arXiv subjects

Xia Hu

Publications and source records attributed to Xia Hu.

At least 109 records · Page 6Linked to original sources

arXiv2025

The Science of Evaluating Foundation Models

The emergent phenomena of large foundation models have revolutionized natural language processing. However, evaluating these models presents significant challenges due to their size, capabilities, and deployment across diverse applications. Existing literature often focuses on individual aspects, such as benchmark performance or specific tasks, but fails to provide a cohesive process that integrates the nuances of diverse use cases with broader ethical and operational considerations. This work focuses on three key aspects: (1) Formalizing the Evaluation Process by providing a structured framework tailored to specific use-case contexts, (2) Offering Actionable Tools and Frameworks such as checklists and templates to ensure thorough, reproducible, and practical evaluations, and (3) Surveying Recent Work with a targeted review of advancements in LLM evaluation, emphasizing real-world applications.

cs.CL↗

arXiv2025

Confident or Seek Stronger: Exploring Uncertainty-Based On-device LLM Routing From Benchmarking to Generalization

Large language models (LLMs) are increasingly deployed and democratized on edge devices. To improve the efficiency of on-device deployment, small language models (SLMs) are often adopted due to their efficient decoding latency and reduced energy consumption. However, these SLMs often generate inaccurate responses when handling complex queries. One promising solution is uncertainty-based SLM routing, offloading high-stakes queries to stronger LLMs when resulting in low-confidence responses on SLM. This follows the principle of "If you lack confidence, seek stronger support" to enhance reliability. Relying on more powerful LLMs is yet effective but increases invocation costs. Therefore, striking a routing balance between efficiency and efficacy remains a critical challenge. Additionally, efficiently generalizing the routing strategy to new datasets remains under-explored. In this paper, we conduct a comprehensive investigation into benchmarking and generalization of uncertainty-driven routing strategies from SLMs to LLMs over 1500+ settings. Our findings highlight: First, uncertainty-correctness alignment in different uncertainty quantification (UQ) methods significantly impacts routing performance. Second, uncertainty distributions depend more on both the specific SLM and the chosen UQ method, rather than downstream data. Building on the insight, we propose a calibration data construction instruction pipeline and open-source a constructed hold-out set to enhance routing generalization on new downstream scenarios. The experimental results indicate calibration data effectively bootstraps routing performance without any new data.

cs.CL↗

arXiv2025

Survey and Improvement Strategies for Gene Prioritization with Large Language Models

Rare diseases are challenging to diagnose due to limited patient data and genetic diversity. Despite advances in variant prioritization, many cases remain undiagnosed. While large language models (LLMs) have performed well in medical exams, their effectiveness in diagnosing rare genetic diseases has not been assessed. To identify causal genes, we benchmarked various LLMs for gene prioritization. Using multi-agent and Human Phenotype Ontology (HPO) classification, we categorized patients based on phenotypes and solvability levels. As gene set size increased, LLM performance deteriorated, so we used a divide-and-conquer strategy to break the task into smaller subsets. At baseline, GPT-4 outperformed other LLMs, achieving near 30% accuracy in ranking causal genes correctly. The multi-agent and HPO approaches helped distinguish confidently solved cases from challenging ones, highlighting the importance of known gene-phenotype associations and phenotype specificity. We found that cases with specific phenotypes or clear associations were more accurately solved. However, we observed biases toward well-studied genes and input order sensitivity, which hindered gene prioritization. Our divide-and-conquer strategy improved accuracy by overcoming these biases. By utilizing HPO classification, novel multi-agent techniques, and our LLM strategy, we improved causal gene identification accuracy compared to our baseline evaluation. This approach streamlines rare disease diagnosis, facilitates reanalysis of unsolved cases, and accelerates gene discovery, supporting the development of targeted diagnostics and therapies.

q-bio.GN↗

arXiv2024

Winner-Take-All Column Row Sampling for Memory Efficient Adaptation of Language Model

With the rapid growth in model size, fine-tuning the large pre-trained language model has become increasingly difficult due to its extensive memory usage. Previous works usually focus on reducing the number of trainable parameters in the network. While the model parameters do contribute to memory usage, the primary memory bottleneck during training arises from storing feature maps, also known as activations, as they are crucial for gradient calculation. Notably, neural networks are usually trained using stochastic gradient descent. We argue that in stochastic optimization, models can handle noisy gradients as long as the gradient estimator is unbiased with reasonable variance. Following this motivation, we propose a new family of unbiased estimators called WTA-CRS, for matrix production with reduced variance, which only requires storing the sub-sampled activations for calculating the gradient. Our work provides both theoretical and experimental evidence that, in the context of tuning transformers, our proposed estimators exhibit lower variance compared to existing ones. By replacing the linear operation with our approximated one in transformers, we can achieve up to 2.7$\times$ peak memory reduction with almost no accuracy drop and enables up to $6.4\times$ larger batch size. Under the same hardware, WTA-CRS enables better down-streaming task performance by applying larger models and/or faster training speed with larger batch sizes.

cs.LG↗

arXiv2024

Gradient Rewiring for Editable Graph Neural Network Training

Deep neural networks are ubiquitously adopted in many applications, such as computer vision, natural language processing, and graph analytics. However, well-trained neural networks can make prediction errors after deployment as the world changes. \textit{Model editing} involves updating the base model to correct prediction errors with less accessible training data and computational resources. Despite recent advances in model editors in computer vision and natural language processing, editable training in graph neural networks (GNNs) is rarely explored. The challenge with editable GNN training lies in the inherent information aggregation across neighbors, which can lead model editors to affect the predictions of other nodes unintentionally. In this paper, we first observe the gradient of cross-entropy loss for the target node and training nodes with significant inconsistency, which indicates that directly fine-tuning the base model using the loss on the target node deteriorates the performance on training nodes. Motivated by the gradient inconsistency observation, we propose a simple yet effective \underline{G}radient \underline{R}ewiring method for \underline{E}ditable graph neural network training, named \textbf{GRE}. Specifically, we first store the anchor gradient of the loss on training nodes to preserve the locality. Subsequently, we rewire the gradient of the loss on the target node to preserve performance on the training node using anchor gradient. Experiments demonstrate the effectiveness of GRE on various model architectures and graph datasets in terms of multiple editing situations. The source code is available at \url{https://github.com/zhimengj0326/Gradient_rewiring_editing}

cs.LG↗

arXiv2024

Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery

Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational tools, leveraging an advanced Transformer model, to unearth noteworthy gene-gene interactions. Despite the efficacy of Transformer models, their parameter intensity presents a bottleneck in data ingestion, hindering data efficiency. To mitigate this, we introduce a novel weighted diversified sampling algorithm. This algorithm computes the diversity score of each data sample in just two passes of the dataset, facilitating efficient subset generation for interaction discovery. Our extensive experimentation demonstrates that by sampling a mere 1\% of the single-cell dataset, we achieve performance comparable to that of utilizing the entire dataset.

cs.AI↗

arXiv2024

KV Cache Compression, But What Must We Give in Return? A Comprehensive Benchmark of Long Context Capable Approaches

Long context capability is a crucial competency for large language models (LLMs) as it mitigates the human struggle to digest long-form texts. This capability enables complex task-solving scenarios such as book summarization, code assistance, and many more tasks that are traditionally manpower-intensive. However, transformer-based LLMs face significant challenges with long context input due to the growing size of the KV cache and the intrinsic complexity of attending to extended inputs; where multiple schools of efficiency-driven approaches - such as KV cache quantization, token dropping, prompt compression, linear-time sequence models, and hybrid architectures - have been proposed to produce efficient yet long context-capable models. Despite these advancements, no existing work has comprehensively benchmarked these methods in a reasonably aligned environment. In this work, we fill this gap by providing a taxonomy of current methods and evaluating 10+ state-of-the-art approaches across seven categories of long context tasks. Our work reveals numerous previously unknown phenomena and offers insights - as well as a friendly workbench - for the future development of long context-capable LLMs. The source code is available at https://github.com/henryzhongsc/longctx_bench.

cs.CL↗

arXiv2024

Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

cs.CL↗

arXiv2024

On the Equivalence of Graph Convolution and Mixup

This paper investigates the relationship between graph convolution and Mixup techniques. Graph convolution in a graph neural network involves aggregating features from neighboring samples to learn representative features for a specific node or sample. On the other hand, Mixup is a data augmentation technique that generates new examples by averaging features and one-hot labels from multiple samples. One commonality between these techniques is their utilization of information from multiple samples to derive feature representation. This study aims to explore whether a connection exists between these two approaches. Our investigation reveals that, under two mild conditions, graph convolution can be viewed as a specialized form of Mixup that is applied during both the training and testing phases. The two conditions are: 1) \textit{Homophily Relabel} - assigning the target node's label to all its neighbors, and 2) \textit{Test-Time Mixup} - Mixup the feature during the test time. We establish this equivalence mathematically by demonstrating that graph convolution networks (GCN) and simplified graph convolution (SGC) can be expressed as a form of Mixup. We also empirically verify the equivalence by training an MLP using the two conditions to achieve comparable performance.

cs.LG↗

arXiv2024

Assessing and Enhancing Large Language Models in Rare Disease Question-answering

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.

cs.CE↗

arXiv2024

KIVI: A Tuning-Free Asymmetric 2bit Quantization for KV Cache

Efficiently serving large language models (LLMs) requires batching of many requests to reduce the cost per request. Yet, with larger batch sizes and longer context lengths, the key-value (KV) cache, which stores attention keys and values to avoid re-computations, significantly increases memory demands and becomes the new bottleneck in speed and memory usage. Additionally, the loading of the KV cache causes the computational core to be idle, which limits the inference speed. A straightforward and effective solution to reduce KV cache size is quantization, which decreases the total bytes taken by KV cache. However, there is a lack of in-depth studies that explore the element distribution of KV cache to understand the hardness and limitation of KV cache quantization. To fill the gap, we conducted a comprehensive study on the element distribution in KV cache of popular LLMs. Our findings indicate that the key cache should be quantized per-channel, i.e., group elements along the channel dimension and quantize them together. In contrast, the value cache should be quantized per-token. From this analysis, we developed a tuning-free 2bit KV cache quantization algorithm named KIVI. With hardware-friendly implementation, KIVI can enable Llama, Falcon, and Mistral models to maintain almost the same quality while using $\mathbf{2.6\times}$ less peak memory (including model weight). This reduction in memory usage enables up to $\mathbf{4\times}$ larger batch size, bringing $\mathbf{2.35\times \sim 3.47\times}$ throughput on real LLM inference workload. The source code is available at https://github.com/jy-yuan/KIVI.

cs.CL↗

arXiv2024

TVE: Learning Meta-attribution for Transferable Vision Explainer

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.

cs.LG↗

arXiv2024

LLM Maybe LongLM: Self-Extend LLM Context Window Without Tuning

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}.

cs.CL↗

arXiv2024

FFB: A Fair Fairness Benchmark for In-Processing Group Fairness Methods

This paper introduces the Fair Fairness Benchmark (\textsf{FFB}), a benchmarking framework for in-processing group fairness methods. Ensuring fairness in machine learning is important for ethical compliance. However, there exist challenges in comparing and developing fairness methods due to inconsistencies in experimental settings, lack of accessible algorithmic implementations, and limited extensibility of current fairness packages and tools. To address these issues, we introduce an open-source standardized benchmark for evaluating in-processing group fairness methods and provide a comprehensive analysis of state-of-the-art methods to ensure different notions of group fairness. This work offers the following key contributions: the provision of flexible, extensible, minimalistic, and research-oriented open-source code; the establishment of unified fairness method benchmarking pipelines; and extensive benchmarking, which yields key insights from $\mathbf{45,079}$ experiments, $\mathbf{14,428}$ GPU hours. We believe that our work will significantly facilitate the growth and development of the fairness research community.

cs.LG↗

arXiv2024

FairLENS: Assessing Fairness in Law Enforcement Speech Recognition

Automatic speech recognition (ASR) techniques have become powerful tools, enhancing efficiency in law enforcement scenarios. To ensure fairness for demographic groups in different acoustic environments, ASR engines must be tested across a variety of speakers in realistic settings. However, describing the fairness discrepancies between models with confidence remains a challenge. Meanwhile, most public ASR datasets are insufficient to perform a satisfying fairness evaluation. To address the limitations, we built FairLENS - a systematic fairness evaluation framework. We propose a novel and adaptable evaluation method to examine the fairness disparity between different models. We also collected a fairness evaluation dataset covering multiple scenarios and demographic dimensions. Leveraging this framework, we conducted fairness assessments on 1 open-source and 11 commercially available state-of-the-art ASR models. Our results reveal that certain models exhibit more biases than others, serving as a fairness guideline for users to make informed choices when selecting ASR models for a given real-world scenario. We further explored model biases towards specific demographic groups and observed that shifts in the acoustic domain can lead to the emergence of new biases.

eess.AS↗

arXiv2024

Omni-SMoLA: Boosting Generalist Multimodal Models with Soft Mixture of Low-rank Experts

Large multi-modal models (LMMs) exhibit remarkable performance across numerous tasks. However, generalist LMMs often suffer from performance degradation when tuned over a large collection of tasks. Recent research suggests that Mixture of Experts (MoE) architectures are useful for instruction tuning, but for LMMs of parameter size around O(50-100B), the prohibitive cost of replicating and storing the expert models severely limits the number of experts we can use. We propose Omni-SMoLA, an architecture that uses the Soft MoE approach to (softly) mix many multimodal low rank experts, and avoids introducing a significant number of new parameters compared to conventional MoE models. The core intuition here is that the large model provides a foundational backbone, while different lightweight experts residually learn specialized knowledge, either per-modality or multimodally. Extensive experiments demonstrate that the SMoLA approach helps improve the generalist performance across a broad range of generative vision-and-language tasks, achieving new SoTA generalist performance that often matches or outperforms single specialized LMM baselines, as well as new SoTA specialist performance.

cs.CV↗

arXiv2024

Learning to Compress Prompt in Natural Language Formats

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.

cs.CL↗

arXiv2024

Feasibility of Identifying Factors Related to Alzheimer's Disease and Related Dementia in Real-World Data

A comprehensive view of factors associated with AD/ADRD will significantly aid in studies to develop new treatments for AD/ADRD and identify high-risk populations and patients for prevention efforts. In our study, we summarized the risk factors for AD/ADRD by reviewing existing meta-analyses and review articles on risk and preventive factors for AD/ADRD. In total, we extracted 477 risk factors in 10 categories from 537 studies. We constructed an interactive knowledge map to disseminate our study results. Most of the risk factors are accessible from structured Electronic Health Records (EHRs), and clinical narratives show promise as information sources. However, evaluating genomic risk factors using RWD remains a challenge, as genetic testing for AD/ADRD is still not a common practice and is poorly documented in both structured and unstructured EHRs. Considering the constantly evolving research on AD/ADRD risk factors, literature mining via NLP methods offers a solution to automatically update our knowledge map.

cs.AI↗