pwc-archive/papers-with-abstracts huggingface dataset:
CoRet: Improved Retriever for Code Editing
Authors: Fabio Fehr, Prabhu Teja Sivaprasad, Luca Franceschi, Giovanni Zappella
Date: 2025-05-30 00:00:00
Tasks: Natural Language Queries, Retrieval

In this paper, we introduce CoRet, a dense retrieval model designed for code-editing tasks that integrates code semantics, repository structure, and call graph dependencies. The model focuses on retrieving relevant portions of a code repository based on natural language queries such as requests to implement new features or fix bugs. These retrieved code chunks can then be presented to a user or to a second code-editing model or agent. To train CoRet, we propose a loss function explicitly designed for repository-level retrieval. On SWE-bench and Long Code Arena's bug localisation datasets, we show that our model substantially improves retrieval recall by at least 15 percentage points over existing models, and ablate the design choices to show their importance in achieving these results.
HELM: Hyperbolic Large Language Models via Mixture-of-Curvature Experts
Authors: Neil He, Rishabh Anand, Hiren Madhu, Ali Maatouk, Smita Krishnaswamy, Leandros Tassiulas, Menglin Yang, Rex Ying
Date: 2025-05-30 00:00:00
Tasks: ARC, General Knowledge, MMLU

Large language models (LLMs) have shown great success in text modeling tasks across domains. However, natural language exhibits inherent semantic hierarchies and nuanced geometric structure, which current LLMs do not capture completely owing to their reliance on Euclidean operations. Recent studies have also shown that not respecting the geometry of token embeddings leads to training instabilities and degradation of generative capabilities. These findings suggest that shifting to non-Euclidean geometries can better align language models with the underlying geometry of text. We thus propose to operate fully in Hyperbolic space, known for its expansive, scale-free, and low-distortion properties. We thus introduce HELM, a family of HypErbolic Large Language Models, offering a geometric rethinking of the Transformer-based LLM that addresses the representational inflexibility, missing set of necessary operations, and poor scalability of existing hyperbolic LMs. We additionally introduce a Mixture-of-Curvature Experts model, HELM-MICE, where each expert operates in a distinct curvature space to encode more fine-grained geometric structure from text, as well as a dense model, HELM-D. For HELM-MICE, we further develop hyperbolic Multi-Head Latent Attention (HMLA) for efficient, reduced-KV-cache training and inference. For both models, we develop essential hyperbolic equivalents of rotary positional encodings and RMS normalization. We are the first to train fully hyperbolic LLMs at billion-parameter scale, and evaluate them on well-known benchmarks such as MMLU and ARC, spanning STEM problem-solving, general knowledge, and commonsense reasoning. Our results show consistent gains from our HELM architectures -- up to 4% -- over popular Euclidean architectures used in LLaMA and DeepSeek, highlighting the efficacy and enhanced reasoning afforded by hyperbolic geometry in large-scale LM pretraining.
Don't Reinvent the Wheel: Efficient Instruction-Following Text Embedding based on Guided Space Transformation
Authors: Yingchaojie Feng, Yiqun Sun, Yandong Sun, Minfeng Zhu, Qiang Huang, Anthony K. H. Tung, Wei Chen
Date: 2025-05-30 00:00:00
Tasks: Instruction Following

In this work, we investigate an important task named instruction-following text embedding, which generates dynamic text embeddings that adapt to user instructions, highlighting specific attributes of text. Despite recent advancements, existing approaches suffer from significant computational overhead, as they require re-encoding the entire corpus for each new instruction. To address this challenge, we propose GSTransform, a novel instruction-following text embedding framework based on Guided Space Transformation. Our key observation is that instruction-relevant information is inherently encoded in generic embeddings but remains underutilized. Instead of repeatedly encoding the corpus for each instruction, GSTransform is a lightweight transformation mechanism that adapts pre-computed embeddings in real time to align with user instructions, guided by a small amount of text data with instruction-focused label annotation. We conduct extensive experiments on three instruction-awareness downstream tasks across nine real-world datasets, demonstrating that GSTransform improves instruction-following text embedding quality over state-of-the-art methods while achieving dramatic speedups of 6~300x in real-time processing on large-scale datasets. The source code is available at https://github.com/YingchaojieFeng/GSTransform.
Unsupervised Evolutionary Cell Type Matching via Entropy-Minimized Optimal Transport
Authors: Mu Qiao
Date: 2025-05-30 00:00:00

Identifying evolutionary correspondences between cell types across species is a fundamental challenge in comparative genomics and evolutionary biology. Existing approaches often rely on either reference-based matching, which imposes asymmetry by designating one species as the reference, or projection-based matching, which may increase computational complexity and obscure biological interpretability at the cell-type level. Here, we present OT-MESH, an unsupervised computational framework leveraging entropy-regularized optimal transport (OT) to systematically determine cross-species cell type homologies. Our method uniquely integrates the Minimize Entropy of Sinkhorn (MESH) technique to refine the OT plan. It begins by selecting genes with high Signal-to-Noise Ratio (SNR) to capture the most informative features, from which a cost matrix is constructed using cosine distances between cell-type centroids. Importantly, the MESH procedure iteratively refines the cost matrix, leading to a transport plan with significantly enhanced sparsity and interpretability of the resulting correspondence matrices. Applied to retinal bipolar cells (BCs) and retinal ganglion cells (RGCs) from mouse and macaque, OT-MESH accurately recovers known evolutionary relationships and uncovers novel correspondences, one of which was independently validated experimentally. Thus, our framework offers a principled, scalable, symmetric, and interpretable solution for evolutionary cell type mapping, facilitating deeper insights into cellular specialization and conservation across species.
REASONING GYM: Reasoning Environments for Reinforcement Learning with Verifiable Rewards
Authors: Zafir Stojanovski, Oliver Stanley, Joe Sharratt, Richard Jones, Abdulhakeem Adefioye, Jean Kaddour, Andreas Köpf
Date: 2025-05-30 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning

We introduce Reasoning Gym (RG), a library of reasoning environments for reinforcement learning with verifiable rewards. It provides over 100 data generators and verifiers spanning multiple domains including algebra, arithmetic, computation, cognition, geometry, graph theory, logic, and various common games. Its key innovation is the ability to generate virtually infinite training data with adjustable complexity, unlike most previous reasoning datasets, which are typically fixed. This procedural generation approach allows for continuous evaluation across varying difficulty levels. Our experimental results demonstrate the efficacy of RG in both evaluating and reinforcement learning of reasoning models.
Supervised Quantum Machine Learning: A Future Outlook from Qubits to Enterprise Applications
Authors: Srikanth Thudumu, Jason Fisher, Hung Du
Date: 2025-05-30 00:00:00
Tasks: Quantum Machine Learning

Supervised Quantum Machine Learning (QML) represents an intersection of quantum computing and classical machine learning, aiming to use quantum resources to support model training and inference. This paper reviews recent developments in supervised QML, focusing on methods such as variational quantum circuits, quantum neural networks, and quantum kernel methods, along with hybrid quantum-classical workflows. We examine recent experimental studies that show partial indications of quantum advantage and describe current limitations including noise, barren plateaus, scalability issues, and the lack of formal proofs of performance improvement over classical methods. The main contribution is a ten-year outlook (2025-2035) that outlines possible developments in supervised QML, including a roadmap describing conditions under which QML may be used in applied research and enterprise systems over the next decade.
A survey of using EHR as real-world evidence for discovering and validating new drug indications
Authors: Nabasmita Talukdar, Xiaodan Zhang, Shreya Paithankar, Hui Wang, Bin Chen
Date: 2025-05-30 00:00:00

Electronic Health Records (EHRs) have been increasingly used as real-world evidence (RWE) to support the discovery and validation of new drug indications. This paper surveys current approaches to EHR-based drug repurposing, covering data sources, processing methodologies, and representation techniques. It discusses study designs and statistical frameworks for evaluating drug efficacy. Key challenges in validation are discussed, with emphasis on the role of large language models (LLMs) and target trial emulation. By synthesizing recent developments and methodological advances, this work provides a foundational resource for researchers aiming to translate real-world data into actionable drug-repurposing evidence.
Drop Dropout on Single-Epoch Language Model Pretraining
Authors: Houjun Liu, John Bauer, Christopher D. Manning
Date: 2025-05-30 00:00:00
Tasks: Language Modeling, Language Modelling, Model Editing, Natural Language Inference, Question Answering

Originally, dropout was seen as a breakthrough regularization technique that reduced overfitting and improved performance in almost all applications of deep learning by reducing overfitting. Yet, single-epoch pretraining tasks common to modern LLMs yield minimal overfitting, leading to dropout not being used for large LLMs. Nevertheless, no thorough empirical investigation has been done on the role of dropout in LM pretraining. Through experiments in single-epoch pretraining of both masked (BERT) and autoregressive (Pythia 160M and 1.4B) LMs with varying levels of dropout, we find that downstream performance in language modeling, morpho-syntax (BLiMP), question answering (SQuAD), and natural-language inference (MNLI) improves when dropout is not applied during pretraining. We additionally find that the recently-introduced "early dropout" also degrades performance over applying no dropout at all. We further investigate the models' editability, and find that models trained without dropout are more successful in gradient-based model editing (MEND) and equivalent in representation-based model editing (ReFT). Therefore, we advocate to drop dropout during single-epoch pretraining.
Inference Acceleration of Autoregressive Normalizing Flows by Selective Jacobi Decoding
Authors: Jiaru Zhang, Juanwu Lu, Ziran Wang, Ruqi Zhang
Date: 2025-05-30 00:00:00

Normalizing flows are promising generative models with advantages such as theoretical rigor, analytical log-likelihood computation, and end-to-end training. However, the architectural constraints to ensure invertibility and tractable Jacobian computation limit their expressive power and practical usability. Recent advancements utilize autoregressive modeling, significantly enhancing expressive power and generation quality. However, such sequential modeling inherently restricts parallel computation during inference, leading to slow generation that impedes practical deployment. In this paper, we first identify that strict sequential dependency in inference is unnecessary to generate high-quality samples. We observe that patches in sequential modeling can also be approximated without strictly conditioning on all preceding patches. Moreover, the models tend to exhibit low dependency redundancy in the initial layer and higher redundancy in subsequent layers. Leveraging these observations, we propose a selective Jacobi decoding (SeJD) strategy that accelerates autoregressive inference through parallel iterative optimization. Theoretical analyses demonstrate the method's superlinear convergence rate and guarantee that the number of iterations required is no greater than the original sequential approach. Empirical evaluations across multiple datasets validate the generality and effectiveness of our acceleration technique. Experiments demonstrate substantial speed improvements up to 4.7 times faster inference while keeping the generation quality and fidelity.
PhySense: Principle-Based Physics Reasoning Benchmarking for Large Language Models
Authors: Yinggan Xu, Yue Liu, Zhiqiang Gao, Changnan Peng, Di Luo
Date: 2025-05-30 00:00:00
Tasks: Benchmarking

Large language models (LLMs) have rapidly advanced and are increasingly capable of tackling complex scientific problems, including those in physics. Despite this progress, current LLMs often fail to emulate the concise, principle-based reasoning characteristic of human experts, instead generating lengthy and opaque solutions. This discrepancy highlights a crucial gap in their ability to apply core physical principles for efficient and interpretable problem solving. To systematically investigate this limitation, we introduce PhySense, a novel principle-based physics reasoning benchmark designed to be easily solvable by experts using guiding principles, yet deceptively difficult for LLMs without principle-first reasoning. Our evaluation across multiple state-of-the-art LLMs and prompt types reveals a consistent failure to align with expert-like reasoning paths, providing insights for developing AI systems with efficient, robust and interpretable principle-based scientific reasoning.
Improving Reliability and Explainability of Medical Question Answering through Atomic Fact Checking in Retrieval-Augmented LLMs
Authors: Juraj Vladika, Annika Domres, Mai Nguyen, Rebecca Moser, Jana Nano, Felix Busch, Lisa C. Adams, Keno K. Bressem, Denise Bernhardt, Stephanie E. Combs, Kai J. Borm, Florian Matthes, Jan C. Peeken
Date: 2025-05-30 00:00:00
Tasks: Fact Checking, Hallucination, Long Form Question Answering, Medical Question Answering, Question Answering, Retrieval-augmented Generation

Large language models (LLMs) exhibit extensive medical knowledge but are prone to hallucinations and inaccurate citations, which pose a challenge to their clinical adoption and regulatory compliance. Current methods, such as Retrieval Augmented Generation, partially address these issues by grounding answers in source documents, but hallucinations and low fact-level explainability persist. In this work, we introduce a novel atomic fact-checking framework designed to enhance the reliability and explainability of LLMs used in medical long-form question answering. This method decomposes LLM-generated responses into discrete, verifiable units called atomic facts, each of which is independently verified against an authoritative knowledge base of medical guidelines. This approach enables targeted correction of errors and direct tracing to source literature, thereby improving the factual accuracy and explainability of medical Q&A. Extensive evaluation using multi-reader assessments by medical experts and an automated open Q&A benchmark demonstrated significant improvements in factual accuracy and explainability. Our framework achieved up to a 40% overall answer improvement and a 50% hallucination detection rate. The ability to trace each atomic fact back to the most relevant chunks from the database provides a granular, transparent explanation of the generated responses, addressing a major gap in current medical AI applications. This work represents a crucial step towards more trustworthy and reliable clinical applications of LLMs, addressing key prerequisites for clinical application and fostering greater confidence in AI-assisted healthcare.
VideoCAD: A Large-Scale Video Dataset for Learning UI Interactions and 3D Reasoning from CAD Software
Authors: Brandon Man, Ghadi Nehme, Md Ferdous Alam, Faez Ahmed
Date: 2025-05-30 00:00:00
Tasks: Question Answering, Spatial Reasoning, Video Understanding, Visual Question Answering, Visual Question Answering (VQA)

Computer-Aided Design (CAD) is a time-consuming and complex process, requiring precise, long-horizon user interactions with intricate 3D interfaces. While recent advances in AI-driven user interface (UI) agents show promise, most existing datasets and methods focus on short, low-complexity tasks in mobile or web applications, failing to capture the demands of professional engineering tools. In this work, we introduce VideoCAD, the first attempt at engineering UI interaction learning for precision tasks. Specifically, VideoCAD is a large-scale synthetic dataset consisting of over 41K annotated video recordings of CAD operations, generated using an automated framework for collecting high-fidelity UI action data from human-made CAD designs. Compared to existing datasets, VideoCAD offers an order of magnitude higher complexity in UI interaction learning for real-world engineering tasks, having up to a 20x longer time horizon than other datasets. We show two important downstream applications of VideoCAD: learning UI interactions from professional precision 3D CAD tools and a visual question-answering (VQA) benchmark designed to evaluate multimodal large language models' (LLM) spatial reasoning and video understanding abilities. To learn the UI interactions, we propose VideoCADFormer - a state-of-the-art model in learning CAD interactions directly from video, which outperforms multiple behavior cloning baselines. Both VideoCADFormer and the VQA benchmark derived from VideoCAD reveal key challenges in the current state of video-based UI understanding, including the need for precise action grounding, multi-modal and spatial reasoning, and long-horizon dependencies.
Vision LLMs Are Bad at Hierarchical Visual Understanding, and LLMs Are the Bottleneck
Authors: Yuwen Tan, Yuan Qing, Boqing Gong
Date: 2025-05-30 00:00:00
Tasks: Question Answering, Visual Question Answering, Visual Question Answering (VQA)

This paper reveals that many state-of-the-art large language models (LLMs) lack hierarchical knowledge about our visual world, unaware of even well-established biology taxonomies. This shortcoming makes LLMs a bottleneck for vision LLMs' hierarchical visual understanding (e.g., recognizing Anemone Fish but not Vertebrate). We arrive at these findings using about one million four-choice visual question answering (VQA) tasks constructed from six taxonomies and four image datasets. Interestingly, finetuning a vision LLM using our VQA tasks reaffirms LLMs' bottleneck effect to some extent because the VQA tasks improve the LLM's hierarchical consistency more than the vision LLM's. We conjecture that one cannot make vision LLMs understand visual concepts fully hierarchical until LLMs possess corresponding taxonomy knowledge.
Harnessing Negative Signals: Reinforcement Distillation from Teacher Data for LLM Reasoning
Authors: Shuyao Xu, Cheng Peng, Jiangxuan Long, Weidi Xu, Wei Chu, Yuan Qi
Date: 2025-05-30 00:00:00
Tasks: Math, Mathematical Reasoning

Recent advances in model distillation demonstrate that data from advanced reasoning models (e.g., DeepSeek-R1, OpenAI's o1) can effectively transfer complex reasoning abilities to smaller, efficient student models. However, standard practices employ rejection sampling, discarding incorrect reasoning examples -- valuable, yet often underutilized data. This paper addresses the critical question: How can both positive and negative distilled reasoning traces be effectively leveraged to maximize LLM reasoning performance in an offline setting? To this end, We propose Reinforcement Distillation (REDI), a two-stage framework. Stage 1 learns from positive traces via Supervised Fine-Tuning (SFT). Stage 2 further refines the model using both positive and negative traces through our proposed REDI objective. This novel objective is a simple, reference-free loss function that outperforms established methods like DPO and SimPO in this distillation context. Our empirical evaluations demonstrate REDI's superiority over baseline Rejection Sampling SFT or SFT combined with DPO/SimPO on mathematical reasoning tasks. Notably, the Qwen-REDI-1.5B model, post-trained on just 131k positive and negative examples from the open Open-R1 dataset, achieves an 83.1% score on MATH-500 (pass@1). Its performance matches or surpasses that of DeepSeek-R1-Distill-Qwen-1.5B (a model post-trained on 800k proprietary data) across various mathematical reasoning benchmarks, establishing a new state-of-the-art for 1.5B models post-trained offline with openly available data.
ProRL: Prolonged Reinforcement Learning Expands Reasoning Boundaries in Large Language Models
Authors: Mingjie Liu, Shizhe Diao, Ximing Lu, Jian Hu, Xin Dong, Yejin Choi, Jan Kautz, Yi Dong
Date: 2025-05-30 00:00:00
Tasks: Reinforcement Learning (RL)

Recent advances in reasoning-centric language models have highlighted reinforcement learning (RL) as a promising method for aligning models with verifiable rewards. However, it remains contentious whether RL truly expands a model's reasoning capabilities or merely amplifies high-reward outputs already latent in the base model's distribution, and whether continually scaling up RL compute reliably leads to improved reasoning performance. In this work, we challenge prevailing assumptions by demonstrating that prolonged RL (ProRL) training can uncover novel reasoning strategies that are inaccessible to base models, even under extensive sampling. We introduce ProRL, a novel training methodology that incorporates KL divergence control, reference policy resetting, and a diverse suite of tasks. Our empirical analysis reveals that RL-trained models consistently outperform base models across a wide range of pass@k evaluations, including scenarios where base models fail entirely regardless of the number of attempts. We further show that reasoning boundary improvements correlates strongly with task competence of base model and training duration, suggesting that RL can explore and populate new regions of solution space over time. These findings offer new insights into the conditions under which RL meaningfully expands reasoning boundaries in language models and establish a foundation for future work on long-horizon RL for reasoning. We release model weights to support further research: https://huggingface.co/nvidia/Nemotron-Research-Reasoning-Qwen-1.5B
Time Blindness: Why Video-Language Models Can't See What Humans Can?
Authors: Ujjwal Upadhyay, Mukul Ranjan, Zhiqiang Shen, Mohamed Elhoseiny
Date: 2025-05-30 00:00:00
Tasks: Temporal Sequences, Video Understanding

Recent advances in vision-language models (VLMs) have made impressive strides in understanding spatio-temporal relationships in videos. However, when spatial information is obscured, these models struggle to capture purely temporal patterns. We introduce $\textbf{SpookyBench}$, a benchmark where information is encoded solely in temporal sequences of noise-like frames, mirroring natural phenomena from biological signaling to covert communication. Interestingly, while humans can recognize shapes, text, and patterns in these sequences with over 98% accuracy, state-of-the-art VLMs achieve 0% accuracy. This performance gap highlights a critical limitation: an over-reliance on frame-level spatial features and an inability to extract meaning from temporal cues. Furthermore, when trained in data sets with low spatial signal-to-noise ratios (SNR), temporal understanding of models degrades more rapidly than human perception, especially in tasks requiring fine-grained temporal reasoning. Overcoming this limitation will require novel architectures or training paradigms that decouple spatial dependencies from temporal processing. Our systematic analysis shows that this issue persists across model scales and architectures. We release SpookyBench to catalyze research in temporal pattern recognition and bridge the gap between human and machine video understanding. Dataset and code has been made available on our project website: https://timeblindness.github.io/.