Chia-Yuan Chang

Guanchu Wang, Junhao Ran, Ruixiang Tang et al.

Despite the impressive capabilities of Large Language Models (LLMs) in general medical domains, questions remain about their performance in diagnosing rare diseases. To answer this question, we aim to assess the diagnostic performance of LLMs in rare diseases, and explore methods to enhance their effectiveness in this area. In this work, we introduce a rare disease question-answering (ReDis-QA) dataset to evaluate the performance of LLMs in diagnosing rare diseases. Specifically, we collected 1360 high-quality question-answer pairs within the ReDis-QA dataset, covering 205 rare diseases. Additionally, we annotated meta-data for each question, facilitating the extraction of subsets specific to any given disease and its property. Based on the ReDis-QA dataset, we benchmarked several open-source LLMs, revealing that diagnosing rare diseases remains a significant challenge for these models. To facilitate retrieval augmentation generation for rare disease diagnosis, we collect the first rare diseases corpus (ReCOP), sourced from the National Organization for Rare Disorders (NORD) database. Specifically, we split the report of each rare disease into multiple chunks, each representing a different property of the disease, including their overview, symptoms, causes, effects, related disorders, diagnosis, and standard therapies. This structure ensures that the information within each chunk aligns consistently with a question. Experiment results demonstrate that ReCOP can effectively improve the accuracy of LLMs on the ReDis-QA dataset by an average of 8%. Moreover, it significantly guides LLMs to generate trustworthy answers and explanations that can be traced back to existing literature.

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.

Chia-Yuan Chang, Yu-Neng Chuang, Guanchu Wang et al.

Domain generalization aims to learn a generalization model that can perform well on unseen test domains by only training on limited source domains. However, existing domain generalization approaches often bring in prediction-irrelevant noise or require the collection of domain labels. To address these challenges, we consider the domain generalization problem from a different perspective by categorizing underlying feature groups into domain-shared and domain-specific features. Nevertheless, the domain-specific features are difficult to be identified and distinguished from the input data. In this work, we propose DomaIn-SPEcific Liberating (DISPEL), a post-processing fine-grained masking approach that can filter out undefined and indistinguishable domain-specific features in the embedding space. Specifically, DISPEL utilizes a mask generator that produces a unique mask for each input data to filter domain-specific features. The DISPEL framework is highly flexible to be applied to any fine-tuned models. We derive a generalization error bound to guarantee the generalization performance by optimizing a designed objective loss. The experimental results on five benchmarks demonstrate DISPEL outperforms existing methods and can further generalize various algorithms.

Hongye Jin, Xiaotian Han, Jingfeng Yang et al.

The evolving sophistication and intricacies of Large Language Models (LLMs) yield unprecedented advancements, yet they simultaneously demand considerable computational resources and incur significant costs. To alleviate these challenges, this paper introduces a novel, simple, and effective method named ``\growlength'' to accelerate the pretraining process of LLMs. Our method progressively increases the training length throughout the pretraining phase, thereby mitigating computational costs and enhancing efficiency. For instance, it begins with a sequence length of 128 and progressively extends to 4096. This approach enables models to process a larger number of tokens within limited time frames, potentially boosting their performance. In other words, the efficiency gain is derived from training with shorter sequences optimizing the utilization of resources. Our extensive experiments with various state-of-the-art LLMs have revealed that models trained using our method not only converge more swiftly but also exhibit superior performance metrics compared to those trained with existing methods. Furthermore, our method for LLMs pretraining acceleration does not require any additional engineering efforts, making it a practical solution in the realm of LLMs.

Yu-Neng Chuang, Kwei-Herng Lai, Ruixiang Tang et al.

Knowledge graph data are prevalent in real-world applications, and knowledge graph neural networks (KGNNs) are essential techniques for knowledge graph representation learning. Although KGNN effectively models the structural information from knowledge graphs, these frameworks amplify the underlying data bias that leads to discrimination towards certain groups or individuals in resulting applications. Additionally, as existing debiasing approaches mainly focus on the entity-wise bias, eliminating the multi-hop relational bias that pervasively exists in knowledge graphs remains an open question. However, it is very challenging to eliminate relational bias due to the sparsity of the paths that generate the bias and the non-linear proximity structure of knowledge graphs. To tackle the challenges, we propose Fair-KGNN, a KGNN framework that simultaneously alleviates multi-hop bias and preserves the proximity information of entity-to-relation in knowledge graphs. The proposed framework is generalizable to mitigate the relational bias for all types of KGNN. We develop two instances of Fair-KGNN incorporating with two state-of-the-art KGNN models, RGCN and CompGCN, to mitigate gender-occupation and nationality-salary bias. The experiments carried out on three benchmark knowledge graph datasets demonstrate that the Fair-KGNN can effectively mitigate unfair situations during representation learning while preserving the predictive performance of KGNN models.

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.

Hongye Jin, Xiaotian Han, Jingfeng Yang et al.

It is well known that LLMs cannot generalize well to long contexts whose lengths are larger than the training sequence length. This poses challenges when employing LLMs for processing long input sequences during inference. In this work, we argue that LLMs themselves have inherent capabilities to handle long contexts without fine-tuning. To achieve this goal, we propose SelfExtend to extend the context window of LLMs by constructing bi-level attention information: the grouped attention and the neighbor attention. The grouped attention captures the dependencies among tokens that are far apart, while neighbor attention captures dependencies among adjacent tokens within a specified range. The two-level attentions are computed based on the original model's self-attention mechanism during inference. With minor code modification, our SelfExtend can effortlessly extend existing LLMs' context window without any fine-tuning. We conduct comprehensive experiments on multiple benchmarks and the results show that our SelfExtend can effectively extend existing LLMs' context window length. The code can be found at \url{https://github.com/datamllab/LongLM}.

Chia-Yuan Chang, Yu-Neng Chuang, Zhimeng Jiang et al.

In real-world applications, machine learning models often become obsolete due to shifts in the joint distribution arising from underlying temporal trends, a phenomenon known as the "concept drift". Existing works propose model-specific strategies to achieve temporal generalization in the near-future domain. However, the diverse characteristics of real-world datasets necessitate customized prediction model architectures. To this end, there is an urgent demand for a model-agnostic temporal domain generalization approach that maintains generality across diverse data modalities and architectures. In this work, we aim to address the concept drift problem from a data-centric perspective to bypass considering the interaction between data and model. Developing such a framework presents non-trivial challenges: (i) existing generative models struggle to generate out-of-distribution future data, and (ii) precisely capturing the temporal trends of joint distribution along chronological source domains is computationally infeasible. To tackle the challenges, we propose the COncept Drift simulAtor (CODA) framework incorporating a predicted feature correlation matrix to simulate future data for model training. Specifically, CODA leverages feature correlations to represent data characteristics at specific time points, thereby circumventing the daunting computational costs. Experimental results demonstrate that using CODA-generated data as training input effectively achieves temporal domain generalization across different model architectures.

Chia-Yuan Chang, Yu-Neng Chuang, Kwei-Herng Lai et al.

Despite the impressive prediction ability, machine learning models show discrimination towards certain demographics and suffer from unfair prediction behaviors. To alleviate the discrimination, extensive studies focus on eliminating the unequal distribution of sensitive attributes via multiple approaches. However, due to privacy concerns, sensitive attributes are often either unavailable or missing in real-world scenarios. Therefore, several existing works alleviate the bias without sensitive attributes. Those studies face challenges, either in inaccurate predictions of sensitive attributes or the need to mitigate unequal distribution of manually defined non-sensitive attributes related to bias. The latter requires strong assumptions about the correlation between sensitive and non-sensitive attributes. As data distribution and task goals vary, the strong assumption on non-sensitive attributes may not be valid and require domain expertise. In this work, we propose an assumption-free framework to detect the related attributes automatically by modeling feature interaction for bias mitigation. The proposed framework aims to mitigate the unfair impact of identified biased feature interactions. Experimental results on four real-world datasets demonstrate that our proposed framework can significantly alleviate unfair prediction behaviors by considering biased feature interactions.

Yu-Neng Chuang, Tianwei Xing, Chia-Yuan Chang et al.

Large language models (LLMs) are great at processing multiple natural language processing tasks, but their abilities are constrained by inferior performance with long context, slow inference speed, and the high cost of computing the results. Deploying LLMs with precise and informative context helps users process large-scale datasets more effectively and cost-efficiently. Existing works rely on compressing long prompt contexts into soft prompts. However, soft prompt compression encounters limitations in transferability across different LLMs, especially API-based LLMs. To this end, this work aims to compress lengthy prompts in the form of natural language with LLM transferability. This poses two challenges: (i) Natural Language (NL) prompts are incompatible with back-propagation, and (ii) NL prompts lack flexibility in imposing length constraints. In this work, we propose a Natural Language Prompt Encapsulation (Nano-Capsulator) framework compressing original prompts into NL formatted Capsule Prompt while maintaining the prompt utility and transferability. Specifically, to tackle the first challenge, the Nano-Capsulator is optimized by a reward function that interacts with the proposed semantics preserving loss. To address the second question, the Nano-Capsulator is optimized by a reward function featuring length constraints. Experimental results demonstrate that the Capsule Prompt can reduce 81.4% of the original length, decrease inference latency up to 4.5x, and save 80.1% of budget overheads while providing transferability across diverse LLMs and different datasets.

Chia-Yuan Chang, Zhimeng Jiang, Vineeth Rakesh et al.

Large Language Models (LLMs) are becoming essential tools for various natural language processing tasks but often suffer from generating outdated or incorrect information. Retrieval-Augmented Generation (RAG) addresses this issue by incorporating external, real-time information retrieval to ground LLM responses. However, the existing RAG systems frequently struggle with the quality of retrieval documents, as irrelevant or noisy documents degrade performance, increase computational overhead, and undermine response reliability. To tackle this problem, we propose Multi-Agent Filtering Retrieval-Augmented Generation (MAIN-RAG), a training-free RAG framework that leverages multiple LLM agents to collaboratively filter and score retrieved documents. Specifically, MAIN-RAG introduces an adaptive filtering mechanism that dynamically adjusts the relevance filtering threshold based on score distributions, effectively minimizing noise while maintaining high recall of relevant documents. The proposed approach leverages inter-agent consensus to ensure robust document selection without requiring additional training data or fine-tuning. Experimental results across four QA benchmarks demonstrate that MAIN-RAG consistently outperforms traditional RAG approaches, achieving a 2-11% improvement in answer accuracy while reducing the number of irrelevant retrieved documents. Quantitative analysis further reveals that our approach achieves superior response consistency and answer accuracy over baseline methods, offering a competitive and practical alternative to training-based solutions.

Yu-Neng Chuang, Guanchu Wang, Chia-Yuan Chang et al.

Large language models (LLMs) increasingly produce natural language explanations, yet these explanations often lack faithfulness, and they do not reliably reflect the evidence the model uses to decide. We introduce FaithLM, a model-agnostic framework that evaluates and improves the faithfulness of LLM explanations without token masking or task-specific heuristics. FaithLM formalizes explanation faithfulness as an intervention property: a faithful explanation should yield a prediction shift when its content is contradicted. Theoretical analysis shows that the resulting contrary-hint score is a sound and discriminative estimator of faithfulness. Building on this principle, FaithLM iteratively refines both the elicitation prompt and the explanation to maximize the measured score. Experiments on three multi-domain datasets and multiple LLM backbones demonstrate that FaithLM consistently increases faithfulness and produces explanations more aligned with human rationales than strong self-explanation baselines. These findings highlight that intervention-based evaluation, coupled with iterative optimization, provides a principled route toward faithful and reliable LLM explanations.

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.

Guanchu Wang, Yu-Neng Chuang, Fan Yang et al.

Explainable machine learning significantly improves the transparency of deep neural networks. However, existing work is constrained to explaining the behavior of individual model predictions, and lacks the ability to transfer the explanation across various models and tasks. This limitation results in explaining various tasks being time- and resource-consuming. To address this problem, we introduce a Transferable Vision Explainer (TVE) that can effectively explain various vision models in downstream tasks. Specifically, the transferability of TVE is realized through a pre-training process on large-scale datasets towards learning the meta-attribution. This meta-attribution leverages the versatility of generic backbone encoders to comprehensively encode the attribution knowledge for the input instance, which enables TVE to seamlessly transfer to explain various downstream tasks, without the need for training on task-specific data. Empirical studies involve explaining three different architectures of vision models across three diverse downstream datasets. The experimental results indicate TVE is effective in explaining these tasks without the need for additional training on downstream data.