arXiv subjects

Yuan Qi

Publications and source records attributed to Yuan Qi.

At least 55 records · Page 3Linked to original sources

arXiv2025

PET2Rep: Towards Vision-Language Model-Drived Automated Radiology Report Generation for Positron Emission Tomography

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficacy metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

eess.IV↗

arXiv2025

ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

q-bio.GN↗

arXiv2025

Count Counts: Motivating Exploration in LLM Reasoning with Count-based Intrinsic Rewards

Reinforcement Learning (RL) has become a compelling way to strengthen the multi step reasoning ability of Large Language Models (LLMs). However, prevalent RL paradigms still lean on sparse outcome-based rewards and limited exploration, which often drives LLMs toward repetitive and suboptimal reasoning patterns. In this paper, we study the central question of how to design exploration for LLM reasoning and introduce MERCI (Motivating Exploration in LLM Reasoning with Count-based Intrinsic Rewards), a novel RL algorithm that augments policy optimization with a principled intrinsic reward. Building on the idea of count-based exploration, MERCI leverages a lightweight Coin Flipping Network (CFN) to estimate the pseudo count and further epistemic uncertainty over reasoning trajectories, and converts them into an intrinsic reward that values novelty while preserving the learning signal from task rewards. We integrate MERCI into some advanced RL frameworks like Group Relative Policy Optimization (GRPO). Experiments on complex reasoning benchmarks demonstrate that MERCI encourages richer and more varied chains of thought, significantly improves performance over strong baselines, and helps the policy escape local routines to discover better solutions. It indicates that our targeted intrinsic motivation can make exploration reliable for language model reasoning.

cs.AI↗

arXiv2025

Infinity Parser: Layout Aware Reinforcement Learning for Scanned Document Parsing

Automated parsing of scanned documents into richly structured, machine-readable formats remains a critical bottleneck in Document AI, as traditional multi-stage pipelines suffer from error propagation and limited adaptability to diverse layouts. We introduce layoutRL, an end-to-end reinforcement learning framework that trains models to be explicitly layout-aware by optimizing a composite reward of normalized edit distance, paragraph count accuracy, and reading order preservation. Leveraging our newly released dataset, Infinity-Doc-55K, which combines 55K high-fidelity synthetic scanned document parsing data with expert-filtered real-world documents, we instantiate layoutRL in a vision-language-model-based parser called Infinity-Parser. Evaluated on English and Chinese benchmarks for OCR, table and formula extraction, and reading order detection, Infinity-Parser achieves new state-of-the-art performance in both accuracy and structural fidelity, outpacing specialist pipelines and general-purpose vision-language models. We will publicly release our code and dataset to accelerate progress in robust document understanding.

cs.CV↗

arXiv2025

Infinity Parser: Layout Aware Reinforcement Learning for Scanned Document Parsing

Document parsing from scanned images into structured formats remains a significant challenge due to its complexly intertwined elements such as text paragraphs, figures, formulas, and tables. Existing supervised fine-tuning methods often struggle to generalize across diverse document types, leading to poor performance, particularly on out-of-distribution data. This issue is further exacerbated by the limited availability of high-quality training data for layout-aware parsing tasks. To address these challenges, we introduce LayoutRL, a reinforcement learning framework that optimizes layout understanding through composite rewards integrating normalized edit distance, paragraph count accuracy, and reading order preservation. To support this training, we construct the Infinity-Doc-400K dataset, which we use to train Infinity-Parser, a vision-language model demonstrating robust generalization across various domains. Extensive evaluations on benchmarks including OmniDocBench, olmOCR-Bench, PubTabNet, and FinTabNet show that Infinity-Parser consistently achieves state-of-the-art performance across a broad range of document types, languages, and structural complexities, substantially outperforming both specialized document parsing systems and general-purpose vision-language models. We will release our code, dataset, and model to facilitate reproducible research in document parsing.

cs.CL↗

arXiv2025

Equivariant Spherical Transformer for Efficient Molecular Modeling

Equivariant Graph Neural Networks (GNNs) have significantly advanced the modeling of 3D molecular structure by leveraging group representations. However, their message passing, heavily relying on Clebsch-Gordan tensor product convolutions, suffers from restricted expressiveness due to the limited non-linearity and low degree of group representations. To overcome this, we introduce the Equivariant Spherical Transformer (EST), a novel plug-and-play framework that applies a Transformer-like architecture to the Fourier spatial domain of group representations. EST achieves higher expressiveness than conventional models while preserving the crucial equivariant inductive bias through a uniform sampling strategy of spherical Fourier transforms. As demonstrated by our experiments on challenging benchmarks like OC20 and QM9, EST-based models achieve state-of-the-art performance. For the complex molecular systems within OC20, small models empowered by EST can outperform some larger models and those using additional data. In addition to demonstrating such strong expressiveness,we provide both theoretical and experimental validation of EST's equivariance as well, paving the way for new research in this area.

cs.LG↗

arXiv2025

Unleashing Flow Policies with Distributional Critics

Flow-based policies have recently emerged as a powerful tool in offline and offline-to-online reinforcement learning, capable of modeling the complex, multimodal behaviors found in pre-collected datasets. However, the full potential of these expressive actors is often bottlenecked by their critics, which typically learn a single, scalar estimate of the expected return. To address this limitation, we introduce the Distributional Flow Critic (DFC), a novel critic architecture that learns the complete state-action return distribution. Instead of regressing to a single value, DFC employs flow matching to model the distribution of return as a continuous, flexible transformation from a simple base distribution to the complex target distribution of returns. By doing so, DFC provides the expressive flow-based policy with a rich, distributional Bellman target, which offers a more stable and informative learning signal. Extensive experiments across D4RL and OGBench benchmarks demonstrate that our approach achieves strong performance, especially on tasks requiring multimodal action distributions, and excels in both offline and offline-to-online fine-tuning compared to existing methods.

cs.LG↗

arXiv2025

SCP-116K: A High-Quality Problem-Solution Dataset and a Generalized Pipeline for Automated Extraction in the Higher Education Science Domain

Recent breakthroughs in large language models (LLMs) exemplified by the impressive mathematical and scientific reasoning capabilities of the o1 model have spotlighted the critical importance of high-quality training data in advancing LLM performance across STEM disciplines. While the mathematics community has benefited from a growing body of curated datasets, the scientific domain at the higher education level has long suffered from a scarcity of comparable resources. To address this gap, we present SCP-116K, a new large-scale dataset of 116,756 high-quality problem-solution pairs, automatically extracted from heterogeneous sources using a streamlined and highly generalizable pipeline. Our approach involves stringent filtering to ensure the scientific rigor and educational level of the extracted materials, while maintaining adaptability for future expansions or domain transfers. By openly releasing both the dataset and the extraction pipeline, we seek to foster research on scientific reasoning, enable comprehensive performance evaluations of new LLMs, and lower the barrier to replicating the successes of advanced models like o1 in the broader science community. We believe SCP-116K will serve as a critical resource, catalyzing progress in high-level scientific reasoning tasks and promoting further innovations in LLM development. The dataset and code are publicly available at https://github.com/AQA6666/SCP-116K-open.

cs.CL↗

arXiv2025

Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generation

Generating physically realistic 3D molecular structures remains a core challenge in molecular generative modeling. While diffusion models equipped with equivariant neural networks have made progress in capturing molecular geometries, they often struggle to produce equilibrium structures that adhere to physical principles such as force field consistency. To bridge this gap, we propose Reinforcement Learning with Physical Feedback (RLPF), a novel framework that extends Denoising Diffusion Policy Optimization to 3D molecular generation. RLPF formulates the task as a Markov decision process and applies proximal policy optimization to fine-tune equivariant diffusion models. Crucially, RLPF introduces reward functions derived from force-field evaluations, providing direct physical feedback to guide the generation toward energetically stable and physically meaningful structures. Experiments on the QM9 and GEOM-drug datasets demonstrate that RLPF significantly improves molecular stability compared to existing methods. These results highlight the value of incorporating physics-based feedback into generative modeling. The code is available at: https://github.com/ZhijianZhou/RLPF/tree/verl_diffusion.

cs.LG↗

arXiv2025

Constraints-Guided Diffusion Reasoner for Neuro-Symbolic Learning

Enabling neural networks to learn complex logical constraints and fulfill symbolic reasoning is a critical challenge. Bridging this gap often requires guiding the neural network's output distribution to move closer to the symbolic constraints. While diffusion models have shown remarkable generative capability across various domains, we employ the powerful architecture to perform neuro-symbolic learning and solve logical puzzles. Our diffusion-based pipeline adopts a two-stage training strategy: the first stage focuses on cultivating basic reasoning abilities, while the second emphasizes systematic learning of logical constraints. To impose hard constraints on neural outputs in the second stage, we formulate the diffusion reasoner as a Markov decision process and innovatively fine-tune it with an improved proximal policy optimization algorithm. We utilize a rule-based reward signal derived from the logical consistency of neural outputs and adopt a flexible strategy to optimize the diffusion reasoner's policy. We evaluate our methodology on some classical symbolic reasoning benchmarks, including Sudoku, Maze, pathfinding and preference learning. Experimental results demonstrate that our approach achieves outstanding accuracy and logical consistency among neural networks.

cs.AI↗

arXiv2025

Efficient Network Automatic Relevance Determination

We propose Network Automatic Relevance Determination (NARD), an extension of ARD for linearly probabilistic models, to simultaneously model sparse relationships between inputs $X \in \mathbb R^{d \times N}$ and outputs $Y \in \mathbb R^{m \times N}$, while capturing the correlation structure among the $Y$. NARD employs a matrix normal prior which contains a sparsity-inducing parameter to identify and discard irrelevant features, thereby promoting sparsity in the model. Algorithmically, it iteratively updates both the precision matrix and the relationship between $Y$ and the refined inputs. To mitigate the computational inefficiencies of the $\mathcal O(m^3 + d^3)$ cost per iteration, we introduce Sequential NARD, which evaluates features sequentially, and a Surrogate Function Method, leveraging an efficient approximation of the marginal likelihood and simplifying the calculation of determinant and inverse of an intermediate matrix. Combining the Sequential update with the Surrogate Function method further reduces computational costs. The computational complexity per iteration for these three methods is reduced to $\mathcal O(m^3+p^3)$, $\mathcal O(m^3 + d^2)$, $\mathcal O(m^3+p^2)$, respectively, where $p \ll d$ is the final number of features in the model. Our methods demonstrate significant improvements in computational efficiency with comparable performance on both synthetic and real-world datasets.

cs.AI↗

arXiv2025

Towards a Universal 3D Medical Multi-modality Generalization via Learning Personalized Invariant Representation

Variations in medical imaging modalities and individual anatomical differences pose challenges to cross-modality generalization in multi-modal tasks. Existing methods often concentrate exclusively on common anatomical patterns, thereby neglecting individual differences and consequently limiting their generalization performance. This paper emphasizes the critical role of learning individual-level invariance, i.e., personalized representation $\mathbb{X}_h$, to enhance multi-modality generalization under both homogeneous and heterogeneous settings. It reveals that mappings from individual biological profile to different medical modalities remain static across the population, which is implied in the personalization process. We propose a two-stage approach: pre-training with invariant representation $\mathbb{X}_h$ for personalization, then fine-tuning for diverse downstream tasks. We provide both theoretical and empirical evidence demonstrating the feasibility and advantages of personalization, showing that our approach yields greater generalizability and transferability across diverse multi-modal medical tasks compared to methods lacking personalization. Extensive experiments further validate that our approach significantly enhances performance in various generalization scenarios.

cs.CV↗

arXiv2025

PAST: A multimodal single-cell foundation model for histopathology and spatial transcriptomics in cancer

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

q-bio.QM↗

arXiv2025

Structure-aware Semantic Discrepancy and Consistency for 3D Medical Image Self-supervised Learning

3D medical image self-supervised learning (mSSL) holds great promise for medical analysis. Effectively supporting broader applications requires considering anatomical structure variations in location, scale, and morphology, which are crucial for capturing meaningful distinctions. However, previous mSSL methods partition images with fixed-size patches, often ignoring the structure variations. In this work, we introduce a novel perspective on 3D medical images with the goal of learning structure-aware representations. We assume that patches within the same structure share the same semantics (semantic consistency) while those from different structures exhibit distinct semantics (semantic discrepancy). Based on this assumption, we propose an mSSL framework named $S^2DC$, achieving Structure-aware Semantic Discrepancy and Consistency in two steps. First, $S^2DC$ enforces distinct representations for different patches to increase semantic discrepancy by leveraging an optimal transport strategy. Second, $S^2DC$ advances semantic consistency at the structural level based on neighborhood similarity distribution. By bridging patch-level and structure-level representations, $S^2DC$ achieves structure-aware representations. Thoroughly evaluated across 10 datasets, 4 tasks, and 3 modalities, our proposed method consistently outperforms the state-of-the-art methods in mSSL.

cs.CV↗

arXiv2025

CENTAUR: Bridging the Impossible Trinity of Privacy, Efficiency, and Performance in Privacy-Preserving Transformer Inference

With the growing deployment of pre-trained models like Transformers on cloud platforms, privacy concerns about model parameters and inference data are intensifying. Existing Privacy-Preserving Transformer Inference (PPTI) frameworks face the "impossible trinity" of balancing privacy, efficiency, and performance: Secure Multi-Party Computation (SMPC)-based approaches ensure strong privacy but suffer from high computational overhead and performance losses; Conversely, permutation-based methods achieve near-plaintext efficiency and accuracy but compromise privacy by exposing sensitive model parameters and intermediate results. Bridging this gap with a single approach presents substantial challenges, motivating the introduction of CENTAUR, a groundbreaking PPTI framework that seamlessly integrates random permutations and SMPC to address the "impossible trinity". By designing efficient PPTI algorithms tailored to the structural properties of Transformer models, CENTAUR achieves an unprecedented balance among privacy, efficiency, and performance. Our experiments demonstrate CENTAUR's ability to resist diverse data reconstruction attacks, achieve plaintext-level inference accuracy, and boost inference speed by 5.0-30.4 times, unlocking new possibilities for secure and efficient AI deployment.

cs.LG↗

arXiv2025

Using Forests in Multivariate Regression Discontinuity Designs

We discuss estimation and inference of conditional treatment effects in regression discontinuity (RD) designs with multiple scores. In addition to local linear regressions and the minimax-optimal estimator more recently proposed by Imbens and Wager (2019), we argue that two variants of random forests, honest regression forests and local linear forests, should be added to the toolkit of applied researchers working with multivariate RD designs; their validity follows from results in Wager and Athey (2018) and Friedberg et al. (2020). We design a systematic Monte Carlo study with data generating processes built both from functional forms that we specify and from Wasserstein Generative Adversarial Networks that closely mimic the observed data. We find no single estimator dominates across all specifications: (i) local linear regressions perform well in univariate settings, but the common practice of reducing multivariate scores to a univariate one can incur under-coverage, possibly due to vanishing density at the transformed cutoff; (ii) good performance of the minimax-optimal estimator depends on accurate estimation of a nuisance parameter and its current implementation only accepts up to two scores; (iii) forest-based estimators are not designed for estimation at boundary points and are susceptible to finite-sample bias, but their flexibility in modeling multivariate scores opens the door to a wide range of empirical applications, as illustrated by an empirical study of COVID-19 hospital funding with three eligibility criteria.

econ.EM↗

arXiv2025

OpenCoder: The Open Cookbook for Top-Tier Code Large Language Models

Large language models (LLMs) for code have become indispensable in various domains, including code generation, reasoning tasks and agent systems. While open-access code LLMs are increasingly approaching the performance levels of proprietary models, high-quality code LLMs suitable for rigorous scientific investigation, particularly those with reproducible data processing pipelines and transparent training protocols, remain limited. The scarcity is due to various challenges, including resource constraints, ethical considerations, and the competitive advantages of keeping models advanced. To address the gap, we introduce OpenCoder, a top-tier code LLM that not only achieves performance comparable to leading models but also serves as an "open cookbook" for the research community. Unlike most prior efforts, we release not only model weights and inference code, but also the reproducible training data, complete data processing pipeline, rigorous experimental ablation results, and detailed training protocols for open scientific research. Through this comprehensive release, we identify the key ingredients for building a top-tier code LLM: (1) code optimized heuristic rules for data cleaning and methods for data deduplication, (2) recall of text corpus related to code and (3) high-quality synthetic data in both annealing and supervised fine-tuning stages. By offering this level of openness, we aim to broaden access to all aspects of a top-tier code LLM, with OpenCoder serving as both a powerful model and an open foundation to accelerate research, and enable reproducible advancements in code AI.

cs.CL↗

arXiv2025

Equivariant Masked Position Prediction for Efficient Molecular Representation

Graph neural networks (GNNs) have shown considerable promise in computational chemistry. However, the limited availability of molecular data raises concerns regarding GNNs' ability to effectively capture the fundamental principles of physics and chemistry, which constrains their generalization capabilities. To address this challenge, we introduce a novel self-supervised approach termed Equivariant Masked Position Prediction (EMPP), grounded in intramolecular potential and force theory. Unlike conventional attribute masking techniques, EMPP formulates a nuanced position prediction task that is more well-defined and enhances the learning of quantum mechanical features. EMPP also bypasses the approximation of the Gaussian mixture distribution commonly used in denoising methods, allowing for more accurate acquisition of physical properties. Experimental results indicate that EMPP significantly enhances performance of advanced molecular architectures, surpassing state-of-the-art self-supervised approaches. Our code is released in https://github.com/ajy112/EMPP

cs.LG↗