TAGMol: Target-Aware Gradient-guided Molecule Generation

3D generative models have shown significant promise in structure-based drug design (SBDD), particularly in discovering ligands tailored to specific target binding sites. Existing algorithms often focus primarily on ligand-target binding, characterized by binding affinity. Moreover, models trained solely on target-ligand distribution may fall short in addressing the broader objectives of drug discovery, such as the development of novel ligands with desired properties like drug-likeness, and synthesizability, underscoring the multifaceted nature of the drug design process. To overcome these challenges, we decouple the problem into molecular generation and property prediction. The latter synergistically guides the diffusion sampling process, facilitating guided diffusion and resulting in the creation of meaningful molecules with the desired properties. We call this guided molecular generation process as TAGMol. Through experiments on benchmark datasets, TAGMol demonstrates superior performance compared to state-of-the-art baselines, achieving a 22% improvement in average Vina Score and yielding favorable outcomes in essential auxiliary properties. This establishes TAGMol as a comprehensive framework for drug generation.

SPEAR : Semi-supervised Data Programming in Python

We present SPEAR, an open-source python library for data programming with semi supervision. The package implements several recent data programming approaches including facility to programmatically label and build training data. SPEAR facilitates weak supervision in the form of heuristics (or rules) and association of noisy labels to the training dataset. These noisy labels are aggregated to assign labels to the unlabeled data for downstream tasks. We have implemented several label aggregation approaches that aggregate the noisy labels and then train using the noisily labeled set in a cascaded manner. Our implementation also includes other approaches that jointly aggregate and train the model. Thus, in our python package, we integrate several cascade and joint data-programming approaches while also providing the facility of data programming by letting the user define labeling functions or rules. The code and tutorial notebooks are available at \url{https://github.com/decile-team/spear}.