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Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel…

Breast cancer is a highly heterogeneous disease with diverse molecular profiles. The PAM50 gene signature is widely recognized as a standard for classifying breast cancer into intrinsic subtypes, enabling more personalized treatment…

Skin cancer is one of the deadly types of cancer and is common in the world. Recently, there has been a huge jump in the rate of people getting skin cancer. For this reason, the number of studies on skin cancer classification with deep…

Less than 1% of protein sequences are structurally and functionally annotated. Natural Language Processing (NLP) community has recently embraced self-supervised learning as a powerful approach to learn representations from unlabeled text,…

We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…

Predicting the mechanical properties of polysulfone (PSF) membranes from structural descriptors remains challenging due to extreme data scarcity typical of experimental studies. To investigate this issue, this study benchmarked…

Chemical synthesis, as a foundational methodology in the creation of transformative molecules, exerts substantial influence across diverse sectors from life sciences to materials and energy. Current chemical synthesis practices emphasize…

Peptide-drug conjugates (PDCs) represent a promising therapeutic avenue for human diseases, particularly in cancer treatment. Systematic elucidation of structure-activity relationships (SARs) and accurate prediction of the activity of PDCs…

Accurate prediction of Drug-Target Affinity (DTA) is crucial for reducing experimental costs and accelerating early screening in computational drug discovery. While sequence-based deep learning methods avoid reliance on costly 3D…

The prediction of tumor progression and chemotherapy response has been recently tackled exploiting Tumor Infiltrating Lymphocytes (TILs) and the nuclear protein Ki67 as prognostic factors. Recently, deep neural networks (DNNs) have been…

Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on…

Molecular property prediction is essential in chemistry, especially for drug discovery applications. However, available molecular property data is often limited, encouraging the transfer of information from related data. Transfer learning…

Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…

With access to large datasets, deep neural networks (DNN) have achieved human-level accuracy in image and speech recognition tasks. However, in chemistry, data is inherently small and fragmented. In this work, we develop an approach of…

In light of the increasing interest in G9a's role in neuroscience, three machine learning (ML) models, that are time efficient and cost effective, were developed to support researchers in this area. The models are based on data provided by…

Machine Learning (ML) and Deep Learning (DL) based framework have evolved rapidly and generated considerable interests for predicting the properties of materials. In this work, we utilize ML-DL framework to predict the electrochemical…

Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for…

Despite the high accuracy of 'black box' deep learning models, drug discovery still relies on protein-ligand interaction principles and heuristics. To improve interpretability of protein-small molecule binding predictions, we developed the…

Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an…

This study introduces a systematic framework to compare the efficacy of Large Language Models (LLMs) for fine-tuning across various cheminformatics tasks. Employing a uniform training methodology, we assessed three well-known…