arXiv subjects

Yu-An Huang

Publications and source records attributed to Yu-An Huang.

6 recordsLinked to original sources

arXiv2026

STAIL: Semantic Text-Anchored Incremental Learning for Medical Imaging via Large Language Models

Deep learning models applied to medical image analysis suffer from severe catastrophic forgetting when continually adapting to new clinical tasks in dynamic environments. Mainstream incremental learning methods typically mitigate this by rehearsing raw historical images. However, this pixel-level rehearsal incurs significant storage overhead, raises privacy concerns, and fails to adequately capture the true data distribution with sparse exemplars. Inspired by human cognitive mechanisms, we propose a novel framework termed Semantic Text-Anchored Incremental Learning (STAIL) for sequential clinical tasks. To overcome the rehearsal bottleneck, STAIL introduces an asymmetric semantic consolidation buffer (SCB). By incorporating a minimal set of image anchors and extensive textual descriptions, the SCB enables dense semantic reconstruction of old tasks at a minimal storage cost. Furthermore, we design an LLM-derived Semantic Anchoring Mechanism (LSAM) that leverages the stable semantic space of frozen large language models as developmental priors. This mechanism explicitly anchors evolving visual features to textual representations, guiding and constraining plasticity and stability at both macroscopic and microscopic levels. Extensive experiments across three heterogeneous medical datasets, covering fundus, ultrasound, and X-ray imaging, demonstrate that STAIL acts as a highly effective plug-and-play module. It comprehensively enhances the performance of various existing baselines, achieving average gains of 2.24\% in AAA-AUC for sustained performance and 3.55\% in BWT-AUC for reduced forgetting. Code is available.

cs.CV↗

arXiv2026

Better Eyes, Better Thoughts: Why Vision Chain-of-Thought Fails in Medicine

Large vision-language models (VLMs) often benefit from chain-of-thought (CoT) prompting in general domains, yet its efficacy in medical vision-language tasks remains underexplored. We report a counter-intuitive trend: on medical visual question answering, CoT frequently underperforms direct answering (DirA) across general-purpose and medical-specific models. We attribute this to a \emph{medical perception bottleneck}: subtle, domain-specific cues can weaken visual grounding, and CoT may compound early perceptual uncertainty rather than correct it. To probe this hypothesis, we introduce two training-free, inference-time grounding interventions: (i) \emph{perception anchoring} via region-of-interest cues and (ii) \emph{description grounding} via high-quality textual guidance. Across multiple benchmarks and model families, these interventions improve accuracy, mitigate CoT degradation, and in several settings reverse the CoT--DirA inversion. Our findings suggest that reliable clinical VLMs require robust visual grounding and cross-modal alignment, beyond extending text-driven reasoning chains. Code is available \href{https://github.com/TianYin123/Better_Eyes_Better_Thoughts}{here}.

cs.CV↗

arXiv2025

Med-REFL: Medical Reasoning Enhancement via Self-Corrected Fine-grained Reflection

Large reasoning models excel in domains like mathematics where intermediate reasoning is straightforward to verify, but struggle to self-correct in medicine fields where evaluating intermediate reasoning is cumbersome and expensive. This verification bottleneck hinders the development of reliable AI reasoners for high-stakes application. Here we propose Med-REFL, a novel framework that learns fine-grained reflection without human labels or model distillation. Med-REFL introduces a deterministic structural assessment of the reasoning space to automatically generate preference data for reflection. By globally evaluating all explored reasoning paths in a tree-of-thoughts, our method quantifies the value of corrective actions, enabling the automated construction of direct preference optimization pairs. This trains the model to recognize and amend its own reasoning fallacies. Extensive experiments show Med-REFL delivers robust gains across diverse models architectures and medical benchmarks, boosting a general-purpose Llama3.1-8B by +5.82% and the state-of-the-art Huatuo-o1 by +4.13% on the MedQA benchmark. Our Med-REFL-8B achieves state-of-the-art performance among 7-8B models while even competing with models twice its size. Crucially, targeted ablations prove its success generalizes to other domains such as logical reasoning and mitigates the `fake reflection' phenomenon in LRMs. Ultimately, our framework provides a scalable solution to the verification bottleneck, paving the way for more reliable AI reasoners in high-stakes domains like medicine. Med-REFL has been made publicly available in https://github.com/TianYin123/Med-REFL.

cs.AI↗

arXiv2025

Graph Structure Learning for Tumor Microenvironment with Cell Type Annotation from non-spatial scRNA-seq data

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however, lack spatial context and rely on incomplete datasets of ligand-receptor interactions (LRIs), limiting accurate cell type annotation and cell-cell communication (CCC) inference. This study addresses these challenges using a novel graph neural network (GNN) model that enhances cell type prediction and cell interaction analysis. Our study utilized a dataset consisting of 49,020 cells from 19 patients across three cancer types: Leukemia, Breast Invasive Carcinoma, and Colorectal Cancer. The proposed scGSL model demonstrated robust performance, achieving an average accuracy of 84.83%, precision of 86.23%, recall of 81.51%, and an F1 score of 80.92% across all datasets. These metrics represent a significant enhancement over existing methods, which typically exhibit lower performance metrics. Additionally, by reviewing existing literature on gene interactions within the TME, the scGSL model proves to robustly identify biologically meaningful gene interactions in an unsupervised manner, validated by significant expression differences in key gene pairs across various cancers. The source code and data used in this paper can be found in https://github.com/LiYuechao1998/scGSL.

q-bio.GN↗

arXiv2025

scBIT: Integrating Single-cell Transcriptomic Data into fMRI-based Prediction for Alzheimer's Disease Diagnosis

Functional MRI (fMRI) and single-cell transcriptomics are pivotal in Alzheimer's disease (AD) research, each providing unique insights into neural function and molecular mechanisms. However, integrating these complementary modalities remains largely unexplored. Here, we introduce scBIT, a novel method for enhancing AD prediction by combining fMRI with single-nucleus RNA (snRNA). scBIT leverages snRNA as an auxiliary modality, significantly improving fMRI-based prediction models and providing comprehensive interpretability. It employs a sampling strategy to segment snRNA data into cell-type-specific gene networks and utilizes a self-explainable graph neural network to extract critical subgraphs. Additionally, we use demographic and genetic similarities to pair snRNA and fMRI data across individuals, enabling robust cross-modal learning. Extensive experiments validate scBIT's effectiveness in revealing intricate brain region-gene associations and enhancing diagnostic prediction accuracy. By advancing brain imaging transcriptomics to the single-cell level, scBIT sheds new light on biomarker discovery in AD research. Experimental results show that incorporating snRNA data into the scBIT model significantly boosts accuracy, improving binary classification by 3.39% and five-class classification by 26.59%. The codes were implemented in Python and have been released on GitHub (https://github.com/77YQ77/scBIT) and Zenodo (https://zenodo.org/records/11599030) with detailed instructions.

q-bio.QM↗

arXiv2025

scGSDR: Harnessing Gene Semantics for Single-Cell Pharmacological Profiling

The rise of single-cell sequencing technologies has revolutionized the exploration of drug resistance, revealing the crucial role of cellular heterogeneity in advancing precision medicine. By building computational models from existing single-cell drug response data, we can rapidly annotate cellular responses to drugs in subsequent trials. To this end, we developed scGSDR, a model that integrates two computational pipelines grounded in the knowledge of cellular states and gene signaling pathways, both essential for understanding biological gene semantics. scGSDR enhances predictive performance by incorporating gene semantics and employs an interpretability module to identify key pathways contributing to drug resistance phenotypes. Our extensive validation, which included 16 experiments covering 11 drugs, demonstrates scGSDR's superior predictive accuracy, when trained with either bulk-seq or scRNA-seq data, achieving high AUROC, AUPR, and F1 Scores. The model's application has extended from single-drug predictions to scenarios involving drug combinations. Leveraging pathways of known drug target genes, we found that scGSDR's cell-pathway attention scores are biologically interpretable, which helped us identify other potential drug-related genes. Literature review of top-ranking genes in our predictions such as BCL2, CCND1, the AKT family, and PIK3CA for PLX4720; and ICAM1, VCAM1, NFKB1, NFKBIA, and RAC1 for Paclitaxel confirmed their relevance. In conclusion, scGSDR, by incorporating gene semantics, enhances predictive modeling of cellular responses to diverse drugs, proving invaluable for scenarios involving both single drug and combination therapies and effectively identifying key resistance-related pathways, thus advancing precision medicine and targeted therapy development.

q-bio.GN↗