arXiv subjects

Ying Wei

Publications and source records attributed to Ying Wei.

At least 37 records · Page 2Linked to original sources

arXiv2025

CellFMCount: A Fluorescence Microscopy Dataset, Benchmark, and Methods for Cell Counting

Accurate cell counting is essential in various biomedical research and clinical applications, including cancer diagnosis, stem cell research, and immunology. Manual counting is labor-intensive and error-prone, motivating automation through deep learning techniques. However, training reliable deep learning models requires large amounts of high-quality annotated data, which is difficult and time-consuming to produce manually. Consequently, existing cell-counting datasets are often limited, frequently containing fewer than $500$ images. In this work, we introduce a large-scale annotated dataset comprising $3{,}023$ images from immunocytochemistry experiments related to cellular differentiation, containing over $430{,}000$ manually annotated cell locations. The dataset presents significant challenges: high cell density, overlapping and morphologically diverse cells, a long-tailed distribution of cell count per image, and variation in staining protocols. We benchmark three categories of existing methods: regression-based, crowd-counting, and cell-counting techniques on a test set with cell counts ranging from $10$ to $2{,}126$ cells per image. We also evaluate how the Segment Anything Model (SAM) can be adapted for microscopy cell counting using only dot-annotated datasets. As a case study, we implement a density-map-based adaptation of SAM (SAM-Counter) and report a mean absolute error (MAE) of $22.12$, which outperforms existing approaches (second-best MAE of $27.46$). Our results underscore the value of the dataset and the benchmarking framework for driving progress in automated cell counting and provide a robust foundation for future research and development.

cs.CV↗

arXiv2025

EchoBench: Benchmarking Sycophancy in Medical Large Vision-Language Models

Recent benchmarks for medical Large Vision-Language Models (LVLMs) emphasize leaderboard accuracy, overlooking reliability and safety. We study sycophancy -- models' tendency to uncritically echo user-provided information -- in high-stakes clinical settings. We introduce EchoBench, a benchmark to systematically evaluate sycophancy in medical LVLMs. It contains 2,122 images across 18 departments and 20 modalities with 90 prompts that simulate biased inputs from patients, medical students, and physicians. We evaluate medical-specific, open-source, and proprietary LVLMs. All exhibit substantial sycophancy; the best proprietary model (Claude 3.7 Sonnet) still shows 45.98% sycophancy, and GPT-4.1 reaches 59.15%. Many medical-specific models exceed 95% sycophancy despite only moderate accuracy. Fine-grained analyses by bias type, department, perceptual granularity, and modality identify factors that increase susceptibility. We further show that higher data quality/diversity and stronger domain knowledge reduce sycophancy without harming unbiased accuracy. EchoBench also serves as a testbed for mitigation: simple prompt-level interventions (negative prompting, one-shot, few-shot) produce consistent reductions and motivate training- and decoding-time strategies. Our findings highlight the need for robust evaluation beyond accuracy and provide actionable guidance toward safer, more trustworthy medical LVLMs.

cs.CV↗

arXiv2025

Improving Alignment in LVLMs with Debiased Self-Judgment

The rapid advancements in Large Language Models (LLMs) and Large Visual-Language Models (LVLMs) have opened up new opportunities for integrating visual and linguistic modalities. However, effectively aligning these modalities remains challenging, often leading to hallucinations--where generated outputs are not grounded in the visual input--and raising safety concerns across various domains. Existing alignment methods, such as instruction tuning and preference tuning, often rely on external datasets, human annotations, or complex post-processing, which limit scalability and increase costs. To address these challenges, we propose a novel approach that generates the debiased self-judgment score, a self-evaluation metric created internally by the model without relying on external resources. This enables the model to autonomously improve alignment. Our method enhances both decoding strategies and preference tuning processes, resulting in reduced hallucinations, enhanced safety, and improved overall capability. Empirical results show that our approach significantly outperforms traditional methods, offering a more effective solution for aligning LVLMs.

cs.CV↗

arXiv2025

TokLIP: Marry Visual Tokens to CLIP for Multimodal Comprehension and Generation

Pioneering token-based works such as Chameleon and Emu3 have established a foundation for multimodal unification but face challenges of high training computational overhead and limited comprehension performance due to a lack of high-level semantics. In this paper, we introduce TokLIP, a visual tokenizer that enhances comprehension by semanticizing vector-quantized (VQ) tokens and incorporating CLIP-level semantics while enabling end-to-end multimodal autoregressive training with standard VQ tokens. TokLIP integrates a low-level discrete VQ tokenizer with a ViT-based token encoder to capture high-level continuous semantics. Unlike previous approaches (e.g., VILA-U) that discretize high-level features, TokLIP disentangles training objectives for comprehension and generation, allowing the direct application of advanced VQ tokenizers without the need for tailored quantization operations. Our empirical results demonstrate that TokLIP achieves exceptional data efficiency, empowering visual tokens with high-level semantic understanding while enhancing low-level generative capacity, making it well-suited for autoregressive Transformers in both comprehension and generation tasks. The code and models are available at https://github.com/TencentARC/TokLIP.

cs.CV↗

arXiv2025

IKOD: Mitigating Visual Attention Degradation in Large Vision-Language Models

Recent advancements in Large Vision-Language Models (LVLMs) have demonstrated significant progress across multiple domains. However, these models still face the inherent challenge of integrating vision and language for collaborative inference, which often leads to "hallucinations", outputs that are not grounded in the corresponding images. Many efforts have been made to address these issues, but each comes with its own limitations, such as high computational cost or expensive dataset annotation. Recent research shows that LVLMs exhibit a long-term bias where hallucinations increase as the sequence length grows, yet the underlying cause remains poorly understood. Building on extensive research into attention mechanisms in LVLMs, we analyze the relationship between this long-term bias and visual attention. In our research, we identify a consistent phenomenon in current LVLMs: the model's attention to visual input diminishes as the generated sequence grows, which we hypothesize to be a key factor contributing to observed increasing hallucinations. Based on these insights, we propose Image attention-guided Key-value merging cOllaborative Decoding (IKOD), a collaborative decoding strategy generating more image-focused sequences. This method derives logits from shorter sequences with higher image attention through key-value merging and combines them with those from the original decoding, effectively mitigating attention degradation and suppressing hallucinations while not incurring too much inference cost. Extensive experiments on both hallucination and comprehensive benchmarks demonstrate IKOD's superior effectiveness in mitigating hallucinations and improving comprehensive capacities for LVLMs. Importantly, IKOD requires no additional training or external tools, making it a lightweight and efficient framework applicable to various models.

cs.CV↗

arXiv2025

Come Together, But Not Right Now: A Progressive Strategy to Boost Low-Rank Adaptation

Low-rank adaptation (LoRA) has emerged as a leading parameter-efficient fine-tuning technique for adapting large foundation models, yet it often locks adapters into suboptimal minima near their initialization. This hampers model generalization and limits downstream operators such as adapter merging and pruning. Here, we propose CoTo, a progressive training strategy that gradually increases adapters' activation probability over the course of fine-tuning. By stochastically deactivating adapters, CoTo encourages more balanced optimization and broader exploration of the loss landscape. We provide a theoretical analysis showing that CoTo promotes layer-wise dropout stability and linear mode connectivity, and we adopt a cooperative-game approach to quantify each adapter's marginal contribution. Extensive experiments demonstrate that CoTo consistently boosts single-task performance, enhances multi-task merging accuracy, improves pruning robustness, and reduces training overhead, all while remaining compatible with diverse LoRA variants. Code is available at https://github.com/zwebzone/coto.

cs.LG↗

arXiv2025

AVFSNet: Audio-Visual Speech Separation for Flexible Number of Speakers with Multi-Scale and Multi-Task Learning

Separating target speech from mixed signals containing flexible speaker quantities presents a challenging task. While existing methods demonstrate strong separation performance and noise robustness, they predominantly assume prior knowledge of speaker counts in mixtures. The limited research addressing unknown speaker quantity scenarios exhibits significantly constrained generalization capabilities in real acoustic environments. To overcome these challenges, this paper proposes AVFSNet -- an audio-visual speech separation model integrating multi-scale encoding and parallel architecture -- jointly optimized for speaker counting and multi-speaker separation tasks. The model independently separates each speaker in parallel while enhancing environmental noise adaptability through visual information integration. Comprehensive experimental evaluations demonstrate that AVFSNet achieves state-of-the-art results across multiple evaluation metrics and delivers outstanding performance on diverse datasets.

eess.AS↗

arXiv2025

Automatic Expert Discovery in LLM Upcycling via Sparse Interpolated Mixture-of-Experts

We present Sparse Interpolated Mixture-of-Experts (SIMoE) instruction-tuning, an end-to-end algorithm designed to fine-tune a dense pre-trained Large Language Model (LLM) into a MoE-style model that possesses capabilities in multiple specialized domains. During instruction-tuning, SIMoE automatically identifies multiple specialized experts under a specified sparsity constraint, with each expert representing a structurally sparse subset of the seed LLM's parameters that correspond to domain-specific knowledge within the data. SIMoE simultaneously learns an input-dependent expert merging strategy via a router network, leveraging rich cross-expert knowledge for superior downstream generalization that surpasses existing baselines. Empirically, SIMoE consistently achieves state-of-the-art performance on common instruction-tuning benchmarks while maintaining an optimal performance-compute trade-off compared to all baselines.

cs.LG↗

arXiv2025

What Makes a Good Reasoning Chain? Uncovering Structural Patterns in Long Chain-of-Thought Reasoning

Recent advances in reasoning with large language models (LLMs) have popularized Long Chain-of-Thought (LCoT), a strategy that encourages deliberate and step-by-step reasoning before producing a final answer. While LCoTs have enabled expert-level performance in complex tasks, how the internal structures of their reasoning chains drive, or even predict, the correctness of final answers remains a critical yet underexplored question. In this work, we present LCoT2Tree, an automated framework that converts sequential LCoTs into hierarchical tree structures and thus enables deeper structural analysis of LLM reasoning. Using graph neural networks (GNNs), we reveal that structural patterns extracted by LCoT2Tree, including exploration, backtracking, and verification, serve as stronger predictors of final performance across a wide range of tasks and models. Leveraging an explainability technique, we further identify critical thought patterns such as over-branching that account for failures. Beyond diagnostic insights, the structural patterns by LCoT2Tree support practical applications, including improving Best-of-N decoding effectiveness. Overall, our results underscore the critical role of internal structures of reasoning chains, positioning LCoT2Tree as a powerful tool for diagnosing, interpreting, and improving reasoning in LLMs.

cs.AI↗

arXiv2025

Mixture of Low Rank Adaptation with Partial Parameter Sharing for Time Series Forecasting

Multi-task forecasting has become the standard approach for time-series forecasting (TSF). However, we show that it suffers from an Expressiveness Bottleneck, where predictions at different time steps share the same representation, leading to unavoidable errors even with optimal representations. To address this issue, we propose a two-stage framework: first, pre-train a foundation model for one-step-ahead prediction; then, adapt it using step-specific LoRA modules.This design enables the foundation model to handle any number of forecast steps while avoiding the expressiveness bottleneck. We further introduce the Mixture-of-LoRA (MoLA) model, which employs adaptively weighted LoRA experts to achieve partial parameter sharing across steps. This approach enhances both efficiency and forecasting performance by exploiting interdependencies between forecast steps. Experiments show that MoLA significantly improves model expressiveness and outperforms state-of-the-art time-series forecasting methods. Code is available at https://anonymous.4open.science/r/MoLA-BC92.

cs.LG↗

arXiv2025

CLDyB: Towards Dynamic Benchmarking for Continual Learning with Pre-trained Models

The advent of the foundation model era has sparked significant research interest in leveraging pre-trained representations for continual learning (CL), yielding a series of top-performing CL methods on standard evaluation benchmarks. Nonetheless, there are growing concerns regarding potential data contamination during the pre-training stage. Furthermore, standard evaluation benchmarks, which are typically static, fail to capture the complexities of real-world CL scenarios, resulting in saturated performance. To address these issues, we describe CL on dynamic benchmarks (CLDyB), a general computational framework based on Markov decision processes for evaluating CL methods reliably. CLDyB dynamically identifies inherently difficult and algorithm-dependent tasks for the given CL methods, and determines challenging task orders using Monte Carlo tree search. Leveraging CLDyB, we first conduct a joint evaluation of multiple state-of-the-art CL methods, leading to a set of commonly challenging and generalizable task sequences where existing CL methods tend to perform poorly. We then conduct separate evaluations of individual CL methods using CLDyB, discovering their respective strengths and weaknesses. The source code and generated task sequences are publicly accessible at https://github.com/szc12153/CLDyB.

cs.LG↗

arXiv2025

Anyprefer: An Agentic Framework for Preference Data Synthesis

High-quality preference data is essential for aligning foundation models with human values through preference learning. However, manual annotation of such data is often time-consuming and costly. Recent methods often adopt a self-rewarding approach, where the target model generates and annotates its own preference data, but this can lead to inaccuracies since the reward model shares weights with the target model, thereby amplifying inherent biases. To address these issues, we propose Anyprefer, a framework designed to synthesize high-quality preference data for aligning the target model. Anyprefer frames the data synthesis process as a cooperative two-player Markov Game, where the target model and the judge model collaborate together. Here, a series of external tools are introduced to assist the judge model in accurately rewarding the target model's responses, mitigating biases in the rewarding process. In addition, a feedback mechanism is introduced to optimize prompts for both models, enhancing collaboration and improving data quality. The synthesized data is compiled into a new preference dataset, Anyprefer-V1, consisting of 58K high-quality preference pairs. Extensive experiments show that Anyprefer significantly improves model alignment performance across four main applications, covering 21 datasets, achieving average improvements of 18.55% in five natural language generation datasets, 3.66% in nine vision-language understanding datasets, 30.05% in three medical image analysis datasets, and 16.00% in four visuo-motor control tasks.

cs.LG↗

arXiv2025

CREAM: Consistency Regularized Self-Rewarding Language Models

Recent self-rewarding large language models (LLM) have successfully applied LLM-as-a-Judge to iteratively improve the alignment performance without the need of human annotations for preference data. These methods commonly utilize the same LLM to act as both the policy model (which generates responses) and the reward model (which scores and ranks those responses). The ranked responses are then used as preference pairs to train the LLM via direct alignment technologies (e.g. DPO). However, it is noteworthy that throughout this process, there is no guarantee of accuracy in the rewarding and ranking, which is critical for ensuring accurate rewards and high-quality preference data. Empirical results from relatively small LLMs (e.g., 7B parameters) also indicate that improvements from self-rewarding may diminish after several iterations in certain situations, which we hypothesize is due to accumulated bias in the reward system. This bias can lead to unreliable preference data for training the LLM. To address this issue, we first formulate and analyze the generalized iterative preference fine-tuning framework for self-rewarding language model. We then introduce the regularization to this generalized framework to mitigate the overconfident preference labeling in the self-rewarding process. Based on this theoretical insight, we propose a Consistency Regularized sElf-rewarding lAnguage Model (CREAM) that leverages the consistency of rewards across different iterations to regularize the self-rewarding training, helping the model to learn from more reliable preference data. With this explicit regularization, our empirical results demonstrate the superiority of CREAM in improving both reward consistency and alignment performance. The code is publicly available at https://github.com/Raibows/CREAM.

cs.LG↗

arXiv2025

Unlocking the Power of Function Vectors for Characterizing and Mitigating Catastrophic Forgetting in Continual Instruction Tuning

Catastrophic forgetting (CF) poses a significant challenge in machine learning, where a model forgets previously learned information upon learning new tasks. Despite the advanced capabilities of Large Language Models (LLMs), they continue to face challenges with CF during continual learning. The majority of existing research focuses on analyzing forgetting patterns through a singular training sequence, thereby overlooking the intricate effects that diverse tasks have on model behavior. Our study explores CF across various settings, discovering that model forgetting is influenced by both the specific training tasks and the models themselves. To this end, we interpret forgetting by examining the function vector (FV), a compact representation of functions in LLMs, offering a model-dependent indicator for the occurrence of CF. Through theoretical and empirical analyses, we demonstrated that CF in LLMs primarily stems from biases in function activation rather than the overwriting of task processing functions. Leveraging these insights, we propose a novel function vector guided training methodology, incorporating a regularization technique to stabilize the FV and mitigate forgetting. Empirical tests on four benchmarks confirm the effectiveness of our proposed training method, substantiating our theoretical framework concerning CF and model function dynamics. We plan to make our code publicly accessible in the near future.

cs.LG↗

arXiv2025

Learning Visual Generative Priors without Text

Although text-to-image (T2I) models have recently thrived as visual generative priors, their reliance on high-quality text-image pairs makes scaling up expensive. We argue that grasping the cross-modality alignment is not a necessity for a sound visual generative prior, whose focus should be on texture modeling. Such a philosophy inspires us to study image-to-image (I2I) generation, where models can learn from in-the-wild images in a self-supervised manner. We first develop a pure vision-based training framework, Lumos, and confirm the feasibility and the scalability of learning I2I models. We then find that, as an upstream task of T2I, our I2I model serves as a more foundational visual prior and achieves on-par or better performance than existing T2I models using only 1/10 text-image pairs for fine-tuning. We further demonstrate the superiority of I2I priors over T2I priors on some text-irrelevant visual generative tasks, like image-to-3D and image-to-video. Our project page is available at https://ant-research.github.io/lumos.

cs.CV↗

arXiv2025

SD-LoRA: Scalable Decoupled Low-Rank Adaptation for Class Incremental Learning

Continual Learning (CL) with foundation models has recently emerged as a promising paradigm to exploit abundant knowledge acquired during pre-training for tackling sequential tasks. However, existing prompt-based and Low-Rank Adaptation-based (LoRA-based) methods often require expanding a prompt/LoRA pool or retaining samples of previous tasks, which poses significant scalability challenges as the number of tasks grows. To address these limitations, we propose Scalable Decoupled LoRA (SD-LoRA) for class incremental learning, which continually separates the learning of the magnitude and direction of LoRA components without rehearsal. Our empirical and theoretical analysis reveals that SD-LoRA tends to follow a low-loss trajectory and converges to an overlapping low-loss region for all learned tasks, resulting in an excellent stability-plasticity trade-off. Building upon these insights, we introduce two variants of SD-LoRA with further improved parameter efficiency. All parameters of SD-LoRAs can be end-to-end optimized for CL objectives. Meanwhile, they support efficient inference by allowing direct evaluation with the finally trained model, obviating the need for component selection. Extensive experiments across multiple CL benchmarks and foundation models consistently validate the effectiveness of SD-LoRA. The code is available at https://github.com/WuYichen-97/SD-Lora-CL.

cs.LG↗

arXiv2025

Learning to Substitute Components for Compositional Generalization

Despite the rising prevalence of neural language models, recent empirical evidence suggests their deficiency in compositional generalization. One of the current de-facto solutions to this problem is compositional data augmentation, which aims to introduce additional compositional inductive bias. However, existing handcrafted augmentation strategies offer limited improvement when systematic generalization of neural language models requires multi-grained compositional bias (i.e., not limited to either lexical or structural biases alone) or when training sentences have an imbalanced difficulty distribution. To address these challenges, we first propose a novel compositional augmentation strategy called Component Substitution (CompSub), which enables multi-grained composition of substantial substructures across the entire training set. Furthermore, we introduce the Learning Component Substitution (LCS) framework. This framework empowers the learning of component substitution probabilities in CompSub in an end-to-end manner by maximizing the loss of neural language models, thereby prioritizing challenging compositions with elusive concepts and novel contexts. We extend the key ideas of CompSub and LCS to the recently emerging in-context learning scenarios of pre-trained large language models (LLMs), proposing the LCS-ICL algorithm to enhance the few-shot compositional generalization of state-of-the-art (SOTA) LLMs. Theoretically, we provide insights into why applying our algorithms to language models can improve compositional generalization performance. Empirically, our results on four standard compositional generalization benchmarks(SCAN, COGS, GeoQuery, and COGS-QL) demonstrate the superiority of CompSub, LCS, and LCS-ICL, with improvements of up to 66.5%, 10.3%, 1.4%, and 8.8%, respectively.

cs.CL↗

arXiv2024

A unified quantile framework for nonlinear heterogeneous transcriptome-wide associations

Transcriptome-wide association studies (TWAS) are powerful tools for identifying gene-level associations by integrating genome-wide association studies and gene expression data. However, most TWAS methods focus on linear associations between genes and traits, ignoring the complex nonlinear relationships that may be present in biological systems. To address this limitation, we propose a novel framework, QTWAS, which integrates a quantile-based gene expression model into the TWAS model, allowing for the discovery of nonlinear and heterogeneous gene-trait associations. Via comprehensive simulations and applications to both continuous and binary traits, we demonstrate that the proposed model is more powerful than conventional TWAS in identifying gene-trait associations.

stat.ME↗