BioMol-MQA: A Multi-Modal Question Answering Dataset For LLM Reasoning Over Bio-Molecular Interactions

Retrieval augmented generation (RAG) has shown great power in improving Large Language Models (LLMs). However, most existing RAG-based LLMs are dedicated to retrieving single modality information, mainly text; while for many real-world problems, such as healthcare, information relevant to queries can manifest in various modalities such as knowledge graph, text (clinical notes), and complex molecular structure. Thus, being able to retrieve relevant multi-modality domain-specific information, and reason and synthesize diverse knowledge to generate an accurate response is important. To address the gap, we present BioMol-MQA, a new question-answering (QA) dataset on polypharmacy, which is composed of two parts (i) a multimodal knowledge graph (KG) with text and molecular structure for information retrieval; and (ii) challenging questions that designed to test LLM capabilities in retrieving and reasoning over multimodal KG to answer questions. Our benchmarks indicate that existing LLMs struggle to answer these questions and do well only when given the necessary background data, signaling the necessity for strong RAG frameworks.

Bridging Source and Target Domains via Link Prediction for Unsupervised Domain Adaptation on Graphs

Graph neural networks (GNNs) have shown great ability for node classification on graphs. However, the success of GNNs relies on abundant labeled data, while obtaining high-quality labels is costly and challenging, especially for newly emerging domains. Hence, unsupervised domain adaptation (UDA), which trains a classifier on the labeled source graph and adapts it to the unlabeled target graph, is attracting increasing attention. Various approaches have been proposed to alleviate the distribution shift between the source and target graphs to facilitate the classifier adaptation. However, most of them simply adopt existing UDA techniques developed for independent and identically distributed data to gain domain-invariant node embeddings for graphs, which do not fully consider the graph structure and message-passing mechanism of GNNs during the adaptation and will fail when label distribution shift exists among domains. In this paper, we proposed a novel framework that adopts link prediction to connect nodes between source and target graphs, which can facilitate message-passing between the source and target graphs and augment the target nodes to have ``in-distribution'' neighborhoods with the source domain. This strategy modified the target graph on the input level to reduce its deviation from the source domain in the embedding space and is insensitive to disproportional label distributions across domains. To prevent the loss of discriminative information in the target graph, we further design a novel identity-preserving learning objective, which guides the learning of the edge insertion module together with reconstruction and adaptation losses. Experimental results on real-world datasets demonstrate the effectiveness of our framework.

Diagnosing and Addressing Pitfalls in KG-RAG Datasets: Toward More Reliable Benchmarking

Knowledge Graph Question Answering (KGQA) systems rely on high-quality benchmarks to evaluate complex multi-hop reasoning. However, despite their widespread use, popular datasets such as WebQSP and CWQ suffer from critical quality issues, including inaccurate or incomplete ground-truth annotations, poorly constructed questions that are ambiguous, trivial, or unanswerable, and outdated or inconsistent knowledge. Through a manual audit of 16 popular KGQA datasets, including WebQSP and CWQ, we find that the average factual correctness rate is only 57 %. To address these issues, we introduce KGQAGen, an LLM-in-the-loop framework that systematically resolves these pitfalls. KGQAGen combines structured knowledge grounding, LLM-guided generation, and symbolic verification to produce challenging and verifiable QA instances. Using KGQAGen, we construct KGQAGen-10k, a ten-thousand scale benchmark grounded in Wikidata, and evaluate a diverse set of KG-RAG models. Experimental results demonstrate that even state-of-the-art systems struggle on this benchmark, highlighting its ability to expose limitations of existing models. Our findings advocate for more rigorous benchmark construction and position KGQAGen as a scalable framework for advancing KGQA evaluation.

Towards Graph Foundation Models: A Transferability Perspective

In recent years, Graph Foundation Models (GFMs) have gained significant attention for their potential to generalize across diverse graph domains and tasks. Some works focus on Domain-Specific GFMs, which are designed to address a variety of tasks within a specific domain, while others aim to create General-Purpose GFMs that extend the capabilities of domain-specific models to multiple domains. Regardless of the type, transferability is crucial for applying GFMs across different domains and tasks. However, achieving strong transferability is a major challenge due to the structural, feature, and distributional variations in graph data. To date, there has been no systematic research examining and analyzing GFMs from the perspective of transferability. To bridge the gap, we present the first comprehensive taxonomy that categorizes and analyzes existing GFMs through the lens of transferability, structuring GFMs around their application scope (domain-specific vs. general-purpose) and their approaches to knowledge acquisition and transfer. We provide a structured perspective on current progress and identify potential pathways for advancing GFM generalization across diverse graph datasets and tasks. We aims to shed light on the current landscape of GFMs and inspire future research directions in GFM development.

How Far are LLMs from Real Search? A Comprehensive Study on Efficiency, Completeness, and Inherent Capabilities

Search plays a fundamental role in problem-solving across various domains, with most real-world decision-making problems being solvable through systematic search. Drawing inspiration from recent discussions on search and learning, we systematically explore the complementary relationship between search and Large Language Models (LLMs) from three perspectives. First, we analyze how learning can enhance search efficiency and propose Search via Learning (SeaL), a framework that leverages LLMs for effective and efficient search. Second, we further extend SeaL to SeaL-C to ensure rigorous completeness during search. Our evaluation across three real-world planning tasks demonstrates that SeaL achieves near-perfect accuracy while reducing search spaces by up to 99.1% compared to traditional approaches. Finally, we explore how far LLMs are from real search by investigating whether they can develop search capabilities independently. Our analysis reveals that while current LLMs struggle with efficient search in complex problems, incorporating systematic search strategies significantly enhances their problem-solving capabilities. These findings not only validate the effectiveness of our approach but also highlight the need for improving LLMs' search abilities for real-world applications.

A General Framework to Enhance Fine-tuning-based LLM Unlearning

Unlearning has been proposed to remove copyrighted and privacy-sensitive data from Large Language Models (LLMs). Existing approaches primarily rely on fine-tuning-based methods, which can be categorized into gradient ascent-based (GA-based) and suppression-based methods. However, they often degrade model utility (the ability to respond to normal prompts). In this work, we aim to develop a general framework that enhances the utility of fine-tuning-based unlearning methods. To achieve this goal, we first investigate the common property between GA-based and suppression-based methods. We unveil that GA-based methods unlearn by distinguishing the target data (i.e., the data to be removed) and suppressing related generations, which is essentially the same strategy employed by suppression-based methods. Inspired by this finding, we introduce Gated Representation UNlearning (GRUN) which has two components: a soft gate function for distinguishing target data and a suppression module using Representation Fine-tuning (ReFT) to adjust representations rather than model parameters. Experiments show that GRUN significantly improves the unlearning and utility. Meanwhile, it is general for fine-tuning-based methods, efficient and promising for sequential unlearning.

Stepwise Perplexity-Guided Refinement for Efficient Chain-of-Thought Reasoning in Large Language Models

Chain-of-Thought (CoT) reasoning, which breaks down complex tasks into intermediate reasoning steps, has significantly enhanced the performance of large language models (LLMs) on challenging tasks. However, the detailed reasoning process in CoT often incurs long generation times and high computational costs, partly due to the inclusion of unnecessary steps. To address this, we propose a method to identify critical reasoning steps using perplexity as a measure of their importance: a step is deemed critical if its removal causes a significant increase in perplexity. Our method enables models to focus solely on generating these critical steps. This can be achieved through two approaches: refining demonstration examples in few-shot CoT or fine-tuning the model using selected examples that include only critical steps. Comprehensive experiments validate the effectiveness of our method, which achieves a better balance between the reasoning accuracy and efficiency of CoT.

LanP: Rethinking the Impact of Language Priors in Large Vision-Language Models

Large Vision-Language Models (LVLMs) have shown impressive performance in various tasks. However, LVLMs suffer from hallucination, which hinders their adoption in the real world. Existing studies emphasized that the strong language priors of LVLMs can overpower visual information, causing hallucinations. However, the positive role of language priors is the key to a powerful LVLM. If the language priors are too weak, LVLMs will struggle to leverage rich parameter knowledge and instruction understanding abilities to complete tasks in challenging visual scenarios where visual information alone is insufficient. Therefore, we propose a benchmark called LanP to rethink the impact of Language Priors in LVLMs. It is designed to investigate how strong language priors are in current LVLMs. LanP consists of 170 images and 340 corresponding well-designed questions. Extensive experiments on 25 popular LVLMs reveal that many LVLMs' language priors are not strong enough to effectively aid question answering when objects are partially hidden. Many models, including GPT-4 Turbo, exhibit an accuracy below 0.5 in such a scenario.

Graph-based Molecular In-context Learning Grounded on Morgan Fingerprints

In-context learning (ICL) effectively conditions large language models (LLMs) for molecular tasks, such as property prediction and molecule captioning, by embedding carefully selected demonstration examples into the input prompt. This approach avoids the computational overhead of extensive pertaining and fine-tuning. However, current prompt retrieval methods for molecular tasks have relied on molecule feature similarity, such as Morgan fingerprints, which do not adequately capture the global molecular and atom-binding relationships. As a result, these methods fail to represent the full complexity of molecular structures during inference. Moreover, small-to-medium-sized LLMs, which offer simpler deployment requirements in specialized systems, have remained largely unexplored in the molecular ICL literature. To address these gaps, we propose a self-supervised learning technique, GAMIC (Graph-Aligned Molecular In-Context learning, which aligns global molecular structures, represented by graph neural networks (GNNs), with textual captions (descriptions) while leveraging local feature similarity through Morgan fingerprints. In addition, we introduce a Maximum Marginal Relevance (MMR) based diversity heuristic during retrieval to optimize input prompt demonstration samples. Our experimental findings using diverse benchmark datasets show GAMIC outperforms simple Morgan-based ICL retrieval methods across all tasks by up to 45%.

A Survey of Calibration Process for Black-Box LLMs

Large Language Models (LLMs) demonstrate remarkable performance in semantic understanding and generation, yet accurately assessing their output reliability remains a significant challenge. While numerous studies have explored calibration techniques, they primarily focus on White-Box LLMs with accessible parameters. Black-Box LLMs, despite their superior performance, pose heightened requirements for calibration techniques due to their API-only interaction constraints. Although recent researches have achieved breakthroughs in black-box LLMs calibration, a systematic survey of these methodologies is still lacking. To bridge this gap, we presents the first comprehensive survey on calibration techniques for black-box LLMs. We first define the Calibration Process of LLMs as comprising two interrelated key steps: Confidence Estimation and Calibration. Second, we conduct a systematic review of applicable methods within black-box settings, and provide insights on the unique challenges and connections in implementing these key steps. Furthermore, we explore typical applications of Calibration Process in black-box LLMs and outline promising future research directions, providing new perspectives for enhancing reliability and human-machine alignment. This is our GitHub link: https://github.com/LiangruXie/Calibration-Process-in-Black-Box-LLMs