Daily Papers

Large Language Models (LLMs) have made notable progress in automated theorem proving, yet existing formal benchmarks remain limited in both mathematical coverage and difficulty. Most are concentrated in areas that are easier to formalize, such as algebra and elementary number theory, and provide limited coverage of subfields that require deeper reasoning, including mathematical analysis. To address this gap, we introduce MA-ProofBench, to the best of our knowledge, the first formal theorem-proving benchmark dedicated to Mathematical Analysis. The benchmark contains 200 formalized theorems covering 6 core topics and 27 subcategories, including measure and integration theory, complex analysis, and functional analysis. The problems are divided into two difficulty levels, an undergraduate level (Level I, 100 problems) and a Ph.D. qualifying level (Level II, 100 problems), to evaluate how well LLMs perform formal reasoning at different mathematical depths. Each problem is constructed through a human-led, LLM-assisted formalization pipeline followed by independent expert review, ensuring that the formal statements remain faithful to the original mathematics. We evaluate a range of recent general-purpose reasoning models and formal theorem provers on MA-ProofBench. However, most models perform poorly: even the best-performing model, GPT-5.5, achieves only 16% Pass@8 on Level I and 5% on Level II, while most models stay close to 0% on Level II. Further analysis identifies Mathlib hallucinations and incomplete proofs as the two dominant failure modes, while an evaluation on the natural-language version of the benchmark exposes a clear gap between informal and formal reasoning. MA-ProofBench is intended to serve as a reliable reference for tracking progress in formal mathematical reasoning in advanced domains.

Automating hardware design could obviate a significant amount of human error from the engineering process and lead to fewer errors. Verilog is a popular hardware description language to model and design digital systems, thus generating Verilog code is a critical first step. Emerging large language models (LLMs) are able to write high-quality code in other programming languages. In this paper, we characterize the ability of LLMs to generate useful Verilog. For this, we fine-tune pre-trained LLMs on Verilog datasets collected from GitHub and Verilog textbooks. We construct an evaluation framework comprising test-benches for functional analysis and a flow to test the syntax of Verilog code generated in response to problems of varying difficulty. Our findings show that across our problem scenarios, the fine-tuning results in LLMs more capable of producing syntactically correct code (25.9% overall). Further, when analyzing functional correctness, a fine-tuned open-source CodeGen LLM can outperform the state-of-the-art commercial Codex LLM (6.5% overall). Training/evaluation scripts and LLM checkpoints are available: https://github.com/shailja-thakur/VGen.

Identifying what individual neurons encode in higher-order visual cortex is an open problem. Responses resist intuitive parameterization, and the deep-network embeddings used in their place are black boxes. Here, we introduce NEURRATOR, a framework that decodes spiking activity into free-form natural-language narration of the viewed scene at single-neuron resolution. A learned encoder maps spike trains from arbitrary subsets of simultaneously-recorded neurons into the patch-embedding space of a frozen CLIP, from which a multimodal language model and sparse autoencoder generates and validates a description with no language-side training. Applied to Neuropixel recordings of mouse visual cortex during natural-movie viewing, NEURRATOR narrates from thousands of neurons, singular cortical regions, local populations, or from a molecularly-defined cell-types. We use this property to (i) quantify how decoding fidelity scales with population size and cortical region, and (ii) "neurrate", in plain language, what individual neurons and genetically-tagged inhibitory cell-types contribute to visual representation. This recasts cell identity from a classification target into a functional probe of the visual system, providing a new unit of biological insights in neural systems.

Recently, significant progress has been made applying machine learning to the problem of table structure inference and extraction from unstructured documents. However, one of the greatest challenges remains the creation of datasets with complete, unambiguous ground truth at scale. To address this, we develop a new, more comprehensive dataset for table extraction, called PubTables-1M. PubTables-1M contains nearly one million tables from scientific articles, supports multiple input modalities, and contains detailed header and location information for table structures, making it useful for a wide variety of modeling approaches. It also addresses a significant source of ground truth inconsistency observed in prior datasets called oversegmentation, using a novel canonicalization procedure. We demonstrate that these improvements lead to a significant increase in training performance and a more reliable estimate of model performance at evaluation for table structure recognition. Further, we show that transformer-based object detection models trained on PubTables-1M produce excellent results for all three tasks of detection, structure recognition, and functional analysis without the need for any special customization for these tasks. Data and code will be released at https://github.com/microsoft/table-transformer.

Relevant information in documents is often summarized in tables, helping the reader to identify useful facts. Most benchmark datasets support either document layout analysis or table understanding, but lack in providing data to apply both tasks in a unified way. We define the task of Contextualized Table Extraction (CTE), which aims to extract and define the structure of tables considering the textual context of the document. The dataset comprises 75k fully annotated pages of scientific papers, including more than 35k tables. Data are gathered from PubMed Central, merging the information provided by annotations in the PubTables-1M and PubLayNet datasets. The dataset can support CTE and adds new classes to the original ones. The generated annotations can be used to develop end-to-end pipelines for various tasks, including document layout analysis, table detection, structure recognition, and functional analysis. We formally define CTE and evaluation metrics, showing which subtasks can be tackled, describing advantages, limitations, and future works of this collection of data. Annotations and code will be accessible a https://github.com/AILab-UniFI/cte-dataset.

Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical impact requires models that generalize across cancer types and capture biologically coherent signals. Prior work is often limited to per-cancer settings and variance-based evaluation, leaving functional relevance underexplored. We introduce HistoPrism, an efficient transformer-based architecture for pan-cancer prediction of gene expression from histology. To evaluate biological meaning, we introduce a pathway-level benchmark, shifting assessment from isolated gene-level variance to coherent functional pathways. HistoPrism not only surpasses prior state-of-the-art models on highly variable genes , but also more importantly, achieves substantial gains on pathway-level prediction, demonstrating its ability to recover biologically coherent transcriptomic patterns. With strong pan-cancer generalization and improved efficiency, HistoPrism establishes a new standard for clinically relevant transcriptomic modeling from routinely available histology.

Despite their widespread success, the application of deep neural networks to functional data remains scarce today. The infinite dimensionality of functional data means standard learning algorithms can be applied only after appropriate dimension reduction, typically achieved via basis expansions. Currently, these bases are chosen a priori without the information for the task at hand and thus may not be effective for the designated task. We instead propose to adaptively learn these bases in an end-to-end fashion. We introduce neural networks that employ a new Basis Layer whose hidden units are each basis functions themselves implemented as a micro neural network. Our architecture learns to apply parsimonious dimension reduction to functional inputs that focuses only on information relevant to the target rather than irrelevant variation in the input function. Across numerous classification/regression tasks with functional data, our method empirically outperforms other types of neural networks, and we prove that our approach is statistically consistent with low generalization error. Code is available at: https://github.com/jwyyy/AdaFNN.

Music is characterized by complex hierarchical structures. Developing a comprehensive model to capture these structures has been a significant challenge in the field of Music Information Retrieval (MIR). Prior research has mainly focused on addressing individual tasks for specific hierarchical levels, rather than providing a unified approach. In this paper, we introduce a versatile, all-in-one model that jointly performs beat and downbeat tracking as well as functional structure segmentation and labeling. The model leverages source-separated spectrograms as inputs and employs dilated neighborhood attentions to capture temporal long-term dependencies, along with non-dilated attentions for local instrumental dependencies. Consequently, the proposed model achieves state-of-the-art performance in all four tasks on the Harmonix Set while maintaining a relatively lower number of parameters compared to recent state-of-the-art models. Furthermore, our ablation study demonstrates that the concurrent learning of beats, downbeats, and segments can lead to enhanced performance, with each task mutually benefiting from the others.

Summary: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarisation and visualisation tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can compare FEA results from multiple studies, making it possible, for example, to highlight patterns of gene expression amongst genes commonly differentially expressed in two sets of conditions, and giving rise to shared enrichments under those conditions. GeneFEAST offers a novel, effective way to address the complexities of linking up many overlapping FEA results to their underlying genes and data, advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments. Availability: GeneFEAST is available at https://github.com/avigailtaylor/GeneFEAST Contact: avigail.taylor@well.ox.ac.uk

It is desirable for statistical models to detect signals of interest independently of their position. If the data is generated by some smooth process, this additional structure should be taken into account. We introduce a new class of neural networks that are shift invariant and preserve smoothness of the data: functional neural networks (FNNs). For this, we use methods from functional data analysis (FDA) to extend multi-layer perceptrons and convolutional neural networks to functional data. We propose different model architectures, show that the models outperform a benchmark model from FDA in terms of accuracy and successfully use FNNs to classify electroencephalography (EEG) data.

Functional linear discriminant analysis (FLDA) is a powerful tool that extends LDA-mediated multiclass classification and dimension reduction to univariate time-series functions. However, in the age of large multivariate and incomplete data, statistical dependencies between features must be estimated in a computationally tractable way, while also dealing with missing data. There is a need for a computationally tractable approach that considers the statistical dependencies between features and can handle missing values. We here develop a multivariate version of FLDA (MUDRA) to tackle this issue and describe an efficient expectation/conditional-maximization (ECM) algorithm to infer its parameters. We assess its predictive power on the "Articulary Word Recognition" data set and show its improvement over the state-of-the-art, especially in the case of missing data. MUDRA allows interpretable classification of data sets with large proportions of missing data, which will be particularly useful for medical or psychological data sets.

Modern automobiles have evolved from just being mechanical machines to having full-fledged electronics systems that enhance vehicle dynamics and driver experience. However, these complex hardware and software systems, if not properly designed, can experience failures that can compromise the safety of the vehicle, its occupants, and the surrounding environment. For example, a system to activate the brakes to avoid a collision saves lives when it functions properly, but could lead to tragic outcomes if the brakes were applied in a way that's inconsistent with the design. Broadly speaking, the analysis performed to minimize such risks falls into a systems engineering domain called Functional Safety. In this paper, we present SafetyLens, a visual data analysis tool to assist engineers and analysts in analyzing automotive Functional Safety datasets. SafetyLens combines techniques including network exploration and visual comparison to help analysts perform domain-specific tasks. This paper presents the design study with domain experts that resulted in the design guidelines, the tool, and user feedback.

Recent work in 3D scene understanding is moving beyond purely spatial analysis toward functional scene understanding. However, existing methods often consider functional relationships between object pairs in isolation, failing to capture the scene-wide interdependence that humans use to resolve ambiguity. We introduce FunFact, a framework for constructing probabilistic open-vocabulary functional 3D scene graphs from posed RGB-D images. FunFact first builds an object- and part-centric 3D map and uses foundation models to propose semantically plausible functional relations. These candidates are converted into factor graph variables and constrained by both LLM-derived common-sense priors and geometric priors. This formulation enables joint probabilistic inference over all functional edges and their marginals, yielding substantially better calibrated confidence scores. To benchmark this setting, we introduce FunThor, a synthetic dataset based on AI2-THOR with part-level geometry and rule-based functional annotations. Experiments on SceneFun3D, FunGraph3D, and FunThor show that FunFact improves node and relation discovery recall and significantly reduces calibration error for ambiguous relations, highlighting the benefits of holistic probabilistic modeling for functional scene understanding. See our project page at https://funfact-scenegraph.github.io/

Plant developmental plasticity, particularly in root system architecture, is fundamental to understanding adaptability and agricultural sustainability. ChronoRoot 2.0 builds upon established low-cost hardware while significantly enhancing software capabilities and usability. The system employs nnUNet architecture for multi-class segmentation, demonstrating significant accuracy improvements while simultaneously tracking six distinct plant structures encompassing root, shoot, and seed components: main root, lateral roots, seed, hypocotyl, leaves, and petiole. This architecture enables easy retraining and incorporation of additional training data without requiring machine learning expertise. The platform introduces dual specialized graphical interfaces: a Standard Interface for detailed architectural analysis with novel gravitropic response parameters, and a Screening Interface enabling high-throughput analysis of multiple plants through automated tracking. Functional Principal Component Analysis integration enables discovery of novel phenotypic parameters through temporal pattern comparison. We demonstrate multi-species analysis, with Arabidopsis thaliana and Solanum lycopersicum, both morphologically distinct plant species. Three use cases in Arabidopsis thaliana and validation with tomato seedlings demonstrate enhanced capabilities: circadian growth pattern characterization, gravitropic response analysis in transgenic plants, and high-throughput etiolation screening across multiple genotypes.ChronoRoot 2.0 maintains the low-cost, modular hardware advantages of its predecessor while dramatically improving accessibility through intuitive graphical interfaces and expanded analytical capabilities. The open-source platform makes sophisticated temporal plant phenotyping more accessible to researchers without computational expertise.

The analysis of non-stationary time-series data requires insight into its local and global patterns with physical interpretability. However, traditional smoothing algorithms, such as B-splines, Savitzky-Golay filtering, and Empirical Mode Decomposition (EMD), lack the ability to perform parametric optimization with guaranteed continuity. In this paper, we propose Functional Continuous Decomposition (FCD), a JAX-accelerated framework that performs parametric, continuous optimization on a wide range of mathematical functions. By using Levenberg-Marquardt optimization to achieve up to C^1 continuous fitting, FCD transforms raw time-series data into M modes that capture different temporal patterns from short-term to long-term trends. Applications of FCD include physics, medicine, financial analysis, and machine learning, where it is commonly used for the analysis of signal temporal patterns, optimized parameters, derivatives, and integrals of decomposition. Furthermore, FCD can be applied for physical analysis and feature extraction with an average SRMSE of 0.735 per segment and a speed of 0.47s on full decomposition of 1,000 points. Finally, we demonstrate that a Convolutional Neural Network (CNN) enhanced with FCD features, such as optimized function values, parameters, and derivatives, achieved 16.8% faster convergence and 2.5% higher accuracy over a standard CNN.

We study a fully connected Hopfield-type associative memory network with online activity-dependent synaptic plasticity, where neural states and synaptic couplings coevolve during retrieval. Using the generating-functional formalism, we derive a dynamical mean-field theory (DMFT) in the large-system limit with extensively many stored random patterns, and show that the many-body dynamics reduces to an effective single-site stochastic process with colored Gaussian crosstalk noise and delayed feedback terms. Numerical solutions of the DMFT equations agree well with direct simulations. We find that moderate plasticity enlarges the basin of attraction and increases the maximum retrievable memory load by generating a positive delayed feedback that stabilizes retrieval against crosstalk noise. However, excessively strong plasticity causes the network to imprint the imperfect initial cue itself, leading to spurious attractors and degraded retrieval performance. Consequently, an optimal plasticity strength emerges from the trade-off between memory stabilization and premature cue imprinting. These results extend the DMFT description of associative memory to networks with coevolving neural and synaptic dynamics.

We present a new dataset, Functional Map of the World (fMoW), which aims to inspire the development of machine learning models capable of predicting the functional purpose of buildings and land use from temporal sequences of satellite images and a rich set of metadata features. The metadata provided with each image enables reasoning about location, time, sun angles, physical sizes, and other features when making predictions about objects in the image. Our dataset consists of over 1 million images from over 200 countries. For each image, we provide at least one bounding box annotation containing one of 63 categories, including a "false detection" category. We present an analysis of the dataset along with baseline approaches that reason about metadata and temporal views. Our data, code, and pretrained models have been made publicly available.

Theory of Mind (ToM), the ability to track others epistemic state, makes humans efficient collaborators. AI agents need the same capacity in multi agent settings, yet existing benchmarks mostly test literal ToM by asking direct belief questions. The ability act optimally on implicit beliefs in embodied environments, called functional ToM, remains largely untested. We introduce EnactToM, an evolving benchmark of 300 embodied multi-agent tasks set in a 3D household with partial observability, private information, and constrained communication. Each task is formally verified for solvability and required epistemic depth, and new tasks are generated increase difficulty as models improve. On the hard split, all seven evaluated frontier models score 0.0% Pass^3 on functional task completion, while averaging 45.0% on literal belief probes. Manual analysis traces 93% of sampled failures to epistemic coordination breakdowns such as withheld information, ignored partner constraints, and misallocated messages, providing a concrete target for future work.

This paper presents LLM-empowered workflow to support Software Defined Vehicle (SDV) software development, covering the aspects of security-aware system topology design, as well as event-driven decision-making code analysis. For code analysis we adopt event chains model which provides formal foundations to systematic validation of functional safety, taking into account the semantic validity of messages exchanged between key components, including both CAN and Vehicle Signal Specification (VSS). Analysis of security aspects for topology relies on synergy with Model-Driven Engineering (MDE) approach and Object Constraint Language (OCL) rules. Both locally deployable and proprietary solution are taken into account for evaluation within Advanced Driver-Assistance Systems (ADAS)-related scenarios.

The change in data distribution over time, also known as concept drift, poses a significant challenge to the reliability of online learning methods. Existing methods typically require model retraining or drift detection, both of which demand high computational costs and are often unsuitable for real-time applications. To address these limitations, a lightweight, fast and efficient random vector functional-link network termed Lite-RVFL is proposed, capable of adapting to concept drift without drift detection and retraining. Lite-RVFL introduces a novel objective function that assigns weights exponentially increasing to new samples, thereby emphasizing recent data and enabling timely adaptation. Theoretical analysis confirms the feasibility of this objective function for drift adaptation, and an efficient incremental update rule is derived. Experimental results on a real-world safety assessment task validate the efficiency, effectiveness in adapting to drift, and potential to capture temporal patterns of Lite-RVFL. The source code is available at https://github.com/songqiaohu/Lite-RVFL.

Multimodal functional neuroimaging enables systematic analysis of brain mechanisms and provides discriminative representations for brain-computer interface (BCI) decoding. However, its acquisition is constrained by high costs and feasibility limitations. Moreover, underrepresentation of specific groups undermines fairness of BCI decoding model. To address these challenges, we propose a unified representation framework for multimodal functional neuroimaging via generative artificial intelligence (AI). By mapping multimodal functional neuroimaging into a unified representation space, the proposed framework is capable of generating data for acquisition-constrained modalities and underrepresented groups. Experiments show that the framework can generate data consistent with real brain activity patterns, provide insights into brain mechanisms, and improve performance on downstream tasks. More importantly, it can enhance model fairness by augmenting data for underrepresented groups. Overall, the framework offers a new paradigm for decreasing the cost of acquiring multimodal functional neuroimages and enhancing the fairness of BCI decoding models.

This study explores the effectiveness of multi-temporal satellite imagery for better functional field boundary delineation using deep learning semantic segmentation architecture on two distinct geographical and multi-scale farming systems of Netherlands and Pakistan. Multidate images of April, August and October 2022 were acquired for PlanetScope and Sentinel-2 in sub regions of Netherlands and November 2022, February and March 2023 for selected area of Dunyapur in Pakistan. For Netherlands, Basic registration crop parcels (BRP) vector layer was used as labeled training data. while self-crafted field boundary vector data were utilized for Pakistan. Four deep learning models with UNET architecture were evaluated using different combinations of multi-date images and NDVI stacks in the Netherlands subregions. A comparative analysis of IoU scores assessed the effectiveness of the proposed multi-date NDVI stack approach. These findings were then applied for transfer learning, using pre-trained models from the Netherlands on the selected area in Pakistan. Additionally, separate models were trained using self-crafted field boundary data for Pakistan, and combined models were developed using data from both the Netherlands and Pakistan. Results indicate that multi-date NDVI stacks provide additional temporal context, reflecting crop growth over different times of the season. The study underscores the critical role of multi-scale ground information from diverse geographical areas in developing robust and universally applicable models for field boundary delineation. The results also highlight the importance of fine spatial resolution for extraction of field boundaries in regions with small scale framing. The findings can be extended to multi-scale implementations for improved automatic field boundary delineation in heterogeneous agricultural environments.

Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically relevant mutations in gene regulatory regions remains a major challenge. Here we introduce Deep VRegulome, a deep-learning method for prediction and interpretation of functionally disruptive variants in the human regulome, which combines 700 DNABERT fine-tuned models, trained on vast amounts of ENCODE gene regulatory regions, with variant scoring, motif analysis, attention-based visualization, and survival analysis. We showcase its application on TCGA glioblastoma WGS dataset in prioritizing survival-associated mutations and regulatory regions. The analysis identified 572 splice-disrupting and 9,837 transcription-factor binding site altering mutations occurring in greater than 10% of glioblastoma samples. Survival analysis linked 1352 mutations and 563 disrupted regulatory regions to patient outcomes, enabling stratification via non-coding mutation signatures. All the code, fine-tuned models, and an interactive data portal are publicly available.

ABACUS (Atomic-orbital Based Ab-initio Computation at USTC) is an open-source software for first-principles electronic structure calculations and molecular dynamics simulations. It mainly features density functional theory (DFT) and molecular dynamics functions and is compatible with both plane-wave basis sets and numerical atomic orbital basis sets. ABACUS serves as a platform that facilitates the integration of various electronic structure methods, such as Kohn-Sham DFT, stochastic DFT, orbital-free DFT, and real-time time-dependent DFT, etc. In addition, with the aid of high-performance computing, ABACUS is designed to perform efficiently and provide massive amounts of first-principles data for generating general-purpose machine learning potentials, such as DPA models. Furthermore, ABACUS serves as an electronic structure platform that interfaces with several AI-assisted algorithms and packages, such as DeePKS-kit, DeePMD, DP-GEN, DeepH, DeePTB, HamGNN, etc.

We give an improved theoretical analysis of score-based generative modeling. Under a score estimate with small L^2 error (averaged across timesteps), we provide efficient convergence guarantees for any data distribution with second-order moment, by either employing early stopping or assuming smoothness condition on the score function of the data distribution. Our result does not rely on any log-concavity or functional inequality assumption and has a logarithmic dependence on the smoothness. In particular, we show that under only a finite second moment condition, approximating the following in reverse KL divergence in epsilon-accuracy can be done in tilde Oleft(d log (1/delta){epsilon}right) steps: 1) the variance-delta Gaussian perturbation of any data distribution; 2) data distributions with 1/delta-smooth score functions. Our analysis also provides a quantitative comparison between different discrete approximations and may guide the choice of discretization points in practice.

Fault attacks are active, physical attacks that an adversary can leverage to alter the control-flow of embedded devices to gain access to sensitive information or bypass protection mechanisms. Due to the severity of these attacks, manufacturers deploy hardware-based fault defenses into security-critical systems, such as secure elements. The development of these countermeasures is a challenging task due to the complex interplay of circuit components and because contemporary design automation tools tend to optimize inserted structures away, thereby defeating their purpose. Hence, it is critical that such countermeasures are rigorously verified post-synthesis. As classical functional verification techniques fall short of assessing the effectiveness of countermeasures, developers have to resort to methods capable of injecting faults in a simulation testbench or into a physical chip. However, developing test sequences to inject faults in simulation is an error-prone task and performing fault attacks on a chip requires specialized equipment and is incredibly time-consuming. To that end, this paper introduces SYNFI, a formal pre-silicon fault verification framework that operates on synthesized netlists. SYNFI can be used to analyze the general effect of faults on the input-output relationship in a circuit and its fault countermeasures, and thus enables hardware designers to assess and verify the effectiveness of embedded countermeasures in a systematic and semi-automatic way. To demonstrate that SYNFI is capable of handling unmodified, industry-grade netlists synthesized with commercial and open tools, we analyze OpenTitan, the first open-source secure element. In our analysis, we identified critical security weaknesses in the unprotected AES block, developed targeted countermeasures, reassessed their security, and contributed these countermeasures back to the OpenTitan repository.

Reinforcement learning with verifiable rewards (RLVR) has significantly improved reasoning in large language models (LLMs), yet the token-level mechanisms underlying these improvements remain unclear. We present a systematic empirical study of RLVR's distributional effects organized around three main analyses: (1) token-level characterization of distributional shifts between base and RL models, (2) the impact of token-level distributional shifts on sequence-level reasoning performance through cross-sampling interventions, and (3) fine-grained mechanics of these shifts at the token level. We find that RL fine-tuning induces highly sparse and targeted changes, with only a small fraction of token distributions exhibiting meaningful divergence between the base and RL policies. We further characterize the structure and evolution of these shifts through analyses of token entropy, positional concentration, and reallocation of probability mass. To assess the functional importance of these sparse changes, we conduct cross-sampling experiments that selectively swap token choices between the base and RL models with varying intervention budgets. We show that inserting only a small fraction of RL-sampled tokens into base generations progressively recovers RL performance gains, while injecting a similarly small number of base token choices into otherwise RL-generated sequences collapses performance to base levels, isolating a small set of token-level decisions directly responsible for RLVR's performance gains. Finally, we explore divergence-weighted variants of the advantage signal as a diagnostic intervention, finding that they can yield improvements over baselines. Together, our results shed light on the distributional changes induced by RLVR and provide a fine-grained, token-level lens for understanding RLVR fine-tuning as a targeted refinement process.

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

Large language models (LLMs) have demonstrated impressive capabilities in code generation, achieving high scores on benchmarks such as HumanEval and MBPP. However, these benchmarks primarily assess functional correctness and neglect broader dimensions of code quality, including security, reliability, readability, and maintainability. In this work, we systematically evaluate the ability of LLMs to generate high-quality code across multiple dimensions using the PythonSecurityEval benchmark. We introduce an iterative static analysis-driven prompting algorithm that leverages Bandit and Pylint to identify and resolve code quality issues. Our experiments with GPT-4o show substantial improvements: security issues reduced from >40% to 13%, readability violations from >80% to 11%, and reliability warnings from >50% to 11% within ten iterations. These results demonstrate that LLMs, when guided by static analysis feedback, can significantly enhance code quality beyond functional correctness.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

For the task of mobility analysis of 3D shapes, we propose joint analysis for simultaneous motion part segmentation and motion attribute estimation, taking a single 3D model as input. The problem is significantly different from those tackled in the existing works which assume the availability of either a pre-existing shape segmentation or multiple 3D models in different motion states. To that end, we develop Shape2Motion which takes a single 3D point cloud as input, and jointly computes a mobility-oriented segmentation and the associated motion attributes. Shape2Motion is comprised of two deep neural networks designed for mobility proposal generation and mobility optimization, respectively. The key contribution of these networks is the novel motion-driven features and losses used in both motion part segmentation and motion attribute estimation. This is based on the observation that the movement of a functional part preserves the shape structure. We evaluate Shape2Motion with a newly proposed benchmark for mobility analysis of 3D shapes. Results demonstrate that our method achieves the state-of-the-art performance both in terms of motion part segmentation and motion attribute estimation.

This study presents a quantitative evaluation of the code quality and security of five prominent Large Language Models (LLMs): Claude Sonnet 4, Claude 3.7 Sonnet, GPT-4o, Llama 3.2 90B, and OpenCoder 8B. While prior research has assessed the functional performance of LLM-generated code, this research tested LLM output from 4,442 Java coding assignments through comprehensive static analysis using SonarQube. The findings suggest that although LLMs can generate functional code, they also introduce a range of software defects, including bugs, security vulnerabilities, and code smells. These defects do not appear to be isolated; rather, they may represent shared weaknesses stemming from systemic limitations within current LLM code generation methods. In particular, critically severe issues, such as hard-coded passwords and path traversal vulnerabilities, were observed across multiple models. These results indicate that LLM-generated code requires verification in order to be considered production-ready. This study found no direct correlation between a model's functional performance (measured by Pass@1 rate of unit tests) and the overall quality and security of its generated code, measured by the number of SonarQube issues in benchmark solutions that passed the functional tests. This suggests that functional benchmark performance score is not a good indicator of overall code quality and security. The goal of this study is not to rank LLM performance but to highlight that all evaluated models appear to share certain weaknesses. Consequently, these findings support the view that static analysis can be a valuable instrument for detecting latent defects and an important safeguard for organizations that deploy AI in software development.

Code Executing Reasoning is becoming a new non-functional metric that assesses the ability of large language models (LLMs) in programming tasks. State-of-the-art frameworks (CodeMind or REval) and benchmarks (CruxEval) usually focus on LLM's prediction of a given code's input/output or intermediate variable states/values on limited programs. However, there is no tool for more in-depth analysis of the results. Without such a tool, the observations about LLM's code execution reasoning cannot be generalized to more datasets, preventing the research community and practitioners from devising the next generation of LLMs with better code execution reasoning abilities. This paper introduces ExeRScope, a series of tools and heuristics to analyze the result of code execution reasoning frameworks to understand better the impact of code properties in the studied benchmarks on the code execution reasoning. With such tooling, analysis can be generalized to code with similar properties without the urgent need to design more benchmarks, which is a cumbersome effort.

Roman Numeral analysis is the important task of identifying chords and their functional context in pieces of tonal music. This paper presents a new approach to automatic Roman Numeral analysis in symbolic music. While existing techniques rely on an intermediate lossy representation of the score, we propose a new method based on Graph Neural Networks (GNNs) that enable the direct description and processing of each individual note in the score. The proposed architecture can leverage notewise features and interdependencies between notes but yield onset-wise representation by virtue of our novel edge contraction algorithm. Our results demonstrate that ChordGNN outperforms existing state-of-the-art models, achieving higher accuracy in Roman Numeral analysis on the reference datasets. In addition, we investigate variants of our model using proposed techniques such as NADE, and post-processing of the chord predictions. The full source code for this work is available at https://github.com/manoskary/chordgnn

The quadratic complexity of attention poses a critical bottleneck for long-context processing, spurring interest in hybrid attention designs. Most open-source hybrid models adopt a layer-wise strategy. Yet, prior work has noted the inherent difficulty of integrating Linear Attention (LA) with Full Attention (FA), suggesting that the design space of attention hybridization remains underexplored. To probe this space, we conduct interpretability analysis and observe that layers exhibit block-wise functional similarity, while individual heads within the same layer display distinct functional specialization despite sharing input features. This head-level heterogeneity suggests that the head dimension provides a natural and principled granularity for fusing heterogeneous attention signals. Building on this insight, we introduce HydraHead, a novel architecture that hybridizes FA and LA along the head axis. HydraHead features two key innovations: (1) an interpretability-driven selection strategy that identifies retrieval-critical heads and preserves FA only for them, and (2) a scale-normalized fusion module that reconciles the distributional gap between FA and LA head outputs. By leveraging a three-stage transfer pipeline with parameter reuse and distillation, we achieve high-performance hybrid models with minimal training overhead. Under a unified training setup, HydraHead outperforms other hybrid designs in long-context tasks while maintaining strong general reasoning. With interpretability-driven head selection, it matches a 3:1 layer-wise hybrid's long-context performance at a 7:1 LA-to-FA ratio. Crucially, trained on only 15B tokens, HydraHead achieves over 69% improvement over the baseline at 512K context length, approaching Qwen3.5, a leading model of comparable size with a native context length of 256K. This highlights the significant scaling potential of head-level hybridization.

The promise of Large Language Models in automated software engineering is often measured by functional correctness, overlooking the critical issue of long term maintainability. This paper presents a systematic audit of technical debt in AI-generated software, revealing that AI does not eliminate flaws but rather introduces a distinct machine signature of defects. Our multi-scale analysis, spanning single-file algorithmic tasks and complex, agent generated systems, identifies a fundamental Reasoning-Complexity Trade-off: as models become more capable, they generate increasingly bloated and coupled code. This architectural decay is so pronounced that we establish a Volume-Quality Inverse Law, where code volume is a near perfect predictor of structural degradation. Crucially, we demonstrate that neither functional correctness nor detailed prompting mitigates this decay. These findings challenge the current paradigm of prompt-driven generation, reframing the central problem of AI-based software engineering from one of code generation to one of architectural complexity management. We conclude that future progress depends on equipping agents with explicit architectural foresight to ensure the software they build is not just functional, but also maintainable.

Recent years have seen a boom in computational approaches to music analysis, yet each one is typically tailored to a specific analytical domain. In this work, we introduce AnalysisGNN, a novel graph neural network framework that leverages a data-shuffling strategy with a custom weighted multi-task loss and logit fusion between task-specific classifiers to integrate heterogeneously annotated symbolic datasets for comprehensive score analysis. We further integrate a Non-Chord-Tone prediction module, which identifies and excludes passing and non-functional notes from all tasks, thereby improving the consistency of label signals. Experimental evaluations demonstrate that AnalysisGNN achieves performance comparable to traditional static-dataset approaches, while showing increased resilience to domain shifts and annotation inconsistencies across multiple heterogeneous corpora.

Several studies have shown that speech and language features, automatically extracted from clinical interviews or spontaneous discourse, have diagnostic value for mental disorders such as schizophrenia and bipolar disorder. They typically make use of a large feature set to train a classifier for distinguishing between two groups of interest, i.e. a clinical and control group. However, a purely data-driven approach runs the risk of overfitting to a particular data set, especially when sample sizes are limited. Here, we first down-select the set of language features to a small subset that is related to a well-validated test of functional ability, the Social Skills Performance Assessment (SSPA). This helps establish the concurrent validity of the selected features. We use only these features to train a simple classifier to distinguish between groups of interest. Linear regression reveals that a subset of language features can effectively model the SSPA, with a correlation coefficient of 0.75. Furthermore, the same feature set can be used to build a strong binary classifier to distinguish between healthy controls and a clinical group (AUC = 0.96) and also between patients within the clinical group with schizophrenia and bipolar I disorder (AUC = 0.83).

Backdoor attacks pose significant security risks for Large Language Models (LLMs), yet the internal mechanisms by which triggers operate remain poorly understood. We present the first mechanistic analysis of language-switching backdoors, studying the GAPperon model family (1B, 8B, 24B parameters) which contains triggers injected during pretraining that cause output language switching. Using activation patching, we localize trigger formation to early layers (7.5-25% of model depth) and identify which attention heads process trigger information. Our central finding is that trigger-activated heads substantially overlap with heads naturally encoding output language across model scales, with Jaccard indices between 0.18 and 0.66 over the top heads identified. This suggests that backdoor triggers do not form isolated circuits but instead co-opt the model's existing language components. These findings have implications for backdoor defense: detection methods may benefit from monitoring known functional components rather than searching for hidden circuits, and mitigation strategies could potentially leverage this entanglement between injected and natural behaviors.

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

Multi-stream transformer architectures have recently been proposed as a promising direction for managing representation collapse and the vanishing gradient problem for residual connections, yet their internal mechanisms remain unexplored. In particular, the recently introduced Manifold-Constrained Hyper-Connections (mHC) architecture posits multiple residual streams with constrained interaction, but lacks in-depth mechanistic analysis. We present the first open-source mHC language model (https://huggingface.co/wgpeng/mhc-780m) and analyze the multiple-stream architecture with a suite of representation-level metrics and causal interventions to probe how parallel streams encode and utilize information. Specifically, we introduce a systematic stream ablation-and-rescue framework that enables direct causal comparison of residual streams during inference. Through targeted pairwise interventions and controlled recovery experiments, we distinguish functional redundancy from asymmetric utilization and reveal how information is distributed across streams beyond what is observable from representational similarity alone.

Across many domains (e.g., IoT, observability, telecommunications, cybersecurity), there is an emerging adoption of conversational data analysis agents that enable users to "talk to your data" to extract insights. Such data analysis agents operate on timeseries data models; e.g., measurements from sensors or events monitoring user clicks and actions in product analytics. We evaluate 6 popular data analysis agents (both open-source and proprietary) on domain-specific data and query types, and find that they fail on stateful and incident-specific queries. We observe two key expressivity gaps in existing evals: domain-customized datasets and domain-specific query types. To enable practitioners in such domains to generate customized and expressive evals for such timeseries data agents, we present AgentFuel. AgentFuel helps domain experts quickly create customized evals to perform end-to-end functional tests. We show that AgentFuel's benchmarks expose key directions for improvement in existing data agent frameworks. We also present anecdotal evidence that using AgentFuel can improve agent performance (e.g., with GEPA). AgentFuel benchmarks are available at https://huggingface.co/datasets/RockfishData/TimeSeriesAgentEvals.

We study the momentum-based minimization of a diffuse perimeter functional on Euclidean spaces and on graphs with applications to semi-supervised classification tasks in machine learning. While the gradient flow in the task at hand is a parabolic partial differential equation, the momentum-method corresponds to a damped hyperbolic PDE, leading to qualitatively and quantitatively different trajectories. Using a convex-concave splitting-based FISTA-type time discretization, we demonstrate empirically that momentum can lead to faster convergence if the time step size is large but not too large. With large time steps, the PDE analysis offers only limited insight into the geometric behavior of solutions and typical hyperbolic phenomena like loss of regularity are not be observed in sample simulations.

The entropic fictitious play (EFP) is a recently proposed algorithm that minimizes the sum of a convex functional and entropy in the space of measures -- such an objective naturally arises in the optimization of a two-layer neural network in the mean-field regime. In this work, we provide a concise primal-dual analysis of EFP in the setting where the learning problem exhibits a finite-sum structure. We establish quantitative global convergence guarantees for both the continuous-time and discrete-time dynamics based on properties of a proximal Gibbs measure introduced in Nitanda et al. (2022). Furthermore, our primal-dual framework entails a memory-efficient particle-based implementation of the EFP update, and also suggests a connection to gradient boosting methods. We illustrate the efficiency of our novel implementation in experiments including neural network optimization and image synthesis.

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

Most text-driven 3D indoor scene synthesis methods generate rooms from object-centric prompts, asking what furniture should be placed rather than how the space is used. Yet in real interior design, a layout is judged by how well it supports its occupants, e.g., their activities and physical needs. We introduce Function2Scene, a framework for generating 3D indoor layouts from functional specifications, i.e., natural-language design briefs describing who will use a room and what they need to do there. Given such a specification, our system parses occupant personas and activities, derives a customized set of functional design constraints from a taxonomy of 17 criteria spanning spatial, ergonomic, activity, and environmental considerations, and uses these constraints to guide layout generation. Rather than relying on an LLM to directly produce a final scene, Function2Scene performs iterative evaluation and refinement through a tool-augmented check-and-repair loop, combining geometric measurements, LLM-based contextual reasoning, and VLM-based visual assessment. Experiments on 30 professionally written interior-design cases show that Function2Scene produces layouts that better satisfy functional requirements than recent LLM-based scene synthesis baselines, with our results preferred in 94.3% of pairwise comparisons. Our work reframes text-driven indoor scene synthesis from placing plausible objects to designing spaces that support human use.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

Transformer-based language models excel at both recall (retrieving memorized facts) and reasoning (performing multi-step inference), but whether these abilities rely on distinct internal mechanisms remains unclear. Distinguishing recall from reasoning is crucial for predicting model generalization, designing targeted evaluations, and building safer interventions that affect one ability without disrupting the other.We approach this question through mechanistic interpretability, using controlled datasets of synthetic linguistic puzzles to probe transformer models at the layer, head, and neuron level. Our pipeline combines activation patching and structured ablations to causally measure component contributions to each task type. Across two model families (Qwen and LLaMA), we find that interventions on distinct layers and attention heads lead to selective impairments: disabling identified "recall circuits" reduces fact-retrieval accuracy by up to 15\% while leaving reasoning intact, whereas disabling "reasoning circuits" reduces multi-step inference by a comparable margin. At the neuron level, we observe task-specific firing patterns, though these effects are less robust, consistent with neuronal polysemanticity.Our results provide the first causal evidence that recall and reasoning rely on separable but interacting circuits in transformer models. These findings advance mechanistic interpretability by linking circuit-level structure to functional specialization and demonstrate how controlled datasets and causal interventions can yield mechanistic insights into model cognition, informing safer deployment of large language models.

Benchmarking the hundreds of functional connectivity (FC) modeling methods on large-scale fMRI datasets is critical for reproducible neuroscience. However, the combinatorial explosion of model-data pairings makes exhaustive evaluation computationally prohibitive, preventing such assessments from becoming a routine pre-analysis step. To break this bottleneck, we reframe the challenge of FC benchmarking by selecting a small, representative core-set whose sole purpose is to preserve the relative performance ranking of FC operators. We formalize this as a ranking-preserving subset selection problem and propose Structure-aware Contrastive Learning for Core-set Selection (SCLCS), a self-supervised framework to select these core-sets. SCLCS first uses an adaptive Transformer to learn each sample's unique FC structure. It then introduces a novel Structural Perturbation Score (SPS) to quantify the stability of these learned structures during training, identifying samples that represent foundational connectivity archetypes. Finally, while SCLCS identifies stable samples via a top-k ranking, we further introduce a density-balanced sampling strategy as a necessary correction to promote diversity, ensuring the final core-set is both structurally robust and distributionally representative. On the large-scale REST-meta-MDD dataset, SCLCS preserves the ground-truth model ranking with just 10% of the data, outperforming state-of-the-art (SOTA) core-set selection methods by up to 23.2% in ranking consistency (nDCG@k). To our knowledge, this is the first work to formalize core-set selection for FC operator benchmarking, thereby making large-scale operators comparisons a feasible and integral part of computational neuroscience. Code is publicly available on https://github.com/lzhan94swu/SCLCS

Effective scientific communication depends on accurate citations that validate sources and guide readers to supporting evidence. Yet academic literature faces mounting challenges: semantic citation errors that misrepresent sources, AI-generated hallucinated references, and traditional citation formats that point to entire papers without indicating which sections substantiate specific claims. We introduce SemanticCite, an AI-powered system that verifies citation accuracy through full-text source analysis while providing rich contextual information via detailed reasoning and relevant text snippets. Our approach combines multiple retrieval methods with a four-class classification system (Supported, Partially Supported, Unsupported, Uncertain) that captures nuanced claim-source relationships and enables appropriate remedial actions for different error types. Our experiments show that fine-tuned lightweight language models achieve performance comparable to large commercial systems with significantly lower computational requirements, making large-scale citation verification practically feasible. The system provides transparent, evidence-based explanations that support user understanding and trust. We contribute a comprehensive dataset of over 1,000 citations with detailed alignments, functional classifications, semantic annotations, and bibliometric metadata across eight disciplines, alongside fine-tuned models and the complete verification framework as open-source software. SemanticCite addresses critical challenges in research integrity through scalable citation verification, streamlined peer review, and quality control for AI-generated content, providing an open-source foundation for maintaining citation accuracy at scale.

Music structure analysis (MSA) underpins music understanding and controllable generation, yet progress has been limited by small, inconsistent corpora. We present SongFormer, a scalable framework that learns from heterogeneous supervision. SongFormer (i) fuses short- and long-window self-supervised audio representations to capture both fine-grained and long-range dependencies, and (ii) introduces a learned source embedding to enable training with partial, noisy, and schema-mismatched labels. To support scaling and fair evaluation, we release SongFormDB, the largest MSA corpus to date (over 10k tracks spanning languages and genres), and SongFormBench, a 300-song expert-verified benchmark. On SongFormBench, SongFormer sets a new state of the art in strict boundary detection (HR.5F) and achieves the highest functional label accuracy, while remaining computationally efficient; it surpasses strong baselines and Gemini 2.5 Pro on these metrics and remains competitive under relaxed tolerance (HR3F). Code, datasets, and model are publicly available.

Prior studies on the emergence in large models have primarily focused on how the functional capabilities of large language models (LLMs) scale with model size. Our research, however, transcends this traditional paradigm, aiming to deepen our understanding of the emergence within LLMs by placing a special emphasis not just on the model size but more significantly on the complex behavior of neuron interactions during the training process. By introducing the concepts of "self-organization" and "multifractal analysis," we explore how neuron interactions dynamically evolve during training, leading to "emergence," mirroring the phenomenon in natural systems where simple micro-level interactions give rise to complex macro-level behaviors. To quantitatively analyze the continuously evolving interactions among neurons in large models during training, we propose the Neuron-based Multifractal Analysis (NeuroMFA). Utilizing NeuroMFA, we conduct a comprehensive examination of the emergent behavior in LLMs through the lens of both model size and training process, paving new avenues for research into the emergence in large models.

Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that discovers shared latent trajectories and subject-specific functional topographies, while modelling temporal correlation in fMRI data. We demonstrate the efficacy of our model in revealing ground truth latent structures using simulated data, and replicate experimental performance of time-segment matching and inter-subject similarity on the publicly available Raider and Sherlock datasets. We further test the utility of our model by analyzing its learned model parameters in the large multi-site SPINS dataset, on a social cognition task from participants with and without schizophrenia.

LLM-integrated software, which embeds or interacts with large language models (LLMs) as functional components, exhibits probabilistic and context-dependent behaviors that fundamentally differ from those of traditional software. This shift introduces a new category of integration defects that arise not only from code errors but also from misaligned interactions among LLM-specific artifacts, including prompts, API calls, configurations, and model outputs. However, existing defect localization techniques are ineffective at identifying these LLM-specific integration defects because they fail to capture cross-layer dependencies across heterogeneous artifacts, cannot exploit incomplete or misleading error traces, and lack semantic reasoning capabilities for identifying root causes. To address these challenges, we propose LIDL, a multi-agent framework for defect localization in LLM-integrated software. LIDL (1) constructs a code knowledge graph enriched with LLM-aware annotations that represent interaction boundaries across source code, prompts, and configuration files, (2) fuses three complementary sources of error evidence inferred by LLMs to surface candidate defect locations, and (3) applies context-aware validation that uses counterfactual reasoning to distinguish true root causes from propagated symptoms. We evaluate LIDL on 146 real-world defect instances collected from 105 GitHub repositories and 16 agent-based systems. The results show that LIDL significantly outperforms five state-of-the-art baselines across all metrics, achieving a Top-3 accuracy of 0.64 and a MAP of 0.48, which represents a 64.1% improvement over the best-performing baseline. Notably, LIDL achieves these gains while reducing cost by 92.5%, demonstrating both high accuracy and cost efficiency.

Pain is a complex and pervasive condition that affects a significant portion of the population. Accurate and consistent assessment is essential for individuals suffering from pain, as well as for developing effective management strategies in a healthcare system. Automatic pain assessment systems enable continuous monitoring, support clinical decision-making, and help minimize patient distress while mitigating the risk of functional deterioration. Leveraging physiological signals offers objective and precise insights into a person's state, and their integration in a multimodal framework can further enhance system performance. This study has been submitted to the Second Multimodal Sensing Grand Challenge for Next-Gen Pain Assessment (AI4PAIN). The proposed approach introduces Tiny-BioMoE, a lightweight pretrained embedding model for biosignal analysis. Trained on 4.4 million biosignal image representations and consisting of only 7.3 million parameters, it serves as an effective tool for extracting high-quality embeddings for downstream tasks. Extensive experiments involving electrodermal activity, blood volume pulse, respiratory signals, peripheral oxygen saturation, and their combinations highlight the model's effectiveness across diverse modalities in automatic pain recognition tasks. The model's architecture (code) and weights are available at https://github.com/GkikasStefanos/Tiny-BioMoE.

Self-supervised learning has greatly facilitated medical image analysis by suppressing the training data requirement for real-world applications. Current paradigms predominantly rely on self-supervision within uni-modal image data, thereby neglecting the inter-modal correlations essential for effective learning of cross-modal image representations. This limitation is particularly significant for naturally grouped multi-modal data, e.g., multi-parametric MRI scans for a patient undergoing various functional imaging protocols in the same study. To bridge this gap, we conduct a novel multi-modal image pre-training with three proxy tasks to facilitate the learning of cross-modality representations and correlations using multi-modal brain MRI scans (over 2.4 million images in 16,022 scans of 3,755 patients), i.e., cross-modal image reconstruction, modality-aware contrastive learning, and modality template distillation. To demonstrate the generalizability of our pre-trained model, we conduct extensive experiments on various benchmarks with ten downstream tasks. The superior performance of our method is reported in comparison to state-of-the-art pre-training methods, with Dice Score improvement of 0.28\%-14.47\% across six segmentation benchmarks and a consistent accuracy boost of 0.65\%-18.07\% in four individual image classification tasks.

In the realm of computer vision and graphics, accurately establishing correspondences between geometric 3D shapes is pivotal for applications like object tracking, registration, texture transfer, and statistical shape analysis. Moving beyond traditional hand-crafted and data-driven feature learning methods, we incorporate spectral methods with deep learning, focusing on functional maps (FMs) and optimal transport (OT). Traditional OT-based approaches, often reliant on entropy regularization OT in learning-based framework, face computational challenges due to their quadratic cost. Our key contribution is to employ the sliced Wasserstein distance (SWD) for OT, which is a valid fast optimal transport metric in an unsupervised shape matching framework. This unsupervised framework integrates functional map regularizers with a novel OT-based loss derived from SWD, enhancing feature alignment between shapes treated as discrete probability measures. We also introduce an adaptive refinement process utilizing entropy regularized OT, further refining feature alignments for accurate point-to-point correspondences. Our method demonstrates superior performance in non-rigid shape matching, including near-isometric and non-isometric scenarios, and excels in downstream tasks like segmentation transfer. The empirical results on diverse datasets highlight our framework's effectiveness and generalization capabilities, setting new standards in non-rigid shape matching with efficient OT metrics and an adaptive refinement module.

Code generation with large language models (LLMs), often termed vibe coding, is increasingly adopted in production but fails to ensure code quality, particularly in security (e.g., SQL injection vulnerabilities) and maintainability (e.g., missing type annotations). Existing methods, such as supervised fine-tuning and rule-based post-processing, rely on labor-intensive annotations or brittle heuristics, limiting their scalability and effectiveness. We propose REAL, a reinforcement learning framework that incentivizes LLMs to generate production-quality code using program analysis-guided feedback. Specifically, REAL integrates two automated signals: (1) program analysis detecting security or maintainability defects and (2) unit tests ensuring functional correctness. Unlike prior work, our framework is prompt-agnostic and reference-free, enabling scalable supervision without manual intervention. Experiments across multiple datasets and model scales demonstrate that REAL outperforms state-of-the-art methods in simultaneous assessments of functionality and code quality. Our work bridges the gap between rapid prototyping and production-ready code, enabling LLMs to deliver both speed and quality.

Decoding approaches are widely used in neuroscience and machine learning to compare stimulus representations across neural systems, such as different brain regions, organisms, and deep learning models. Popular methods include decoding (perceptual) manifolds and alignment metrics such as Representational Similarity Analysis (RSA) and Dynamic Similarity Analysis (DSA), where similarity in decoding representations is interpreted as evidence for similar computation. This paper demonstrates a fundamental weakness behind this approach: it is misleading to assume that representational geometry is representative of a neuronal population as a whole, when such representations may actually be shaped by a very small subset of neurons. We show that the complementary encoding paradigm addresses this issue directly: it characterizes how neurons are organized globally in terms of their responses to a set of data, providing insight into how the decoding representation is implemented by neurons within a population. We demonstrate across experiments in biological systems and deep learning models that (i) surprisingly, similar decoding behavior and high representational alignment can arise from small, non-representative subpopulations of neurons; and critically, (ii) alignment metrics are insensitive to encoding manifold topology (how function is distributed across neurons), despite this being a key signature of differentiation across biological systems. A controlled MNIST experiment provides causal evidence: decoding metrics remain unchanged even when encoding topology is causally manipulated via the training loss. Overall, similarity in decoding behavior, as measured by classic alignment metrics, does not imply similarity in function or computation, motivating the use of encoding manifolds as a complementary tool for comparing neural systems.

The advancement of graph-based malware analysis is critically limited by the absence of large-scale datasets that capture the inherent hierarchical structure of software. Existing methods often oversimplify programs into single level graphs, failing to model the crucial semantic relationship between high-level functional interactions and low-level instruction logic. To bridge this gap, we introduce \dataset, the largest public hierarchical graph dataset for malware analysis, comprising over 200M Control Flow Graphs (CFGs) nested within 595K Function Call Graphs (FCGs). This two-level representation preserves structural semantics essential for building robust detectors resilient to code obfuscation and malware evolution. We demonstrate HiGraph's utility through a large-scale analysis that reveals distinct structural properties of benign and malicious software, establishing it as a foundational benchmark for the community. The dataset and tools are publicly available at https://higraph.org.

Migrating existing C programs into Rust is increasingly desired, as Rust offers superior memory safety while maintaining C's high performance. However, vastly different features between C and Rust--e.g., distinct definitions and usages of pointers and references--pose significant challenges beyond mere syntactic translation. Existing automated translation tools, such as C2Rust, may rely too much on syntactic, template-based translation and generate unsafe Rust code that is hard for human developers to read, maintain, or even compile. More semantic-aware translation that produces safer, idiomatic, and runnable Rust code is much needed. This paper introduces a novel dependency-guided and large language model (LLM)-based C-to-Rust translation approach, RustMap, based on three key ideas: (1) Utilize LLM capabilities to produce idiomatic Rust code from given small pieces of C code, (2) Mitigate LLM limitations in handling large codebases by breaking project-scale C programs into smaller units for translation according to their usage dependencies and composing them into a runnable Rust program, and (3) Enhance the correctness of the translated Rust program by using test cases to check input/output equivalence, isolate faulty code when execution states deviate, and iteratively refine the translation using feedback from compilation and test errors. We empirically evaluate RustMap on 126 real-world programs, including 125 from Rosetta Code and a 7000+ line bzip2 implementation using GPT-4o as the LLM. RustMap shows promising results, guiding GPT-4o to produce idiomatic, readable, and functional Rust code with significantly less unsafe code than other tools, and revealing non-trivial translation patterns reusable for future research.

Elucidating the functional effect of missense variants is of crucial importance, yet challenging. To understand the impact of such variants, we fine-tuned the ESM2 protein language model to classify 20 protein features at amino acid resolution. We used the resulting models to: 1) identify protein features that are enriched in either pathogenic or benign missense variants, 2) compare the characteristics of proteins with reference or alternate alleles to understand how missense variants affect protein functionality. We show that our model can be used to reclassify some variants of unknown significance. We also demonstrate the usage of our models for understanding the potential effect of variants on protein features.

The rapid advancement of AI technology has led to widespread applications of agent systems across various domains. However, the need for detailed architecture design poses significant challenges in designing and operating these systems. This paper introduces a taxonomy focused on the architectures of foundation-model-based agents, addressing critical aspects such as functional capabilities and non-functional qualities. We also discuss the operations involved in both design-time and run-time phases, providing a comprehensive view of architectural design and operational characteristics. By unifying and detailing these classifications, our taxonomy aims to improve the design of foundation-model-based agents. Additionally, the paper establishes a decision model that guides critical design and runtime decisions, offering a structured approach to enhance the development of foundation-model-based agents. Our contributions include providing a structured architecture design option and guiding the development process of foundation-model-based agents, thereby addressing current fragmentation in the field.

Reinforcement learning (RL) with verifiable rewards has become a standard post-training stage for boosting visual reasoning in vision-language models, yet it remains unclear what capabilities RL actually improves compared with supervised fine-tuning as cold-start initialization (IN). End-to-end benchmark gains conflate multiple factors, making it difficult to attribute improvements to specific skills. To bridge the gap, we propose a Frankenstein-style analysis framework including: (i) functional localization via causal probing; (ii) update characterization via parameter comparison; and (iii) transferability test via model merging. Instead, RL induces a consistent inference-time shift primarily in mid-to-late layers, and these mid-to-late refinements are both transferable (via merging) and necessary (via freezing) for RL gains. Overall, our results suggest that RL's reliable contribution in visual reasoning is not a uniform enhancement of visual perception, but a systematic refinement of mid-to-late transformer computation that improves vision-to-reasoning alignment and reasoning performance, highlighting the limitations of benchmark-only evaluation for understanding multimodal reasoning improvements.

This paper investigates how Transformer language models (LMs) fine-tuned for acceptability classification capture linguistic features. Our approach uses the best practices of topological data analysis (TDA) in NLP: we construct directed attention graphs from attention matrices, derive topological features from them, and feed them to linear classifiers. We introduce two novel features, chordality, and the matching number, and show that TDA-based classifiers outperform fine-tuning baselines. We experiment with two datasets, CoLA and RuCoLA in English and Russian, typologically different languages. On top of that, we propose several black-box introspection techniques aimed at detecting changes in the attention mode of the LMs during fine-tuning, defining the LM's prediction confidences, and associating individual heads with fine-grained grammar phenomena. Our results contribute to understanding the behavior of monolingual LMs in the acceptability classification task, provide insights into the functional roles of attention heads, and highlight the advantages of TDA-based approaches for analyzing LMs. We release the code and the experimental results for further uptake.

Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To address this gap, we introduce SciHorizon-GENE, a large-scale gene-centric benchmark constructed from authoritative biological databases. The benchmark integrates curated knowledge for over 190K human genes and comprises more than 540K questions covering diverse gene-to-function reasoning scenarios relevant to cell type annotation, functional interpretation, and mechanism-oriented analysis. Motivated by behavioral patterns observed in preliminary examinations, SciHorizon-GENE evaluates LLMs along four biologically critical perspectives: research attention sensitivity, hallucination tendency, answer completeness, and literature influence, explicitly targeting failure modes that limit the safe adoption of LLMs in biological interpretation pipelines. We systematically evaluate a wide range of state-of-the-art general-purpose and biomedical LLMs, revealing substantial heterogeneity in gene-level reasoning capabilities and persistent challenges in generating faithful, complete, and literature-grounded functional interpretations. Our benchmark establishes a systematic foundation for analyzing LLM behavior at the gene scale and offers insights for model selection and development, with direct relevance to knowledge-enhanced biological interpretation.

Large Language Models (LLMs) are increasingly deployed as active participants on public social media platforms, yet their behavior in these unconstrained social environments remains largely unstudied. Existing datasets, drawn primarily from private chat interfaces, lack the multi-party dynamics and public visibility crucial for understanding real-world performance. To address this gap, we introduce @GrokSet, a large-scale dataset of over 1 million tweets involving the @Grok LLM on X. Our analysis reveals a distinct functional shift: rather than serving as a general assistant, the LLM is frequently invoked as an authoritative arbiter in high-stakes, polarizing political debates. However, we observe a persistent engagement gap: despite this visibility, the model functions as a low-status utility, receiving significantly less social validation (likes, replies) than human peers. Finally, we find that this adversarial context exposes shallow alignment: users bypass safety filters not through complex jailbreaks, but through simple persona adoption and tone mirroring. We release @GrokSet as a critical resource for studying the intersection of AI agents and societal discourse.

We introduce DafnyCOMP, a benchmark for evaluating large language models (LLMs) on compositional specification generation in Dafny. Unlike prior benchmarks that focus on single-function tasks, DafnyCOMP targets programs composed of multiple interacting functions with data dependencies, requiring reasoning across component boundaries. The benchmark consists of 300 automatically synthesized multi-function programs. We evaluate several state-of-the-art LLM families and find that, while they perform well on single-function verification, their performance drops sharply on compositional tasks. Analysis reveals systematic failures in cross-functional reasoning, including fragile specifications, misalignment between implementations and proofs, and unstable reasoning. DafnyCOMP thus provides a diagnostic tool for measuring progress toward reliable, verifiable, and compositional code generation with LLMs.

Agentic coding tools receive goals written in natural language as input, break them down into specific tasks, and write or execute the actual code with minimal human intervention. Central to this process are agent context files ("READMEs for agents") that provide persistent, project-level instructions. In this paper, we conduct the first large-scale empirical study of 2,303 agent context files from 1,925 repositories to characterize their structure, maintenance, and content. We find that these files are not static documentation but complex, difficult-to-read artifacts that evolve like configuration code, maintained through frequent, small additions. Our content analysis of 16 instruction types shows that developers prioritize functional context, such as build and run commands (62.3%), implementation details (69.9%), and architecture (67.7%). We also identify a significant gap: non-functional requirements like security (14.5%) and performance (14.5%) are rarely specified. These findings indicate that while developers use context files to make agents functional, they provide few guardrails to ensure that agent-written code is secure or performant, highlighting the need for improved tooling and practices.

Game generation is an emerging application of coding agents, requiring models to transform natural-language specifications into playable interactive systems. Unlike traditional coding tasks, game generation takes place within a game engine, where scripts, scenes, assets, rendering, and runtime interactions must jointly produce coherent gameplay. We formalize end-to-end game generation as the problem of producing a complete game artifact that realizes a specification through observable player-game interaction in a target environment. We argue that evaluating this setting requires three desiderata: Engine Grounding, Artifact Completeness, and Interactive Verification. We propose an interaction-grounded evaluation framework that assesses executable gameplay through replayed demonstrations and rubric-guided multimodal judging. We instantiate this framework as GameCraft-Bench, a benchmark comprising 140 Godot tasks across 15 game families. Evaluations of frontier coding agents show that end-to-end game generation remains highly challenging: the strongest agent achieves only 41.46%, and most agents score below 40%. Further analysis reveals that while agents often implement recognizable mechanics, they struggle to deliver complete games with sufficient content, functional visual feedback, and coherent presentation. See https://tongxuluo.github.io/gamecraft-bench-website for demos, code, and data.

Multimodal Large Language Models (MLLMs) excel at utilizing digital APIs and increasingly serve as the "brain" of embodied AI, instructing robots to interact with the physical world. In such embodied settings, a central capability is the use of physical tools, which underpins MLLMs' ability to assist humans in real-world tasks. Despite the importance, MLLMs' proficiency in physical tool use remains largely unexplored. To address this gap, we introduce PhysTool-Bench, the first physical tool-use benchmark designed to evaluate MLLMs' ability to comprehend real-world scenarios, identify physical tools, and plan their use. PhysTool-Bench comprises 2,510 queries over 2,678 real-world physical tools spanning diverse domains, including manufacturing, electrical work, agriculture, and healthcare. Concretely, models are evaluated along two primary dimensions: 1) recognizing all physical tools present in the scene, and 2) planning the tool selection and use sequence based on the instruction and visual context. Across 13 leading MLLMs, even the strongest model (Gemini-3.1-Pro) identifies only 58.7% of tools in a scene and completes merely 21.0% of queries end-to-end. Our analysis reveals a two-level deficit: MLLMs struggle to perceive tools in realistic scenes, and the much larger drop at the planning stage further indicates a lack of functional commonsense for mapping perceived tools onto task semantics, pinpointing a critical bottleneck for the development of practical embodied AI.

The paradigm of LLM-as-a-judge is emerging as a scalable and efficient alternative to human evaluation, demonstrating strong performance on well-defined tasks. However, its reliability in open-ended tasks with dynamic environments and complex interactions remains unexplored. To bridge the gap, we introduce WebDevJudge, a systematic benchmark for assessing LLM-as-a-judge performance in web development, with support for both non-interactive evaluation based on static observations and continuous interactive evaluation with a dynamic web environment. WebDevJudge comprises human preference labels over paired web implementations, annotated with structured and query-grounded rubrics to ensure high-quality ground truth. Using this benchmark, we comprehensively evaluate various evaluators, including LLMs, MLLMs, and agentic workflows. We systematically investigate the impact of different paradigms and guidance mechanisms. Our experiments reveal a significant gap between LLM judges and human experts. In-depth analysis indicates this gap stems from fundamental model limitations, including failures in recognizing functional equivalence, verifying task feasibility, and mitigating bias. Overall, WebDevJudge presents a significant challenge to LLM-as-a-judge, offering insights to guide future research toward developing more reliable and capable automated evaluators for complicated scenarios. Code and data are available at https://github.com/lcy2723/WebDevJudge.

Despite recent progress made by large language models in code generation, they still struggle with programs that meet complex requirements. Recent work utilizes plan-and-solve decomposition to decrease the complexity and leverage self-tests to refine the generated program. Yet, planning deep-inside requirements in advance can be challenging, and the tests need to be accurate to accomplish self-improvement. To this end, we propose FunCoder, a code generation framework incorporating the divide-and-conquer strategy with functional consensus. Specifically, FunCoder recursively branches off sub-functions as smaller goals during code generation, represented by a tree hierarchy. These sub-functions are then composited to attain more complex objectives. Additionally, we designate functions via a consensus formed by identifying similarities in program behavior, mitigating error propagation. FunCoder outperforms state-of-the-art methods by +9.8% on average in HumanEval, MBPP, xCodeEval and MATH with GPT-3.5 and GPT-4. Moreover, our method demonstrates superiority on smaller models: With FunCoder, StableCode-3b surpasses GPT-3.5 by +18.6% and achieves 97.7% of GPT-4's performance on HumanEval. Further analysis reveals that our proposed dynamic function decomposition is capable of handling complex requirements, and the functional consensus prevails over self-testing in correctness evaluation.

The choice of activation function plays a critical role in neural networks, yet most architectures still rely on fixed, uniform activation functions across all neurons. We introduce SmartMixed, a two-phase training strategy that allows networks to learn optimal per-neuron activation functions while preserving computational efficiency at inference. In the first phase, neurons adaptively select from a pool of candidate activation functions (ReLU, Sigmoid, Tanh, Leaky ReLU, ELU, SELU) using a differentiable hard-mixture mechanism. In the second phase, each neuron's activation function is fixed according to the learned selection, resulting in a computationally efficient network that supports continued training with optimized vectorized operations. We evaluate SmartMixed on the MNIST dataset using feedforward neural networks of varying depths. The analysis shows that neurons in different layers exhibit distinct preferences for activation functions, providing insights into the functional diversity within neural architectures.

LLMs exhibit promising Social Intelligence (SI) in modeling human behavior, raising the need to evaluate LLMs' SI and their discrepancy with humans. SI equips humans with interpersonal abilities to behave wisely in navigating social interactions to achieve social goals. This presents an operational evaluation paradigm: outcome-oriented goal achievement evaluation and process-oriented interpersonal ability evaluation, which existing work fails to address. To this end, we propose SocialEval, a script-based bilingual SI benchmark, integrating outcome- and process-oriented evaluation by manually crafting narrative scripts. Each script is structured as a world tree that contains plot lines driven by interpersonal ability, providing a comprehensive view of how LLMs navigate social interactions. Experiments show that LLMs fall behind humans on both SI evaluations, exhibit prosociality, and prefer more positive social behaviors, even if they lead to goal failure. Analysis of LLMs' formed representation space and neuronal activations reveals that LLMs have developed ability-specific functional partitions akin to the human brain.

This paper investigates a novel lossy compression framework operating under logarithmic loss, designed to handle situations where the reconstruction distribution diverges from the source distribution. This framework is especially relevant for applications that require joint compression and retrieval, and in scenarios involving distributional shifts due to processing. We show that the proposed formulation extends the classical minimum entropy coupling framework by integrating a bottleneck, allowing for a controlled degree of stochasticity in the coupling. We explore the decomposition of the Minimum Entropy Coupling with Bottleneck (MEC-B) into two distinct optimization problems: Entropy-Bounded Information Maximization (EBIM) for the encoder, and Minimum Entropy Coupling (MEC) for the decoder. Through extensive analysis, we provide a greedy algorithm for EBIM with guaranteed performance, and characterize the optimal solution near functional mappings, yielding significant theoretical insights into the structural complexity of this problem. Furthermore, we illustrate the practical application of MEC-B through experiments in Markov Coding Games (MCGs) under rate limits. These games simulate a communication scenario within a Markov Decision Process, where an agent must transmit a compressed message from a sender to a receiver through its actions. Our experiments highlight the trade-offs between MDP rewards and receiver accuracy across various compression rates, showcasing the efficacy of our method compared to conventional compression baseline.

LLM-based coding agents rely on skills, pre-packaged instruction sets that extend agent capabilities, yet every token of skill content injected into the context window incurs both monetary cost and attention dilution. To understand the severity of this problem, we conduct a large-scale empirical study of 55,315 publicly available skills and find systemic inefficiencies: 26.4\% lack routing descriptions entirely, over 60\% of body content is non-actionable, and reference files can inject tens of thousands of tokens per invocation. Motivated by these findings, we present SkillReducer, a two-stage optimization framework. Stage~1 optimizes the routing layer by compressing verbose descriptions and generating missing ones via adversarial delta debugging. Stage~2 restructures skill bodies through taxonomy-driven classification and progressive disclosure, separating actionable core rules from supplementary content loaded on demand, validated by faithfulness checks and a self-correcting feedback loop. Evaluated on 600 skills and the SkillsBench benchmark, SkillReducer achieves 48\% description compression and 39\% body compression while improving functional quality by 2.8\%, revealing a less-is-more effect where removing non-essential content reduces distraction in the context window. These benefits transfer across five models from four families with a mean retention of 0.965, and generalize to an independent agent framework.

Modern large language models leverage Mixture-of-Experts (MoE) architectures for efficient scaling, but face a critical challenge: functionally similar experts are often selected simultaneously, creating redundant computation and limiting effective model capacity. Existing auxiliary balance loss methods improve token distribution but fail to address the underlying expert diversity problem. We introduce GatePro, a novel parameter-free method that directly promotes expert selection diversity. GatePro identifies the most similar expert pairs and introduces localized competition mechanisms, preventing redundant expert co-activation while maintaining natural expert specialization. Our comprehensive evaluation demonstrates GatePro's effectiveness across model scales and benchmarks. Analysis demonstrates GatePro's ability to achieve enhanced expert diversity, where experts develop more distinct and complementary capabilities, avoiding functional redundancy. This approach can be deployed hot-swappable during any training phase without additional learnable parameters, offering a practical solution for improving MoE effectiveness.

Long-form answers, consisting of multiple sentences, can provide nuanced and comprehensive answers to a broader set of questions. To better understand this complex and understudied task, we study the functional structure of long-form answers collected from three datasets, ELI5, WebGPT and Natural Questions. Our main goal is to understand how humans organize information to craft complex answers. We develop an ontology of six sentence-level functional roles for long-form answers, and annotate 3.9k sentences in 640 answer paragraphs. Different answer collection methods manifest in different discourse structures. We further analyze model-generated answers -- finding that annotators agree less with each other when annotating model-generated answers compared to annotating human-written answers. Our annotated data enables training a strong classifier that can be used for automatic analysis. We hope our work can inspire future research on discourse-level modeling and evaluation of long-form QA systems.

With the widespread deployment of large language models (LLMs) such as GPT4, BART, and LLaMA, the need for a system that can intelligently select the most suitable model for specific tasks while balancing cost, latency, accuracy, and ethical considerations has become increasingly important. Recognizing that not all tasks necessitate models with over 100 billion parameters, we introduce OptiRoute, an advanced model routing engine designed to dynamically select and route tasks to the optimal LLM based on detailed user-defined requirements. OptiRoute captures both functional (e.g., accuracy, speed, cost) and non-functional (e.g., helpfulness, harmlessness, honesty) criteria, leveraging lightweight task analysis and complexity estimation to efficiently match tasks with the best-fit models from a diverse array of LLMs. By employing a hybrid approach combining k-nearest neighbors (kNN) search and hierarchical filtering, OptiRoute optimizes for user priorities while minimizing computational overhead. This makes it ideal for real-time applications in cloud-based ML platforms, personalized AI services, and regulated industries.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

Advances in peptide identification are revolutionizing our ability to decipher protein functions and accelerate therapeutic discovery. We present PDeepPP, a deep learning framework that integrates pretrained protein language models with parallel transformer-CNN architectures, achieving state-of-the-art performance in peptide characterization tasks. The model's hybrid architecture demonstrates unique capabilities in capturing both local sequence motifs and global structural features, as evidenced by 29% improved cluster separation in UMAP visualizations compared to conventional approaches. Evaluated across 33 biological recognition tasks - including post-translational modification site prediction and bioactive peptide identification - PDeepPP outperformed existing methods in 25 tasks with average AUC improvements of 4.2%. Notably, it achieved 0.9726 accuracy with PR AUC 0.9977 in antimicrobial peptide detection while reducing false negatives by 37.5% in antimalarial recognition scenarios. This framework enables accurate large-scale peptide analysis, achieving 218* acceleration over sequence-alignment-based methods while maintaining 99.5% specificity in critical glycosylation site detection.PDeepPP establishes a new paradigm for computational peptide analysis through its synergistic architecture design, enabling rapid yet precise functional annotation that bridges molecular pattern recognition with translational biomedical applications.We have made our implementation, including code, data, and pretrained models, publicly available via GitHub (https://github.com/fondress/PDeepPP) and Hugging Face (https://huggingface.co/fondress/PDeppPP).

Brain-Computer Interface (BCI) systems allow users to perform actions by translating their brain activity into commands. Such systems usually need a training phase, consisting in training a classification algorithm to discriminate between mental states using specific features from the recorded signals. This phase of feature selection and training is crucial for BCI performance and presents specific constraints to be met in a clinical context, such as post-stroke rehabilitation. In this paper, we present HappyFeat, a software making Motor Imagery (MI) based BCI experiments easier, by gathering all necessary manipulations and analysis in a single convenient GUI and via automation of experiment or analysis parameters. The resulting workflow allows for effortlessly selecting the best features, helping to achieve good BCI performance in time-constrained environments. Alternative features based on Functional Connectivity can be used and compared or combined with Power Spectral Density, allowing a network-oriented approach. We then give details of HappyFeat's main mechanisms, and a review of its performances in typical use cases. We also show that it can be used as an efficient tool for comparing different metrics extracted from the signals, to train the classification algorithm. To this end, we show a comparison between the commonly-used Power Spectral Density and network metrics based on Functional Connectivity. HappyFeat is available as an open-source project which can be freely downloaded on GitHub.

Large language model (LLM) agents execute tasks through multi-step workflows that combine planning, memory, and tool use. While this design enables autonomy, it also expands the attack surface for backdoor threats. Backdoor triggers injected into specific stages of an agent workflow can persist through multiple intermediate states and adversely influence downstream outputs. However, existing studies remain fragmented and typically analyze individual attack vectors in isolation, leaving the cross-stage interaction and propagation of backdoor triggers poorly understood from an agent-centric perspective. To fill this gap, we propose BackdoorAgent, a modular and stage-aware framework that provides a unified, agent-centric view of backdoor threats in LLM agents. BackdoorAgent structures the attack surface into three functional stages of agentic workflows, including planning attacks, memory attacks, and tool-use attacks, and instruments agent execution to enable systematic analysis of trigger activation and propagation across different stages. Building on this framework, we construct a standardized benchmark spanning four representative agent applications: Agent QA, Agent Code, Agent Web, and Agent Drive, covering both language-only and multimodal settings. Our empirical analysis shows that triggers implanted at a single stage can persist across multiple steps and propagate through intermediate states. For instance, when using a GPT-based backbone, we observe trigger persistence in 43.58\% of planning attacks, 77.97\% of memory attacks, and 60.28\% of tool-stage attacks, highlighting the vulnerabilities of the agentic workflow itself to backdoor threats. To facilitate reproducibility and future research, our code and benchmark are publicly available at GitHub.

Understanding the property of neural populations (or voxels) in the human brain can advance our comprehension of human perceptual and cognitive processing capabilities and contribute to developing brain-inspired computer models. Recent encoding models using deep neural networks (DNNs) have successfully predicted voxel-wise activity. However, interpreting the properties that explain voxel responses remains challenging because of the black-box nature of DNNs. As a solution, we propose LLM-assisted Visual Cortex Captioning (LaVCa), a data-driven approach that uses large language models (LLMs) to generate natural-language captions for images to which voxels are selective. By applying LaVCa for image-evoked brain activity, we demonstrate that LaVCa generates captions that describe voxel selectivity more accurately than the previously proposed method. Furthermore, the captions generated by LaVCa quantitatively capture more detailed properties than the existing method at both the inter-voxel and intra-voxel levels. Furthermore, a more detailed analysis of the voxel-specific properties generated by LaVCa reveals fine-grained functional differentiation within regions of interest (ROIs) in the visual cortex and voxels that simultaneously represent multiple distinct concepts. These findings offer profound insights into human visual representations by assigning detailed captions throughout the visual cortex while highlighting the potential of LLM-based methods in understanding brain representations. Please check out our webpage at https://sites.google.com/view/lavca-llm/

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.

As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization. Although the proportionality between the language model size and the richness of its learned representations is validated, we prioritize accessibility and pursue a path of data-efficient, cost-reduced, and knowledge-guided optimization. Through over twenty experiments ranging from masking, architecture, and pre-training data, we derive insights from protein-specific experimentation into building a model that interprets the language of life, optimally. We present Ankh, the first general-purpose PLM trained on Google's TPU-v4 surpassing the state-of-the-art performance with fewer parameters (<10% for pre-training, <7% for inference, and <30% for the embedding dimension). We provide a representative range of structure and function benchmarks where Ankh excels. We further provide a protein variant generation analysis on High-N and One-N input data scales where Ankh succeeds in learning protein evolutionary conservation-mutation trends and introducing functional diversity while retaining key structural-functional characteristics. We dedicate our work to promoting accessibility to research innovation via attainable resources.

Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used approaches such as Density Functional Theory (DFT) frequently fail for this task due to deficiencies that are well recognized. However, for high-fidelity approaches, creating large datasets of energies and forces for reactive processes to train machine learning interatomic potentials or force fields is daunting. For example, the use of the unrestricted coupled cluster level of theory has previously been seen as unfeasible due to high computational costs, the lack of analytical gradients in many computational codes, and additional challenges such as constructing suitable basis set corrections for forces. In this work, we develop new methods and workflows to overcome the challenges inherent to automating unrestricted coupled cluster calculations. Using these advancements, we create a dataset of gas-phase reactions containing energies and forces for 3119 different organic molecules configurations calculated at the gold-standard level of unrestricted CCSD(T) (coupled cluster singles doubles and perturbative triples). With this dataset, we provide an analysis of the differences between the density functional and unrestricted CCSD(T) descriptions. We develop a transferable machine learning interatomic potential for gas-phase reactions, trained on unrestricted CCSD(T) data, and demonstrate the advantages of transitioning away from DFT data. Transitioning from training to DFT to training to UCCSD(T) datasets yields an improvement of more than 0.1 eV/Å in force accuracy and over 0.1 eV in activation energy reproduction.

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

Despite the rapid growth of machine learning research, corresponding code implementations are often unavailable, making it slow and labor-intensive for researchers to reproduce results and build upon prior work. In the meantime, recent Large Language Models (LLMs) excel at understanding scientific documents and generating high-quality code. Inspired by this, we introduce PaperCoder, a multi-agent LLM framework that transforms machine learning papers into functional code repositories. PaperCoder operates in three stages: planning, where it constructs a high-level roadmap, designs the system architecture with diagrams, identifies file dependencies, and generates configuration files; analysis, which focuses on interpreting implementation-specific details; and generation, where modular, dependency-aware code is produced. Moreover, each phase is instantiated through a set of specialized agents designed to collaborate effectively across the pipeline. We then evaluate PaperCoder on generating code implementations from machine learning papers based on both model-based and human evaluations, specifically from the original paper authors, with author-released repositories as ground truth if available. Our results demonstrate the effectiveness of PaperCoder in creating high-quality, faithful implementations. Furthermore, it consistently shows strengths in the recently released PaperBench benchmark, surpassing strong baselines by substantial margins.

Everyday tasks come with a target, and pretraining models around this target is what turns them into experts. In this paper, we study target-oriented language model (LM) pretraining by introducing Neuron-Activated Graph Ranking (NAG-based Ranking), a training-free and interpretable framework for target pretraining data selection. Rather than using black-box representations, our approach directly characterizes each target input by a sparse set of high-impact neurons in any off-the-shelf LLMs. Concretely, we quantify neuron impact and select the most influential neurons across layers into a compact Neuron-Activated Graph (NAG), and rank candidate data by NAG similarity to target examples. We conduct experiments across six benchmarks, where our NAG-based Ranking improves target-oriented pretraining by 4.9% on average over random sampling, and also outperforms state-of-the-art baselines by 5.3% accuracy on HellaSwag. It also remains effective under a more applicable multi-target setting, where our best setup surpasses two baselines by 1.1% and 4.1%, respectively. Furthermore, we provide a comprehensive analysis on why and how our NAG works, e.g., deactivating NAG-selected neurons (only 0.12% of all) causes a 23.5% performance collapse, and restricting NAG to the final layer incurs a 4.1% average drop, indicating that NAG captures a sparse "functional backbone" for learning target features. We release the code at https://github.com/asillycat/NAG.

Discovering governing equations from observational data remains a fundamental challenge in scientific modeling, particularly when the underlying mathematical structure is unknown. Traditional sparse identification methods like SINDy excel at discovering parsimonious models but require researchers to specify candidate basis functions a priori, a limitation that often leads to model failure when critical terms are omitted or when systems exhibit unconventional dynamics. Purely symbolic regression approaches offer unlimited flexibility but struggle with noise sensitivity and frequently produce overly complex, unstable equations. We present AutoSINDy, a hybrid Discovery-then-Solve framework that combines the exploratory power of symbolic regression with the robust sparsity-promoting capabilities of SINDy. Our method operates in three stages: (1) PySR-based symbolic regression discovers candidate functional forms from bootstrapped data chunks; (2) a curation pipeline decomposes, expands, and filters these expressions using collinearity analysis to construct a minimal yet comprehensive library; and (3) SINDy identifies sparse governing equations from this custom-tailored library. Extensive experiments across canonical nonlinear systems demonstrate that AutoSINDy consistently recovers ground-truth equations even under high observational noise, achieving a ground-truth recovery rate of 92.8% across all trials. Compared with standard SINDy using enriched libraries and standalone symbolic regression, AutoSINDy achieves higher predictive accuracy, superior generalization to unseen trajectories, and substantially lower symbolic complexity.

Integration of artificial intelligent (AI) agents in higher education is transforming teaching, learning and administrative processes. Although existing AI agents effectively support individual tasks, their implementation remains fragmented and inefficient for handling the complexity of educational institutions. This highlights a significant research gap: the lack of integrated eco-system-level agentic multi-agent AI platform capable of coordinated planning, reasoning, and adaptive decision-making across multiple educational functions. This paper presents a forward-looking perspective on agentic multi-agent AI platform in higher education, consisting interconnected autonomous, goal driven agents that support learning, teaching, and institutional operations. It addresses timely and critical questions: Can agentic AI represent the next generation of intelligent systems in tertiary education? Can they collectively support seamless coordinated operations across teaching, learning and administrative support? To what extent can such systems foster inclusive and equitable learning for diverse learners with special educational needs? To ground this perspective, a thematic analysis of existing literature identifies four dominant themes: task-specific fragmented AI tools, the transition from single-agent to multi-agent systems, limited cross-functional integration, and insufficient focus on inclusivity and accessibility. Findings reveal a clear gap between current AI implementations and the needs of holistic, learner-centered educational ecosystem. The paper synthesizes challenges and outlines future research directions for scalable human-aligned, and inclusive agentic AI platform. The significant contribution is the incorporation of inclusive learning perspectives, highlighting how coordinated agentic multi-agent platform can support diverse learners through adaptive, multimodal interventions.

GPU kernels are critical for ML performance but difficult to optimize across diverse accelerators. We present KForge, a platform-agnostic framework built on two collaborative LLM-based agents: a generation agent that produces and iteratively refines programs through compilation and correctness feedback, and a performance analysis agent that interprets profiling data to guide optimization. This agent-based architecture requires only a single-shot example to target new platforms. We make three key contributions: (1) introducing an iterative refinement system where the generation agent and performance analysis agent collaborate through functional and optimization passes, interpreting diverse profiling data (from programmatic APIs to GUI-based tools) to generate actionable recommendations that guide program synthesis for arbitrary accelerators; (2) demonstrating that the generation agent effectively leverages cross-platform knowledge transfer, where a reference implementation from one architecture substantially improves generation quality for different hardware targets; and (3) validating the platform-agnostic nature of our approach by demonstrating effective program synthesis across fundamentally different parallel computing platforms: NVIDIA CUDA and Apple Metal.

Prompts are the interface for eliciting the capabilities of large language models (LLMs). Understanding their structure and components is critical for analyzing LLM behavior and optimizing performance. However, the field lacks a comprehensive framework for systematic prompt analysis and understanding. We introduce PromptPrism, a linguistically-inspired taxonomy that enables prompt analysis across three hierarchical levels: functional structure, semantic component, and syntactic pattern. We show the practical utility of PromptPrism by applying it to three applications: (1) a taxonomy-guided prompt refinement approach that automatically improves prompt quality and enhances model performance across a range of tasks; (2) a multi-dimensional dataset profiling method that extracts and aggregates structural, semantic, and syntactic characteristics from prompt datasets, enabling comprehensive analysis of prompt distributions and patterns; (3) a controlled experimental framework for prompt sensitivity analysis by quantifying the impact of semantic reordering and delimiter modifications on LLM performance. Our experimental results validate the effectiveness of our taxonomy across these applications, demonstrating that PromptPrism provides a foundation for refining, profiling, and analyzing prompts.

We introduce Brain-JEPA, a brain dynamics foundation model with the Joint-Embedding Predictive Architecture (JEPA). This pioneering model achieves state-of-the-art performance in demographic prediction, disease diagnosis/prognosis, and trait prediction through fine-tuning. Furthermore, it excels in off-the-shelf evaluations (e.g., linear probing) and demonstrates superior generalizability across different ethnic groups, surpassing the previous large model for brain activity significantly. Brain-JEPA incorporates two innovative techniques: Brain Gradient Positioning and Spatiotemporal Masking. Brain Gradient Positioning introduces a functional coordinate system for brain functional parcellation, enhancing the positional encoding of different Regions of Interest (ROIs). Spatiotemporal Masking, tailored to the unique characteristics of fMRI data, addresses the challenge of heterogeneous time-series patches. These methodologies enhance model performance and advance our understanding of the neural circuits underlying cognition. Overall, Brain-JEPA is paving the way to address pivotal questions of building brain functional coordinate system and masking brain activity at the AI-neuroscience interface, and setting a potentially new paradigm in brain activity analysis through downstream adaptation.

Deep residual architectures, such as ResNet and the Transformer, have enabled models of unprecedented depth, yet a formal understanding of why depth is so effective remains an open question. A popular intuition, following Veit et al. (2016), is that these residual networks behave like ensembles of many shallower models. Our key finding is an explicit analytical formula that verifies this ensemble perspective, proving that increasing network depth is mathematically equivalent to expanding the size of this implicit ensemble. Furthermore, our expansion reveals a hierarchical ensemble structure in which the combinatorial growth of computation paths leads to an explosion in the output signal, explaining the historical necessity of normalization layers in training deep models. This insight offers a first principles explanation for the historical dependence on normalization layers and sheds new light on a family of successful normalization-free techniques like SkipInit and Fixup. However, while these previous approaches infer scaling factors through optimizer analysis or a heuristic analogy to Batch Normalization, our work offers the first explanation derived directly from the network's inherent functional structure. Specifically, our Residual Expansion Theorem reveals that scaling each residual module provides a principled solution to taming the combinatorial explosion inherent to these architectures. We further show that this scaling acts as a capacity controls that also implicitly regularizes the model's complexity.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Instruction tuning has recently been recognized as an effective way of aligning Large Language Models (LLMs) to enhance their generalization ability across various tasks. However, when tuning publicly accessible, centralized LLMs with private instruction data, privacy concerns are inevitable. While direct transfer of parameterized modules between models is a plausible approach to address this, its implications and effectiveness need further exploration. This paper focuses on Offsite-Tuning (OFT), a representative technique that transfers transformer blocks between centralized LLMs and downstream emulators. Given the limited understanding of the underlying mechanism of OFT, we perform an empirical analysis on LLMs from the perspectives of representation and functional similarity. Interestingly, our findings reveal a unique modular structure within the layers of LLMs that appears to emerge as the model size expands. Simultaneously, we note subtle but potentially significant changes in representation and intermediate predictions across the layers. Inspired by these observations, we propose CRaSh, involving Clustering, Removing, and Sharing, a training-free strategy to derive improved emulators from LLMs. CRaSh significantly boosts performance of OFT with billions of parameters. Furthermore, we investigate the optimal solutions yielded by fine-tuning with and without full model through the lens of loss landscape. Our findings demonstrate a linear connectivity among these optima falling over the same basin, thereby highlighting the effectiveness of CRaSh and OFT. The source code is publicly available at https://github.com/TsinghuaC3I/CRaSh.

Rust's compile-time safety guarantees make it ideal for safety-critical systems, creating demand for translating legacy C codebases to Rust. While various approaches have emerged for this task, they face inherent trade-offs: rule-based solutions face challenges in meeting code safety and idiomaticity requirements, while LLM-based solutions often fail to generate semantically equivalent Rust code, due to the heavy dependencies of modules across the entire codebase. Recent studies have revealed that both solutions are limited to small-scale programs. In this paper, we propose EvoC2Rust, an automated framework for converting entire C projects to equivalent Rust ones. EvoC2Rust employs a skeleton-guided translation strategy for project-level translation. The pipeline consists of three evolutionary stages: 1) it first decomposes the C project into functional modules, employs a feature-mapping-enhanced LLM to transform definitions and macros and generates type-checked function stubs, which form a compilable Rust skeleton; 2) it then incrementally translates the function, replacing the corresponding stub placeholder; 3) finally, it repairs compilation errors by integrating LLM and static analysis. Through evolutionary augmentation, EvoC2Rust combines the advantages of both rule-based and LLM-based solutions. Our evaluation on open-source benchmarks and six industrial projects demonstrates EvoC2Rust's superior performance in project-level C-to-Rust translation. On average, it achieves 17.24% and 14.32% improvements in syntax and semantic accuracy over the LLM-based approaches, along with a 96.79% higher code safety rate than the rule-based tools. At the module level, EvoC2Rust reaches 92.25% compilation and 89.53% test pass rates on industrial projects, even for complex codebases and long functions.

Large language models increasingly expose reasoning traces, yet their underlying cognitive structure and steps remain difficult to identify and analyze beyond surface-level statistics. We adopt Schoenfeld's Episode Theory as an inductive, intermediate-scale lens and introduce ThinkARM (Anatomy of Reasoning in Models), a scalable framework that explicitly abstracts reasoning traces into functional reasoning steps such as Analysis, Explore, Implement, Verify, etc. When applied to mathematical problem solving by diverse models, this abstraction reveals reproducible thinking dynamics and structural differences between reasoning and non-reasoning models, which are not apparent from token-level views. We further present two diagnostic case studies showing that exploration functions as a critical branching step associated with correctness, and that efficiency-oriented methods selectively suppress evaluative feedback steps rather than uniformly shortening responses. Together, our results demonstrate that episode-level representations make reasoning steps explicit, enabling systematic analysis of how reasoning is structured, stabilized, and altered in modern language models.

Unlike human-engineered systems such as aeroplanes, where each component's role and dependencies are well understood, the inner workings of AI models remain largely opaque, hindering verifiability and undermining trust. This paper introduces SemanticLens, a universal explanation method for neural networks that maps hidden knowledge encoded by components (e.g., individual neurons) into the semantically structured, multimodal space of a foundation model such as CLIP. In this space, unique operations become possible, including (i) textual search to identify neurons encoding specific concepts, (ii) systematic analysis and comparison of model representations, (iii) automated labelling of neurons and explanation of their functional roles, and (iv) audits to validate decision-making against requirements. Fully scalable and operating without human input, SemanticLens is shown to be effective for debugging and validation, summarizing model knowledge, aligning reasoning with expectations (e.g., adherence to the ABCDE-rule in melanoma classification), and detecting components tied to spurious correlations and their associated training data. By enabling component-level understanding and validation, the proposed approach helps bridge the "trust gap" between AI models and traditional engineered systems. We provide code for SemanticLens on https://github.com/jim-berend/semanticlens and a demo on https://semanticlens.hhi-research-insights.eu.

In the field of urban planning, existing Vision-Language Models (VLMs) frequently fail to effectively analyze and evaluate planning maps, despite the critical importance of these visual elements for urban planners and related educational contexts. Planning maps, which visualize land use, infrastructure layouts, and functional zoning, require specialized understanding of spatial configurations, regulatory requirements, and multi-scale analysis. To address this challenge, we introduce PlanGPT-VL, the first domain-specific Vision-Language Model tailored specifically for urban planning maps. PlanGPT-VL employs three innovative approaches: (1) PlanAnno-V framework for high-quality VQA data synthesis, (2) Critical Point Thinking to reduce hallucinations through structured verification, and (3) comprehensive training methodology combining Supervised Fine-Tuning with frozen vision encoder parameters. Through systematic evaluation on our proposed PlanBench-V benchmark, we demonstrate that PlanGPT-VL significantly outperforms general-purpose state-of-the-art VLMs in specialized planning map interpretation tasks, offering urban planning professionals a reliable tool for map analysis, assessment, and educational applications while maintaining high factual accuracy. Our lightweight 7B parameter model achieves comparable performance to models exceeding 72B parameters, demonstrating efficient domain specialization without sacrificing performance.

Large language models routinely hallucinate APIs and mislocalize edits, while language servers compute verified, IDE-grade facts about real code. We present Lanser-CLI, a CLI-first orchestration layer that pins and mediates a Language Server Protocol (LSP) server for coding agents and CI, exposing deterministic, replayable workflows. Our position is that language servers provide not only structural information (definitions, references, types, diagnostics) but also an actionable process reward: machine-checked, step-wise signals that align an agent's planning loop with program reality. In this work, Lanser-CLI contributes: (i) a robust addressing scheme beyond brittle "file:line:col" via a Selector DSL (symbolic, AST-path, and content-anchored selectors) with a principled relocation algorithm; (ii) deterministic Analysis Bundles that normalize Language Server responses and capture environment/capability metadata with stable content hashes; (iii) a safety envelope for mutating operations (rename, code actions) with preview, workspace jails, and Git-aware, transactional apply; and (iv) a process-reward functional derived from Language Server facts (diagnostic deltas, disambiguation confidence, and safe-apply checks) that is computable online and replayable offline. We formalize determinism under frozen snapshots and establish a monotonicity property for the process reward, making it suitable for process supervision and counterfactual analysis. Project Page: https://github.com/yifanzhang-pro/lanser-cli

We introduce a new functional space U designed to contain all classical arithmetic functions (Mobius, von Mangoldt, Euler phi, divisor functions, Dirichlet characters, etc.). The norm of U combines a Hilbert-type component, based on square summability of Dirichlet coefficients for every s > 1, with a Banach component controlling logarithmic averages of partial sums. We prove that U is a complete Banach space which embeds continuously all standard Hilbert spaces of Dirichlet series and allows natural actions of Dirichlet convolution and shift operators. This framework provides a unified analytic setting for classical and modern problems in multiplicative number theory.

Visual encoding and decoding models act as gateways to understanding the neural mechanisms underlying human visual perception. Typically, visual encoding models that predict brain activity from stimuli and decoding models that reproduce stimuli from brain activity are treated as distinct tasks, requiring separate models and training procedures. This separation is inefficient and fails to model the consistency between encoding and decoding processes. To address this limitation, we propose NeuroFlow, the first unified framework that jointly models visual encoding and decoding from neural activity within a single flow model. NeuroFlow introduces two key components: (1) NeuroVAE is designed as a variational backbone to model neural variability and establish a compact, semantically structured latent space for bidirectional modeling across visual and neural modalities. (2) Cross-modal Flow Matching (XFM) bypasses the typical paradigm of noise-to-data diffusion guided by a specific modality condition, instead learning a reversibly consistent flow model between visual and neural latent distributions. For the first time, visual encoding and decoding are reformulated as a time-dependent, reversible process within a shared latent space for unified modeling. Empirical results demonstrate that NeuroFlow achieves superior overall performance in visual encoding and decoding tasks with higher computational efficiency compared to any isolated methods. We further analyze principal factors that steer the model toward encoding-decoding consistency and, through brain functional analyses, demonstrate that NeuroFlow captures consistent activation patterns underlying neural variability. NeuroFlow marks a major step toward unified visual encoding and decoding from neural activity, providing mechanistic insights that inform future bidirectional visual brain-computer interfaces.

Learning mappings between infinite-dimensional function spaces, or operator learning, is essential for many machine learning applications. Although transformer-based operators are popular, they often rely on token-wise attention. These methods treat continuous fields as discrete tokens and usually ignore the global functional structure. We introduce Functional Attention, which reinterprets attention as a functional correspondence between adaptive bases. Inspired by geometric functional maps, our method replaces softmax affinities with structured linear operators. This yields a compact, generalizable, resolution-invariant representation that explicitly captures global dependencies. Experiments demonstrate that Functional Attention can match state-of-the-art performance in many operator learning tasks, including solving PDEs, 3D segmentation, and regression, while remaining robust to varying discretizations. Project page is available at https://github.com/xjffff/FUNCATTN.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

Transformers, and the attention mechanism in particular, have become ubiquitous in machine learning. Their success in modeling nonlocal, long-range correlations has led to their widespread adoption in natural language processing, computer vision, and time series problems. Neural operators, which map spaces of functions into spaces of functions, are necessarily both nonlinear and nonlocal if they are universal; it is thus natural to ask whether the attention mechanism can be used in the design of neural operators. Motivated by this, we study transformers in the function space setting. We formulate attention as a map between infinite dimensional function spaces and prove that the attention mechanism as implemented in practice is a Monte Carlo or finite difference approximation of this operator. The function space formulation allows for the design of transformer neural operators, a class of architectures designed to learn mappings between function spaces. In this paper, we state and prove the first universal approximation result for transformer neural operators, using only a slight modification of the architecture implemented in practice. The prohibitive cost of applying the attention operator to functions defined on multi-dimensional domains leads to the need for more efficient attention-based architectures. For this reason we also introduce a function space generalization of the patching strategy from computer vision, and introduce a class of associated neural operators. Numerical results, on an array of operator learning problems, demonstrate the promise of our approaches to function space formulations of attention and their use in neural operators.

The Functional Machine Calculus (Heijltjes 2022) is a new approach to unifying the imperative and functional programming paradigms. It extends the lambda-calculus, preserving the key features of confluent reduction and typed termination, to embed computational effects, evaluation strategies, and control flow operations. The first instalment modelled sequential higher-order computation with global store, input/output, probabilities, and non-determinism, and embedded both the call-by-name and call-by-value lambda-calculus, as well as Moggi's computational metalanguage and Levy's call-by-push-value. The present paper extends the calculus from sequential to branching and looping control flow. This allows the faithful embedding of a minimal but complete imperative language, including conditionals, exception handling, and iteration, as well as constants and algebraic data types. The calculus is defined through a simple operational semantics, extending the (simplified) Krivine machine for the lambda-calculus with multiple operand stacks to model effects and a continuation stack to model sequential, branching, and looping computation. It features a confluent reduction relation and a system of simple types that guarantees termination of the machine and strong normalization of reduction (in the absence of iteration). These properties carry over to the embedded imperative language, providing a unified functional-imperative model of computation that supports simple types, a direct and intuitive operational semantics, and a confluent reduction semantics.

In this paper, we examine the solvability of a functional equation in a Lipschitz space. As an application, we use our result to determine the existence and uniqueness of solutions to an equation describing a specific type of choice behavior model for the learning process of the paradise fish. Finally, we present some concrete examples where, using numerical techniques, we obtain approximations to the solution of the functional equation. As the straightforward Picard's iteration can be very expensive, we show that an analytical suboptimal least-squares approximation can be chosen in practice, resulting in very good accuracy.

A wide range of scientific problems, such as those described by continuous-time dynamical systems and partial differential equations (PDEs), are naturally formulated on function spaces. While function spaces are typically infinite-dimensional, deep learning has predominantly advanced through applications in computer vision and natural language processing that focus on mappings between finite-dimensional spaces. Such fundamental disparities in the nature of the data have limited neural networks from achieving a comparable level of success in scientific applications as seen in other fields. Neural operators are a principled way to generalize neural networks to mappings between function spaces, offering a pathway to replicate deep learning's transformative impact on scientific problems. For instance, neural operators can learn solution operators for entire classes of PDEs, e.g., physical systems with different boundary conditions, coefficient functions, and geometries. A key factor in deep learning's success has been the careful engineering of neural architectures through extensive empirical testing. Translating these neural architectures into neural operators allows operator learning to enjoy these same empirical optimizations. However, prior neural operator architectures have often been introduced as standalone models, not directly derived as extensions of existing neural network architectures. In this paper, we identify and distill the key principles for constructing practical implementations of mappings between infinite-dimensional function spaces. Using these principles, we propose a recipe for converting several popular neural architectures into neural operators with minimal modifications. This paper aims to guide practitioners through this process and details the steps to make neural operators work in practice. Our code can be found at https://github.com/neuraloperator/NNs-to-NOs

Deep functional maps have recently emerged as a powerful tool for solving non-rigid shape correspondence tasks. Methods that use this approach combine the power and flexibility of the functional map framework, with data-driven learning for improved accuracy and generality. However, most existing methods in this area restrict the learning aspect only to the feature functions and still rely on axiomatic modeling for formulating the training loss or for functional map regularization inside the networks. This limits both the accuracy and the applicability of the resulting approaches only to scenarios where assumptions of the axiomatic models hold. In this work, we show, for the first time, that both in-network regularization and functional map training can be replaced with data-driven methods. For this, we first train a generative model of functional maps in the spectral domain using score-based generative modeling, built from a large collection of high-quality maps. We then exploit the resulting model to promote the structural properties of ground truth functional maps on new shape collections. Remarkably, we demonstrate that the learned models are category-agnostic, and can fully replace commonly used strategies such as enforcing Laplacian commutativity or orthogonality of functional maps. Our key technical contribution is a novel distillation strategy from diffusion models in the spectral domain. Experiments demonstrate that our learned regularization leads to better results than axiomatic approaches for zero-shot non-rigid shape matching. Our code is available at: https://github.com/daidedou/diffumatch/

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

The Functional Machine Calculus (Heijltjes 2022) is an extension of the lambda-calculus that preserves confluent reduction and typed termination, while enabling both call-by-name and call-by-value reduction behaviour and encoding the computational effects of mutable higher-order store, input/output, and probabilistic computation. In this note the calculus is extended to capture exception handling and loop constructs.

Unsupervised learning with functional data is an emerging paradigm of machine learning research with applications to computer vision, climate modeling and physical systems. A natural way of modeling functional data is by learning operators between infinite dimensional spaces, leading to discretization invariant representations that scale independently of the sample grid resolution. Here we present Variational Autoencoding Neural Operators (VANO), a general strategy for making a large class of operator learning architectures act as variational autoencoders. For this purpose, we provide a novel rigorous mathematical formulation of the variational objective in function spaces for training. VANO first maps an input function to a distribution over a latent space using a parametric encoder and then decodes a sample from the latent distribution to reconstruct the input, as in classic variational autoencoders. We test VANO with different model set-ups and architecture choices for a variety of benchmarks. We start from a simple Gaussian random field where we can analytically track what the model learns and progressively transition to more challenging benchmarks including modeling phase separation in Cahn-Hilliard systems and real world satellite data for measuring Earth surface deformation.

We propose a new class of generative diffusion models, called functional diffusion. In contrast to previous work, functional diffusion works on samples that are represented by functions with a continuous domain. Functional diffusion can be seen as an extension of classical diffusion models to an infinite-dimensional domain. Functional diffusion is very versatile as images, videos, audio, 3D shapes, deformations, \etc, can be handled by the same framework with minimal changes. In addition, functional diffusion is especially suited for irregular data or data defined in non-standard domains. In our work, we derive the necessary foundations for functional diffusion and propose a first implementation based on the transformer architecture. We show generative results on complicated signed distance functions and deformation functions defined on 3D surfaces.

This paper presents the Functional Machine Calculus (FMC) as a simple model of higher-order computation with "reader/writer" effects: higher-order mutable store, input/output, and probabilistic and non-deterministic computation. The FMC derives from the lambda-calculus by taking the standard operational perspective of a call-by-name stack machine as primary, and introducing two natural generalizations. One, "locations", introduces multiple stacks, which each may represent an effect and so enable effect operators to be encoded into the abstraction and application constructs of the calculus. The second, "sequencing", is known from kappa-calculus and concatenative programming languages, and introduces the imperative notions of "skip" and "sequence". This enables the encoding of reduction strategies, including call-by-value lambda-calculus and monadic constructs. The encoding of effects into generalized abstraction and application means that standard results from the lambda-calculus may carry over to effects. The main result is confluence, which is possible because encoded effects reduce algebraically rather than operationally. Reduction generates the familiar algebraic laws for state, and unlike in the monadic setting, reader/writer effects combine seamlessly. A system of simple types confers termination of the machine.

Functional data play a pivotal role across science and engineering, yet their infinite-dimensional nature makes representation learning challenging. Conventional statistical models depend on pre-chosen basis expansions or kernels, limiting the flexibility of data-driven discovery, while many deep-learning pipelines treat functions as fixed-grid vectors, ignoring inherent continuity. In this paper, we introduce Functional Attention with a Mixture-of-Experts (FAME), an end-to-end, fully data-driven framework for function-on-function regression. FAME forms continuous attention by coupling a bidirectional neural controlled differential equation with MoE-driven vector fields to capture intra-functional continuity, and further fuses change to inter-functional dependencies via multi-head cross attention. Extensive experiments on synthetic and real-world functional-regression benchmarks show that FAME achieves state-of-the-art accuracy, strong robustness to arbitrarily sampled discrete observations of functions.

We consider the problem of approximating a function from L^2 by an element of a given m-dimensional space V_m, associated with some feature map varphi, using evaluations of the function at random points x_1,dots,x_n. After recalling some results on optimal weighted least-squares using independent and identically distributed points, we consider weighted least-squares using projection determinantal point processes (DPP) or volume sampling. These distributions introduce dependence between the points that promotes diversity in the selected features varphi(x_i). We first provide a generalized version of volume-rescaled sampling yielding quasi-optimality results in expectation with a number of samples n = O(mlog(m)), that means that the expected L^2 error is bounded by a constant times the best approximation error in L^2. Also, further assuming that the function is in some normed vector space H continuously embedded in L^2, we further prove that the approximation is almost surely bounded by the best approximation error measured in the H-norm. This includes the cases of functions from L^infty or reproducing kernel Hilbert spaces. Finally, we present an alternative strategy consisting in using independent repetitions of projection DPP (or volume sampling), yielding similar error bounds as with i.i.d. or volume sampling, but in practice with a much lower number of samples. Numerical experiments illustrate the performance of the different strategies.