Sirui Ding

Daochen Zha, Kwei-Herng Lai, Qiaoyu Tan et al.

Imbalanced learning is a fundamental challenge in data mining, where there is a disproportionate ratio of training samples in each class. Over-sampling is an effective technique to tackle imbalanced learning through generating synthetic samples for the minority class. While numerous over-sampling algorithms have been proposed, they heavily rely on heuristics, which could be sub-optimal since we may need different sampling strategies for different datasets and base classifiers, and they cannot directly optimize the performance metric. Motivated by this, we investigate developing a learning-based over-sampling algorithm to optimize the classification performance, which is a challenging task because of the huge and hierarchical decision space. At the high level, we need to decide how many synthetic samples to generate. At the low level, we need to determine where the synthetic samples should be located, which depends on the high-level decision since the optimal locations of the samples may differ for different numbers of samples. To address the challenges, we propose AutoSMOTE, an automated over-sampling algorithm that can jointly optimize different levels of decisions. Motivated by the success of SMOTE~\cite{chawla2002smote} and its extensions, we formulate the generation process as a Markov decision process (MDP) consisting of three levels of policies to generate synthetic samples within the SMOTE search space. Then we leverage deep hierarchical reinforcement learning to optimize the performance metric on the validation data. Extensive experiments on six real-world datasets demonstrate that AutoSMOTE significantly outperforms the state-of-the-art resampling algorithms. The code is at https://github.com/daochenzha/autosmote

Yi Fang, Haoran Xu, Jiaxin Han et al.

Foundation models have revolutionized various fields such as natural language processing (NLP) and computer vision (CV). While efforts have been made to transfer the success of the foundation models in general AI domains to biology, existing works focus on directly adopting the existing foundation model architectures from general machine learning domains without a systematic design considering the unique physicochemical and structural properties of each biological data modality. This leads to suboptimal performance, as these repurposed architectures struggle to capture the long-range dependencies, sparse information, and complex underlying ``grammars'' inherent to biological data. To address this gap, we introduce BioArc, a novel framework designed to move beyond intuition-driven architecture design towards principled, automated architecture discovery for biological foundation models. Leveraging Neural Architecture Search (NAS), BioArc systematically explores a vast architecture design space, evaluating architectures across multiple biological modalities while rigorously analyzing the interplay between architecture, tokenization, and training strategies. This large-scale analysis identifies novel, high-performance architectures, allowing us to distill a set of empirical design principles to guide future model development. Furthermore, to make the best of this set of discovered principled architectures, we propose and compare several architecture prediction methods that effectively and efficiently predict optimal architectures for new biological tasks. Overall, our work provides a foundational resource and a principled methodology to guide the creation of the next generation of task-specific and foundation models for biology.

Shuang Zhou, Zidu Xu, Mian Zhang et al.

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the increasing attention in this field, a holistic view is still lacking. Many critical aspects remain unclear, such as the diseases and clinical data to which LLMs have been applied, the LLM techniques employed, and the evaluation methods used. In this article, we perform a comprehensive review of LLM-based methods for disease diagnosis. Our review examines the existing literature across various dimensions, including disease types and associated clinical specialties, clinical data, LLM techniques, and evaluation methods. Additionally, we offer recommendations for applying and evaluating LLMs for diagnostic tasks. Furthermore, we assess the limitations of current research and discuss future directions. To our knowledge, this is the first comprehensive review for LLM-based disease diagnosis.

Sirui Ding, Ruixiang Tang, Daochen Zha et al.

Liver transplant is an essential therapy performed for severe liver diseases. The fact of scarce liver resources makes the organ assigning crucial. Model for End-stage Liver Disease (MELD) score is a widely adopted criterion when making organ distribution decisions. However, it ignores post-transplant outcomes and organ/donor features. These limitations motivate the emergence of machine learning (ML) models. Unfortunately, ML models could be unfair and trigger bias against certain groups of people. To tackle this problem, this work proposes a fair machine learning framework targeting graft failure prediction in liver transplant. Specifically, knowledge distillation is employed to handle dense and sparse features by combining the advantages of tree models and neural networks. A two-step debiasing method is tailored for this framework to enhance fairness. Experiments are conducted to analyze unfairness issues in existing models and demonstrate the superiority of our method in both prediction and fairness performance.

Chia-Yuan Chang, Jiayi Yuan, Sirui Ding et al.

Clinical trials are indispensable in developing new treatments, but they face obstacles in patient recruitment and retention, hindering the enrollment of necessary participants. To tackle these challenges, deep learning frameworks have been created to match patients to trials. These frameworks calculate the similarity between patients and clinical trial eligibility criteria, considering the discrepancy between inclusion and exclusion criteria. Recent studies have shown that these frameworks outperform earlier approaches. However, deep learning models may raise fairness issues in patient-trial matching when certain sensitive groups of individuals are underrepresented in clinical trials, leading to incomplete or inaccurate data and potential harm. To tackle the issue of fairness, this work proposes a fair patient-trial matching framework by generating a patient-criterion level fairness constraint. The proposed framework considers the inconsistency between the embedding of inclusion and exclusion criteria among patients of different sensitive groups. The experimental results on real-world patient-trial and patient-criterion matching tasks demonstrate that the proposed framework can successfully alleviate the predictions that tend to be biased.

Sirui Ding, Qiaoyu Tan, Chia-yuan Chang et al.

Organ transplant is the essential treatment method for some end-stage diseases, such as liver failure. Analyzing the post-transplant cause of death (CoD) after organ transplant provides a powerful tool for clinical decision making, including personalized treatment and organ allocation. However, traditional methods like Model for End-stage Liver Disease (MELD) score and conventional machine learning (ML) methods are limited in CoD analysis due to two major data and model-related challenges. To address this, we propose a novel framework called CoD-MTL leveraging multi-task learning to model the semantic relationships between various CoD prediction tasks jointly. Specifically, we develop a novel tree distillation strategy for multi-task learning, which combines the strength of both the tree model and multi-task learning. Experimental results are presented to show the precise and reliable CoD predictions of our framework. A case study is conducted to demonstrate the clinical importance of our method in the liver transplant.

Shenghan Zhang, Haoxuan Li, Ruixiang Tang et al.

Detailed phenotype information is fundamental to accurate diagnosis and risk estimation of diseases. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from the heterogeneous EHR data remains a challenge. In this work, we present PheME, an Ensemble framework using Multi-modality data of structured EHRs and unstructured clinical notes for accurate Phenotype prediction. Firstly, we employ multiple deep neural networks to learn reliable representations from the sparse structured EHR data and redundant clinical notes. A multi-modal model then aligns multi-modal features onto the same latent space to predict phenotypes. Secondly, we leverage ensemble learning to combine outputs from single-modal models and multi-modal models to improve phenotype predictions. We choose seven diseases to evaluate the phenotyping performance of the proposed framework. Experimental results show that using multi-modal data significantly improves phenotype prediction in all diseases, the proposed ensemble learning framework can further boost the performance.

Shuang Zhou, Mingquan Lin, Sirui Ding et al.

Automatic differential diagnosis (DDx) is an essential medical task that generates a list of potential diseases as differentials based on patient symptom descriptions. In practice, interpreting these differential diagnoses yields significant value but remains under-explored. Given the powerful capabilities of large language models (LLMs), we investigated using LLMs for interpretable DDx. Specifically, we curated the first DDx dataset with expert-derived interpretation on 570 clinical notes. Besides, we proposed Dual-Inf, a novel framework that enabled LLMs to conduct bidirectional inference (i.e., from symptoms to diagnoses and vice versa) for DDx interpretation. Both human and automated evaluation validated its efficacy in predicting and elucidating differentials across four base LLMs. In addition, Dual-Inf could reduce interpretation errors and hold promise for rare disease explanations. To the best of our knowledge, it is the first work that customizes LLMs for DDx explanation and comprehensively evaluates their interpretation performance. Overall, our study bridges a critical gap in DDx interpretation and enhances clinical decision-making.

Yi Fang, Bowen Jin, Jiacheng Shen et al.

The rapid development of Multimodal Large Language Models (MLLMs) has enabled the integration of multiple modalities, including texts and images, within the large language model (LLM) framework. However, texts and images are usually interconnected, forming a multimodal attributed graph (MMAG). It is underexplored how MLLMs can incorporate the relational information (\textit{i.e.}, graph structure) and semantic information (\textit{i.e.,} texts and images) on such graphs for multimodal comprehension and generation. In this paper, we propose GraphGPT-o, which supports omni-multimodal understanding and creation on MMAGs. We first comprehensively study linearization variants to transform semantic and structural information as input for MLLMs. Then, we propose a hierarchical aligner that enables deep graph encoding, bridging the gap between MMAGs and MLLMs. Finally, we explore the inference choices, adapting MLLM to interleaved text and image generation in graph scenarios. Extensive experiments on three datasets from different domains demonstrate the effectiveness of our proposed method. Datasets and codes will be open-sourced upon acceptance.

Yuhao Xu, Xiaoda Wang, Jiaying Lu et al.

Electrocardiogram (ECG) analysis plays a vital role in the early detection, monitoring, and management of various cardiovascular conditions. While existing models have achieved notable success in ECG interpretation, they fail to leverage the interrelated nature of various cardiac abnormalities. Conversely, developing a specific model capable of extracting all relevant features for multiple ECG tasks remains a significant challenge. Large-scale foundation models, though powerful, are not typically pretrained on ECG data, making full re-training or fine-tuning computationally expensive. To address these challenges, we propose EnECG(Mixture of Experts-based Ensemble Learning for ECG Multi-tasks), an ensemble-based framework that integrates multiple specialized foundation models, each excelling in different aspects of ECG interpretation. Instead of relying on a single model or single task, EnECG leverages the strengths of multiple specialized models to tackle a variety of ECG-based tasks. To mitigate the high computational cost of full re-training or fine-tuning, we introduce a lightweight adaptation strategy: attaching dedicated output layers to each foundation model and applying Low-Rank Adaptation (LoRA) only to these newly added parameters. We then adopt a Mixture of Experts (MoE) mechanism to learn ensemble weights, effectively combining the complementary expertise of individual models. Our experimental results demonstrate that by minimizing the scope of fine-tuning, EnECG can help reduce computational and memory costs while maintaining the strong representational power of foundation models. This framework not only enhances feature extraction and predictive performance but also ensures practical efficiency for real-world clinical applications. The code is available at https://github.com/yuhaoxu99/EnECG.git.

Yuhao Xu, Jiaying Lu, Sirui Ding et al.

In the process of patient diagnosis, non-invasive measurements are widely used due to their low risks and quick results. Electrocardiogram (ECG), as a non-invasive method to collect heart activities, is used to diagnose cardiac conditions. Analyzing the ECG typically requires domain expertise, which is a roadblock to applying artificial intelligence (AI) for healthcare. Through advances in self-supervised learning and foundation models, AI systems can now acquire and leverage domain knowledge without relying solely on human expertise. However, there is a lack of comprehensive analyses over the foundation models' performance on ECG. This study aims to answer the research question: "Are Foundation Models Useful for ECG Analysis?" To address it, we evaluate language/general time-series/ECG foundation models in comparison with time-series deep learning models. The experimental results show that general time-series/ECG foundation models achieve a top performance rate of 80%, indicating their effectiveness in ECG analysis. In-depth analyses and insights are provided along with comprehensive experimental results. This study highlights the limitations and potential of foundation models in advancing physiological waveform analysis. The data and code for this benchmark are publicly available at https://github.com/yuhaoxu99/ECGMultitasks-Benchmark.

Yuyan Liu, Sirui Ding, Sheng Zhou et al.

Molecular property prediction (MPP) is a fundamental and crucial task in drug discovery. However, prior methods are limited by the requirement for a large number of labeled molecules and their restricted ability to generalize for unseen and new tasks, both of which are essential for real-world applications. To address these challenges, we present MolecularGPT for few-shot MPP. From a perspective on instruction tuning, we fine-tune large language models (LLMs) based on curated molecular instructions spanning over 1000 property prediction tasks. This enables building a versatile and specialized LLM that can be adapted to novel MPP tasks without any fine-tuning through zero- and few-shot in-context learning (ICL). MolecularGPT exhibits competitive in-context reasoning capabilities across 10 downstream evaluation datasets, setting new benchmarks for few-shot molecular prediction tasks. More importantly, with just two-shot examples, MolecularGPT can outperform standard supervised graph neural network methods on 4 out of 7 datasets. It also excels state-of-the-art LLM baselines by up to 15.7% increase on classification accuracy and decrease of 17.9 on regression metrics (e.g., RMSE) under zero-shot. This study demonstrates the potential of LLMs as effective few-shot molecular property predictors. The code is available at https://github.com/NYUSHCS/MolecularGPT.

Yi Fang, Dongzhe Fan, Sirui Ding et al.

Representation learning on text-attributed graphs (TAGs), where nodes are represented by textual descriptions, is crucial for textual and relational knowledge systems and recommendation systems. Currently, state-of-the-art embedding methods for TAGs primarily focus on fine-tuning language models (e.g., BERT) using structure-aware training signals. While effective, these methods are tailored for individual TAG and cannot generalize across various graph scenarios. Given the shared textual space, leveraging multiple TAGs for joint fine-tuning, aligning text and graph structure from different aspects, would be more beneficial. Motivated by this, we introduce a novel Unified Graph Language Model (UniGLM) framework, the first graph embedding model that generalizes well to both in-domain and cross-domain TAGs. Specifically, UniGLM is trained over multiple TAGs with different domains and scales using self-supervised contrastive learning. UniGLM includes an adaptive positive sample selection technique for identifying structurally similar nodes and a lazy contrastive module that is devised to accelerate training by minimizing repetitive encoding calculations. Extensive empirical results across 9 benchmark TAGs demonstrate UniGLM's efficacy against leading embedding baselines in terms of generalization (various downstream tasks and backbones) and transfer learning (in and out of domain scenarios). The code is available at https://github.com/NYUSHCS/UniGLM.

Daochen Zha, Zaid Pervaiz Bhat, Yi-Wei Chen et al.

Action recognition is an important task for video understanding with broad applications. However, developing an effective action recognition solution often requires extensive engineering efforts in building and testing different combinations of the modules and their hyperparameters. In this demo, we present AutoVideo, a Python system for automated video action recognition. AutoVideo is featured for 1) highly modular and extendable infrastructure following the standard pipeline language, 2) an exhaustive list of primitives for pipeline construction, 3) data-driven tuners to save the efforts of pipeline tuning, and 4) easy-to-use Graphical User Interface (GUI). AutoVideo is released under MIT license at https://github.com/datamllab/autovideo

Shaojie Wang, Sirui Ding, Na Zou

Recent advances in large language models (LLMs) have revolutionized natural language processing, yet evaluating their intrinsic linguistic understanding remains challenging. Moving beyond specialized evaluation tasks, we propose an information-theoretic framework grounded in mutual information (MI) to achieve this. We formalize the understanding as MI between an input sentence and its latent representation (sentence-level MI), measuring how effectively input information is preserved in latent representation. Given that LLMs learn embeddings for individual tokens, we decompose sentence-level MI into token-level MI between tokens and sentence embeddings, establishing theoretical bounds connecting these measures. Based on this foundation, we theoretically derive a computable lower bound for token-level MI using Fano's inequality, which directly relates to token-level recoverability-the ability to predict original tokens from sentence embedding. We implement this recoverability task to comparatively measure MI across different LLMs, revealing that encoder-only models consistently maintain higher information fidelity than their decoder-only counterparts, with the latter exhibiting a distinctive late-layer "forgetting" pattern where mutual information is first enhanced and then discarded. Moreover, fine-tuning to maximize token-level recoverability consistently improves understanding ability of LLMs on tasks without task-specific supervision, demonstrating that mutual information can serve as a foundation for understanding and improving language model capabilities.

Yu-Neng Chuang, Songchen Li, Jiayi Yuan et al.

Time Series Forecasting (TSF) has long been a challenge in time series analysis. Inspired by the success of Large Language Models (LLMs), researchers are now developing Large Time Series Models (LTSMs)-universal transformer-based models that use autoregressive prediction-to improve TSF. However, training LTSMs on heterogeneous time series data poses unique challenges, including diverse frequencies, dimensions, and patterns across datasets. Recent endeavors have studied and evaluated various design choices aimed at enhancing LTSM training and generalization capabilities. However, these design choices are typically studied and evaluated in isolation and are not benchmarked collectively. In this work, we introduce LTSM-Bundle, a comprehensive toolbox, and benchmark for training LTSMs, spanning pre-processing techniques, model configurations, and dataset configuration. It modularized and benchmarked LTSMs from multiple dimensions, encompassing prompting strategies, tokenization approaches, training paradigms, base model selection, data quantity, and dataset diversity. Furthermore, we combine the most effective design choices identified in our study. Empirical results demonstrate that this combination achieves superior zero-shot and few-shot performances compared to state-of-the-art LTSMs and traditional TSF methods on benchmark datasets.

Haofan Wang, Zifan Wang, Mengnan Du et al.

Recently, increasing attention has been drawn to the internal mechanisms of convolutional neural networks, and the reason why the network makes specific decisions. In this paper, we develop a novel post-hoc visual explanation method called Score-CAM based on class activation mapping. Unlike previous class activation mapping based approaches, Score-CAM gets rid of the dependence on gradients by obtaining the weight of each activation map through its forward passing score on target class, the final result is obtained by a linear combination of weights and activation maps. We demonstrate that Score-CAM achieves better visual performance and fairness for interpreting the decision making process. Our approach outperforms previous methods on both recognition and localization tasks, it also passes the sanity check. We also indicate its application as debugging tools. Official code has been released.