XAI meets Biology: A Comprehensive Review of Explainable AI in Bioinformatics Applications

Artificial intelligence (AI), particularly machine learning and deep learning models, has significantly impacted bioinformatics research by offering powerful tools for analyzing complex biological data. However, the lack of interpretability and transparency of these models presents challenges in leveraging these models for deeper biological insights and for generating testable hypotheses. Explainable AI (XAI) has emerged as a promising solution to enhance the transparency and interpretability of AI models in bioinformatics. This review provides a comprehensive analysis of various XAI techniques and their applications across various bioinformatics domains including DNA, RNA, and protein sequence analysis, structural analysis, gene expression and genome analysis, and bioimaging analysis. We introduce the most pertinent machine learning and XAI methods, then discuss their diverse applications and address the current limitations of available XAI tools. By offering insights into XAI's potential and challenges, this review aims to facilitate its practical implementation in bioinformatics research and help researchers navigate the landscape of XAI tools.

Trustworthy Representation Learning Across Domains

As AI systems have obtained significant performance to be deployed widely in our daily live and human society, people both enjoy the benefits brought by these technologies and suffer many social issues induced by these systems. To make AI systems good enough and trustworthy, plenty of researches have been done to build guidelines for trustworthy AI systems. Machine learning is one of the most important parts for AI systems and representation learning is the fundamental technology in machine learning. How to make the representation learning trustworthy in real-world application, e.g., cross domain scenarios, is very valuable and necessary for both machine learning and AI system fields. Inspired by the concepts in trustworthy AI, we proposed the first trustworthy representation learning across domains framework which includes four concepts, i.e, robustness, privacy, fairness, and explainability, to give a comprehensive literature review on this research direction. Specifically, we first introduce the details of the proposed trustworthy framework for representation learning across domains. Second, we provide basic notions and comprehensively summarize existing methods for the trustworthy framework from four concepts. Finally, we conclude this survey with insights and discussions on future research directions.

Fair Attribute Completion on Graph with Missing Attributes

Tackling unfairness in graph learning models is a challenging task, as the unfairness issues on graphs involve both attributes and topological structures. Existing work on fair graph learning simply assumes that attributes of all nodes are available for model training and then makes fair predictions. In practice, however, the attributes of some nodes might not be accessible due to missing data or privacy concerns, which makes fair graph learning even more challenging. In this paper, we propose FairAC, a fair attribute completion method, to complement missing information and learn fair node embeddings for graphs with missing attributes. FairAC adopts an attention mechanism to deal with the attribute missing problem and meanwhile, it mitigates two types of unfairness, i.e., feature unfairness from attributes and topological unfairness due to attribute completion. FairAC can work on various types of homogeneous graphs and generate fair embeddings for them and thus can be applied to most downstream tasks to improve their fairness performance. To our best knowledge, FairAC is the first method that jointly addresses the graph attribution completion and graph unfairness problems. Experimental results on benchmark datasets show that our method achieves better fairness performance with less sacrifice in accuracy, compared with the state-of-the-art methods of fair graph learning. Code is available at: https://github.com/donglgcn/FairAC.

Towards Explainable Visual Anomaly Detection

Anomaly detection and localization of visual data, including images and videos, are of great significance in both machine learning academia and applied real-world scenarios. Despite the rapid development of visual anomaly detection techniques in recent years, the interpretations of these black-box models and reasonable explanations of why anomalies can be distinguished out are scarce. This paper provides the first survey concentrated on explainable visual anomaly detection methods. We first introduce the basic background of image-level anomaly detection and video-level anomaly detection, followed by the current explainable approaches for visual anomaly detection. Then, as the main content of this survey, a comprehensive and exhaustive literature review of explainable anomaly detection methods for both images and videos is presented. Finally, we discuss several promising future directions and open problems to explore on the explainability of visual anomaly detection.