Yifang Ma

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.

Xuyang Wu, Yuan Wang, Hsin-Tai Wu et al.

Large vision-language models (LVLMs) have recently achieved significant progress, demonstrating strong capabilities in open-world visual understanding. However, it is not yet clear how LVLMs address demographic biases in real life, especially the disparities across attributes such as gender, skin tone, age and race. In this paper, We empirically investigate \emph{visual fairness} in several mainstream LVLMs by auditing their performance disparities across demographic attributes using public fairness benchmark datasets (e.g., FACET, UTKFace). Our fairness evaluation framework employs direct and single-choice question prompt on visual question-answering/classification tasks. Despite advancements in visual understanding, our zero-shot prompting results show that both open-source and closed-source LVLMs continue to exhibit fairness issues across different prompts and demographic groups. Furthermore, we propose a potential multi-modal Chain-of-thought (CoT) based strategy for unfairness mitigation, applicable to both open-source and closed-source LVLMs. This approach enhances transparency and offers a scalable solution for addressing fairness, providing a solid foundation for future research and practical efforts in unfairness mitigation. The dataset and code used in this study are publicly available at this GitHub Repository.

Yi Fang, Dongzhe Fan, Daochen Zha et al.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

Yuan Wang, Xuyang Wu, Hsin-Tai Wu et al.

The integration of Large Language Models (LLMs) in information retrieval has raised a critical reevaluation of fairness in the text-ranking models. LLMs, such as GPT models and Llama2, have shown effectiveness in natural language understanding tasks, and prior works (e.g., RankGPT) have also demonstrated that the LLMs exhibit better performance than the traditional ranking models in the ranking task. However, their fairness remains largely unexplored. This paper presents an empirical study evaluating these LLMs using the TREC Fair Ranking dataset, focusing on the representation of binary protected attributes such as gender and geographic location, which are historically underrepresented in search outcomes. Our analysis delves into how these LLMs handle queries and documents related to these attributes, aiming to uncover biases in their ranking algorithms. We assess fairness from both user and content perspectives, contributing an empirical benchmark for evaluating LLMs as the fair ranker.

Yuanfu Sun, Zhengnan Ma, Yi Fang et al.

The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.

Dongzhe Fan, Yi Fang, Jiajin Liu et al.

Large Language Models (LLMs) have demonstrated substantial efficacy in advancing graph-structured data analysis. Prevailing LLM-based graph methods excel in adapting LLMs to text-rich graphs, wherein node attributes are text descriptions. However, their applications to multimodal graphs--where nodes are associated with diverse attribute types, such as texts and images--remain underexplored, despite their ubiquity in real-world scenarios. To bridge the gap, we introduce the Multimodal Large Language and Graph Assistant (MLaGA), an innovative model that adeptly extends LLM capabilities to facilitate reasoning over complex graph structures and multimodal attributes. We first design a structure-aware multimodal encoder to align textual and visual attributes within a unified space through a joint graph pre-training objective. Subsequently, we implement a multimodal instruction-tuning approach to seamlessly integrate multimodal features and graph structures into the LLM through lightweight projectors. Extensive experiments across multiple datasets demonstrate the effectiveness of MLaGA compared to leading baseline methods, achieving superior performance in diverse graph learning tasks under both supervised and transfer learning scenarios.

Huei-Chung Hu, Xuyang Wu, Yuan Wang et al.

Numerous works concerning head pose estimation (HPE) offer algorithms or proposed neural network-based approaches for extracting Euler angles from either facial key points or directly from images of the head region. However, many works failed to provide clear definitions of the coordinate systems and Euler or Tait-Bryan angles orders in use. It is a well-known fact that rotation matrices depend on coordinate systems, and yaw, roll, and pitch angles are sensitive to their application order. Without precise definitions, it becomes challenging to validate the correctness of the output head pose and drawing routines employed in prior works. In this paper, we thoroughly examined the Euler angles defined in the 300W-LP dataset, head pose estimation such as 3DDFA-v2, 6D-RepNet, WHENet, etc, and the validity of their drawing routines of the Euler angles. When necessary, we infer their coordinate system and sequence of yaw, roll, pitch from provided code. This paper presents (1) code and algorithms for inferring coordinate system from provided source code, code for Euler angle application order and extracting precise rotation matrices and the Euler angles, (2) code and algorithms for converting poses from one rotation system to another, (3) novel formulae for 2D augmentations of the rotation matrices, and (4) derivations and code for the correct drawing routines for rotation matrices and poses. This paper also addresses the feasibility of defining rotations with right-handed coordinate system in Wikipedia and SciPy, which makes the Euler angle extraction much easier for full-range head pose research.

Subramaniam Vincent, Phoebe Wang, Zhan Shi et al.

Since the launch of ChatGPT in late 2022, the capacities of Large Language Models and their evaluation have been in constant discussion and evaluation both in academic research and in the industry. Scenarios and benchmarks have been developed in several areas such as law, medicine and math (Bommasani et al., 2023) and there is continuous evaluation of model variants. One area that has not received sufficient scenario development attention is journalism, and in particular journalistic sourcing and ethics. Journalism is a crucial truth-determination function in democracy (Vincent, 2023), and sourcing is a crucial pillar to all original journalistic output. Evaluating the capacities of LLMs to annotate stories for the different signals of sourcing and how reporters justify them is a crucial scenario that warrants a benchmark approach. It offers potential to build automated systems to contrast more transparent and ethically rigorous forms of journalism with everyday fare. In this paper we lay out a scenario to evaluate LLM performance on identifying and annotating sourcing in news stories on a five-category schema inspired from journalism studies (Gans, 2004). We offer the use case, our dataset and metrics and as the first step towards systematic benchmarking. Our accuracy findings indicate LLM-based approaches have more catching to do in identifying all the sourced statements in a story, and equally, in matching the type of sources. An even harder task is spotting source justifications.