ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction

In this work, we propose the novel Prototypical Graph Regression Self-explainable Trees (ProGReST) model, which combines prototype learning, soft decision trees, and Graph Neural Networks. In contrast to other works, our model can be used to address various challenging tasks, including compound property prediction. In ProGReST, the rationale is obtained along with prediction due to the model's built-in interpretability. Additionally, we introduce a new graph prototype projection to accelerate model training. Finally, we evaluate PRoGReST on a wide range of chemical datasets for molecular property prediction and perform in-depth analysis with chemical experts to evaluate obtained interpretations. Our method achieves competitive results against state-of-the-art methods.Comment: In the review proces

Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions

Graph representation learning (GRL) has emerged as a pivotal field that has contributed significantly to breakthroughs in various fields, including biomedicine. The objective of this survey is to review the latest advancements in GRL methods and their applications in the biomedical field. We also highlight key challenges currently faced by GRL and outline potential directions for future research.Comment: Accepted by 2023 IMIA Yearbook of Medical Informatic

Navigating Healthcare Insights: A Birds Eye View of Explainability with Knowledge Graphs

Knowledge graphs (KGs) are gaining prominence in Healthcare AI, especially in drug discovery and pharmaceutical research as they provide a structured way to integrate diverse information sources, enhancing AI system interpretability. This interpretability is crucial in healthcare, where trust and transparency matter, and eXplainable AI (XAI) supports decision making for healthcare professionals. This overview summarizes recent literature on the impact of KGs in healthcare and their role in developing explainable AI models. We cover KG workflow, including construction, relationship extraction, reasoning, and their applications in areas like Drug-Drug Interactions (DDI), Drug Target Interactions (DTI), Drug Development (DD), Adverse Drug Reactions (ADR), and bioinformatics. We emphasize the importance of making KGs more interpretable through knowledge-infused learning in healthcare. Finally, we highlight research challenges and provide insights for future directions.Comment: IEEE AIKE 2023, 8 Page

A Survey on Explainability of Graph Neural Networks

Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and recommendation systems. However, combining feature information and combinatorial graph structures has led to complex non-linear GNN models. Consequently, this has increased the challenges of understanding the workings of GNNs and the underlying reasons behind their predictions. To address this, numerous explainability methods have been proposed to shed light on the inner mechanism of the GNNs. Explainable GNNs improve their security and enhance trust in their recommendations. This survey aims to provide a comprehensive overview of the existing explainability techniques for GNNs. We create a novel taxonomy and hierarchy to categorize these methods based on their objective and methodology. We also discuss the strengths, limitations, and application scenarios of each category. Furthermore, we highlight the key evaluation metrics and datasets commonly used to assess the explainability of GNNs. This survey aims to assist researchers and practitioners in understanding the existing landscape of explainability methods, identifying gaps, and fostering further advancements in interpretable graph-based machine learning.Comment: submitted to Bulletin of the IEEE Computer Society Technical Committee on Data Engineerin

Deep learning techniques for biomedical data processing

The interest in Deep Learning (DL) has seen an exponential growth in the last ten years, producing a significant increase in both theoretical and applicative studies. On the one hand, the versatility and the ability to tackle complex tasks have led to the rapid and widespread diffusion of DL technologies. On the other hand, the dizzying increase in the availability of biomedical data has made classical analyses, carried out by human experts, progressively more unlikely. Contextually, the need for efficient and reliable automatic tools to support clinicians, at least in the most demanding tasks, has become increasingly pressing. In this survey, we will introduce a broad overview of DL models and their applications to biomedical data processing, specifically to medical image analysis, sequence processing (RNA and proteins) and graph modeling of molecular data interactions. First, the fundamental key concepts of DL architectures will be introduced, with particular reference to neural networks for structured data, convolutional neural networks, generative adversarial models, and siamese architectures. Subsequently, their applicability for the analysis of different types of biomedical data will be shown, in areas ranging from diagnostics to the understanding of the characteristics underlying the process of transcription and translation of our genetic code, up to the discovery of new drugs. Finally, the prospects and future expectations of DL applications to biomedical data will be discussed

Graph Representation Learning in Biomedicine

Biomedical networks are universal descriptors of systems of interacting elements, from protein interactions to disease networks, all the way to healthcare systems and scientific knowledge. With the remarkable success of representation learning in providing powerful predictions and insights, we have witnessed a rapid expansion of representation learning techniques into modeling, analyzing, and learning with such networks. In this review, we put forward an observation that long-standing principles of networks in biology and medicine -- while often unspoken in machine learning research -- can provide the conceptual grounding for representation learning, explain its current successes and limitations, and inform future advances. We synthesize a spectrum of algorithmic approaches that, at their core, leverage graph topology to embed networks into compact vector spaces, and capture the breadth of ways in which representation learning is proving useful. Areas of profound impact include identifying variants underlying complex traits, disentangling behaviors of single cells and their effects on health, assisting in diagnosis and treatment of patients, and developing safe and effective medicines