Ruixiang Tang

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

The exponential growth in scholarly publications necessitates advanced tools for efficient article retrieval, especially in interdisciplinary fields where diverse terminologies are used to describe similar research. Traditional keyword-based search engines often fall short in assisting users who may not be familiar with specific terminologies. To address this, we present a knowledge graph-based paper search engine for biomedical research to enhance the user experience in discovering relevant queries and articles. The system, dubbed DiscoverPath, employs Named Entity Recognition (NER) and part-of-speech (POS) tagging to extract terminologies and relationships from article abstracts to create a KG. To reduce information overload, DiscoverPath presents users with a focused subgraph containing the queried entity and its neighboring nodes and incorporates a query recommendation system, enabling users to iteratively refine their queries. The system is equipped with an accessible Graphical User Interface that provides an intuitive visualization of the KG, query recommendations, and detailed article information, enabling efficient article retrieval, thus fostering interdisciplinary knowledge exploration. DiscoverPath is open-sourced at https://github.com/ynchuang/DiscoverPath.

Jiayi Yuan, Ruixiang Tang, Xiaoqian Jiang et al.

The process of matching patients with suitable clinical trials is essential for advancing medical research and providing optimal care. However, current approaches face challenges such as data standardization, ethical considerations, and a lack of interoperability between Electronic Health Records (EHRs) and clinical trial criteria. In this paper, we explore the potential of large language models (LLMs) to address these challenges by leveraging their advanced natural language generation capabilities to improve compatibility between EHRs and clinical trial descriptions. We propose an innovative privacy-aware data augmentation approach for LLM-based patient-trial matching (LLM-PTM), which balances the benefits of LLMs while ensuring the security and confidentiality of sensitive patient data. Our experiments demonstrate a 7.32% average improvement in performance using the proposed LLM-PTM method, and the generalizability to new data is improved by 12.12%. Additionally, we present case studies to further illustrate the effectiveness of our approach and provide a deeper understanding of its underlying principles.

Yuqing Zhou, Ruixiang Tang, Ziyu Yao et al.

Language models (LMs), despite their advances, often depend on spurious correlations, undermining their accuracy and generalizability. This study addresses the overlooked impact of subtler, more complex shortcuts that compromise model reliability beyond oversimplified shortcuts. We introduce a comprehensive benchmark that categorizes shortcuts into occurrence, style, and concept, aiming to explore the nuanced ways in which these shortcuts influence the performance of LMs. Through extensive experiments across traditional LMs, large language models, and state-of-the-art robust models, our research systematically investigates models' resilience and susceptibilities to sophisticated shortcuts. Our benchmark and code can be found at: https://github.com/yuqing-zhou/shortcut-learning-in-text-classification.

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.

Mingyu Jin, Kai Mei, Wujiang Xu et al.

Large language models (LLMs) have achieved remarkable success in contextual knowledge understanding. In this paper, we show that these concentrated massive values consistently emerge in specific regions of attention queries (Q) and keys (K) while not having such patterns in values (V) in various modern transformer-based LLMs (Q, K, and V mean the representations output by the query, key, and value layers respectively). Through extensive experiments, we further demonstrate that these massive values play a critical role in interpreting contextual knowledge (knowledge obtained from the current context window) rather than in retrieving parametric knowledge stored within the model's parameters. Our further investigation of quantization strategies reveals that ignoring these massive values leads to a pronounced drop in performance on tasks requiring rich contextual understanding, aligning with our analysis. Finally, we trace the emergence of concentrated massive values and find that such concentration is caused by Rotary Positional Encoding (RoPE), which has appeared since the first layers. These findings shed new light on how Q and K operate in LLMs and offer practical insights for model design and optimization. The Code is Available at https://github.com/MingyuJ666/Rope_with_LLM.

Mingyu Jin, Weidi Luo, Sitao Cheng et al.

Large Language Models (LLMs) have demonstrated strong performance in handling complex tasks requiring both extensive knowledge and reasoning abilities. However, the existing LLM inference pipeline operates as an opaque process without explicit separation between knowledge retrieval and reasoning steps, making the model's decision-making process unclear and disorganized. This ambiguity can lead to issues such as hallucinations and knowledge forgetting, which significantly impact the reliability of LLMs in high-stakes domains. In this paper, we propose a new inference paradigm that decomposes the complex inference process into two distinct and clear actions: (1) memory recall: which retrieves relevant knowledge, and (2) reasoning: which performs logical steps based on the recalled knowledge. To facilitate this decomposition, we introduce two special tokens memory and reason, guiding the model to distinguish between steps that require knowledge retrieval and those that involve reasoning. Our experiment results show that this decomposition not only improves model performance but also enhances the interpretability of the inference process, enabling users to identify sources of error and refine model responses effectively. The code is available at https://github.com/MingyuJ666/Disentangling-Memory-and-Reasoning.

Zicong He, Boxuan Zhang, Weihao Liu et al.

The meteoric rise of foundation models (FMs) has expanded their capabilities far beyond conventional tasks. Creativity, long regarded as a hallmark of human intelligence and a driver of innovation, is now increasingly recognized as a critical dimension of machine intelligence in the era of generative FMs, complementing traditional measures of accuracy. However, existing evaluation frameworks for creativity remain fragmented, relying on ad hoc metrics not firmly grounded in established theories. To address this gap, we introduce C^2-Eval, a holistic benchmark for unified assessment of creativity in FMs. C^2-Eval distinguishes between two complementary forms of creativity: convergent creativity, where tasks admit constrained solutions (e.g., code generation), and divergent creativity, where tasks are open-ended (e.g., storytelling). It evaluates both dimensions using fine-grained criteria derived from social-science theory, focusing on Usefulness, Originality, and Surprise (U-O-S). Through extensive experiments on leading proprietary and open-source models, we analyze trade-offs in their creative capabilities. Our results highlight both the strengths and challenges of current FMs in pursuing a creative machine mind, showing that C^2-Eval is an effective lens for examining the evolving landscape of creative AI.

Yanshu Li, Yi Cao, Hongyang He et al.

Multimodal in-context learning (ICL) equips Large Vision-language Models (LVLMs) with the ability to adapt to new tasks via multiple user-provided demonstrations, without requiring any model parameter updates. However, its effectiveness is constrained by the token-intensive nature of multimodal inputs and the complexity of cross-modal few-shot reasoning, which together hinder LVLMs from extracting useful patterns from demonstrations. To address these challenges, we propose \textbf{M$^2$IV}, a novel representation engineering approach that replaces explicit token-level demonstrations with a set of learnable Multimodal In-context Vectors directly injected into the residual streams of LVLMs. By analyzing the distinct roles of multi-head attention (MHA) and multi-layer perceptrons (MLP) in the ICL process, we design a training strategy that enables M$^2$IV to perform fine-grained semantic distillation and robust cross-modal representation learning. M$^2$IV not only improves performance across diverse tasks and LVLMs but also significantly reduces token overhead, enabling graceful scaling to many-shot scenarios. To further enhance usability, we introduce \textbf{VLibrary}, a repository that stores trained M$^2$IVs for flexible retrieval and injection. With VLibrary, users can steer pre-trained LVLMs in a customized manner that meets diverse requirements. Extensive experiments demonstrate that M$^2$IV consistently outperforms vanilla ICL and prior representation engineering baselines, achieving an average accuracy gain of 3.74\% with substantial improvements in overall efficiency.

Matthew Neeley, Guantong Qi, Guanchu Wang et al.

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.

Qipan Xu, Zhenting Wang, Xiaoxiao He et al.

Generative AI models, renowned for their ability to synthesize high-quality content, have sparked growing concerns over the improper generation of copyright-protected material. While recent studies have proposed various approaches to address copyright issues, the capability of large vision-language models (LVLMs) to detect copyright infringements remains largely unexplored. In this work, we focus on evaluating the copyright detection abilities of state-of-the-art LVLMs using a various set of image samples. Recognizing the absence of a comprehensive dataset that includes both IP-infringement samples and ambiguous non-infringement negative samples, we construct a benchmark dataset comprising positive samples that violate the copyright protection of well-known IP figures, as well as negative samples that resemble these figures but do not raise copyright concerns. This dataset is created using advanced prompt engineering techniques. We then evaluate leading LVLMs using our benchmark dataset. Our experimental results reveal that LVLMs are prone to overfitting, leading to the misclassification of some negative samples as IP-infringement cases. In the final section, we analyze these failure cases and propose potential solutions to mitigate the overfitting problem.

Liwei Che, Tony Qingze Liu, Jing Jia et al.

Despite their remarkable potential, Large Vision-Language Models (LVLMs) still face challenges with object hallucination, a problem where their generated outputs mistakenly incorporate objects that do not actually exist. Although most works focus on addressing this issue within the language-model backbone, our work shifts the focus to the image input source, investigating how specific image tokens contribute to hallucinations. Our analysis reveals a striking finding: a small subset of image tokens with high attention scores are the primary drivers of object hallucination. By removing these hallucinatory image tokens (only 1.5% of all image tokens), the issue can be effectively mitigated. This finding holds consistently across different models and datasets. Building on this insight, we introduce EAZY, a novel, training-free method that automatically identifies and Eliminates hAllucinations by Zeroing out hallucinatorY image tokens. We utilize EAZY for unsupervised object hallucination detection, achieving 15% improvement compared to previous methods. Additionally, EAZY demonstrates remarkable effectiveness in mitigating hallucinations while preserving model utility and seamlessly adapting to various LVLM architectures.

Zeru Shi, Yingjia Wan, Zhenting Wang et al.

Motivated by the puzzling observation that inserting long sequences of meaningless tokens before the query prompt can consistently enhance LLM reasoning performance, this work analyzes the underlying mechanism driving this phenomenon and based on these insights proposes a more principled method that allows for similar performance gains. First, we find that the improvements arise from a redistribution of activations in the LLM's MLP layers, where near zero activations become less frequent while large magnitude activations increase. This redistribution enhances the model's representational capacity by suppressing weak signals and promoting stronger, more informative ones. Building on this insight, we propose the Activation Redistribution Module (ARM), a lightweight inference-time technique that modifies activations directly without altering the input sequence. ARM adaptively identifies near-zero activations after the non-linear function and shifts them outward, implicitly reproducing the beneficial effects of meaningless tokens in a controlled manner. Extensive experiments across diverse benchmarks and model architectures clearly show that ARM consistently improves LLM performance on reasoning tasks while requiring only a few lines of simple code to implement. Our findings deliver both a clear mechanistic explanation for the unexpected benefits of meaningless tokens and a simple yet effective technique that harnesses activation redistribution to further improve LLM performance.

Yanbo Fang, Ruixiang Tang

Understanding how large language models (LLMs) acquire, retain, and apply knowledge remains an open challenge. This paper introduces a novel framework, K-(CSA)^2, which categorizes LLM knowledge along two dimensions: correctness and confidence. The framework defines six categories of knowledge, ranging from highly confident correctness to confidently held misconceptions, enabling a nuanced evaluation of model comprehension beyond binary accuracy. Using this framework, we demonstrate how techniques like chain-of-thought prompting and reinforcement learning with human feedback fundamentally alter the knowledge structures of internal (pre-trained) and external (context-dependent) knowledge in LLMs. CoT particularly enhances base model performance and shows synergistic benefits when applied to aligned LLMs. Moreover, our layer-wise analysis reveals that higher layers in LLMs encode more high-confidence knowledge, while low-confidence knowledge tends to emerge in middle-to-lower layers.