arXiv research

New dataset $abla^2$DFT for drug-like molecules benchmarks neural network potentials.

BOAT optimizes multiple antibody properties efficiently.

We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them on a latent space. As a proof of concept, we demonstrate that it can be used to generate drug-like molecules w…

Deep generative models are attracting great attention as a new promising approach for molecular design. All models reported so far are based on either variational autoencoder (VAE) or generative adversarial network (GAN). Here we propose a new type model based on an adversarially regularized autoencoder (ARAE). It basi…

A new RL framework optimizes drug-like molecules synthetically.

Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To augment the compound design process we introduce Mol-CycleGAN - a CycleGAN-based model that generates optimized compo…

Although machine learning has been successfully used to propose novel molecules that satisfy desired properties, it is still challenging to explore a large chemical space efficiently. In this paper, we present a conditional molecular design method that facilitates generating new molecules with desired properties. The p…

CogMol designs novel drug-like molecules for SARS-CoV-2 targets.

Paper proposes a method to design molecules with specific properties.

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph generation, whose goal is to discover novel molecules with desired properties such as …

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph recurrent generative model for molecular structures. Our model generates diverse …

BERT learns molecular substructures for chemistry problems.

DECAF optimizes molecular graphs for ensemble properties, improving drug design accuracy.

Sparse molecular representations improve interpretability in graph neural networks.

Optimising discrete data for a desired characteristic using gradient-based methods involves projecting the data into a continuous latent space and carrying out optimisation in this space. Carrying out global optimisation is difficult as optimisers are likely to follow gradients into regions of the latent space that the…

Molecule optimization is about generating molecule $Y$ with more desirable properties based on an input molecule $X$. The state-of-the-art approaches partition the molecules into a large set of substructures $S$ and grow the new molecule structure by iteratively predicting which substructure from $S$ to add. However, s…

We present a framework, which we call Molecule Deep $Q$-Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double $Q$-learning and randomized value functions). We directly define modifications on molecules, thereby ensuring 100…

Benchmark proposes to assess molecule docking efficiency.

Optimizes latent space of VAEs using decoder uncertainty to generate valid objects.

A new drug embedding method using hierarchical drug relations and chemical structures.

HLTF generates chemically valid 3D molecules with improved topology control.

This abstract reviews recent methods for predicting protein-ligand binding affinity.

Q-SAVI model improves drug discovery accuracy with prior knowledge of chemical space.

Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well …

Alzheimer's disease (AD) is the most common neurodegenerative disease in older people. Despite considerable efforts to find a cure for AD, there is a 99.6% failure rate of clinical trials for AD drugs, likely because AD patients cannot easily be identified at early stages. This project investigated machine learning app…

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on either 1-D or 2-D representations of typically small, drug-like molecules. Howev…

Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a drug-like molecule to a given target. These models require expert-level knowled…

According to Cobanoglu et al and Murphy, it is now widely acknowledged that the single target paradigm (one protein or target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - that is, i…

Groups with Property (T) have fiber products with Property (T).

We prove recognition theorems for codimension one manifold factors of dimension $n \geq 4$. In particular, we formalize topographical methods and introduce three ribbons properties: the crinkled ribbons property, the twisted crinkled ribbons property, and the fuzzy ribbons property. We show that $X \times \mathbb{R}$ i…

The study shows that several properties are not profinite invariants.

We show that all finite-dimensional resolvable generalized manifolds with the piecewise disjoint arc-disk property are codimension one manifold factors. We then show how the piecewise disjoint arc-disk property and other general position properties that detect codimension one manifold factors are related. We also note …

The paper explores higher property T in lattices and its connections to geometric phenomena.

Asymptotic property C was introduced by Dranishnikov to study spaces with infinite asymptotic dimension. We show that asymptotic property C is preserved by infinite products. We also show that countable restricted direct products of countable groups with finite asymptotic dimension have asymptotic property C. Then we i…

Groups of importance in group theory have flexible stability properties.

This paper generalizes property (QT) to a broader class of groups.

Proves a vanishing property for symplectic manifold cohomology.

Survey on foliations and diffeomorphism groups.

We prove extension theorems for several geometric properties such as asymptotic property C (APC), finite decomposition complexity (FDC), strict finite decomposition complexity (sFDC) which are weakenings of Gromov's finite asymptotic dimension (FAD). The context of all theorems is a finitely generated group $G$ with a …

Study generalizes property elicitation to imprecise probabilities.

Introduces bounded scale measure and generalizes property A.

Study cohomological and metric properties of non-Kähler complex manifolds.

The paper explores the twisted Rokhlin property in mapping class groups of surfaces.

The balance property is crucial for insurance pricing, ensuring total actuarial price equals loss. Maximum likelihood GLMs fulfill it, but Lindholm-Wüthrich suggests three methods, with constrained GLM being superior.

We prove some general results about quasi-actions on trees and define Property (QFA), which is analogous to Serre's Property (FA), but in the coarse setting. This property is shown to hold for a class of groups, including $SL(n,\Z)$ for $n\geq 3$. We also give a way of thinking about Property (QFA) by breaking it down …

We present examples of metric spaces that are not Riemannian manifolds nor dimensionally homogeneous that satisfy the Tetrahedral Property. In spite of that, Euclidean cones over metric spaces with small diameter do not satisfy this property. We extend Sormani's Tetrahedral Property to a less restrictive property and p…

The paper examines curvature properties of twistor spaces.

Study Finsler metric measure manifolds' concentration properties.