A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Generative model learns to create molecules with multiple properties using interpretable substructures.
MoFlow generates chemically valid molecular graphs from latent representations.
We seek to automate the design of molecules based on specific chemical properties. Our primary contributions are a simpler method for generating SMILES strings guaranteed to be chemically valid, using a combination of a new context-free grammar for SMILES and additional masking logic; and casting the molecular property…
Deep neural networks improve chemical reactor control using MPC.
Molecular optimization aims to discover novel molecules with desirable properties. Two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecu…
GraphAF generates chemically valid molecules efficiently and accurately.
Chemical databases store information in text representations, and the SMILES format is a universal standard used in many cheminformatics software. Encoded in each SMILES string is structural information that can be used to predict complex chemical properties. In this work, we develop SMILES2vec, a deep RNN that automat…
Hyperbolic volume correlates with chemical properties of fullerenes.
MEGAN models chemical reactions as graph edits, improving synthesis planning.
With access to large datasets, deep neural networks (DNN) have achieved human-level accuracy in image and speech recognition tasks. However, in chemistry, data is inherently small and fragmented. In this work, we develop an approach of using rule-based knowledge for training ChemNet, a transferable and generalizable de…
Deep Learning has been shown to learn efficient representations for structured data such as image, text or audio. In this chapter, we present neural network architectures that are able to learn efficient representations of molecules and materials. In particular, the continuous-filter convolutional network SchNet accura…
With the rise of deep neural networks for quantum chemistry applications, there is a pressing need for architectures that, beyond delivering accurate predictions of chemical properties, are readily interpretable by researchers. Here, we describe interpretation techniques for atomistic neural networks on the example of …
We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two deep neural networks - generative and predictive - that are trained separately b…
NLP techniques improve drug discovery by analyzing chemical and protein text.
Proposes SPCA to incorporate structural constraints in model identification.
Generative neural network designs novel 3D molecules with specified properties.
Machine learning advances chemistry and materials science by enabling large-scale exploration of chemical space based on quantum chemical calculations. While these models supply fast and accurate predictions of atomistic chemical properties, they do not explicitly capture the electronic degrees of freedom of a molecule…
Improved molecular property prediction using WL embedding in GNNs.
Generating molecules with desired chemical properties is important for drug discovery. The use of generative neural networks is promising for this task. However, from visual inspection, it often appears that generated samples lack diversity. In this paper, we quantify this internal chemical diversity, and we raise the …
Bio-oil molecule assessment is essential for the sustainable development of chemicals and transportation fuels. These oxygenated molecules have adequate carbon, hydrogen, and oxygen atoms that can be used for developing new value-added molecules (chemicals or transportation fuels). One motivation for our study stems fr…
Geometric approach to thermodynamics of chemical reaction networks.
Proposes a new model to predict polymer properties by integrating various data types.
Chemical autoencoders are attractive models as they combine chemical space navigation with possibilities for de-novo molecule generation in areas of interest. This enables them to produce focused chemical libraries around a single lead compound for employment early in a drug discovery project. Here it is shown that the…
HLTF generates chemically valid 3D molecules with improved topology control.
New method predicts activity coefficients for binary mixtures without using physical descriptors.
MatGAN uses GAN to efficiently generate new inorganic materials.
New method finds graphene nanocrystals with reduced DFT calculations.
Surrogate models improve chemical process equipment design and optimization.
Rank-based Bayesian Optimization improves molecule selection in chemical systems.
Functional groups (FGs) are molecular substructures that are served as a foundation for analyzing and predicting chemical properties of molecules. Automatic discovery of FGs will impact various fields of research, including medicinal chemistry and material sciences, by reducing the amount of lab experiments required fo…
Framework separates chemical and structural contributions to aqueous solubility.
A framework separates chemical and structural contributions to aqueous solubility.
We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings …
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the Chemical Master Equation. Despite its simple structur…
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of fragments required for chemical accuracy is still prohibitively expensive for ab-initio MBE to compete with force fi…
Deep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is possible to side-step expensive search procedures in the discrete and vast space of chemical structures. We introduce MolGAN, an imp…
Machine learning recreates the periodic table from element properties.
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a…
MoleculeSTM learns from molecule structures and texts for better drug design.
The paper develops a Gaussian process model for predicting chemical efficacy.
Modof-pipe optimizes molecules by modifying a single site, outperforming state-of-the-art methods.
Nuclear magnetic resonance (NMR) spectroscopy exploits the magnetic properties of atomic nuclei to discover the structure, reaction state and chemical environment of molecules. We propose a probabilistic generative model and inference procedures for NMR spectroscopy. Specifically, we use a weighted sum of trigonometric…
CANs improve GANs by enforcing structured constraints during training.
Structural Causal Models (SCMs) provide a popular causal modeling framework. In this work, we show that SCMs are not flexible enough to give a complete causal representation of dynamical systems at equilibrium. Instead, we propose a generalization of the notion of an SCM, that we call Causal Constraints Model (CCM), an…
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 …
This review discusses challenges and solutions for AI in chemical engineering.
Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approa…
A new RL framework optimizes drug-like molecules synthetically.