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One reason pretraining on self-supervised linguistic tasks is effective is that it teaches models features that are helpful for language understanding. However, we want pretrained models to learn not only to represent linguistic features,…

Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…

AI for drug discovery has been a research hotspot in recent years, and SMILES-based language models has been increasingly applied in drug molecular design. However, no work has explored whether and how language models understand the…

Pathology text mining is a challenging task given the reporting variability and constant new findings in cancer sub-type definitions. However, successful text mining of a large pathology database can play a critical role to advance 'big…

Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction…

We propose to develop deep learning models that can predict Pareto optimal dose distributions by using any given set of beam angles, along with patient anatomy, as input to train the deep neural networks. We implement and compare two deep…

Accurately modeling the protein fitness landscapes holds great importance for protein engineering. Recently, due to their capacity and representation ability, pre-trained protein language models have achieved state-of-the-art performance in…

Machine-learning interatomic potentials (MLIPs) have enabled molecular dynamics at near ab initio accuracy, yet remain limited to energies and forces by construction, leaving electronic observables such as dipole moments and…

DPD-Cancer is a graph-attention deep learning framework for predicting small-molecule DPD-Cancer is a graph-attention deep learning framework for predicting small-molecule anti-cancer activity across the NCI-60 panel, trained and evaluated…

Supervised learning models, also known as quantitative structure-activity regression (QSAR) models, are increasingly used in assisting the process of preclinical, small molecule drug discovery. The models are trained on data consisting of a…

Drug combination therapy has become a increasingly promising method in the treatment of cancer. However, the number of possible drug combinations is so huge that it is hard to screen synergistic drug combinations through wet-lab…

The incredible capabilities of generative artificial intelligence models have inevitably led to their application in the domain of drug discovery. Within this domain, the vastness of chemical space motivates the development of more…

Machine learning approaches have become popular for molecular modeling tasks, including molecular force fields and properties prediction. Traditional supervised learning methods suffer from scarcity of labeled data for particular tasks,…

The advent of digital pathology presents opportunities for computer vision for fast, accurate, and objective solutions for histopathological images and aid in knowledge discovery. This work uses deep learning to predict genomic biomarkers -…

Multimodal deep learning has improved prognostic accuracy for brain tumours by integrating histopathology and genomic data, yet the contribution of volumetric MRI within unified survival frameworks remains unexplored. This pilot study…

The goal of the present study is to analyze an application of deep learning models in order to augment the diagnostic performance of oral squamous cell carcinoma (OSCC) with a longitudinal cohort study using the Histopathological Imaging…

Motivation: Tumor classification using Imaging Mass Spectrometry (IMS) data has a high potential for future applications in pathology. Due to the complexity and size of the data, automated feature extraction and classification steps are…

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…

Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the…

Machine learning has been widely verified and applied in chemoinformatics, and have achieved outstanding results in the prediction, modification, and optimization of luminescence, magnetism, and electrode materials. Here, we propose a…