Lu Zhou

Yuchen Ren, Zhengyu Zhao, Chenhao Lin et al.

Transferable adversarial examples are known to cause threats in practical, black-box attack scenarios. A notable approach to improving transferability is using integrated gradients (IG), originally developed for model interpretability. In this paper, we find that existing IG-based attacks have limited transferability due to their naive adoption of IG in model interpretability. To address this limitation, we focus on the IG integration path and refine it in three aspects: multiplicity, monotonicity, and diversity, supported by theoretical analyses. We propose the Multiple Monotonic Diversified Integrated Gradients (MuMoDIG) attack, which can generate highly transferable adversarial examples on different CNN and ViT models and defenses. Experiments validate that MuMoDIG outperforms the latest IG-based attack by up to 37.3\% and other state-of-the-art attacks by 8.4\%. In general, our study reveals that migrating established techniques to improve transferability may require non-trivial efforts. Code is available at \url{https://github.com/RYC-98/MuMoDIG}.

Yichun Feng, Jiawei Wang, Ruikun He et al.

Knowledge graphs and large language models (LLMs) are key tools for biomedical knowledge integration and reasoning, facilitating structured organization of scientific articles and discovery of complex semantic relationships. However, current methods face challenges: knowledge graph construction is limited by complex terminology, data heterogeneity, and rapid knowledge evolution, while LLMs show limitations in retrieval and reasoning, making it difficult to uncover cross-document associations and reasoning pathways. To address these issues, we propose a pipeline that uses LLMs to construct a biomedical knowledge graph (BioStrataKG) from large-scale articles and builds a cross-document question-answering dataset (BioCDQA) to evaluate latent knowledge retrieval and multi-hop reasoning. We then introduce Integrated and Progressive Retrieval-Augmented Reasoning (IP-RAR) to enhance retrieval accuracy and knowledge reasoning. IP-RAR maximizes information recall through Integrated Reasoning-based Retrieval and refines knowledge via Progressive Reasoning-based Generation, using self-reflection to achieve deep thinking and precise contextual understanding. Experiments show that IP-RAR improves document retrieval F1 score by 20\% and answer generation accuracy by 25\% over existing methods. This framework helps doctors efficiently integrate treatment evidence for personalized medication plans and enables researchers to analyze advancements and research gaps, accelerating scientific discovery and decision-making.

Yang Liu, Lu Zhou, Ruikun He et al.

The surge in multimodal single-cell omics data exposes limitations in traditional, manually defined analysis workflows. AI agents offer a paradigm shift, enabling adaptive planning, executable code generation, traceable decisions, and real-time knowledge fusion. However, the lack of a comprehensive benchmark critically hinders progress. We introduce a novel benchmarking evaluation system to rigorously assess agent capabilities in single-cell omics analysis. This system comprises: a unified platform compatible with diverse agent frameworks and LLMs; multidimensional metrics assessing cognitive program synthesis, collaboration, execution efficiency, bioinformatics knowledge integration, and task completion quality; and 50 diverse real-world single-cell omics analysis tasks spanning multi-omics, species, and sequencing technologies. Our evaluation reveals that Grok-3-beta achieves state-of-the-art performance among tested agent frameworks. Multi-agent frameworks significantly enhance collaboration and execution efficiency over single-agent approaches through specialized role division. Attribution analyses of agent capabilities identify that high-quality code generation is crucial for task success, and self-reflection has the most significant overall impact, followed by retrieval-augmented generation (RAG) and planning. This work highlights persistent challenges in code generation, long-context handling, and context-aware knowledge retrieval, providing a critical empirical foundation and best practices for developing robust AI agents in computational biology.

Md Kamruzzaman Sarker, Lu Zhou, Aaron Eberhart et al.

Neuro-Symbolic Artificial Intelligence -- the combination of symbolic methods with methods that are based on artificial neural networks -- has a long-standing history. In this article, we provide a structured overview of current trends, by means of categorizing recent publications from key conferences. The article is meant to serve as a convenient starting point for research on the general topic.

Aaron Eberhart, Monireh Ebrahimi, Lu Zhou et al.

We present a new approach to integrating deep learning with knowledge-based systems that we believe shows promise. Our approach seeks to emulate reasoning structure, which can be inspected part-way through, rather than simply learning reasoner answers, which is typical in many of the black-box systems currently in use. We demonstrate that this idea is feasible by training a long short-term memory (LSTM) artificial neural network to learn EL+ reasoning patterns with two different data sets. We also show that this trained system is resistant to noise by corrupting a percentage of the test data and comparing the reasoner's and LSTM's predictions on corrupt data with correct answers.