Related papers: Drug Discovery with Dynamic Goal-aware Fragments

Recently, utilizing reinforcement learning (RL) to generate molecules with desired properties has been highlighted as a promising strategy for drug design. A molecular docking program - a physical simulation that estimates protein-small…

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes…

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…

Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly…

Data is a central component of machine learning and causal inference tasks. The availability of large amounts of data from sources such as open data repositories, data lakes and data marketplaces creates an opportunity to augment data and…

Generative Flow Networks, or GFlowNets, offer a promising framework for molecular design, but their internal decision policies remain opaque. This limits adoption in drug discovery, where chemists require clear and interpretable rationales…

It remains a challenging task to generate a vast variety of novel compounds with desirable pharmacological properties. In this work, a generative network complex (GNC) is proposed as a new platform for designing novel compounds, predicting…

Drug discovery is a complex, multi-step pipeline that remains heavily dependent on manual, experience-driven operations; meanwhile, existing customized artificial intelligence tools are fragmented across web applications, desktop software,…

In the field of computational molecule generation, an essential task in the discovery of new chemical compounds, fragment-based deep generative models are a leading approach, consistently achieving state-of-the-art results in molecular…

Chemical space exploration underlies drug discovery, yet most generative models treat chemical space as a fixed, implicitly learned distribution, focusing on sampling molecules rather than deliberately designing the space itself. We…

Existing drug discovery pipelines take 5-10 years and cost billions of dollars. Computational approaches aim to sample from regions of the whole molecular and solid-state compounds called chemical space which could be on the order of 1060 .…

The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…

Recent advancements in generative models have established state-of-the-art benchmarks in the generation of molecules and novel drug candidates. Despite these successes, a significant gap persists between generative models and the…

Most earlier 3D structure-based molecular generation approaches follow an atom-wise paradigm, incrementally adding atoms to a partially built molecular fragment within protein pockets. These methods, while effective in designing tightly…

Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…

Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage,…

To mitigate the hallucination and knowledge deficiency in large language models (LLMs), Knowledge Graph (KG)-based Retrieval-Augmented Generation (RAG) has shown promising potential by utilizing KGs as external resource to enhance LLMs…

The capability of the human to pay attention to both coarse and fine-grained regions has been applied to computer vision tasks. Motivated by that, we propose a collaborative learning framework in the complex domain for monaural noise…

Conventional generative models for materials discovery are predominantly trained and validated using data from Density Functional Theory (DFT) with approximate exchange-correlation functionals. This creates a fundamental bottleneck: these…

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…