arXiv subjects

Junzhou Huang

Publications and source records attributed to Junzhou Huang.

At least 37 records · Page 2Linked to original sources

arXiv2025

Leveraging Gait Patterns as Biomarkers: An attention-guided Deep Multiple Instance Learning Network for Scoliosis Classification

Scoliosis is a spinal curvature disorder that is difficult to detect early and can compress the chest cavity, impacting respiratory function and cardiac health. Especially for adolescents, delayed detection and treatment result in worsening compression. Traditional scoliosis detection methods heavily rely on clinical expertise, and X-ray imaging poses radiation risks, limiting large-scale early screening. We propose an Attention-Guided Deep Multi-Instance Learning method (Gait-MIL) to effectively capture discriminative features from gait patterns, which is inspired by ScoNet-MT's pioneering use of gait patterns for scoliosis detection. We evaluate our method on the first large-scale dataset based on gait patterns for scoliosis classification. The results demonstrate that our study improves the performance of using gait as a biomarker for scoliosis detection, significantly enhances detection accuracy for the particularly challenging Neutral cases, where subtle indicators are often overlooked. Our Gait-MIL also performs robustly in imbalanced scenarios, making it a promising tool for large-scale scoliosis screening.

cs.CV↗

arXiv2025

InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

cs.LG↗

arXiv2025

DELST: Dual Entailment Learning for Hyperbolic Image-Gene Pretraining in Spatial Transcriptomics

Spatial transcriptomics (ST) maps gene expression within tissue at individual spots, making it a valuable resource for multimodal representation learning. Additionally, ST inherently contains rich hierarchical information both across and within modalities. For instance, different spots exhibit varying numbers of nonzero gene expressions, corresponding to different levels of cellular activity and semantic hierarchies. However, existing methods rely on contrastive alignment of image-gene pairs, failing to accurately capture the intricate hierarchical relationships in ST data. Here, we propose DELST, the first framework to embed hyperbolic representations while modeling hierarchy for image-gene pretraining at two levels: (1) Cross-modal entailment learning, which establishes an order relationship between genes and images to enhance image representation generalization; (2) Intra-modal entailment learning, which encodes gene expression patterns as hierarchical relationships, guiding hierarchical learning across different samples at a global scale and integrating biological insights into single-modal representations. Extensive experiments on ST benchmarks annotated by pathologists demonstrate the effectiveness of our framework, achieving improved predictive performance compared to existing methods. Our code and models are available at: https://github.com/XulinChen/DELST.

cs.CV↗

arXiv2025

Natural Language-Assisted Multi-modal Medication Recommendation

Combinatorial medication recommendation(CMR) is a fundamental task of healthcare, which offers opportunities for clinical physicians to provide more precise prescriptions for patients with intricate health conditions, particularly in the scenarios of long-term medical care. Previous research efforts have sought to extract meaningful information from electronic health records (EHRs) to facilitate combinatorial medication recommendations. Existing learning-based approaches further consider the chemical structures of medications, but ignore the textual medication descriptions in which the functionalities are clearly described. Furthermore, the textual knowledge derived from the EHRs of patients remains largely underutilized. To address these issues, we introduce the Natural Language-Assisted Multi-modal Medication Recommendation(NLA-MMR), a multi-modal alignment framework designed to learn knowledge from the patient view and medication view jointly. Specifically, NLA-MMR formulates CMR as an alignment problem from patient and medication modalities. In this vein, we employ pretrained language models(PLMs) to extract in-domain knowledge regarding patients and medications, serving as the foundational representation for both modalities. In the medication modality, we exploit both chemical structures and textual descriptions to create medication representations. In the patient modality, we generate the patient representations based on textual descriptions of diagnosis, procedure, and symptom. Extensive experiments conducted on three publicly accessible datasets demonstrate that NLA-MMR achieves new state-of-the-art performance, with a notable average improvement of 4.72% in Jaccard score. Our source code is publicly available on https://github.com/jtan1102/NLA-MMR_CIKM_2024.

cs.AI↗

arXiv2025

GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction

Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and exhaustive wet lab experiments. Existing methods of automatic function annotation or prediction mainly focus on protein function prediction with sequence, 3D-structures or protein family information. In this study, we propose to tackle the gene function prediction problem by exploring Gene Ontology graph and annotation with BERT (GoBERT) to decipher the underlying relationships among gene functions. Our proposed novel function prediction task utilizes existing functions as inputs and generalizes the function prediction to gene and gene products. Specifically, two pre-train tasks are designed to jointly train GoBERT to capture both explicit and implicit relations of functions. Neighborhood prediction is a self-supervised multi-label classification task that captures the explicit function relations. Specified masking and recovering task helps GoBERT in finding implicit patterns among functions. The pre-trained GoBERT possess the ability to predict novel functions for various gene and gene products based on known functional annotations. Extensive experiments, biological case studies, and ablation studies are conducted to demonstrate the superiority of our proposed GoBERT.

cs.LG↗

arXiv2024

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers

Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual datasets to ensure reliable results. Ontology graphs, neatly organized domain terminology graphs, provide ideal sources for domain facts. However, available gene ontology annotations are currently distributed across various databases without unified identifiers for genes and gene products. To address these challenges, we introduce Unified Entrez Gene Identifier Dataset and Benchmarks (UniEntrezDB), the first systematic effort to unify large-scale public Gene Ontology Annotations (GOA) from various databases using unique gene identifiers. UniEntrezDB includes a pre-training dataset and four downstream tasks designed to comprehensively evaluate gene embedding performance from gene, protein, and cell levels, ultimately enhancing the reliability and applicability of LLMs in gene research and other professional settings.

cs.DB↗

arXiv2024

Compositional Image Retrieval via Instruction-Aware Contrastive Learning

Composed Image Retrieval (CIR) involves retrieving a target image based on a composed query of an image paired with text that specifies modifications or changes to the visual reference. CIR is inherently an instruction-following task, as the model needs to interpret and apply modifications to the image. In practice, due to the scarcity of annotated data in downstream tasks, Zero-Shot CIR (ZS-CIR) is desirable. While existing ZS-CIR models based on CLIP have shown promising results, their capability in interpreting and following modification instructions remains limited. Some research attempts to address this by incorporating Large Language Models (LLMs). However, these approaches still face challenges in effectively integrating multimodal information and instruction understanding. To tackle above challenges, we propose a novel embedding method utilizing an instruction-tuned Multimodal LLM (MLLM) to generate composed representation, which significantly enhance the instruction following capability for a comprehensive integration between images and instructions. Nevertheless, directly applying MLLMs introduces a new challenge since MLLMs are primarily designed for text generation rather than embedding extraction as required in CIR. To address this, we introduce a two-stage training strategy to efficiently learn a joint multimodal embedding space and further refining the ability to follow modification instructions by tuning the model in a triplet dataset similar to the CIR format. Extensive experiments on four public datasets: FashionIQ, CIRR, GeneCIS, and CIRCO demonstrates the superior performance of our model, outperforming state-of-the-art baselines by a significant margin. Codes are available at the GitHub repository.

cs.CV↗

arXiv2024

CARES: A Comprehensive Benchmark of Trustworthiness in Medical Vision Language Models

Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing significant risks for future model deployment. In this paper, we introduce CARES and aim to comprehensively evaluate the Trustworthiness of Med-LVLMs across the medical domain. We assess the trustworthiness of Med-LVLMs across five dimensions, including trustfulness, fairness, safety, privacy, and robustness. CARES comprises about 41K question-answer pairs in both closed and open-ended formats, covering 16 medical image modalities and 27 anatomical regions. Our analysis reveals that the models consistently exhibit concerns regarding trustworthiness, often displaying factual inaccuracies and failing to maintain fairness across different demographic groups. Furthermore, they are vulnerable to attacks and demonstrate a lack of privacy awareness. We publicly release our benchmark and code in https://cares-ai.github.io/.

cs.LG↗

arXiv2024

Distribution-Free Fair Federated Learning with Small Samples

As federated learning gains increasing importance in real-world applications due to its capacity for decentralized data training, addressing fairness concerns across demographic groups becomes critically important. However, most existing machine learning algorithms for ensuring fairness are designed for centralized data environments and generally require large-sample and distributional assumptions, underscoring the urgent need for fairness techniques adapted for decentralized and heterogeneous systems with finite-sample and distribution-free guarantees. To address this issue, this paper introduces FedFaiREE, a post-processing algorithm developed specifically for distribution-free fair learning in decentralized settings with small samples. Our approach accounts for unique challenges in decentralized environments, such as client heterogeneity, communication costs, and small sample sizes. We provide rigorous theoretical guarantees for both fairness and accuracy, and our experimental results further provide robust empirical validation for our proposed method.

stat.ML↗

arXiv2024

PathM3: A Multimodal Multi-Task Multiple Instance Learning Framework for Whole Slide Image Classification and Captioning

In the field of computational histopathology, both whole slide images (WSIs) and diagnostic captions provide valuable insights for making diagnostic decisions. However, aligning WSIs with diagnostic captions presents a significant challenge. This difficulty arises from two main factors: 1) Gigapixel WSIs are unsuitable for direct input into deep learning models, and the redundancy and correlation among the patches demand more attention; and 2) Authentic WSI diagnostic captions are extremely limited, making it difficult to train an effective model. To overcome these obstacles, we present PathM3, a multimodal, multi-task, multiple instance learning (MIL) framework for WSI classification and captioning. PathM3 adapts a query-based transformer to effectively align WSIs with diagnostic captions. Given that histopathology visual patterns are redundantly distributed across WSIs, we aggregate each patch feature with MIL method that considers the correlations among instances. Furthermore, our PathM3 overcomes data scarcity in WSI-level captions by leveraging limited WSI diagnostic caption data in the manner of multi-task joint learning. Extensive experiments with improved classification accuracy and caption generation demonstrate the effectiveness of our method on both WSI classification and captioning task.

cs.CV↗

arXiv2024

Enhancing Multimodal Large Language Models with Multi-instance Visual Prompt Generator for Visual Representation Enrichment

Multimodal Large Language Models (MLLMs) have achieved SOTA performance in various visual language tasks by fusing the visual representations with LLMs leveraging some visual adapters. In this paper, we first establish that adapters using query-based Transformers such as Q-former is a simplified Multi-instance Learning method without considering instance heterogeneity/correlation. We then propose a general component termed Multi-instance Visual Prompt Generator (MIVPG) to incorporate enriched visual representations into LLMs by taking advantage of instance correlation between images or patches for the same sample. Quantatitive evaluation on three public vision-language (VL) datasets from different scenarios shows that the proposed MIVPG improves Q-former in main VL tasks.

cs.CV↗

arXiv2024

Spectrum-Aware Parameter Efficient Fine-Tuning for Diffusion Models

Adapting large-scale pre-trained generative models in a parameter-efficient manner is gaining traction. Traditional methods like low rank adaptation achieve parameter efficiency by imposing constraints but may not be optimal for tasks requiring high representation capacity. We propose a novel spectrum-aware adaptation framework for generative models. Our method adjusts both singular values and their basis vectors of pretrained weights. Using the Kronecker product and efficient Stiefel optimizers, we achieve parameter-efficient adaptation of orthogonal matrices. We introduce Spectral Orthogonal Decomposition Adaptation (SODA), which balances computational efficiency and representation capacity. Extensive evaluations on text-to-image diffusion models demonstrate SODA's effectiveness, offering a spectrum-aware alternative to existing fine-tuning methods.

cs.CV↗

arXiv2024

Segment Any Cell: A SAM-based Auto-prompting Fine-tuning Framework for Nuclei Segmentation

In the rapidly evolving field of AI research, foundational models like BERT and GPT have significantly advanced language and vision tasks. The advent of pretrain-prompting models such as ChatGPT and Segmentation Anything Model (SAM) has further revolutionized image segmentation. However, their applications in specialized areas, particularly in nuclei segmentation within medical imaging, reveal a key challenge: the generation of high-quality, informative prompts is as crucial as applying state-of-the-art (SOTA) fine-tuning techniques on foundation models. To address this, we introduce Segment Any Cell (SAC), an innovative framework that enhances SAM specifically for nuclei segmentation. SAC integrates a Low-Rank Adaptation (LoRA) within the attention layer of the Transformer to improve the fine-tuning process, outperforming existing SOTA methods. It also introduces an innovative auto-prompt generator that produces effective prompts to guide segmentation, a critical factor in handling the complexities of nuclei segmentation in biomedical imaging. Our extensive experiments demonstrate the superiority of SAC in nuclei segmentation tasks, proving its effectiveness as a tool for pathologists and researchers. Our contributions include a novel prompt generation strategy, automated adaptability for diverse segmentation tasks, the innovative application of Low-Rank Attention Adaptation in SAM, and a versatile framework for semantic segmentation challenges.

eess.IV↗

arXiv2023

MIVC: Multiple Instance Visual Component for Visual-Language Models

Vision-language models have been widely explored across a wide range of tasks and achieve satisfactory performance. However, it's under-explored how to consolidate entity understanding through a varying number of images and to align it with the pre-trained language models for generative tasks. In this paper, we propose MIVC, a general multiple instance visual component to bridge the gap between various image inputs with off-the-shelf vision-language models by aggregating visual representations in a permutation-invariant fashion through a neural network. We show that MIVC could be plugged into the visual-language models to improve the model performance consistently on visual question answering, classification and captioning tasks on a public available e-commerce dataset with multiple images per product. Furthermore, we show that the component provides insight into the contribution of each image to the downstream tasks.

cs.CV↗

arXiv2023

ChatGraph: Interpretable Text Classification by Converting ChatGPT Knowledge to Graphs

ChatGPT, as a recently launched large language model (LLM), has shown superior performance in various natural language processing (NLP) tasks. However, two major limitations hinder its potential applications: (1) the inflexibility of finetuning on downstream tasks and (2) the lack of interpretability in the decision-making process. To tackle these limitations, we propose a novel framework that leverages the power of ChatGPT for specific tasks, such as text classification, while improving its interpretability. The proposed framework conducts a knowledge graph extraction task to extract refined and structural knowledge from the raw data using ChatGPT. The rich knowledge is then converted into a graph, which is further used to train an interpretable linear classifier to make predictions. To evaluate the effectiveness of our proposed method, we conduct experiments on four datasets. The result shows that our method can significantly improve the performance compared to directly utilizing ChatGPT for text classification tasks. And our method provides a more transparent decision-making process compared with previous text classification methods.

cs.CL↗

arXiv2023

Structure-Aware DropEdge Towards Deep Graph Convolutional Networks

It has been discovered that Graph Convolutional Networks (GCNs) encounter a remarkable drop in performance when multiple layers are piled up. The main factor that accounts for why deep GCNs fail lies in over-smoothing, which isolates the network output from the input with the increase of network depth, weakening expressivity and trainability. In this paper, we start by investigating refined measures upon DropEdge -- an existing simple yet effective technique to relieve over-smoothing. We term our method as DropEdge++ for its two structure-aware samplers in contrast to DropEdge: layer-dependent sampler and feature-dependent sampler. Regarding the layer-dependent sampler, we interestingly find that increasingly sampling edges from the bottom layer yields superior performance than the decreasing counterpart as well as DropEdge. We theoretically reveal this phenomenon with Mean-Edge-Number (MEN), a metric closely related to over-smoothing. For the feature-dependent sampler, we associate the edge sampling probability with the feature similarity of node pairs, and prove that it further correlates the convergence subspace of the output layer with the input features. Extensive experiments on several node classification benchmarks, including both full- and semi- supervised tasks, illustrate the efficacy of DropEdge++ and its compatibility with a variety of backbones by achieving generally better performance over DropEdge and the no-drop version.

cs.LG↗

arXiv2023

Noise-robust Graph Learning by Estimating and Leveraging Pairwise Interactions

Teaching Graph Neural Networks (GNNs) to accurately classify nodes under severely noisy labels is an important problem in real-world graph learning applications, but is currently underexplored. Although pairwise training methods have demonstrated promise in supervised metric learning and unsupervised contrastive learning, they remain less studied on noisy graphs, where the structural pairwise interactions (PI) between nodes are abundant and thus might benefit label noise learning rather than the pointwise methods. This paper bridges the gap by proposing a pairwise framework for noisy node classification on graphs, which relies on the PI as a primary learning proxy in addition to the pointwise learning from the noisy node class labels. Our proposed framework PI-GNN contributes two novel components: (1) a confidence-aware PI estimation model that adaptively estimates the PI labels, which are defined as whether the two nodes share the same node labels, and (2) a decoupled training approach that leverages the estimated PI labels to regularize a node classification model for robust node classification. Extensive experiments on different datasets and GNN architectures demonstrate the effectiveness of PI-GNN, yielding a promising improvement over the state-of-the-art methods. Code is publicly available at https://github.com/TianBian95/pi-gnn.

cs.LG↗

arXiv2023

Deep learning-based approach to reveal tumor mutational burden status from whole slide images across multiple cancer types

Tumor mutational burden (TMB) is a potential genomic biomarker of immunotherapy. However, TMB detected through whole exome sequencing lacks clinical penetration in low-resource settings. In this study, we proposed a multi-scale deep learning framework to address the detection of TMB status from routinely used whole slide images for a multiple cancer TMB prediction model (MC- TMB). The MC-TMB achieved a mean area under the curve (AUC) of 0.818 (0.804-0.831) in the cross-validation cohort, which showed superior performance to each single-scale model. The improvements of MC-TMB over the single-tumor models were also confirmed by the ablation tests on x10 magnification, and the highly concerned regions typically correspond to dense lymphocytic infiltration and heteromorphic tumor cells. MC-TMB algorithm also exhibited good generalization on the external validation cohort with an AUC of 0.732 (0.683-0.761), and better performance when compared to other methods. In conclusion, we proposed a deep learning-based approach to reveal tumor mutational burden status from routinely used pathological slides across multiple cancer types.

cs.CV↗