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Wei Ju

Publications and source records attributed to Wei Ju.

At least 19 recordsLinked to original sources
arXiv2026

Do Pathology Vision-Language Models Truly See Pathology?

Pathology vision-language models (VLMs) have recently progressed rapidly and are commonly evaluated by answer accuracy on pathology VQA benchmarks. However, we dig into current evaluations and identify three overlooked issues: 1) Visual evidence is not always necessary. For instance, Gemini-3-Pro achieves 53.5% average accuracy across 5 VQA benchmarks without any visual input. 2) Domain training can improve accuracy without proportional gains in visual binding. Compared with Qwen2.5-VL-7B, Patho-R1-7B exhibits a 5.8-point lower multimodal gain and a 3.7-point lower attention IoU. 3) Entity-level attention is diffuse and weakly query-specific. On PathVG, attention maps remain highly correlated across different entity queries. These issues can lead to substantial misjudgments of pathology VLMs' actual multimodal capabilities. To this end, we present PathBind, a benchmark comprising 2,600 samples: PathBind-VQA with 1,500 questions across six dimensions, PathBind-PTA with 600 questions from a private pathology teaching atlas, and PathBind-Grounding with 500 expert-curated region-level samples. Each component undergoes task-specific automated filtering and expert review to reduce textual shortcuts and improve entity-region correspondence. We evaluate 18 representative VLMs on VQA samples of PathBind and five existing pathology VQA benchmarks, and further evaluate 10 VLMs on PathBind-Grounding and PathVG. Results show that current pathology VLMs still exhibit a substantial gap between answer-side performance and visual-semantic binding.

cs.CV↗
arXiv2026

Von Mises-Fisher Mixture Model with Dynamic Shrinkage for Realistic Test-Time Transduction

A range of methods aim to enhance the performance of vision-language models (VLMs) at test time. Among them, transduction has emerged as a promising paradigm due to its strong compatibility and efficiency. However, realistic evaluations often involve highly imbalanced class distributions, which cause performance degradation or even collapse. In this work, we systematically revisit transduction from the perspective of penalized likelihood estimation (PLE), showing that PLE with a KL-divergence anchor term naturally yields an adaptive shrinkage behavior between prior anchors and empirical estimates. From this viewpoint, the brittleness of transductive methods can be attributed to the absence of anchoring mechanism and static modeling of the shrinkage strength. Therefore, we propose Mixture of Von Mises-Fisher Models with Dynamic Shrinkage (MOON). MOON is built upon a mixture of von Mises-Fisher distributions to model feature representations on the unit hypersphere. To handle imbalance, MOON dynamically adjusts the shrinkage strength using zero-shot priors at both instance and class levels. Thus, it suppresses unreliable assignments and prevents harmful updates from outlier classes, thereby mitigating negative transfer. MOON is model-agnostic, training-free, and requires no task-specific hyperparameter tuning. Extensive experiments further validate the advantage of MOON in both performance and efficiency. Our code is available at https://github.com/walawalagoose/MOON

cs.CV↗
arXiv2026

scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.

cs.LG↗
arXiv2026

PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion

Macrocyclic peptides are promising therapeutic candidates for intracellular targets, but their design requires simultaneous control over non-natural monomer chemistry, ring topology, membrane permeability, and target binding. Existing SMILES- or HELM-string generative models either operate in long atom-level sequence spaces or treat monomers as symbolic tokens with limited chemical grounding. We introduce PepALD, an Autoregressive Latent Diffusion (ALD) foundation model for \textit{de novo} macrocyclic peptide generation. The model represents HELM monomers with structured chemical embeddings, generates each residue through context-conditioned diffusion in chemically informed latent space, predicts R-group-aware ring closures during autoregressive generation, and aligns the denoiser to affinity rewards using winner-protected diffusion-adapted preference optimization. In silico experiments demonstrate PepALD's generation quality and reward-optimization performance against representative peptide generation baselines.

cs.LG↗
arXiv2026

BRIDGE: Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks

Motivation: Gene regulatory network inference from single-cell RNA sequencing (scRNA-seq) data is important for uncovering cell-state-specific transcriptional programs. However, scRNA-seq measurements are sparse and noisy, and experimentally validated TF-target interactions remain limited, making reliable inference challenging. Although graph neural networks have advanced GRN prediction, existing methods often rely on biologically unconstrained graph augmentation, such as random edge perturbation, and insufficiently control information transfer between genes and cells. These limitations may distort regulatory structures and weaken robustness under noisy and weakly supervised settings. Results: To address these issues, we propose an innovative framework named Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks (BRIDGE). BRIDGE extracts gene and cell representations from the expression matrix and its matrix dual, and performs contrastive learning in the gene space and cell space between self and neighbors across the co-expression-refined regulatory view and the original graph. It then applies heterogeneous gated encoding to adaptively regulate information transfer between genes and cells, enabling robust transcription factor-to-target gene prediction. Experiments on benchmark datasets spanning three network types and seven cell types show that BRIDGE achieves state-of-the-art AUROC and AUPRC in most settings. In particular, on Specific networks, BRIDGE improves average AUPRC by 5% over the second-best baseline, GCLink. In cross-cell-type few-shot transfer, BRIDGE consistently outperforms GCLink and GENELink across all six target cell types. A case study on hESC further supports the biological relevance of the predictions, with 9 of the top 10 and 46 of the top 100 novel TF-target interactions validated by ChIPBase.

q-bio.MN↗
arXiv2026

Interests Burn-down Diffusion Process for Personalized Collaborative Filtering

Generative methods have gained widespread attention in Collaborative Filtering (CF) tasks for their ability to produce high-quality personalized samples aligned with users' interests. Among them, diffusion generative models have raised increasing attention in recommendation field. Despite that the pioneering efforts have applied the conventional diffusion process to model diffusive user interests, the incongruity between the Gaussian noise and the subtle nature of user's personalized interaction behavior has led to sub-optimal results. To this end, we introduce a specifically-tailored diffusion scheme for interaction systems, namely the interests burn-down process. The interests burn-down process delineates the decay of user interests towards candidate items, complemented by its reverse burn-up process that yields personalized recommendation for users. The inherent burn-down nature of this process adeptly models the diffusive user interests, aligning seamlessly with the requirements of CF tasks. We present a novel recommendation method StageCF to illustrate the superiority of this newly proposed diffusion process. Experimental results have demonstrated the effectiveness of StageCF against existing generative and diffusion-based baseline methods. Furthermore, comprehensive studies validate the functionality of interests burn-down process, shedding light on its capacity to generate personalized interactions.

cs.IR↗
arXiv2026

CMGL: Confidence-guided Multi-omics Graph Learning for Cancer Subtype Classification

Motivation: Multi-omics integration can improve cancer subtyping, but modality informativeness and noise vary across cancer types and patients. Existing graph-based methods optimize modality weights jointly with the classification objective and therefore lack independent reliability estimates, so low-quality omics distort patient similarity graphs and amplify noise through message passing. Results: We propose CMGL, a two-stage framework that estimates per-sample modality reliability through evidential deep learning and uses the frozen confidence scores to guide cross-omics fusion and graph construction. On four MLOmics cancer-subtype tasks and the 32-class pan-cancer task, CMGL consistently improves over the strongest baseline, surpassing it by 4.03% in average accuracy on the four single-cancer tasks. Its representations recover the PAM50 intrinsic subtypes of breast invasive carcinoma (BRCA), and the BRCA-trained model transfers without fine-tuning to kidney renal clear cell carcinoma (KIRC), stratifying patients into prognostically distinct groups.

cs.LG↗
arXiv2026

Robust LLM-based Audio-Visual Speech Recognition with Sparse Modality Alignment and Visual Unit-Guided Refinement

Audio-Visual Speech Recognition (AVSR) integrates acoustic and visual information to enhance robustness in adverse acoustic conditions. Recent advances in Large Language Models (LLMs) have yielded competitive automatic speech recognition performance and shown effectiveness for AVSR. However, prior approaches project audio and visual features independently or apply shallow fusion, limiting cross-modal alignment and complementary exchange while increasing the LLM's computational load. To address this, we propose AVUR-LLM, an LLM-based Audio-Visual Speech Recognition via Sparse Modality Alignment and Visual Unit-Guided Refinement. Experiments on LRS3 demonstrate state-of-the-art results for AVSR. Under additive-noise conditions at 0 dB SNR, it achieves 37% relative improvement over the baseline system.

cs.SD↗
arXiv2026

Identifying and Correcting Label Noise for Robust GNNs via Influence Contradiction

Graph Neural Networks (GNNs) have shown remarkable capabilities in learning from graph-structured data with various applications such as social analysis and bioinformatics. However, the presence of label noise in real scenarios poses a significant challenge in learning robust GNNs, and their effectiveness can be severely impacted when dealing with noisy labels on graphs, often stemming from annotation errors or inconsistencies. To address this, in this paper we propose a novel approach called ICGNN that harnesses the structure information of the graph to effectively alleviate the challenges posed by noisy labels. Specifically, we first design a novel noise indicator that measures the influence contradiction score (ICS) based on the graph diffusion matrix to quantify the credibility of nodes with clean labels, such that nodes with higher ICS values are more likely to be detected as having noisy labels. Then we leverage the Gaussian mixture model to precisely detect whether the label of a node is noisy or not. Additionally, we develop a soft strategy to combine the predictions from neighboring nodes on the graph to correct the detected noisy labels. At last, pseudo-labeling for abundant unlabeled nodes is incorporated to provide auxiliary supervision signals and guide the model optimization. Experiments on benchmark datasets show the superiority of our approach over competitive baselines in noisy label scenarios.

cs.LG↗
arXiv2026

DeepEra: A Deep Evidence Reranking Agent for Scientific Retrieval-Augmented Generated Question Answering

With the rapid growth of scientific literature, scientific question answering (SciQA) has become increasingly critical for exploring and utilizing scientific knowledge. Retrieval-Augmented Generation (RAG) enhances LLMs by incorporating knowledge from external sources, thereby providing credible evidence for scientific question answering. But existing retrieval and reranking methods remain vulnerable to passages that are semantically similar but logically irrelevant, often reducing factual reliability and amplifying hallucinations.To address this challenge, we propose a Deep Evidence Reranking Agent (DeepEra) that integrates step-by-step reasoning, enabling more precise evaluation of candidate passages beyond surface-level semantics. To support systematic evaluation, we construct SciRAG-SSLI (Scientific RAG - Semantically Similar but Logically Irrelevant), a large-scale dataset comprising about 300K SciQA instances across 10 subjects, constructed from 10M scientific corpus. The dataset combines naturally retrieved contexts with systematically generated distractors to test logical robustness and factual grounding. Comprehensive evaluations confirm that our approach achieves superior retrieval performance compared to leading rerankers. To our knowledge, this work is the first to comprehensively study and empirically validate innegligible SSLI issues in two-stage RAG frameworks.

cs.CL↗
arXiv2025

WhisperVC: Decoupled Cross-Domain Alignment and Speech Generation for Low-Resource Whisper-to-Normal Conversion

Whispered speech lacks vocal-fold excitation, making intelligible conversion challenging. We propose WhisperVC, a three-stage framework for low-resource whisper-to-normal (W2N) conversion that decouples cross-domain alignment from speech generation. Stage 1 uses limited paired whisper-normal data with a content encoder and a Conformer-based variational autoencoder (VAE) with soft-DTW alignment to learn domain-invariant semantic representations. Stage 2, trained only on normal speech, employs a Length-Channel Aligner and a two-stage speaker-conditioned mel generator for timbre and prosody modeling. Stage 3 fine-tunes a HiFi-GAN vocoder for waveform synthesis. Experimental results on AISHELL6-Whisper show competitive quality (DNSMOS 3.07, UTMOS 2.83, CER 16.93%) and WavLM speaker similarity (0.95). The framework also supports privacy-preserving communication as well as non-vocal communication and a rehabilitation tool for post-surgical vocal-fold patients. Samples are available online.

eess.AS↗
arXiv2025

A Survey on Efficient Large Language Model Training: From Data-centric Perspectives

Post-training of Large Language Models (LLMs) is crucial for unlocking their task generalization potential and domain-specific capabilities. However, the current LLM post-training paradigm faces significant data challenges, including the high costs of manual annotation and diminishing marginal returns on data scales. Therefore, achieving data-efficient post-training has become a key research question. In this paper, we present the first systematic survey of data-efficient LLM post-training from a data-centric perspective. We propose a taxonomy of data-efficient LLM post-training methods, covering data selection, data quality enhancement, synthetic data generation, data distillation and compression, and self-evolving data ecosystems. We summarize representative approaches in each category and outline future research directions. By examining the challenges in data-efficient LLM post-training, we highlight open problems and propose potential research avenues. We hope our work inspires further exploration into maximizing the potential of data utilization in large-scale model training. Paper List: https://github.com/luo-junyu/Awesome-Data-Efficient-LLM

cs.CL↗
arXiv2025

Rewarding the Journey, Not Just the Destination: A Composite Path and Answer Self-Scoring Reward Mechanism for Test-Time Reinforcement Learning

Reinforcement Learning (RL) has emerged as a powerful paradigm for advancing Large Language Models (LLMs), achieving remarkable performance in complex reasoning domains such as mathematics and code generation. However, current RL methods face a fundamental scalability bottleneck due to their heavy reliance on human-curated preference data or labeled datasets for reward modeling. To overcome this limitation, we explore RL on unlabeled data where models learn autonomously from continuous experience streams. The core challenge in this setting lies in reliable reward estimation without ground-truth supervision. Existing approaches like Test-Time RL address this through self-consistent consensus, but risk reinforcing incorrect pseudo-labels derived from majority voting. We introduce COMPASS (Composite Path and Answer Self-Scoring), a novel test-time reward mechanism that operates without external supervision. COMPASS integrates two complementary components: the Dual-Calibration Answer Reward (DCAR), which stabilizes training by establishing trustworthy pseudo-labels through confidence and credibility calibration, and the Decisive Path Reward (DPR), which directly optimizes the reasoning process quality beyond mere outcome supervision. By jointly reinforcing trustworthy consensus answers and highly decisive reasoning chains, the COMPASS systematically enhances the model's analytical capabilities. Extensive experiments show that COMPASS achieves significant and consistent performance gains across diverse reasoning tasks and model architectures, advancing a more scalable direction for LLMs to learn from continuous experience.

cs.LG↗
arXiv2025

Robust Audio-Visual Target Speaker Extraction with Emotion-Aware Multiple Enrollment Fusion

Audio-Visual Target Speaker Extraction (AVTSE) is crucial for cocktail party scenarios. Leveraging multiple cues --such as utterance-level speaker embeddings or steady face images, and frame-level lip motion or facial expression features --can significantly improve performance. However, real-world applications often suffer from intermittent signal loss, especially for frame-level cues. This paper systematically investigates the robustness of multi-enrollment fusion under varying degrees of modality missing. Results show that while full multimodal fusion excels under ideal conditions, its performance degrades sharply when encountering unseen modalities missing during the testing. Crucially, training with a high missing rate dramatically enhances robustness, maintaining stable performance even under severe test-time modality missing. We demonstrate that fusing the complementary one frame of face image with frame-level lip features achieves both strong performance and robustness for the AVTSE task. The model and codes are shared.

eess.AS↗
arXiv2025

SciRerankBench: Benchmarking Rerankers Towards Scientific Retrieval-Augmented Generated LLMs

Scientific literature question answering is a pivotal step towards new scientific discoveries. Recently, \textit{two-stage} retrieval-augmented generated large language models (RAG-LLMs) have shown impressive advancements in this domain. Such a two-stage framework, especially the second stage (reranker), is particularly essential in the scientific domain, where subtle differences in terminology may have a greatly negative impact on the final factual-oriented or knowledge-intensive answers. Despite this significant progress, the potential and limitations of these works remain unexplored. In this work, we present a Scientific Rerank-oriented RAG Benchmark (SciRerankBench), for evaluating rerankers within RAG-LLMs systems, spanning five scientific subjects. To rigorously assess the reranker performance in terms of noise resilience, relevance disambiguation, and factual consistency, we develop three types of question-context-answer (Q-C-A) pairs, i.e., Noisy Contexts (NC), Semantically Similar but Logically Irrelevant Contexts (SSLI), and Counterfactual Contexts (CC). Through systematic evaluation of 13 widely used rerankers on five families of LLMs, we provide detailed insights into their relative strengths and limitations. To the best of our knowledge, SciRerankBench is the first benchmark specifically developed to evaluate rerankers within RAG-LLMs, which provides valuable observations and guidance for their future development.

cs.CL↗
arXiv2025

Sparse Causal Discovery with Generative Intervention for Unsupervised Graph Domain Adaptation

Unsupervised Graph Domain Adaptation (UGDA) leverages labeled source domain graphs to achieve effective performance in unlabeled target domains despite distribution shifts. However, existing methods often yield suboptimal results due to the entanglement of causal-spurious features and the failure of global alignment strategies. We propose SLOGAN (Sparse Causal Discovery with Generative Intervention), a novel approach that achieves stable graph representation transfer through sparse causal modeling and dynamic intervention mechanisms. Specifically, SLOGAN first constructs a sparse causal graph structure, leveraging mutual information bottleneck constraints to disentangle sparse, stable causal features while compressing domain-dependent spurious correlations through variational inference. To address residual spurious correlations, we innovatively design a generative intervention mechanism that breaks local spurious couplings through cross-domain feature recombination while maintaining causal feature semantic consistency via covariance constraints. Furthermore, to mitigate error accumulation in target domain pseudo-labels, we introduce a category-adaptive dynamic calibration strategy, ensuring stable discriminative learning. Extensive experiments on multiple real-world datasets demonstrate that SLOGAN significantly outperforms existing baselines.

cs.LG↗
arXiv2025

MARCO: Meta-Reflection with Cross-Referencing for Code Reasoning

The ability to reason is one of the most fundamental capabilities of large language models (LLMs), enabling a wide range of downstream tasks through sophisticated problem-solving. A critical aspect of this is code reasoning, which involves logical reasoning with formal languages (i.e., programming code). In this paper, we enhance this capability of LLMs by exploring the following question: how can an LLM agent become progressively smarter in code reasoning with each solution it proposes, thereby achieving substantial cumulative improvement? Most existing research takes a static perspective, focusing on isolated problem-solving using frozen LLMs. In contrast, we adopt a cognitive-evolving perspective and propose a novel framework named Meta-Reflection with Cross-Referencing (MARCO) that enables the LLM to evolve dynamically during inference through self-improvement. From the perspective of human cognitive development, we leverage both knowledge accumulation and lesson sharing. In particular, to accumulate knowledge during problem-solving, we propose meta-reflection that reflects on the reasoning paths of the current problem to obtain knowledge and experience for future consideration. Moreover, to effectively utilize the lessons from other agents, we propose cross-referencing that incorporates the solution and feedback from other agents into the current problem-solving process. We conduct experiments across various datasets in code reasoning, and the results demonstrate the effectiveness of MARCO.

cs.CL↗
arXiv2025

Dynamic Bundling with Large Language Models for Zero-Shot Inference on Text-Attributed Graphs

Large language models (LLMs) have been used in many zero-shot learning problems, with their strong generalization ability. Recently, adopting LLMs in text-attributed graphs (TAGs) has drawn increasing attention. However, the adoption of LLMs faces two major challenges: limited information on graph structure and unreliable responses. LLMs struggle with text attributes isolated from the graph topology. Worse still, they yield unreliable predictions due to both information insufficiency and the inherent weakness of LLMs (e.g., hallucination). Towards this end, this paper proposes a novel method named Dynamic Text Bundling Supervision (DENSE) that queries LLMs with bundles of texts to obtain bundle-level labels and uses these labels to supervise graph neural networks. Specifically, we sample a set of bundles, each containing a set of nodes with corresponding texts of close proximity. We then query LLMs with the bundled texts to obtain the label of each bundle. Subsequently, the bundle labels are used to supervise the optimization of graph neural networks, and the bundles are further refined to exclude noisy items. To justify our design, we also provide theoretical analysis of the proposed method. Extensive experiments across ten datasets validate the effectiveness of the proposed method.

cs.LG↗