Finally, we propose deep learning baselines on four machine learning tasks to study AirfRANS under different constraints for generalization considerations: big and scarce data regime, Reynolds number, and angle of attack extrapolation.

Poisoning pretraining data can introduce harmful behaviors to LMs that are difficult to detect and mitigate. Prior work on poisoning pretraining data has largely exploited established data sources such as Wikipedia, which do not represent the large scale and heterogeneity typical of pretraining corpora, and has ignored the interaction between poisoned data and data curation pipelines. We demonstrate that poisoning attacks on pretraining data are feasible beyond this limited setting through an existing web-scale content injection mechanism: public discussion interfaces. Additionally, to measure whether malicious content is included after web crawling and data curation, we introduce HalfLife, a novel analysis for estimating adversarial content inclusion in web-crawl based LM training data. We use HalfLife to explore the feasibility of poisoning pretraining corpora at web scale through open discussion interfaces. Our analysis demonstrates the importance of estimating whether poison injections are included in pretraining data, and establishes third-party webpage content as a possible vector for attacking language model pretraining.

Memory is not merely the storage of data; it is the scaffolding of reality. When biological memory fades, the world does not simply turn black; it regresses into an unrecognizable chaos. Echoes of the Prior is an interactive installation that attempts to visualize this subjective phenomenology of forgetting. By inducing controlled synaptic decay within a Feed-Forward 3D Reconstruction model, we create an artistic analogy for the erosion of the brain's predictive priors. We position the Neural Network not as a tool for engineering, but as a cognitive proxy - a silicon brain whose structural degeneration evokes the disorienting, poetic, and terrifying experience of losing one's grip on the world. Ultimately, we offer this framework as a catalyst, inviting the wider community to explore the uncharted potential of neuromorphic aesthetics in visualizing the fragility of intelligence. Interactive demo see https://decart-4d.github.io/.

Correlative computational microscopy is accelerating the mapping of dynamic biological systems by integrating morphological and molecular measurements across spatial scales, from organelles to entire organisms. Visualization, measurement, and prediction of interactions among the components of biological systems can be accelerated by generalist computational imaging frameworks that relax the trade-offs imposed by multiplex dynamic imaging. This work reports a generalist framework for wave optical imaging of the architectural order (waveOrder) among biomolecules for encoding and decoding multiple specimen properties from a minimal set of acquired channels, with or without fluorescent labels. waveOrder expresses material properties in terms of elegant physically motivated basis vectors directly interpretable as phase, absorption, birefringence, diattenuation, and fluorophore density; and it expresses image data in terms of directly measurable Stokes parameters. We report a corresponding multi-channel reconstruction algorithm to recover specimen properties in multiple contrast modes. With this framework, we implement multiple 3D computational microscopy methods, including quantitative phase imaging, quantitative label-free imaging with phase and polarization, and fluorescence deconvolution imaging, across scales ranging from organelles to whole zebrafish. These advances are available via an extensible open-source computational imaging library, waveOrder, and a napari plugin, recOrder.

Consumer electronics used to follow the miniaturization trend described by Moore's Law. Despite increased processing power in Microcontroller Units (MCUs), MCUs used in the smallest appliances are still not capable of running even moderately big, state-of-the-art artificial neural networks (ANNs) especially in time-sensitive scenarios. In this work, we present a novel method called Scattered Online Inference (SOI) that aims to reduce the computational complexity of ANNs. SOI leverages the continuity and seasonality of time-series data and model predictions, enabling extrapolation for processing speed improvements, particularly in deeper layers. By applying compression, SOI generates more general inner partial states of ANN, allowing skipping full model recalculation at each inference.

Reinforcement learning often needs to deal with the exponential growth of states and actions when exploring optimal control in high-dimensional spaces (often known as the curse of dimensionality). In this work, we address this issue by learning the inherent structure of action-wise similar MDP to appropriately balance the performance degradation versus sample/computational complexity. In particular, we partition the action spaces into multiple groups based on the similarity in transition distribution and reward function, and build a linear decomposition model to capture the difference between the intra-group transition kernel and the intra-group rewards. Both our theoretical analysis and experiments reveal a surprising and counter-intuitive result: while a more refined grouping strategy can reduce the approximation error caused by treating actions in the same group as identical, it also leads to increased estimation error when the size of samples or the computation resources is limited. This finding highlights the grouping strategy as a new degree of freedom that can be optimized to minimize the overall performance loss. To address this issue, we formulate a general optimization problem for determining the optimal grouping strategy, which strikes a balance between performance loss and sample/computational complexity. We further propose a computationally efficient method for selecting a nearly-optimal grouping strategy, which maintains its computational complexity independent of the size of the action space.

Computational Fluid Dynamics (CFD) is an essential simulation tool in various engineering disciplines, but it often requires substantial domain expertise and manual configuration, creating barriers to entry. We present Foam-Agent, a multi-agent framework that automates complex OpenFOAM-based CFD simulation workflows from natural language inputs. Our innovation includes (1) a hierarchical multi-index retrieval system with specialized indices for different simulation aspects, (2) a dependency-aware file generation system that provides consistency management across configuration files, and (3) an iterative error correction mechanism that diagnoses and resolves simulation failures without human intervention. Through comprehensive evaluation on the dataset of 110 simulation tasks, Foam-Agent achieves an 83.6% success rate with Claude 3.5 Sonnet, significantly outperforming existing frameworks (55.5% for MetaOpenFOAM and 37.3% for OpenFOAM-GPT). Ablation studies demonstrate the critical contribution of each system component, with the specialized error correction mechanism providing a 36.4% performance improvement. Foam-Agent substantially lowers the CFD expertise threshold while maintaining modeling accuracy, demonstrating the potential of specialized multi-agent systems to democratize access to complex scientific simulation tools. The code is public at https://github.com/csml-rpi/Foam-Agent

A DJ mix is a sequence of music tracks concatenated seamlessly, typically rendered for audiences in a live setting by a DJ on stage. As a DJ mix is produced in a studio or the live version is recorded for music streaming services, computational methods to analyze DJ mixes, for example, extracting track information or understanding DJ techniques, have drawn research interests. Many of previous works are, however, limited to identifying individual tracks in a mix or segmenting it, and the sizes of the datasets are usually small. In this paper, we provide an in-depth analysis of DJ music by aligning a mix to its original music tracks. We set up the subsequence alignment such that the audio features are less sensitive to the tempo or key change of the original track in a mix. This approach provides temporally tight mix-to-track matching from which we can obtain cue-points, transition length, mix segmentation, and musical changes in DJ performance. Using 1,557 mixes from 1001Tracklists including 13,728 tracks and 20,765 transitions, we conduct the proposed analysis and show a wide range of statistics, which may elucidate the creative process of DJ music making.

As the artificial intelligence (AI) supply chain grows more complex, AI systems and models are increasingly likely to incorporate externally-sourced ingredients such as datasets and other models. In such cases, determining whether or not an AI system or model complies with the EU AI Act will require gathering compliance-related metadata about both the AI system or model at-large as well as those externally-supplied ingredients. There must then be an analysis that looks across all of this metadata to render a prediction about the compliance of the overall AI system or model. Up until now, this process has not been automated. Thus, it has not been possible to make real-time compliance determinations in scenarios where doing so would be advantageous, such as the iterative workflows of today's AI developers, search and acquisition of AI ingredients on communities like Hugging Face, federated and continuous learning, and more. To address this shortcoming, we introduce a highly automated system for AI Act compliance analysis. This system has two key elements. First is an interlocking set of computational artifacts that capture compliance-related metadata about both: (1) the AI system or model at-large; (2) any constituent ingredients such as datasets and models. Second is an automated analysis algorithm that operates across those computational artifacts to render a run-time prediction about whether or not the overall AI system or model complies with the AI Act. Working together, these elements promise to enhance and accelerate AI Act compliance assessments.

Chain-of-Thought (CoT) prompting has improved the reasoning performance of large language models (LLMs), but it remains unclear why it works and whether it is the unique mechanism for triggering reasoning in large language models. In this work, we study this question by directly analyzing and intervening on the internal representations of LLMs with Sparse Autoencoders (SAEs), identifying a small set of latent features that are causally associated with LLM reasoning behavior. Across multiple model families and reasoning benchmarks, we find that steering a single reasoning-related latent feature can substantially improve accuracy without explicit CoT prompting. For large models, latent steering achieves performance comparable to standard CoT prompting while producing more efficient outputs. We further observe that this reasoning-oriented internal state is triggered early in generation and can override prompt-level instructions that discourage explicit reasoning. Overall, our results suggest that multi-step reasoning in LLMs is supported by latent internal activations that can be externally activated, while CoT prompting is one effective, but not unique, way of activating this mechanism rather than its necessary cause.

Social networks are creating a digital world in which the cognitive, emotional, and pragmatic value of the imagery of human faces and bodies is arguably changing. However, researchers in the digital humanities are often ill-equipped to study these phenomena at scale. This work presents FRESCO (Face Representation in E-Societies through Computational Observation), a framework designed to explore the socio-cultural implications of images on social media platforms at scale. FRESCO deconstructs images into numerical and categorical variables using state-of-the-art computer vision techniques, aligning with the principles of visual semiotics. The framework analyzes images across three levels: the plastic level, encompassing fundamental visual features like lines and colors; the figurative level, representing specific entities or concepts; and the enunciation level, which focuses particularly on constructing the point of view of the spectator and observer. These levels are analyzed to discern deeper narrative layers within the imagery. Experimental validation confirms the reliability and utility of FRESCO, and we assess its consistency and precision across two public datasets. Subsequently, we introduce the FRESCO score, a metric derived from the framework's output that serves as a reliable measure of similarity in image content.

The advent of pre-trained Language Models (LMs) has markedly advanced natural language processing, but their efficacy in out-of-distribution (OOD) scenarios remains a significant challenge. Computational argumentation (CA), modeling human argumentation processes, is a field notably impacted by these challenges because complex annotation schemes and high annotation costs naturally lead to resources barely covering the multiplicity of available text sources and topics. Due to this data scarcity, generalization to data from uncovered covariant distributions is a common challenge for CA tasks like stance detection or argument classification. This work systematically assesses LMs' capabilities for such OOD scenarios. While previous work targets specific OOD types like topic shifts or OOD uniformly, we address three prevalent OOD scenarios in CA: topic shift, domain shift, and language shift. Our findings challenge the previously asserted general superiority of in-context learning (ICL) for OOD. We find that the efficacy of such learning paradigms varies with the type of OOD. Specifically, while ICL excels for domain shifts, prompt-based fine-tuning surpasses for topic shifts. To sum up, we navigate the heterogeneity of OOD scenarios in CA and empirically underscore the potential of base-sized LMs in overcoming these challenges.

With the rapid advancements in multimodal generative technology, Affective Computing research has provoked discussion about the potential consequences of AI systems equipped with emotional intelligence. Affective Computing involves the design, evaluation, and implementation of Emotion AI and related technologies aimed at improving people's lives. Designing a computational model in affective computing requires vast amounts of multimodal data, including RGB images, video, audio, text, and physiological signals. Moreover, Affective Computing research is deeply engaged with ethical considerations at various stages-from training emotionally intelligent models on large-scale human data to deploying these models in specific applications. Fundamentally, the development of any AI system must prioritize its impact on humans, aiming to augment and enhance human abilities rather than replace them, while drawing inspiration from human intelligence in a safe and responsible manner. The MRAC 2024 Track 1 workshop seeks to extend these principles from controlled, small-scale lab environments to real-world, large-scale contexts, emphasizing responsible development. The workshop also aims to highlight the potential implications of generative technology, along with the ethical consequences of its use, to researchers and industry professionals. To the best of our knowledge, this is the first workshop series to comprehensively address the full spectrum of multimodal, generative affective computing from a responsible AI perspective, and this is the second iteration of this workshop. Webpage: https://react-ws.github.io/2024/

When workers lose jobs to AI-driven restructuring, two very different conversations happen on X (formerly Twitter) at the same time. Tech executives and AI researchers talk about productivity, transformation, and opportunity. Laid-off workers and labour critics talk about job loss, uncertainty, and fear. This paper asks a simple question: which conversation gets more reach? We report three studies using two collection methods and 763 tweets from 20 named public accounts. Study 1 used keyword-based collection (n=392) and found no significant difference between corpora (p=0.891), revealing that keyword search is too noisy for this task. Study 2 used account-based collection (n=96) and found a 3.12x mean amplification advantage for capital discourse over labour discourse (p=0.000003, Cohen's d=0.555). Study 3 combined both methods (n=763) and confirmed the finding at 4.18x mean and 10.77x median amplification ratio (p<0.000001). Critically, after normalising for follower count, the asymmetry persists at 2.69x (p=0.000009, Cohen's d=0.491), demonstrating that the effect is not simply a consequence of capital accounts having larger audiences. The finding is robust across all tested amplification metric weightings. We introduce the Amplification Ratio and Amplification Normalisation Index as simple metrics for measuring platform-level discourse inequality. A cross-platform replication on Reddit (n=647 posts) did not replicate the finding, suggesting the asymmetry may be specific to X's account-based amplification architecture. We discuss the methodological implications for cross-platform discourse analysis.

Consider the following process: Take any four-digit number which has at least two distinct digits. Then, rearrange the digits of the original number in ascending and descending order, take these two numbers, and find the difference between the two. Finally, repeat this routine using the difference as the new four-digit number. In 1949, D. R. Kaprekar became the first to discover that this process, known as the Kaprekar Routine, would always yield 6174 within 7 iterations. Since this number remains unchanged after an application of the Kaprekar Routine, it became known as Kaprekar's Constant. Previous works have shown that the only base 10 Kaprekar's Constants are 495 and 6174, the 3-digit and 4-digit case. However, little attention has been given to other bases or determining which digit cases and which bases have a Kaprekar's Constant. This paper analyzes the behavior of the Kaprekar Routine in the 3-digit case, deriving an expression for all 3-digit Kaprekar Constants. In addition, the author developed a series of C++ programs to analyze the paths integers followed to their respective Kaprekar's Constant. Surprisingly, it was determined from this program that the most commonly required number of iterations required to reach Kaprekar's Constant for 3-digit integers was consistently 3, regardless of base. When loaded as a matrix, the iteration requirement data demonstrates a precise recurring relationship reminiscent of Pascal's Triangle.

Understanding when learning is statistically possible yet computationally hard is a central challenge in high-dimensional statistics. In this work, we investigate this question in the context of single- and multi-index models, classes of functions widely studied as benchmarks to probe the ability of machine learning methods to discover features in high-dimensional data. Our main contribution is to show that a Noise Sensitivity Exponent (NSE) - a simple quantity determined by the activation function - governs the existence and magnitude of statistical-to-computational gaps within a broad regime of these models. We first establish that, in single-index models with large additive noise, the onset of a computational bottleneck is fully characterized by the NSE. We then demonstrate that the same exponent controls a statistical-computational gap in the specialization transition of large separable multi-index models, where individual components become learnable. Finally, in hierarchical multi-index models, we show that the NSE governs the optimal computational rate in which different directions are sequentially learned. Taken together, our results identify the NSE as a unifying property linking noise robustness, computational hardness, and feature specialization in high-dimensional learning.

Sensitivity to staining variation remains a major barrier to deploying computational pathology (CPath) models as hematoxylin and eosin (H&E) staining varies across laboratories, requiring systematic assessment of how this variability affects model prediction. In this work, we developed a three-step protocol for evaluating robustness to H&E staining variation in CPath models. Step 1: Select reference staining conditions, Step 2: Characterize test set staining properties, Step 3: Apply CPath model(s) under simulated reference staining conditions. Here, we first created a new reference staining library based on the PLISM dataset. As an exemplary use case, we applied the protocol to assess the robustness properties of 306 microsatellite instability (MSI) classification models on the unseen SurGen colorectal cancer dataset (n=738), including 300 attention-based multiple instance learning models trained on the TCGA-COAD/READ datasets across three feature extractors (UNI2-h, H-Optimus-1, Virchow2), alongside six public MSI classification models. Classification performance was measured as AUC, and robustness as the min-max AUC range across four simulated staining conditions (low/high H&E intensity, low/high H&E color similarity). Across models and staining conditions, classification performance ranged from AUC 0.769-0.911 (Δ = 0.142). Robustness ranged from 0.007-0.079 (Δ = 0.072), and showed a weak inverse correlation with classification performance (Pearson r=-0.22, 95% CI [-0.34, -0.11]). Thus, we show that the proposed evaluation protocol enables robustness-informed CPath model selection and provides insight into performance shifts across H&E staining conditions, supporting the identification of operational ranges for reliable model deployment. Code is available at https://github.com/CTPLab/staining-robustness-evaluation .

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

Computational notebooks such as Jupyter Notebook have become data scientists' de facto programming environments. Many visualization researchers and practitioners have developed interactive visualization tools that support notebooks. However, little is known about the appropriate design of visual analytics (VA) tools in notebooks. To bridge this critical research gap, we investigate the design strategies in this space by analyzing 159 notebook VA tools and their users' feedback. Our analysis encompasses 62 systems from academic papers and 103 systems sourced from a pool of 55k notebooks containing interactive visualizations that we obtain via scraping 8.6 million notebooks on GitHub. We also examine findings from 15 user studies and user feedback in 379 GitHub issues. Through this work, we identify unique design opportunities and considerations for future notebook VA tools, such as using and manipulating multimodal data in notebooks as well as balancing the degree of visualization-notebook integration. Finally, we develop SuperNOVA, an open-source interactive tool to help researchers explore existing notebook VA tools and search for related work.

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding real-time researcher guidance. This paper introduces Deep Research, a multi-agent system enabling interactive scientific investigation with turnaround times measured in minutes. The architecture comprises specialized agents for planning, data analysis, literature search, and novelty detection, unified through a persistent world state that maintains context across iterative research cycles. Two operational modes support different workflows: semi-autonomous mode with selective human checkpoints, and fully autonomous mode for extended investigations. Evaluation on the BixBench computational biology benchmark demonstrated state-of-the-art performance, achieving 48.8% accuracy on open response and 64.4% on multiple-choice evaluation, exceeding existing baselines by 14 to 26 percentage points. Analysis of architectural constraints, including open access literature limitations and challenges inherent to automated novelty assessment, informs practical deployment considerations for AI-assisted scientific workflows.

Multiple instance learning (MIL) is the most widely used framework in computational pathology, encompassing sub-typing, diagnosis, prognosis, and more. However, the existing MIL paradigm typically requires an offline instance feature extractor, such as a pre-trained ResNet or a foundation model. This approach lacks the capability for feature fine-tuning within the specific downstream tasks, limiting its adaptability and performance. To address this issue, we propose a Re-embedded Regional Transformer (R^2T) for re-embedding the instance features online, which captures fine-grained local features and establishes connections across different regions. Unlike existing works that focus on pre-training powerful feature extractor or designing sophisticated instance aggregator, R^2T is tailored to re-embed instance features online. It serves as a portable module that can seamlessly integrate into mainstream MIL models. Extensive experimental results on common computational pathology tasks validate that: 1) feature re-embedding improves the performance of MIL models based on ResNet-50 features to the level of foundation model features, and further enhances the performance of foundation model features; 2) the R^2T can introduce more significant performance improvements to various MIL models; 3) R^2T-MIL, as an R^2T-enhanced AB-MIL, outperforms other latest methods by a large margin.The code is available at: https://github.com/DearCaat/RRT-MIL.

Autonomous computational pathology (ACP) converts high-level pathology analysis goals into executable, traceable and clinically bounded workflows. Realizing this capability requires adapting general agentic harness systems to pathology-specific tasks, tools, evidence standards and clinical claim boundaries. We contribute ACP-Bench, a framework that adapts existing harness systems from computational pathology support toward ACP workflow capability. ACP-Bench evaluates 41 pathology workflow tasks, including 24 biomarker, 7 morphology and 10 prognosis tasks spanning 6 body-system groups and 9 endpoint families. The benchmark evaluates 9 models and 3 harness groups (Claude Code, Codex and Open Code), yielding 369 complete trajectories. ACP-Bench evaluates each trajectory across workflow execution, diagnostic performance and clinical-boundary alignment, combining expert-adjudicated process audits, diagnostic assessment and pathologist-validated safety review. Across evaluated systems, workflow initiation, task interpretation and diagnostic reporting were more mature than tool-bound execution, result binding and reflective workflow revision, and formal end-to-end completion remained rare. ACP-Bench provides a reusable standard for auditing whether agentic systems can operationalize pathology workflows before claims of reliable clinical autonomy.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

State Space Models (SSMs) have emerged as a promising alternative to Transformers for long-context sequence modeling, offering linear O(N) computational complexity compared to the Transformer's quadratic O(N^2) scaling. This paper presents a comprehensive benchmarking study comparing the Mamba SSM against the LLaMA Transformer on long-context sequences, using dyadic therapy sessions as a representative test case. We evaluate both architectures across two dimensions: (1) computational efficiency, where we measure memory usage and inference speed from 512 to 8,192 tokens, and (2) representational efficiency, where we analyze hidden state dynamics and attention patterns. Our findings provide actionable insights for practitioners working with long-context applications, establishing precise conditions under which SSMs offer advantages over Transformers.

Pre-trained encoders for offline feature extraction followed by multiple instance learning (MIL) aggregators have become the dominant paradigm in computational pathology (CPath), benefiting cancer diagnosis and prognosis. However, performance limitations arise from the absence of encoder fine-tuning for downstream tasks and disjoint optimization with MIL. While slide-level supervised end-to-end (E2E) learning is an intuitive solution to this issue, it faces challenges such as high computational demands and suboptimal results. These limitations motivate us to revisit E2E learning. We argue that prior work neglects inherent E2E optimization challenges, leading to performance disparities compared to traditional two-stage methods. In this paper, we pioneer the elucidation of optimization challenge caused by sparse-attention MIL and propose a novel MIL called ABMILX. It mitigates this problem through global correlation-based attention refinement and multi-head mechanisms. With the efficient multi-scale random patch sampling strategy, an E2E trained ResNet with ABMILX surpasses SOTA foundation models under the two-stage paradigm across multiple challenging benchmarks, while remaining computationally efficient (<10 RTX3090 hours). We show the potential of E2E learning in CPath and calls for greater research focus in this area. The code is https://github.com/DearCaat/E2E-WSI-ABMILX.

Automation of humor detection and rating has interesting use cases in modern technologies, such as humanoid robots, chatbots, and virtual assistants. In this paper, we propose a novel approach for detecting and rating humor in short texts based on a popular linguistic theory of humor. The proposed technical method initiates by separating sentences of the given text and utilizing the BERT model to generate embeddings for each one. The embeddings are fed to separate lines of hidden layers in a neural network (one line for each sentence) to extract latent features. At last, the parallel lines are concatenated to determine the congruity and other relationships between the sentences and predict the target value. We accompany the paper with a novel dataset for humor detection consisting of 200,000 formal short texts. In addition to evaluating our work on the novel dataset, we participated in a live machine learning competition focused on rating humor in Spanish tweets. The proposed model obtained F1 scores of 0.982 and 0.869 in the humor detection experiments which outperform general and state-of-the-art models. The evaluation performed on two contrasting settings confirm the strength and robustness of the model and suggests two important factors in achieving high accuracy in the current task: 1) usage of sentence embeddings and 2) utilizing the linguistic structure of humor in designing the proposed model.

Large language model (LLM)-based systems are becoming increasingly popular for solving tasks by constructing executable workflows that interleave LLM calls, information retrieval, tool use, code execution, memory updates, and verification. This survey reviews recent methods for designing and optimizing such workflows, which we treat as agentic computation graphs (ACGs). We organize the literature based on when workflow structure is determined, where structure refers to which components or agents are present, how they depend on each other, and how information flows between them. This lens distinguishes static methods, which fix a reusable workflow scaffold before deployment, from dynamic methods, which select, generate, or revise the workflow for a particular run before or during execution. We further organize prior work along three dimensions: when structure is determined, what part of the workflow is optimized, and which evaluation signals guide optimization (e.g., task metrics, verifier signals, preferences, or trace-derived feedback). We also distinguish reusable workflow templates, run-specific realized graphs, and execution traces, separating reusable design choices from the structures actually deployed in a given run and from realized runtime behavior. Finally, we outline a structure-aware evaluation perspective that complements downstream task metrics with graph-level properties, execution cost, robustness, and structural variation across inputs. Our goal is to provide a clear vocabulary, a unified framework for positioning new methods, a more comparable view of existing body of literature, and a more reproducible evaluation standard for future work in workflow optimizations for LLM agents.

The advent of foundation models (FMs) as an emerging suite of AI techniques has struck a wave of opportunities in computational healthcare. The interactive nature of these models, guided by pre-training data and human instructions, has ignited a data-centric AI paradigm that emphasizes better data characterization, quality, and scale. In healthcare AI, obtaining and processing high-quality clinical data records has been a longstanding challenge, ranging from data quantity, annotation, patient privacy, and ethics. In this survey, we investigate a wide range of data-centric approaches in the FM era (from model pre-training to inference) towards improving the healthcare workflow. We discuss key perspectives in AI security, assessment, and alignment with human values. Finally, we offer a promising outlook of FM-based analytics to enhance the performance of patient outcome and clinical workflow in the evolving landscape of healthcare and medicine. We provide an up-to-date list of healthcare-related foundation models and datasets at https://github.com/Yunkun-Zhang/Data-Centric-FM-Healthcare .

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

We revisit the longstanding open problem of implementing Nakamoto's proof-of-work (PoW) consensus based on a real-world computational task T(x) (as opposed to artificial random hashing), in a truly permissionless setting where the miner itself chooses the input x. The challenge in designing such a Proof-of-Useful-Work (PoUW) protocol, is using the native computation of T(x) to produce a PoW certificate with prescribed hardness and with negligible computational overhead over the worst-case complexity of T(cdot) -- This ensures malicious miners cannot ``game the system" by fooling the verifier to accept with higher probability compared to honest miners (while using similar computational resources). Indeed, obtaining a PoUW with O(1)-factor overhead is trivial for any task T, but also useless. Our main result is a PoUW for the task of Matrix Multiplication MatMul(A,B) of arbitrary matrices with 1+o(1) multiplicative overhead compared to naive MatMul (even in the presence of Fast Matrix Multiplication-style algorithms, which are currently impractical). We conjecture that our protocol has optimal security in the sense that a malicious prover cannot obtain any significant advantage over an honest prover. This conjecture is based on reducing hardness of our protocol to the task of solving a batch of low-rank random linear equations which is of independent interest. Since MatMuls are the bottleneck of AI compute as well as countless industry-scale applications, this primitive suggests a concrete design of a new L1 base-layer protocol, which nearly eliminates the energy-waste of Bitcoin mining -- allowing GPU consumers to reduce their AI training and inference costs by ``re-using" it for blockchain consensus, in exchange for block rewards (2-for-1). This blockchain is currently under construction.

Large language models (LLMs) demonstrate remarkable reasoning capabilities, yet their stateless architecture fundamentally limits deployment in long-horizon research workflows requiring multi-session continuity and quantitative rigor. Here we present Ensemble QSP, a multi-agent framework featuring a three-layer hierarchical memory architecture that keeps injected context bounded and constant in project duration (mid-term project state: median 301 tokens, max 4,050, across 104 runs) by capping each state category and evicting completed work, enabling continuous autonomous operation without context degradation. The system orchestrates five specialist worker agents under domain-expert principal investigators, enforcing physical constraints through physics-based checklists and structured-domain knowledge. Comprehensive benchmarking demonstrates robust autonomous pharmacokinetic-pharmacodynamic model selection without human intervention, consistent result quality across both lower-cost and frontier LLMs, improved PK parameter recovery relative to single-agent baselines, and stable model selection across linguistically diverse prompts of the same task. Feature-level ablation across physiologically based pharmacokinetic (PBPK) models spanning a broad complexity range shows that PI-agent oversight improves debugging efficiency while preserving final accuracy across conditions. The architecture is structurally domain-agnostic, adding a new scientific domain requires only a new PI agent configuration.

The ability to resolve complex physical phenomena with high fidelity and at low computational cost is central to addressing key challenges in modern engineering. A prime example lies in hypersonic flows, where the precise prediction of the full flowfield topology, in particular with respect to shock wave location and intensity, is critical. Yet supersonic and hypersonic flows continue to be a stumbling block for traditional reduced-order models and neural emulators that struggle to capture steep gradients in flow states with physical consistency in applications of industrial relevance. To that end, we introduce a fully GPU based workflow that integrates accelerated data generation with the training of neural emulators augmented by uncertainty quantification and physics-aware refinement. Our workflow is enabled by a differentiable high-fidelity solver (JAX-Fluids) which we employ for rapid dataset creation and residual-based improvement of the neural emulator to enhance physical consistency. Building on this framework, we first present a suite of model architectures and analyze their scaling behavior to expose their strengths and shortcomings. We then show that residual-based refinement enables training on cases where only mesh and input parameters are available, substantially reducing residuals and improving physical consistency. Together, differentiable simulation and residual-based refinement yield physics emulators that remain reliable beyond their training distribution, a key requirement for deploying surrogates in real-world engineering design loops.

Long contexts challenge transformers: attention scores dilute across thousands of tokens, critical information is often lost in the middle, and models struggle to adapt to novel patterns at inference time. Recent work on test-time adaptation addresses this by maintaining a form of working memory -- transient parameters updated on the current context -- but existing approaches rely on uniform write policies that waste computation on low-utility regions and suffer from high gradient variance across semantically heterogeneous contexts. In this work, we reframe test-time adaptation as a budget-constrained memory consolidation problem, focusing on which parts of the context should be consolidated into working memory under limited computation. We propose Gdwm (Gated Differentiable Working Memory), a framework that introduces a write controller to gate the consolidation process. The controller estimates Contextual Utility, an information-theoretic measure of long-range contextual dependence, and allocates gradient steps accordingly while maintaining global coverage. Experiments on ZeroSCROLLS and LongBench v2 demonstrate that Gdwm achieves comparable or superior performance with 4times fewer gradient steps than uniform baselines, establishing a new efficiency-performance Pareto frontier for test-time adaptation.

Training large language models (LLMs) with increasingly long and varying sequence lengths introduces severe load imbalance challenges in large-scale data-parallel training. Recent frameworks attempt to mitigate these issues through data reorganization or hybrid parallel strategies. However, they often overlook how computational and communication costs scale with sequence length, resulting in suboptimal performance. We identify three critical challenges: (1) varying computation-to-communication ratios across sequences of different lengths in distributed attention, (2) mismatch between static NIC-GPU affinity and dynamic parallel workloads, and (3) distinct optimal partitioning strategies required for quadratic attention versus linear components. To address these challenges, we present Zeppelin, a novel training system that integrates three key techniques: (1) a hierarchical sequence partitioning method for the attention module that reduces communication overhead and balances computation, supported by an efficient attention engine that applies divergent parallel strategies; (2) a routing layer that orchestrates inter-node transfers to fully utilize NIC bandwidth; and (3) a remapping layer that transforms sequence layouts between attention and linear modules, ensuring high computational efficiency across both. Comprehensive evaluations across diverse configurations show that Zeppelin delivers an average 2.80x speedup over state-of-the-art methods.

Financial tasks are pivotal to global economic stability; however, their execution faces challenges including labor intensive processes, low error tolerance, data fragmentation, and tool limitations. Although large language models (LLMs) have succeeded in various natural language processing tasks and have shown potential in automating workflows through reasoning and contextual understanding, current benchmarks for evaluating LLMs in finance lack sufficient domain-specific data, have simplistic task design, and incomplete evaluation frameworks. To address these gaps, this article presents FinMaster, a comprehensive financial benchmark designed to systematically assess the capabilities of LLM in financial literacy, accounting, auditing, and consulting. Specifically, FinMaster comprises three main modules: i) FinSim, which builds simulators that generate synthetic, privacy-compliant financial data for companies to replicate market dynamics; ii) FinSuite, which provides tasks in core financial domains, spanning 183 tasks of various types and difficulty levels; and iii) FinEval, which develops a unified interface for evaluation. Extensive experiments over state-of-the-art LLMs reveal critical capability gaps in financial reasoning, with accuracy dropping from over 90% on basic tasks to merely 40% on complex scenarios requiring multi-step reasoning. This degradation exhibits the propagation of computational errors, where single-metric calculations initially demonstrating 58% accuracy decreased to 37% in multimetric scenarios. To the best of our knowledge, FinMaster is the first benchmark that covers full-pipeline financial workflows with challenging tasks. We hope that FinMaster can bridge the gap between research and industry practitioners, driving the adoption of LLMs in real-world financial practices to enhance efficiency and accuracy.

Configuring computational fluid dynamics (CFD) simulations typically demands extensive domain expertise, limiting broader access. Although large language models (LLMs) have advanced scientific computing, their use in automating CFD workflows is underdeveloped. We introduce a novel approach centered on domain-specific LLM adaptation. By fine-tuning Qwen2.5-7B-Instruct on NL2FOAM, our custom dataset of 28716 natural language-to-OpenFOAM configuration pairs with chain-of-thought (CoT) annotations, we enable direct translation from natural language descriptions to executable CFD setups. A multi-agent framework orchestrates the process, autonomously verifying inputs, generating configurations, running simulations, and correcting errors. Evaluation on a benchmark of 21 diverse flow cases demonstrates state-of-the-art performance, achieving 88.7% solution accuracy and 82.6% first-attempt success rate. This significantly outperforms larger general-purpose models like Qwen2.5-72B-Instruct, DeepSeek-R1, and Llama3.3-70B-Instruct, while also requiring fewer correction iterations and maintaining high computational efficiency. The results highlight the critical role of domain-specific adaptation in deploying LLM assistants for complex engineering workflows. Our code and fine-tuned model have been deposited at https://github.com/YYgroup/AutoCFD.

Machine Learning (ML) has the potential to revolutionise the field of automotive aerodynamics, enabling split-second flow predictions early in the design process. However, the lack of open-source training data for realistic road cars, using high-fidelity CFD methods, represents a barrier to their development. To address this, a high-fidelity open-source (CC-BY-SA) public dataset for automotive aerodynamics has been generated, based on 500 parametrically morphed variants of the widely-used DrivAer notchback generic vehicle. Mesh generation and scale-resolving CFD was executed using consistent and validated automatic workflows representative of the industrial state-of-the-art. Geometries and rich aerodynamic data are published in open-source formats. To our knowledge, this is the first large, public-domain dataset for complex automotive configurations generated using high-fidelity CFD.

Recent work investigates whether LMs learn human-like linguistic generalizations and representations from developmentally plausible amounts of data. Yet, the basic linguistic units processed in these LMs are determined by subword-based tokenization, which limits their validity as models of learning at and below the word level. In this paper, we explore the potential of tokenization-free, phoneme- and grapheme-based language models. We demonstrate that small models based on the Llama architecture can achieve strong linguistic performance on standard syntactic and novel lexical/phonetic benchmarks when trained with character-level vocabularies. We further show that phoneme-based models almost match grapheme-based models in standard tasks and novel evaluations. Our findings suggest a promising direction for creating more linguistically plausible language models that are better suited for computational studies of language acquisition and processing.

In natural language processing, a recently popular line of work explores how to best report the experimental results of neural networks. One exemplar publication, titled "Show Your Work: Improved Reporting of Experimental Results," advocates for reporting the expected validation effectiveness of the best-tuned model, with respect to the computational budget. In the present work, we critically examine this paper. As far as statistical generalizability is concerned, we find unspoken pitfalls and caveats with this approach. We analytically show that their estimator is biased and uses error-prone assumptions. We find that the estimator favors negative errors and yields poor bootstrapped confidence intervals. We derive an unbiased alternative and bolster our claims with empirical evidence from statistical simulation. Our codebase is at http://github.com/castorini/meanmax.

Enhancing the reasoning capabilities of large language models (LLMs) typically relies on massive computational resources and extensive datasets, limiting accessibility for resource-constrained settings. Our study investigates the potential of reinforcement learning (RL) to improve reasoning in small LLMs, focusing on a 1.5-billion-parameter model, DeepSeek-R1-Distill-Qwen-1.5B, under strict constraints: training on 4 NVIDIA A40 GPUs (48 GB VRAM each) within 24 hours. Adapting the Group Relative Policy Optimization (GRPO) algorithm and curating a compact, high-quality mathematical reasoning dataset, we conducted three experiments to explore model behavior and performance. Our results demonstrate rapid reasoning gains - e.g., AMC23 accuracy rising from 63% to 80% and AIME24 reaching 46.7%, surpassing o1-preview - using only 7,000 samples and a $42 training cost, compared to thousands of dollars for baseline models. However, challenges such as optimization instability and length constraints emerged with prolonged training. These findings highlight the efficacy of RL-based fine-tuning for small LLMs, offering a cost-effective alternative to large-scale approaches. We release our code and datasets as open-source resources, providing insights into trade-offs and laying a foundation for scalable, reasoning-capable LLMs in resource-limited environments. All are available at https://github.com/knoveleng/open-rs.

Uterine diseases represent an important category of gynecologic pathology and require accurate histopathological assessment for diagnosis and treatment planning. Whole-slide images (WSI) have enabled the digital transformation of pathology workflows and provided new opportunities for artificial intelligence (AI) in computational pathology. In particular, multimodal models that jointly analyze histopathology images and pathology reports have shown promising potential for automated pathology report generation and AI-assisted diagnosis. However, the development of such systems remains limited by the scarcity of datasets that pair whole-slide images with clinically meaningful pathology reports. Instead, existing pathology datasets focus on patch- or slide-level annotations of a single endpoint (e.g., disease class), which do not fully capture the rich information in full clinical diagnostic workflow reports. Here, we introduce TUM-Uteria, a uterine pathology dataset comprising WSIs paired with diagnostic pathology reports at both the case and slide levels, collected from a tertiary medical center. The dataset contains 216 clinical cases, comprising 455 slide-level WSI-report pairs. The dataset underwent a structured multi-stage validation procedure involving board-certified pathologists to ensure reliable annotations. TUM-Uteria supports research in computational pathology, including whole-slide image analysis, multimodal learning, and automated pathology report generation.

Multi-Agent Systems (MAS) built on large language models typically solve complex tasks by coordinating multiple agents through workflows. Existing approaches generates workflows either at task level or query level, but their relative costs and benefits remain unclear. After rethinking and empirical analyses, we show that query-level workflow generation is not always necessary, since a small set of top-K best task-level workflows together already covers equivalent or even more queries. We further find that exhaustive execution-based task-level evaluation is both extremely token-costly and frequently unreliable. Inspired by the idea of self-evolution and generative reward modeling, we propose a low-cost task-level generation framework SCALE, which means \textbf{S}elf prediction of the optimizer with few shot \textbf{CAL}ibration for \textbf{E}valuation instead of full validation execution. Extensive experiments demonstrate that SCALE maintains competitive performance, with an average degradation of just 0.61\% compared to existing approach across multiple datasets, while cutting overall token usage by up to 83\%.

We investigate continued pretraining of LLMs for language adaptation on a tight academic budget: a setting in which only a few GPUs can be used in parallel, for a heavily constrained duration. We focus on adapting Mistral-7B to German or Arabic and evaluate several techniques to improve efficiency and effectiveness in this setting. Our German models adapted on this tight compute budget underperform compared to the base Mistral-7B, while our Arabic models outperform several baselines, showing that for sufficiently well-represented languages, continued pretraining for specialization is not always helpful. Our main findings focus on training precision and tokenizer swapping. Our results show that pure bfloat16 training is a viable alternative to mixed-precision training, while being much faster when only using a few GPUs. Swapping the tokenizer for a specialized one yields more efficient tokenization and is competitive with the original tokenizer, which already contains some German tokens, but did not significantly increase performance for German. Code and model weights are available at on GitHub.

This paper presents the computational challenge on differential geometry and topology that happened within the ICLR 2021 workshop "Geometric and Topological Representation Learning". The competition asked participants to provide creative contributions to the fields of computational geometry and topology through the open-source repositories Geomstats and Giotto-TDA. The challenge attracted 16 teams in its two month duration. This paper describes the design of the challenge and summarizes its main findings.

We present a quantum algorithm for portfolio optimization. We discuss the market data input, the processing of such data via quantum operations, and the output of financially relevant results. Given quantum access to the historical record of returns, the algorithm determines the optimal risk-return tradeoff curve and allows one to sample from the optimal portfolio. The algorithm can in principle attain a run time of {rm poly}(log(N)), where N is the size of the historical return dataset. Direct classical algorithms for determining the risk-return curve and other properties of the optimal portfolio take time {rm poly}(N) and we discuss potential quantum speedups in light of the recent works on efficient classical sampling approaches.

Text-to-image diffusion models particularly Stable Diffusion, have revolutionized the field of computer vision. However, the synthesis quality often deteriorates when asked to generate images that faithfully represent complex prompts involving multiple attributes and objects. While previous studies suggest that blended text embeddings lead to improper attribute binding, few have explored this in depth. In this work, we critically examine the limitations of the CLIP text encoder in understanding attributes and investigate how this affects diffusion models. We discern a phenomenon of attribute bias in the text space and highlight a contextual issue in padding embeddings that entangle different concepts. We propose Magnet, a novel training-free approach to tackle the attribute binding problem. We introduce positive and negative binding vectors to enhance disentanglement, further with a neighbor strategy to increase accuracy. Extensive experiments show that Magnet significantly improves synthesis quality and binding accuracy with negligible computational cost, enabling the generation of unconventional and unnatural concepts.

The rapidly-developing intersection of machine learning (ML) with high-energy physics (HEP) presents both opportunities and challenges to our community. Far beyond applications of standard ML tools to HEP problems, genuinely new and potentially revolutionary approaches are being developed by a generation of talent literate in both fields. There is an urgent need to support the needs of the interdisciplinary community driving these developments, including funding dedicated research at the intersection of the two fields, investing in high-performance computing at universities and tailoring allocation policies to support this work, developing of community tools and standards, and providing education and career paths for young researchers attracted by the intellectual vitality of machine learning for high energy physics.

Recent research has leveraged large language model multi-agent systems for complex problem-solving while trying to reduce the manual effort required to build them, driving the development of automated agent workflow optimization methods. However, existing methods remain inflexible due to representational limitations, a lack of adaptability, and poor scalability when relying on discrete optimization techniques. We address these challenges with ScoreFlow, a simple yet high-performance framework that leverages efficient gradient-based optimization in a continuous space. ScoreFlow incorporates Score-DPO, a novel variant of the direct preference optimization method that accounts for quantitative feedback. Across six benchmarks spanning question answering, coding, and mathematical reasoning, ScoreFlow achieves an 8.2% improvement over existing baselines. Moreover, it empowers smaller models to outperform larger ones with lower inference costs. Project: https://github.com/Gen-Verse/ScoreFlow

While coreference resolution is attracting more interest than ever from computational literature researchers, representative datasets of fully annotated long documents remain surprisingly scarce. In this paper, we introduce a new annotated corpus of three full-length French novels, totaling over 285,000 tokens. Unlike previous datasets focused on shorter texts, our corpus addresses the challenges posed by long, complex literary works, enabling evaluation of coreference models in the context of long reference chains. We present a modular coreference resolution pipeline that allows for fine-grained error analysis. We show that our approach is competitive and scales effectively to long documents. Finally, we demonstrate its usefulness to infer the gender of fictional characters, showcasing its relevance for both literary analysis and downstream NLP tasks.

This paper describes the first-ever open-source high-fidelity CFD dataset of a high-lift aircraft for the purpose of AI surrogate model development. The dataset is composed of 1800 samples, arising from 180 geometry variants and 10 angles of attack for the high-lift NASA Common Research Model (CRM) geometry, used within the AIAA High-Lift Prediction Workshop series. One of the novelties of this dataset is the use of a GPU-accelerated high-fidelity explicit, wall-modeled LES approach for each simulation, using solution-adapted grids between 300M and 500M cells. This ensures the greatest possible accuracy given known challenges in steady-state RANS approaches for these portions of the flight envelope. The entire dataset (geometries, time-averaged volume and surface variables and integral forces) are available, free of charge with a permissive open-source license (CC-BY-4.0). By making this data publicly available, we aim to accelerate the research and development of AI surrogate modeling within the aerospace industry.

The rapid evolution of large language models (LLMs) is transforming artificial intelligence into autonomous research partners, yet a critical gap persists in complex scientific domains such as combustion modeling. Here, practical AI assistance requires the seamless integration of domain literature knowledge with robust execution capabilities for expertise-intensive tools such as computational fluid dynamics (CFD) codes. To bridge this gap, we introduce FlamePilot, an LLM agent designed to empower combustion modeling research through automated and self-corrective CFD workflows. FlamePilot differentiates itself through an architecture that leverages atomic tools to ensure the robust setup and execution of complex simulations in both OpenFOAM and extended frameworks such as DeepFlame. The system is also capable of learning from scientific articles, extracting key information to guide the simulation from initial setup to optimized results. Validation on a public benchmark shows FlamePilot achieved a perfect 1.0 executability score and a 0.438 success rate, surpassing the prior best reported agent scores of 0.625 and 0.250, respectively. Furthermore, a detailed case study on Moderate or Intense Low-oxygen Dilution (MILD) combustion simulation demonstrates its efficacy as a collaborative research copilot, where FlamePilot autonomously translated a research paper into a configured simulation, conducted the simulation, post-processed the results, proposed evidence-based refinements, and managed a multi-step parameter study to convergence under minimal human intervention. By adopting a transparent and interpretable paradigm, FlamePilot establishes a foundational framework for AI-empowered combustion modeling, fostering a collaborative partnership where the agent manages workflow orchestration, freeing the researcher for high-level analysis.

Ex-post harmonisation is one of many data preprocessing processes used to combine the increasingly vast and diverse sources of data available for research and analysis. Documenting provenance and ensuring the quality of multi-source datasets is vital for ensuring trustworthy scientific research and encouraging reuse of existing harmonisation efforts. However, capturing and communicating statistically relevant properties of harmonised datasets is difficult without a universal standard for describing harmonisation operations. Our paper combines mathematical and computer science perspectives to address this need. The Crossmaps Framework defines a new approach for transforming existing variables collected under a specific measurement or classification standard to an imputed counterfactual variable indexed by some target standard. It uses computational graphs to separate intended transformation logic from actual data transformations, and avoid the risk of syntactically valid data manipulation scripts resulting in statistically questionable data. In this paper, we introduce the Crossmaps Framework through the example of ex-post harmonisation of aggregated statistics in the social sciences. We define a new provenance task abstraction, the crossmap transform, and formalise two associated objects, the shared mass array and the crossmap. We further define graph, matrix and list encodings of crossmaps and discuss resulting implications for understanding statistical properties of ex-post harmonisation and designing error minimising workflows.

The advancement in generative AI could be boosted with more accessible mathematics. Beyond human-AI chat, large language models (LLMs) are emerging in programming, algorithm discovery, and theorem proving, yet their genomics application is limited. This project introduces Math Agents and mathematical embedding as fresh entries to the "Moore's Law of Mathematics", using a GPT-based workflow to convert equations from literature into LaTeX and Python formats. While many digital equation representations exist, there's a lack of automated large-scale evaluation tools. LLMs are pivotal as linguistic user interfaces, providing natural language access for human-AI chat and formal languages for large-scale AI-assisted computational infrastructure. Given the infinite formal possibility spaces, Math Agents, which interact with math, could potentially shift us from "big data" to "big math". Math, unlike the more flexible natural language, has properties subject to proof, enabling its use beyond traditional applications like high-validation math-certified icons for AI alignment aims. This project aims to use Math Agents and mathematical embeddings to address the ageing issue in information systems biology by applying multiscalar physics mathematics to disease models and genomic data. Generative AI with episodic memory could help analyse causal relations in longitudinal health records, using SIR Precision Health models. Genomic data is suggested for addressing the unsolved Alzheimer's disease problem.

Vast efforts have been devoted to creating high-performance few-shot learners, i.e., large-scale pretrained language models (PLMs) that perform well with little downstream task training data. Training PLMs has incurred significant cost, but utilizing the few-shot learners is still challenging due to their enormous size. This work focuses on a crucial question: How to make effective use of these few-shot learners? We propose LMTurk, a novel approach that treats few-shot learners as crowdsourcing workers. The rationale is that crowdsourcing workers are in fact few-shot learners: They are shown a few illustrative examples to learn about a task and then start annotating. LMTurk employs few-shot learners built upon PLMs as workers. We show that the resulting annotations can be utilized to train models that solve the task well and are small enough to be deployable in practical scenarios. Active learning is integrated into LMTurk to reduce the amount of queries made to PLMs, minimizing the computational cost of running PLM inference passes. Altogether, LMTurk is an important step towards making effective use of current PLMs.

What is the current state-of-the-art for image restoration and enhancement applied to degraded images acquired under less than ideal circumstances? Can the application of such algorithms as a pre-processing step to improve image interpretability for manual analysis or automatic visual recognition to classify scene content? While there have been important advances in the area of computational photography to restore or enhance the visual quality of an image, the capabilities of such techniques have not always translated in a useful way to visual recognition tasks. Consequently, there is a pressing need for the development of algorithms that are designed for the joint problem of improving visual appearance and recognition, which will be an enabling factor for the deployment of visual recognition tools in many real-world scenarios. To address this, we introduce the UG^2 dataset as a large-scale benchmark composed of video imagery captured under challenging conditions, and two enhancement tasks designed to test algorithmic impact on visual quality and automatic object recognition. Furthermore, we propose a set of metrics to evaluate the joint improvement of such tasks as well as individual algorithmic advances, including a novel psychophysics-based evaluation regime for human assessment and a realistic set of quantitative measures for object recognition performance. We introduce six new algorithms for image restoration or enhancement, which were created as part of the IARPA sponsored UG^2 Challenge workshop held at CVPR 2018. Under the proposed evaluation regime, we present an in-depth analysis of these algorithms and a host of deep learning-based and classic baseline approaches. From the observed results, it is evident that we are in the early days of building a bridge between computational photography and visual recognition, leaving many opportunities for innovation in this area.

Mixture-of-Experts (MoE) has been demonstrated as an efficient method to scale up models. By dynamically and sparsely selecting activated experts, MoE can effectively reduce computational costs. Despite the success, we observe that many tokens in the MoE models have uncertain routing results. These tokens have nearly equal scores for choosing each expert, and we demonstrate that this uncertainty can lead to incorrect selections. Inspired by the Global Workspace Theory (GWT), we propose a new fine-tuning method, GW-MoE, to address this issue. The core idea is to broadcast the uncertain tokens across experts during fine-tuning. Therefore, these tokens can acquire the necessary knowledge from any expert during inference and become less sensitive to the choice. GW-MoE does not introduce additional inference overhead. We validate that GW can mitigate the uncertain problem and consistently improve in different tasks (text classification, question answering, summarization, code generation, and mathematical problem solving) and model sizes (650M and 8B parameters).

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

The accelerated adoption of digital pathology and advances in deep learning have enabled the development of powerful models for various pathology tasks across a diverse array of diseases and patient cohorts. However, model training is often difficult due to label scarcity in the medical domain and the model's usage is limited by the specific task and disease for which it is trained. Additionally, most models in histopathology leverage only image data, a stark contrast to how humans teach each other and reason about histopathologic entities. We introduce CONtrastive learning from Captions for Histopathology (CONCH), a visual-language foundation model developed using diverse sources of histopathology images, biomedical text, and notably over 1.17 million image-caption pairs via task-agnostic pretraining. Evaluated on a suite of 13 diverse benchmarks, CONCH can be transferred to a wide range of downstream tasks involving either or both histopathology images and text, achieving state-of-the-art performance on histology image classification, segmentation, captioning, text-to-image and image-to-text retrieval. CONCH represents a substantial leap over concurrent visual-language pretrained systems for histopathology, with the potential to directly facilitate a wide array of machine learning-based workflows requiring minimal or no further supervised fine-tuning.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

The trade-off between regret and computational cost is a fundamental problem for online kernel regression, and previous algorithms worked on the trade-off can not keep optimal regret bounds at a sublinear computational complexity. In this paper, we propose two new algorithms, AOGD-ALD and NONS-ALD, which can keep nearly optimal regret bounds at a sublinear computational complexity, and give sufficient conditions under which our algorithms work. Both algorithms dynamically maintain a group of nearly orthogonal basis used to approximate the kernel mapping, and keep nearly optimal regret bounds by controlling the approximate error. The number of basis depends on the approximate error and the decay rate of eigenvalues of the kernel matrix. If the eigenvalues decay exponentially, then AOGD-ALD and NONS-ALD separately achieves a regret of O(L(f)) and O(d_{eff}(mu)T) at a computational complexity in O(ln^2{T}). If the eigenvalues decay polynomially with degree pgeq 1, then our algorithms keep the same regret bounds at a computational complexity in o(T) in the case of p>4 and pgeq 10, respectively. L(f) is the cumulative losses of f and d_{eff}(mu) is the effective dimension of the problem. The two regret bounds are nearly optimal and are not comparable.