Related papers: Transcriptome-Conditioned Personalized De Novo Dru…

Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

In this work we present a deep learning approach to conduct hypothesis-free, transcriptomics-based matching of drugs for diseases. Our proposed neural network architecture is trained on approved drug-disease indications, taking as input the…

Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline.…

A key aim of systems biology is the reconstruction of molecular networks, however we do not yet have networks that integrate information from all datasets available for a particular clinical condition. This is in part due to the limited…

The pathogenesis and progression of many tumors, including hematologic malignancies is highly dependent on enhanced lipogenesis. De novo fatty-acid synthesis permits accelerated proliferation of tumor cells by providing structural…

Glioblastomas, constituting over 50% of malignant brain tumors, are highly aggressive brain tumors that pose substantial treatment challenges due to their rapid progression and resistance to standard therapies. The methylation status of the…

With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating…

Finding drug-like compounds with high bioactivity is essential for drug discovery, but the task is complicated by the high cost of chemical synthesis and validation. With their outstanding performance in de novo drug design, deep generative…

Longer timelines and lower success rates of drug candidates limit the productivity of clinical trials in the pharmaceutical industry. Promising de novo drug design techniques help solve this by exploring a broader chemical space,…

A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning…

Domain-aware machine learning (ML) models have been increasingly adopted for accelerating small molecule therapeutic design in the recent years. These models have been enabled by significant advancement in state-of-the-art artificial…

Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but…

Generation of drug-like molecules with high binding affinity to target proteins remains a difficult and resource-intensive task in drug discovery. Existing approaches primarily employ reinforcement learning, Markov sampling, or deep…

Machine learning (ML) has been playing important roles in drug discovery in the past years by providing (pre-)screening tools for prioritising chemical compounds to pass through wet lab experiments. One of the main ML tasks in drug…

Breast cancer (BC) remains a significant global health challenge, with personalized treatment selection complicated by the disease's molecular and clinical heterogeneity. BC treatment decisions rely on various patient-specific clinical…

De novo molecule generation allows the search for more drug-like hits across a vast chemical space. However, lead optimization is still required, and the process of optimizing molecular structures faces the challenge of balancing structural…

De novo molecule generation can suffer from data inefficiency; requiring large amounts of training data or many sampled data points to conduct objective optimization. The latter is a particular disadvantage when combining deep generative…

Single-cell datasets often lack individual cell labels, making it challenging to identify cells associated with disease. To address this, we introduce Mixture Modeling for Multiple Instance Learning (MMIL), an expectation maximization…

Computing atomic-scale properties of chemically disordered materials requires an efficient exploration of their vast configuration space. Traditional approaches such as Monte Carlo or Special Quasirandom Structures either entail sampling an…