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Not only automation of manufacturing processes but also automation of automation procedures itself become increasingly relevant to automation research. In this context, automated capability assessment, mainly leveraged by deep learning…

The unprecedented performance of machine learning models in recent years, particularly Deep Learning and transformer models, has resulted in their application in various domains such as finance, healthcare, and education. However, the…

Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…

The implementation of Artificial Intelligence (AI) systems in the manufacturing domain enables higher production efficiency, outstanding performance, and safer operations, leveraging powerful tools such as deep learning and reinforcement…

Explainable AI (XAI) methods identify which features are relevant to a model's predictions but often fail to clarify why certain decisions are made. In this work, we present a novel method that integrates causality with argument-based…

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…

Protein structures and functions are determined by a contiguous arrangement of amino acid sequences. Designing novel protein sequences and structures with desired geometry and functions is a complex task with large state spaces. Here we…

Deep Learning is a state-of-the-art technique to make inference on extensive or complex data. As a black box model due to their multilayer nonlinear structure, Deep Neural Networks are often criticized to be non-transparent and their…

Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to…

PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…

Black box systems for automated decision making, often based on machine learning over (big) data, map a user's features into a class or a score without exposing the reasons why. This is problematic not only for lack of transparency, but…

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…

Deep learning-based prediction of protein-ligand complexes has advanced significantly with the development of architectures such as AlphaFold3, Boltz-1, Chai-1, Protenix, and NeuralPlexer. Multiple sequence alignment (MSA) has been a key…

The goal of Protein Structure Prediction (PSP) problem is to predict a protein's 3D structure (confirmation) from its amino acid sequence. The problem has been a 'holy grail' of science since the Noble prize-winning work of Anfinsen…

Financial forecasting increasingly uses large neural network models, but their opacity raises challenges for trust and regulatory compliance. We present several approaches to explainable and reliable AI in finance. \emph{First}, we describe…

Studies on manufacturing cost prediction based on deep learning have begun in recent years, but the cost prediction rationale cannot be explained because the models are still used as a black box. This study aims to propose a manufacturing…

AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from…

While machine learning techniques have been successfully applied in several fields, the black-box nature of the models presents challenges for interpreting and explaining the results. We develop a new framework called Adaptive Explainable…

With the long term accumulation of high quality educational data, artificial intelligence has shown excellent performance in knowledge tracing. However, due to the lack of interpretability and transparency of some algorithms, this approach…

The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the…