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Goal-directed molecular generation requires satisfying heterogeneous constraints such as protein--ligand compatibility and multi-objective drug-like properties, yet existing methods often optimize these constraints in isolation, failing to…
Medication recommendation targets to provide a proper set of medicines according to patients' diagnoses, which is a critical task in clinics. Currently, the recommendation is manually conducted by doctors. However, for complicated cases,…
It is increasingly common in many types of natural and physical systems (especially biological systems) to have different types of measurements performed on the same underlying system. In such settings, it is important to align the…
Modern generative models achieve excellent quality in a variety of tasks including image or text generation and chemical molecule modeling. However, existing methods often lack the essential ability to generate examples with requested…
Numerous challenges in science and engineering can be framed as optimization tasks, including the maximization of reaction yields, the optimization of molecular and materials properties, and the fine-tuning of automated hardware protocols.…
This paper proposes a latent prompt Transformer model for solving challenging optimization problems such as molecule design, where the goal is to find molecules with optimal values of a target chemical or biological property that can be…
Drug targets are the main focus of drug discovery due to their key role in disease pathogenesis. Computational approaches are widely applied to drug development because of the increasing availability of biological molecular datasets.…
For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state of the…
Complex networks theory has commonly been used for modelling and understanding the interactions taking place between the elements composing complex systems. More recently, the use of generative models has gained momentum, as they allow…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…
Automated Machine Learning encompasses a set of meta-algorithms intended to design and apply machine learning techniques (e.g., model selection, hyperparameter tuning, model assessment, etc.). TPOT, a software for optimizing machine…
Cell heterogeneity plays an important role in patient responses to drug treatments. In many cancers, it is associated with poor treatment outcomes. Many modern drug combination therapies aim to exploit cell heterogeneity, but determining…
Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the…
Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo design flow matching or diffusion-based models are limited to…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
Recent advances in generative models have made exploring design spaces easier for de novo molecule generation. However, popular generative models like GANs and normalizing flows face challenges such as training instabilities due to…
Modeling the joint distribution of data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic benefits reaching beyond purely generative or predictive models.…
Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…
One of the challenging problems in sequence generation tasks is the optimized generation of sequences with specific desired goals. Current sequential generative models mainly generate sequences to closely mimic the training data, without…