Related papers: ExplainableFold: Understanding AlphaFold Predictio…

European Law now requires AI to be explainable in the context of adverse decisions affecting European Union (EU) citizens. At the same time, it is expected that there will be increasing instances of AI failure as it operates on imperfect…

Using machine learning in high-stakes applications often requires predictions to be accompanied by explanations comprehensible to the domain user, who has ultimate responsibility for decisions and outcomes. Recently, a new framework for…

The need for transparency of predictive systems based on Machine Learning algorithms arises as a consequence of their ever-increasing proliferation in the industry. Whenever black-box algorithmic predictions influence human affairs, the…

There has been a growing interest in model-agnostic methods that can make deep learning models more transparent and explainable to a user. Some researchers recently argued that for a machine to achieve a certain degree of human-level…

Artificial intelligence (AI) in the form of deep learning bears promise for drug discovery and chemical biology, $\textit{e.g.}$, to predict protein structure and molecular bioactivity, plan organic synthesis, and design molecules…

AlphaFold, a groundbreaking protein prediction model, has revolutionized protein structure prediction, populating the AlphaFold Protein Database (AFDB) with millions of predicted structures. However, AlphaFold's accuracy in predicting…

How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…

Recent developments in Artificial Intelligence (AI) and their applications in critical industries such as healthcare, fin-tech and cybersecurity have led to a surge in research in explainability in AI. Innovative research methods are being…

A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…

The integration of artificial intelligence into business processes has significantly enhanced decision-making capabilities across various industries such as finance, healthcare, and retail. However, explaining the decisions made by these AI…

Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…

This paper explores interpretability techniques for two of the most successful learning algorithms in medical decision-making literature: deep neural networks and random forests. We applied these algorithms in a real-world medical dataset…

Interpretability, explainability and transparency are key issues to introducing Artificial Intelligence methods in many critical domains: This is important due to ethical concerns and trust issues strongly connected to reliability,…

AlphaFold can be used for both single-chain and multi-chain protein structure prediction, while the latter becomes extremely challenging as the number of chains increases. In this work, by taking each chain as a node and assembly actions as…

Transparency is an essential requirement of machine learning based decision making systems that are deployed in real world. Often, transparency of a given system is achieved by providing explanations of the behavior and predictions of the…

Explaining the predictions of a deep neural network is a nontrivial task, yet high-quality explanations for predictions are often a prerequisite for practitioners to trust these models. Counterfactual explanations aim to explain predictions…

Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic resolution in some…

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially…

Explaining recommendations enables users to understand whether recommended items are relevant to their needs and has been shown to increase their trust in the system. More generally, if designing explainable machine learning models is key…

Artificial Intelligence (AI) has become essential for analyzing complex data and solving highly-challenging tasks. It is being applied across numerous disciplines beyond computer science, including Food Engineering, where there is a growing…