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The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…

Protein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast…

The amyloid state of proteins is widely studied with relevancy in neurology, biochemistry, and biotechnology. In contrast with amorphous aggregation, the amyloid state has a well-defined structure, consisting of parallel and anti-parallel…

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…

Pre-trained large language models (LLM) have emerged as a powerful tool for simulating various scenarios and generating output given specific instructions and multimodal input. In this work, we analyze the specific use of LLM to enhance a…

Large language models (LLMs) have demonstrated that large-scale pretraining enables systems to adapt rapidly to new problems with little supervision in the language domain. This success, however, has not translated as effectively to the…

Deep learning has become a powerful tool in computational biology, revolutionising the analysis and interpretation of biological data over time. In our article review, we delve into various aspects of deep learning in computational biology.…

In this letter, we use large language models (LLMs) to develop a high-performing and robust beam prediction method. We formulate the millimeter wave (mmWave) beam prediction problem as a time series forecasting task, where the historical…

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional…

Protein language models (PLMs) have transformed sequence-based protein analysis, yet most applications rely only on final-layer embeddings, which may overlook biologically meaningful information encoded in earlier layers. We systematically…

Large Language Models (LLMs) inherit explicit and implicit biases from their training datasets. Identifying and mitigating biases in LLMs is crucial to ensure fair outputs, as they can perpetuate harmful stereotypes and misinformation. This…

Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further…

Methods from artificial intelligence (AI), in general, and machine learning, in particular, have kept conquering new territories in numerous areas of science. Most of the applications of these techniques are restricted to the classification…

In the domain of network biology, the interactions among heterogeneous genomic and molecular entities are represented through networks. Link prediction (LP) methodologies are instrumental in inferring missing or prospective associations…

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…

Deep-learning models such as Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) have been successfully used for process-mining tasks. They have achieved better performance for different predictive tasks than traditional…

Language models (LMs) are machine learning models designed to predict linguistic patterns by estimating the probability of word sequences based on large-scale datasets, such as text. LMs have a wide range of applications in natural language…

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet,…

Data-driven modeling based on Machine Learning (ML) is becoming a central component of protein engineering workflows. This perspective presents the elements necessary to develop effective, reliable, and reproducible ML models, and a set of…

Large language models (LLMs) have been widely employed across various application domains, yet their black-box nature poses significant challenges to understanding how these models process input data internally to make predictions. In this…