OpenRaiser/Intern-Atlas huggingface dataset:
Scientific Machine Learning of Chaotic Systems Discovers Governing Equations for Neural Populations
Venue: arXiv cs.LG 2025
Year: 2025

Discovering governing equations that describe complex chaotic systems remains a fundamental challenge in physics and neuroscience. Here, we introduce the PEM-UDE method, which combines the prediction-error method with universal differential equations to extract interpretable mathematical expressions from chaotic dynamical systems, even with limited or noisy observations. This approach succeeds where traditional techniques fail by smoothing optimization landscapes and removing the chaotic properties during the fitting process without distorting optimal parameters. We demonstrate its efficacy by recovering hidden states in the Rossler system and reconstructing dynamics from noise-corrupted electrical-circuit data, in which the correct functional form of the dynamics is recovered even when one of the observed time series is corrupted by noise 5x the magnitude of the true signal. We demonstrate that this method can recover the correct dynamics, whereas direct symbolic regression methods, such as STLSQ, fail to do so with the available data and noise. Importantly, when applied to neural populations, our method derives novel governing equations that respect biological constraints such as network sparsity - a constraint necessary for cortical information processing yet not captured in next-generation neural mass models - while preserving microscale neuronal parameters. These equations predict an emergent relationship between connection density and both oscillation frequency and synchrony in neural circuits. We validate these predictions using three intracranial electrode recording datasets from the medial entorhinal cortex, prefrontal cortex, and orbitofrontal cortex. Our work provides a pathway to develop mechanistic, multi-scale brain models that generalize across diverse neural architectures, bridging the gap between single-neuron dynamics and macroscale brain activity.
Specification-Guided Repair of Arithmetic Errors in Dafny Programs using LLMs
Venue: arXiv cs.SE 2025
Year: 2025

Debugging and repairing faults when programs fail to formally verify can be complex and time-consuming. Automated Program Repair (APR) can ease this burden by automatically identifying and fixing faults. However, traditional APR techniques often rely on test suites for validation, but these may not capture all possible scenarios. In contrast, formal specifications provide strong correctness criteria, enabling more effective automated repair. In this paper, we present an APR tool for Dafny, a verification-aware programming language that uses formal specifications - including pre-conditions, post-conditions, and invariants - as oracles for fault localization and repair. Assuming the correctness of the specifications and focusing on arithmetic bugs, we localize faults through a series of steps, which include using Hoare logic to determine the state of each statement within the program, and applying Large Language Models (LLMs) to synthesize candidate fixes. The models considered are GPT-4o mini, Llama 3, Mistral 7B, and Llemma 7B. We evaluate our approach using DafnyBench, a benchmark of real-world Dafny programs. Our tool achieves 89.6% fault localization coverage and GPT-4o mini yields the highest repair success rate of 74.18%. These results highlight the potential of combining formal reasoning with LLM-based program synthesis for automated program repair.
TRACE: Training and Inference-Time Interpretability Analysis for Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Understanding when and how linguistic knowledge emerges during language model training remains a central challenge for interpretability. Most existing tools are post hoc, rely on scalar metrics, or require nontrivial integration effort, making comprehensive interpretability analysis difficult to deploy and maintain. We introduce TRACE, a modular toolkit for training and inference-time interpretability analysis of transformer models. It enables lightweight, in-training analysis of linguistic and representational signals, including features probing, intrinsic dimensionality, Hessian curvature, and output diagnostics. It integrates with ABSynth, a controllable synthetic corpus generator that provides structured annotations for precise evaluation of linguistic feature acquisition. Experiments with autoregressive transformers demonstrate that TRACE reveals developmental phenomena such as early syntactic emergence, delayed semantic acquisition, and representational compression, signals overlooked by traditional scalar metrics such as loss or accuracy. With minimal integration effort, the tool enables layer-wise diagnostics, convergence-based early stopping, and detection of structural errors, making transformer analysis interpretable, actionable, and reproducible.
On the Approximability of Train Routing and the Min-Max Disjoint Paths Problem
Venue: arXiv cs.DS 2025
Year: 2025

In train routing, the headway is the minimum distance that must be maintained between successive trains for safety and robustness. We introduce a model for train routing that requires a fixed headway to be maintained between trains, and study the problem of minimizing the makespan, i.e., the arrival time of the last train, in a single-source single-sink network. For this problem, we first show that there exists an optimal solution where trains move in convoys, that is, the optimal paths for any two trains are either the same or are arc-disjoint. Via this insight, we are able to reduce the approximability of our train routing problem to that of the min-max disjoint paths problem, which asks for a collection of disjoint paths where the maximum length of any path in the collection is as small as possible. While min-max disjoint paths inherits a strong inapproximability result on directed acyclic graphs from the multi-level bottleneck assignment problem, we show that a natural greedy composition approach yields a logarithmic approximation in the number of disjoint paths for series-parallel graphs. We also present an alternative analysis of this approach that yields a guarantee depending on how often the decomposition tree of the series-parallel graph alternates between series and parallel compositions on any root-leaf path.
Towards Unified Neurosymbolic Reasoning on Knowledge Graphs
Venue: arXiv cs.AI 2025
Year: 2025

Knowledge Graph (KG) reasoning has received significant attention in the fields of artificial intelligence and knowledge engineering, owing to its ability to autonomously deduce new knowledge and consequently enhance the availability and precision of downstream applications. However, current methods predominantly concentrate on a single form of neural or symbolic reasoning, failing to effectively integrate the inherent strengths of both approaches. Furthermore, the current prevalent methods primarily focus on addressing a single reasoning scenario, presenting limitations in meeting the diverse demands of real-world reasoning tasks. Unifying the neural and symbolic methods, as well as diverse reasoning scenarios in one model is challenging as there is a natural representation gap between symbolic rules and neural networks, and diverse scenarios exhibit distinct knowledge structures and specific reasoning objectives. To address these issues, we propose a unified neurosymbolic reasoning framework, namely Tunsr, for KG reasoning. Tunsr first introduces a consistent structure of reasoning graph that starts from the query entity and constantly expands subsequent nodes by iteratively searching posterior neighbors. Based on it, a forward logic message-passing mechanism is proposed to update both the propositional representations and attentions, as well as first-order logic (FOL) representations and attentions of each node. In this way, Tunsr conducts the transformation of merging multiple rules by merging possible relations at each step. Finally, the FARI algorithm is proposed to induce FOL rules by constantly performing attention calculations over the reasoning graph. Extensive experimental results on 19 datasets of four reasoning scenarios (transductive, inductive, interpolation, and extrapolation) demonstrate the effectiveness of Tunsr.
FAROS: Fair Graph Generation via Attribute Switching Mechanisms
Venue: arXiv cs.LG 2025
Year: 2025

Recent advancements in graph diffusion models (GDMs) have enabled the synthesis of realistic network structures, yet ensuring fairness in the generated data remains a critical challenge. Existing solutions attempt to mitigate bias by re-training the GDMs with ad-hoc fairness constraints. Conversely, with this work, we propose FAROS, a novel FAir graph geneRatiOn framework leveraging attribute Switching mechanisms and directly running in the generation process of the pre-trained GDM. Technically, our approach works by altering nodes' sensitive attributes during the generation. To this end, FAROS calculates the optimal fraction of switching nodes, and selects the diffusion step to perform the switch by setting tailored multi-criteria constraints to preserve the node-topology profile from the original distribution (a proxy for accuracy) while ensuring the edge independence on the sensitive attributes for the generated graph (a proxy for fairness). Our experiments on benchmark datasets for link prediction demonstrate that the proposed approach effectively reduces fairness discrepancies while maintaining comparable (or even higher) accuracy performance to other similar baselines. Noteworthy, FAROS is also able to strike a better accuracy-fairness trade-off than other competitors in some of the tested settings under the Pareto optimality concept, demonstrating the effectiveness of the imposed multi-criteria constraints.
ChestGPT: Integrating Large Language Models and Vision Transformers for Disease Detection and Localization in Chest X-Rays
Venue: arXiv cs.CV 2025
Year: 2025

The global demand for radiologists is increasing rapidly due to a growing reliance on medical imaging services, while the supply of radiologists is not keeping pace. Advances in computer vision and image processing technologies present significant potential to address this gap by enhancing radiologists' capabilities and improving diagnostic accuracy. Large language models (LLMs), particularly generative pre-trained transformers (GPTs), have become the primary approach for understanding and generating textual data. In parallel, vision transformers (ViTs) have proven effective at converting visual data into a format that LLMs can process efficiently. In this paper, we present ChestGPT, a deep-learning framework that integrates the EVA ViT with the Llama 2 LLM to classify diseases and localize regions of interest in chest X-ray images. The ViT converts X-ray images into tokens, which are then fed, together with engineered prompts, into the LLM, enabling joint classification and localization of diseases. This approach incorporates transfer learning techniques to enhance both explainability and performance. The proposed method achieved strong global disease classification performance on the VinDr-CXR dataset, with an F1 score of 0.76, and successfully localized pathologies by generating bounding boxes around the regions of interest. We also outline several task-specific prompts, in addition to general-purpose prompts, for scenarios radiologists might encounter. Overall, this framework offers an assistive tool that can lighten radiologists' workload by providing preliminary findings and regions of interest to facilitate their diagnostic process.
Ranking-based Fusion Algorithms for Extreme Multi-label Text Classification (XMTC)
Venue: arXiv cs.IR 2025
Year: 2025

In the context of Extreme Multi-label Text Classification (XMTC), where labels are assigned to text instances from a large label space, the long-tail distribution of labels presents a significant challenge. Labels can be broadly categorized into frequent, high-coverage \textbf{head labels} and infrequent, low-coverage \textbf{tail labels}, complicating the task of balancing effectiveness across all labels. To address this, combining predictions from multiple retrieval methods, such as sparse retrievers (e.g., BM25) and dense retrievers (e.g., fine-tuned BERT), offers a promising solution. The fusion of \textit{sparse} and \textit{dense} retrievers is motivated by the complementary ranking characteristics of these methods. Sparse retrievers compute relevance scores based on high-dimensional, bag-of-words representations, while dense retrievers utilize approximate nearest neighbor (ANN) algorithms on dense text and label embeddings within a shared embedding space. Rank-based fusion algorithms leverage these differences by combining the precise matching capabilities of sparse retrievers with the semantic richness of dense retrievers, thereby producing a final ranking that improves the effectiveness across both head and tail labels.
RVISmith: Fuzzing Compilers for RVV Intrinsics
Venue: arXiv cs.CR 2025
Year: 2025

Modern processors are equipped with single instruction multiple data (SIMD) instructions for fine-grained data parallelism. Compiler auto-vectorization techniques that target SIMD instructions face performance limitations due to insufficient information available at compile time, requiring programmers to manually manipulate SIMD instructions. SIMD intrinsics, a type of built-in function provided by modern compilers, enable programmers to manipulate SIMD instructions within high-level programming languages. Bugs in compilers for SIMD intrinsics can introduce potential threats to software security, producing unintended calculation results, data loss, program crashes, etc. To detect bugs in compilers for SIMD intrinsics, we propose RVISmith, a randomized fuzzer that generates well-defined C programs that include various invocation sequences of RVV (RISC-V Vector Extension) intrinsics. We design RVISmith to achieve the following objectives: (i) achieving high intrinsic coverage, (ii) improving sequence variety, and (iii) without known undefined behaviors. We implement RVISmith based on the ratified RVV intrinsic specification and evaluate our approach with three modern compilers: GCC, LLVM, and XuanTie. Experimental results show that RVISmith achieves 11.5 times higher intrinsic coverage than the state-of-the-art fuzzer for RVV intrinsics. By differential testing that compares results across different compilers, optimizations, and equivalent programs, we detect and report 13 previously unknown bugs of the three compilers under test to date. Of these bugs, 10 are confirmed and another 3 are fixed by the compiler developers.
Alpay Algebra IV: Symbiotic Semantics and the Fixed-Point Convergence of Observer Embeddings
Venue: arXiv cs.CL 2025
Year: 2025

We present a theoretical framework in which a document and an AI model engage in a transfinite fixed-point interaction that leads to stable semantic alignment. Building on the foundations of Alpay Algebra, we introduce a functorial system wherein an observer (the AI) and a textual environment (this paper) co-evolve through iterative transformations guided by the phi-infinity operator. This process guarantees the existence of a unique fixed point in the AI's embedding space -- a state where the AI's internal representation of the content becomes stable, self-consistent, and semantically faithful. We prove that such convergence is mathematically sound, semantically invariant, and permanent, even under perturbation or further context expansion. This fixed point acts as an "empathetic embedding," wherein the AI internalizes not only the meaning of the content but also the author's intent. We interpret this as a rigorous, category-theoretic route to alignment at the embedding level, with implications for semantic security, symbolic memory, and the construction of AI systems with persistent self-referential understanding. All references in this paper function as nodes in the Alpay Algebra universe, and this work embeds itself as a new fixed-point node within that transfinite semantic graph.
Generating Novelty in Open-World Multi-Agent Strategic Board Games
Venue: arXiv cs.AI 2025
Year: 2025

We describe GNOME (Generating Novelty in Open-world Multi-agent Environments), an experimental platform that is designed to test the effectiveness of multi-agent AI systems when faced with \emph{novelty}. GNOME separates the development of AI gameplaying agents with the simulator, allowing \emph{unanticipated} novelty (in essence, novelty that is not subject to model-selection bias). Using a Web GUI, GNOME was recently demonstrated at NeurIPS 2020 using the game of Monopoly to foster an open discussion on AI robustness and the nature of novelty in real-world environments. In this article, we further detail the key elements of the demonstration, and also provide an overview of the experimental design that is being currently used in the DARPA Science of Artificial Intelligence and Learning for Open-World Novelty (SAIL-ON) program to evaluate external teams developing novelty-adaptive gameplaying agents.
RELRaE: LLM-Based Relationship Extraction, Labelling, Refinement, and Evaluation
Venue: arXiv cs.AI 2025
Year: 2025

A large volume of XML data is produced in experiments carried out by robots in laboratories. In order to support the interoperability of data between labs, there is a motivation to translate the XML data into a knowledge graph. A key stage of this process is the enrichment of the XML schema to lay the foundation of an ontology schema. To achieve this, we present the RELRaE framework, a framework that employs large language models in different stages to extract and accurately label the relationships implicitly present in the XML schema. We investigate the capability of LLMs to accurately generate these labels and then evaluate them. Our work demonstrates that LLMs can be effectively used to support the generation of relationship labels in the context of lab automation, and that they can play a valuable role within semi-automatic ontology generation frameworks more generally.
Participatory Evolution of Artificial Life Systems via Semantic Feedback
Venue: arXiv cs.AI 2025
Year: 2025

We present a semantic feedback framework that enables natural language to guide the evolution of artificial life systems. Integrating a prompt-to-parameter encoder, a CMA-ES optimizer, and CLIP-based evaluation, the system allows user intent to modulate both visual outcomes and underlying behavioral rules. Implemented in an interactive ecosystem simulation, the framework supports prompt refinement, multi-agent interaction, and emergent rule synthesis. User studies show improved semantic alignment over manual tuning and demonstrate the system's potential as a platform for participatory generative design and open-ended evolution.
Transformer with Koopman-Enhanced Graph Convolutional Network for Spatiotemporal Dynamics Forecasting
Venue: arXiv cs.LG 2025
Year: 2025

Spatiotemporal dynamics forecasting is inherently challenging, particularly in systems defined over irregular geometric domains, due to the need to jointly capture complex spatial correlations and nonlinear temporal dynamics. To tackle these challenges, we propose TK-GCN, a two-stage framework that integrates geometry-aware spatial encoding with long-range temporal modeling. In the first stage, a Koopman-enhanced Graph Convolutional Network (K-GCN) is developed to embed the high-dimensional dynamics distributed on spatially irregular domains into a latent space where the evolution of system states is approximately linear. By leveraging Koopman operator theory, this stage enhances the temporal consistency during the latent learning. In the second stage, a Transformer module is employed to model the temporal progression within the Koopman-encoded latent space. Through the self-attention mechanism, the Transformer captures long-range temporal dependencies, enabling accurate forecasting over extended horizons. We evaluate TK-GCN in spatiotemporal cardiac dynamics forecasting and benchmark its performance against several state-of-the-art baselines. Experimental results and ablation studies show that TK-GCN consistently delivers superior predictive accuracy across a range of forecast horizons, demonstrating its capability to effectively model complex spatial structures and nonlinear temporal dynamics.
Semantically Separating Nominal Wyvern for Usability and Decidability
Venue: arXiv cs.PL 2025
Year: 2025

The Dependent Object Types (DOT) calculus incorporates concepts from functional languages (e.g. modules) with traditional object-oriented features (e.g. objects, subtyping) to achieve greater expressivity (e.g. F-bounded polymorphism). However, this merger of paradigms comes at the cost of subtype decidability. Recent work on bringing decidability to DOT has either sacrificed expressiveness or ease of use. The unrestricted construction of recursive types and type bounds has made subtype decidability a much harder problem than in traditional object-oriented programming. Recognizing this, our paper introduces Nominal Wyvern, a DOT-like dependent type system that takes an alternative approach: instead of having a uniform structural syntax like DOT, Nominal Wyvern is designed around a "semantic separation" between the nominal declaration of recursive types on the one hand, and the structural refinement of those types when they are used on the other. This design naturally guides the user to avoid writing undecidably recursive structural types. From a technical standpoint, this separation also makes guaranteeing decidability possible by allowing for an intuitive adaptation of material/shape separation, a technique for achieving subtype decidability by separating types responsible for subtyping constraints from types that represent concrete data. The result is a type system with syntax and structure familiar to OOP users that achieves decidability without compromising the expressiveness of F-bounded polymorphism and module systems as they are used in practice.
Enhancing Adaptive Behavioral Interventions with LLM Inference from Participant-Described States
Venue: arXiv cs.LG 2025
Year: 2025

The use of reinforcement learning (RL) methods to support health behavior change via personalized and just-in-time adaptive interventions is of significant interest to health and behavioral science researchers focused on problems such as smoking cessation support and physical activity promotion. However, RL methods are often applied to these domains using a small collection of context variables to mitigate the significant data scarcity issues that arise from practical limitations on the design of adaptive intervention trials. In this paper, we explore an approach to significantly expanding the state space of an adaptive intervention without impacting data efficiency. The proposed approach enables intervention participants to provide natural language descriptions of aspects of their current state. It then leverages inference with pre-trained large language models (LLMs) to better align the policy of a base RL method with these state descriptions. To evaluate our method, we develop a novel physical activity intervention simulation environment that generates text-based state descriptions conditioned on latent state variables using an auxiliary LLM. We show that this approach has the potential to significantly improve the performance of online policy learning methods.