Yiqiao Jin

Yiqiao Jin, Yunsheng Bai, Yanqiao Zhu et al. · gatech

Open Source Software (OSS) is forming the spines of technology infrastructures, attracting millions of talents to contribute. Notably, it is challenging and critical to consider both the developers' interests and the semantic features of the project code to recommend appropriate development tasks to OSS developers. In this paper, we formulate the novel problem of code recommendation, whose purpose is to predict the future contribution behaviors of developers given their interaction history, the semantic features of source code, and the hierarchical file structures of projects. Considering the complex interactions among multiple parties within the system, we propose CODER, a novel graph-based code recommendation framework for open source software developers. CODER jointly models microscopic user-code interactions and macroscopic user-project interactions via a heterogeneous graph and further bridges the two levels of information through aggregation on file-structure graphs that reflect the project hierarchy. Moreover, due to the lack of reliable benchmarks, we construct three large-scale datasets to facilitate future research in this direction. Extensive experiments show that our CODER framework achieves superior performance under various experimental settings, including intra-project, cross-project, and cold-start recommendation. We will release all the datasets, code, and utilities for data retrieval upon the acceptance of this work.

Yijia Xiao, Yiqiao Jin, Yushi Bai et al. · gatech, tsinghua

The proliferation of Large Language Models (LLMs) has driven considerable interest in fine-tuning them with domain-specific data to create specialized language models. Nevertheless, such domain-specific fine-tuning data often contains contextually sensitive personally identifiable information (PII). Direct fine-tuning of LLMs on this data without privacy protection poses a risk of data leakage of sensitive PII during inference time. To address this challenge, we introduce Contextual Privacy Protection Language Models (PrivacyMind), a novel paradigm for fine-tuning LLMs that effectively injects domain-specific knowledge while safeguarding inference-time data privacy. Our work offers a theoretical analysis for model design and benchmarks various techniques such as corpus curation, penalty-based unlikelihood in training loss, instruction-based tuning, etc. Extensive experiments across diverse datasets and scenarios demonstrate the effectiveness of our approaches. In particular, instruction tuning with both positive and negative examples stands out as a promising method, effectively protecting private data while enhancing the model's knowledge. Our work underscores the potential for Large Language Models as robust contextual privacy protection learners. The complete code and data for the work can be found at https://github.com/Yijia-Xiao/PrivacyMind.

Qinlin Zhao, Jindong Wang, Yixuan Zhang et al.

Large language models (LLMs) have been widely used as agents to complete different tasks, such as personal assistance or event planning. While most of the work has focused on cooperation and collaboration between agents, little work explores competition, another important mechanism that promotes the development of society and economy. In this paper, we seek to examine the competition dynamics in LLM-based agents. We first propose a general framework for studying the competition between agents. Then, we implement a practical competitive environment using GPT-4 to simulate a virtual town with two types of agents, restaurant agents and customer agents. Specifically, the restaurant agents compete with each other to attract more customers, where competition encourages them to transform, such as cultivating new operating strategies. Simulation experiments reveal several interesting findings at the micro and macro levels, which align well with existing market and sociological theories. We hope that the framework and environment can be a promising testbed to study competition that fosters understanding of society. Code is available at: https://github.com/microsoft/competeai.

Yiqiao Jin, Mohit Chandra, Gaurav Verma et al. · gatech

Large language models (LLMs) are transforming the ways the general public accesses and consumes information. Their influence is particularly pronounced in pivotal sectors like healthcare, where lay individuals are increasingly appropriating LLMs as conversational agents for everyday queries. While LLMs demonstrate impressive language understanding and generation proficiencies, concerns regarding their safety remain paramount in these high-stake domains. Moreover, the development of LLMs is disproportionately focused on English. It remains unclear how these LLMs perform in the context of non-English languages, a gap that is critical for ensuring equity in the real-world use of these systems.This paper provides a framework to investigate the effectiveness of LLMs as multi-lingual dialogue systems for healthcare queries. Our empirically-derived framework XlingEval focuses on three fundamental criteria for evaluating LLM responses to naturalistic human-authored health-related questions: correctness, consistency, and verifiability. Through extensive experiments on four major global languages, including English, Spanish, Chinese, and Hindi, spanning three expert-annotated large health Q&A datasets, and through an amalgamation of algorithmic and human-evaluation strategies, we found a pronounced disparity in LLM responses across these languages, indicating a need for enhanced cross-lingual capabilities. We further propose XlingHealth, a cross-lingual benchmark for examining the multilingual capabilities of LLMs in the healthcare context. Our findings underscore the pressing need to bolster the cross-lingual capacities of these models, and to provide an equitable information ecosystem accessible to all.

Changyu Chen, Xiting Wang, Yiqiao Jin et al. · gatech

In reinforcement learning (RL), there are two major settings for interacting with the environment: online and offline. Online methods explore the environment at significant time cost, and offline methods efficiently obtain reward signals by sacrificing exploration capability. We propose semi-offline RL, a novel paradigm that smoothly transits from offline to online settings, balances exploration capability and training cost, and provides a theoretical foundation for comparing different RL settings. Based on the semi-offline formulation, we present the RL setting that is optimal in terms of optimization cost, asymptotic error, and overfitting error bound. Extensive experiments show that our semi-offline approach is efficient and yields comparable or often better performance compared with state-of-the-art methods.

Yijia Xiao, Edward Sun, Yiqiao Jin et al.

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research. To streamline this process, we introduce ProteinGPT, a state-of-the-art multimodal large language model for proteins that enables users to upload protein sequences and/or structures for comprehensive analysis and responsive inquiries. ProteinGPT integrates protein sequence and structure encoders with linear projection layers to ensure precise representation adaptation and leverages a large language model (LLM) to generate accurate, contextually relevant responses. To train ProteinGPT, we constructed a large-scale dataset of 132,092 proteins, each annotated with 20-30 property tags and 5-10 QA pairs per protein, and optimized the instruction-tuning process using GPT-4o. Experiments demonstrate that ProteinGPT effectively generates informative responses to protein-related questions, achieving high performance on both semantic and lexical metrics and significantly outperforming baseline models and general-purpose LLMs in understanding and responding to protein-related queries. Our code and data are available at https://github.com/ProteinGPT/ProteinGPT.

Yiqiao Jin, Xiting Wang, Yaru Hao et al. · gatech

In this paper, we move towards combining large parametric models with non-parametric prototypical networks. We propose prototypical fine-tuning, a novel prototypical framework for fine-tuning pretrained language models (LM), which automatically learns a bias to improve predictive performance for varying data sizes, especially low-resource settings. Our prototypical fine-tuning approach can automatically adjust the model capacity according to the number of data points and the model's inherent attributes. Moreover, we propose four principles for effective prototype fine-tuning towards the optimal solution. Experimental results across various datasets show that our work achieves significant performance improvements under various low-resource settings, as well as comparable and usually better performances in high-resource scenarios.

Vibhor Agarwal, Yiqiao Jin, Mohit Chandra et al. · gatech

Large language models (LLMs) are starting to complement traditional information seeking mechanisms such as web search. LLM-powered chatbots like ChatGPT are gaining prominence among the general public. AI chatbots are also increasingly producing content on social media platforms. However, LLMs are also prone to hallucinations, generating plausible yet factually incorrect or fabricated information. This becomes a critical problem when laypeople start seeking information about sensitive issues such as healthcare. Existing works in LLM hallucinations in the medical domain mainly focus on testing the medical knowledge of LLMs through standardized medical exam questions which are often well-defined and clear-cut with definitive answers. However, these approaches may not fully capture how these LLMs perform during real-world interactions with patients. This work conducts a pioneering study on hallucinations in LLM-generated responses to real-world healthcare queries from patients.We introduce MedHalu, a novel medical hallucination benchmark featuring diverse health-related topics and hallucinated responses from LLMs, with detailed annotation of the hallucination types and text spans. We also propose MedHaluDetect, a comprehensive framework for evaluating LLMs' abilities to detect hallucinations. Furthermore, we study the vulnerability to medical hallucinations among three groups -- medical experts, LLMs, and laypeople. Notably, LLMs significantly underperform human experts and, in some cases, even laypeople in detecting medical hallucinations. To improve hallucination detection, we propose an expert-in-the-loop approach that integrates expert reasoning into LLM inputs, significantly improving hallucination detection for all LLMs, including a 6.3% macro-F1 improvement for GPT-4. Our code and dataset are available at https://netsys.surrey.ac.uk/datasets/medhalu/.

Yiqiao Jin, Minje Choi, Gaurav Verma et al. · gatech

Social media platforms are hubs for multimodal information exchange, encompassing text, images, and videos, making it challenging for machines to comprehend the information or emotions associated with interactions in online spaces. Multimodal Large Language Models (MLLMs) have emerged as a promising solution to these challenges, yet they struggle to accurately interpret human emotions and complex content such as misinformation. This paper introduces MM-Soc, a comprehensive benchmark designed to evaluate MLLMs' understanding of multimodal social media content. MM-Soc compiles prominent multimodal datasets and incorporates a novel large-scale YouTube tagging dataset, targeting a range of tasks from misinformation detection, hate speech detection, and social context generation. Through our exhaustive evaluation on ten size-variants of four open-source MLLMs, we have identified significant performance disparities, highlighting the need for advancements in models' social understanding capabilities. Our analysis reveals that, in a zero-shot setting, various types of MLLMs generally exhibit difficulties in handling social media tasks. However, MLLMs demonstrate performance improvements post fine-tuning, suggesting potential pathways for improvement. Our code and data are available at https://github.com/claws-lab/MMSoc.git.

Yijia Xiao, Wanjia Zhao, Junkai Zhang et al.

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

Neng Kai Nigel Neo, Yeon-Chang Lee, Yiqiao Jin et al.

The Fair Graph Anomaly Detection (FairGAD) problem aims to accurately detect anomalous nodes in an input graph while avoiding biased predictions against individuals from sensitive subgroups. However, the current literature does not comprehensively discuss this problem, nor does it provide realistic datasets that encompass actual graph structures, anomaly labels, and sensitive attributes. To bridge this gap, we introduce a formal definition of the FairGAD problem and present two novel datasets constructed from the social media platforms Reddit and Twitter. These datasets comprise 1.2 million and 400,000 edges associated with 9,000 and 47,000 nodes, respectively, and leverage political leanings as sensitive attributes and misinformation spreaders as anomaly labels. We demonstrate that our FairGAD datasets significantly differ from the synthetic datasets used by the research community. Using our datasets, we investigate the performance-fairness trade-off in nine existing GAD and non-graph AD methods on five state-of-the-art fairness methods. Our code and datasets are available at https://github.com/nigelnnk/FairGAD

Yiqiao Jin, Stefano Petrangeli, Yu Shen et al.

Graphical User Interface (GUI) agents are autonomous systems that interpret and generate actions, enabling intelligent user assistance and automation. Effective training of these agent presents unique challenges, such as sparsity in supervision signals, scalability for large datasets, and the need for nuanced user understanding. We propose stateful screen schema, an efficient representation of GUI interactions that captures key user actions and intentions over time. Building on this foundation, we introduce ScreenLLM, a set of multimodal large language models (MLLMs) tailored for advanced UI understanding and action prediction. Extensive experiments on both open-source and proprietary models show that ScreenLLM accurately models user behavior and predicts actions. Our work lays the foundation for scalable, robust, and intelligent GUI agents that enhance user interaction in diverse software environments.

Kartik Sharma, Yiqiao Jin, Rakshit Trivedi et al.

Large language models (LLMs) acquire knowledge across diverse domains such as science, history, and geography encountered during generative pre-training. However, due to their stochasticity, it is difficult to predict what LLMs have acquired. Prior work has developed different ways to probe this knowledge by investigating the hidden representations, crafting specific task prompts, curating representative samples, and estimating their uncertainty. However, these methods require making forward passes through the underlying model to probe the LLM's knowledge about a specific fact, making them computationally expensive and time-consuming. To bridge this gap, we propose $\textbf{PEEK}$ or $\textbf{P}$roxy $\textbf{E}$mbeddings to $\textbf{E}$stimate $\textbf{K}$nowledge of LLMs, by leveraging the pre-trained embedding models that effectively encode factual knowledge as text or graphs as proxies for LLMs. First, we identify a training set of facts known by LLMs through various probing strategies and then adapt embedding models to predict the LLM outputs with a linear decoder layer. Comprehensive evaluation on $3$ Wikipedia-derived datasets, $4$ LLMs, and $7$ embedding models shows that embeddings can predict LLM knowledge on a held-out set with up to 90 % accuracy. Furthermore, we find that sentence embedding models are more suitable than graph embeddings to predict LLM knowledge, shedding light on the underlying representation of the factual landscape. Thus, we believe that knowledge-adapted embeddings can be used to identify knowledge gaps in LLMs at scale and can provide deeper insights into LLMs' internal inductive bias. The code and data are made available at https://github.com/claws-lab/peek.

Yiqiao Jin, Kartik Sharma, Vineeth Rakesh et al.

Retrieval-augmented Generation (RAG) extends large language models (LLMs) with external knowledge but faces key challenges: restricted effective context length and redundancy in retrieved documents. Pure compression-based approaches reduce input size but often discard fine-grained details essential for factual accuracy. We propose SARA, a unified RAG framework that balances local precision and global knowledge coverage under tight context budgets. SARA combines natural-language text snippets with semantic compression vectors to jointly enhance context efficiency and answer correctness. It represents contexts at two complementary levels: 1) fine-grained natural-language spans that preserve critical entities and numerical values, and 2) compact, interpretable vectors that summarize high-level semantics. An iterative evidence-selection module employs the compression vectors for dynamic reranking of contexts. Across 9 datasets and 5 open-source LLMs spanning 3 model families (Mistral, Llama, and Gemma), SARA consistently improves answer relevance (+17.71), answer correctness (+13.72), and semantic similarity (+15.53), demonstrating the importance of integrating textual and compressed representations for robust, context-efficient RAG.

Yiqiao Jin, Andrew Zhao, Yeon-Chang Lee et al.

We developed DyGETViz, a novel framework for effectively visualizing dynamic graphs (DGs) that are ubiquitous across diverse real-world systems. This framework leverages recent advancements in discrete-time dynamic graph (DTDG) models to adeptly handle the temporal dynamics inherent in dynamic graphs. DyGETViz effectively captures both micro- and macro-level structural shifts within these graphs, offering a robust method for representing complex and massive dynamic graphs. The application of DyGETViz extends to a diverse array of domains, including ethology, epidemiology, finance, genetics, linguistics, communication studies, social studies, and international relations. Through its implementation, DyGETViz has revealed or confirmed various critical insights. These include the diversity of content sharing patterns and the degree of specialization within online communities, the chronological evolution of lexicons across decades, and the distinct trajectories exhibited by aging-related and non-related genes. Importantly, DyGETViz enhances the accessibility of scientific findings to non-domain experts by simplifying the complexities of dynamic graphs. Our framework is released as an open-source Python package for use across diverse disciplines. Our work not only addresses the ongoing challenges in visualizing and analyzing DTDG models but also establishes a foundational framework for future investigations into dynamic graph representation and analysis across various disciplines.

Shudong Liu, Yiqiao Jin, Cheng Li et al.

Vision-language models (VLMs) have advanced human-AI interaction but struggle with cultural understanding, often misinterpreting symbols, gestures, and artifacts due to biases in predominantly Western-centric training data. In this paper, we construct CultureVerse, a large-scale multimodal benchmark covering 19, 682 cultural concepts, 188 countries/regions, 15 cultural concepts, and 3 question types, with the aim of characterizing and improving VLMs' multicultural understanding capabilities. Then, we propose CultureVLM, a series of VLMs fine-tuned on our dataset to achieve significant performance improvement in cultural understanding. Our evaluation of 16 models reveals significant disparities, with a stronger performance in Western concepts and weaker results in African and Asian contexts. Fine-tuning on our CultureVerse enhances cultural perception, demonstrating cross-cultural, cross-continent, and cross-dataset generalization without sacrificing performance on models' general VLM benchmarks. We further present insights on cultural generalization and forgetting. We hope that this work could lay the foundation for more equitable and culturally aware multimodal AI systems.

Sejoon Oh, Yiqiao Jin, Megha Sharma et al. · gatech

Multimodal large language models (MLLMs) have revolutionized vision-language understanding but remain vulnerable to multimodal jailbreak attacks, where adversarial inputs are meticulously crafted to elicit harmful or inappropriate responses. We propose UniGuard, a novel multimodal safety guardrail that jointly considers the unimodal and cross-modal harmful signals. UniGuard trains a multimodal guardrail to minimize the likelihood of generating harmful responses in a toxic corpus. The guardrail can be seamlessly applied to any input prompt during inference with minimal computational costs. Extensive experiments demonstrate the generalizability of UniGuard across multiple modalities, attack strategies, and multiple state-of-the-art MLLMs, including LLaVA, Gemini Pro, GPT-4o, MiniGPT-4, and InstructBLIP. Notably, this robust defense mechanism maintains the models' overall vision-language understanding capabilities.

Guancheng Wan, Lucheng Fu, Haoxin Liu et al.

The performance of Large Language Models (LLMs) hinges on carefully engineered prompts. However, prevailing prompt optimization methods, ranging from heuristic edits and reinforcement learning to evolutionary search, primarily target point-wise accuracy. They seldom enforce paraphrase invariance or searching stability, and therefore cannot remedy this brittleness in practice. Automated prompt search remains brittle: small, semantically preserving paraphrases often cause large performance swings. We identify this brittleness as the textual sharpness of the prompt landscape. In this work, we provide the first formal treatment of textual sharpness in the discrete, semantic space of prompts, together with an operational robustness criterion over a semantic neighborhood; the design is black-box or API-only, requiring no gradients to update the model's parameters. Then we introduce TARE (Textual Sharpness-Aware Evolving), a derivative-free framework that alternates between an inner, sampling-based adversarial search that stresses a prompt with hard paraphrases and an outer, robust selection that prefers candidates whose neighborhoods remain strong. We further propose ATARE, which learns anisotropic weights to shape the semantic neighborhood and adapts its radius over time to balance exploration and fidelity. Diverse tasks evaluate our methods, whose design for minimizing textual sharpness gap leads to prompts that preserve accuracy under paraphrasing, outperforming accuracy-only prompt search while remaining computationally practical.

Jiaxi Yang, Mengqi Zhang, Yiqiao Jin et al. · amazon-science

Large Language Model-based Multi-Agent Systems (MASs) have emerged as a powerful paradigm for tackling complex tasks through collaborative intelligence. However, the topology of these systems--how agents in MASs should be configured, connected, and coordinated--remains largely unexplored. In this position paper, we call for a paradigm shift toward \emph{topology-aware MASs} that explicitly model and dynamically optimize the structure of inter-agent interactions. We identify three fundamental components--agents, communication links, and overall topology--that collectively determine the system's adaptability, efficiency, robustness, and fairness. To operationalize this vision, we introduce a systematic three-stage framework: 1) agent selection, 2) structure profiling, and 3) topology synthesis. This framework not only provides a principled foundation for designing MASs but also opens new research frontiers across language modeling, reinforcement learning, graph learning, and generative modeling to ultimately unleash their full potential in complex real-world applications. We conclude by outlining key challenges and opportunities in MASs evaluation. We hope our framework and perspectives offer critical new insights in the era of agentic AI.

Yibo Hu, Yiqiao Jin, Meng Ye et al.

In today's cross-platform social media landscape, understanding factors that drive engagement for multimodal content, especially text paired with visuals, remains complex. This study investigates how rewriting Reddit post titles adapted from YouTube video titles affects user engagement. First, we build and analyze a large dataset of Reddit posts sharing YouTube videos, revealing that 21% of post titles are minimally modified. Statistical analysis demonstrates that title rewrites measurably improve engagement. Second, we design a controlled, multi-phase experiment to rigorously isolate the effects of textual variations by neutralizing confounding factors like video popularity, timing, and community norms. Comprehensive statistical tests reveal that effective title rewrites tend to feature emotional resonance, lexical richness, and alignment with community-specific norms. Lastly, pairwise ranking prediction experiments using a fine-tuned BERT classifier achieves 74% accuracy, significantly outperforming near-random baselines, including GPT-4o. These results validate that our controlled dataset effectively minimizes confounding effects, allowing advanced models to both learn and demonstrate the impact of textual features on engagement. By bridging quantitative rigor with qualitative insights, this study uncovers engagement dynamics and offers a robust framework for future cross-platform, multimodal content strategies.

Yiqiao Jin, Xiting Wang, Ruichao Yang et al.

The detection of fake news often requires sophisticated reasoning skills, such as logically combining information by considering word-level subtle clues. In this paper, we move towards fine-grained reasoning for fake news detection by better reflecting the logical processes of human thinking and enabling the modeling of subtle clues. In particular, we propose a fine-grained reasoning framework by following the human information-processing model, introduce a mutual-reinforcement-based method for incorporating human knowledge about which evidence is more important, and design a prior-aware bi-channel kernel graph network to model subtle differences between pieces of evidence. Extensive experiments show that our model outperforms the state-of-the-art methods and demonstrate the explainability of our approach.