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Researchers have recently achieved significant advances in deep learning techniques, which in turn has substantially advanced other research disciplines, such as natural language processing, image processing, speech recognition, and…
Predicting whether a molecule can cross the blood-brain barrier (BBB) is a key step in early-stage neuro-pharmaceutical design, directly influencing the efficiency and success rate of drug development. Traditional methods based on…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…
Deep learning is very effective at jointly learning feature representations and classification models, especially when dealing with high dimensional input patterns. Probabilistic logic reasoning, on the other hand, is capable to take…
Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…
Proteins are essential components of all living organisms and play a critical role in cellular survival. They have a broad range of applications, from clinical treatments to material engineering. This versatility has spurred the development…
Geometry problem solving, a crucial aspect of mathematical reasoning, is vital across various domains, including education, the assessment of AI's mathematical abilities, and multimodal capability evaluation. The recent surge in deep…
Recently, deep feedforward neural networks have achieved considerable success in modeling biological sensory processing, in terms of reproducing the input-output map of sensory neurons. However, such models raise profound questions about…
In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…
Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…
Over the last several years, the field of natural language processing has been propelled forward by an explosion in the use of deep learning models. This survey provides a brief introduction to the field and a quick overview of deep…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…
Process mining enables the reconstruction and evaluation of business processes based on digital traces in IT systems. An increasingly important technique in this context is process prediction. Given a sequence of events of an ongoing trace,…
The transformation towards renewable energy and feedstock supply in the chemical industry requires new conceptual process design approaches. Recently, breakthroughs in artificial intelligence offer opportunities to accelerate this…
Deep Learning has revolutionized the fields of computer vision, natural language understanding, speech recognition, information retrieval and more. However, with the progressive improvements in deep learning models, their number of…