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.
Recent studies illustrate how machine learning (ML) can be used to bypass a core challenge of molecular modeling: the tradeoff between accuracy and computational cost. Here, we assess multiple ML approaches for predicting the atomization energy of organic molecules. Our resulting models learn the difference between low…
Transfer learning boosts chemically accurate neural network potentials for organic molecules.
In applications such as molecule design or drug discovery, it is desirable to have an algorithm which recommends new candidate molecules based on the results of past tests. These molecules first need to be synthesized and then tested for objective properties. We describe ChemBO, a Bayesian optimization framework for ge…
We introduce multiscale invariant dictionaries to estimate quantum chemical energies of organic molecules, from training databases. Molecular energies are invariant to isometric atomic displacements, and are Lipschitz continuous to molecular deformations. Similarly to density functional theory (DFT), the molecule is re…
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models a…
Atoms and molecules are important conceptual entities we invented to understand the physical world around us. The key to their usefulness lies in the organization of nuclear and electronic degrees of freedom into a single dynamical variable whose time evolution we can better imagine. The use of such effective variables…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees that the molecules can actually be synthesized in practice. We propose a new molecu…
Paper introduces a graph-based approach for retrosynthesis prediction.
A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance of kernel ridge regression models on well-studied data sets of small organic mole…
METRO predicts reactions using minimal templates, reducing computational overhead and achieving state-of-the-art results.
Organic Solar Cells are a promising technology for solving the clean energy crisis in the world. However, generating candidate chemical compounds for solar cells is a time-consuming process requiring thousands of hours of laboratory analysis. For a solar cell, the most important property is the power conversion efficie…
The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers from coverage and eff…
A neural network and evolutionary algorithm framework designs nonlinear optical molecules.
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 …
Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we require generative models that guide our search towards systems with desired proper…
We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy…
We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over hierarchical terms. These terms are generated from a neural network--a composit…
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based neural network architectures have emerged in recent years as the most successful …
Gryffin optimizes categorical variables in materials design, leveraging expert knowledge.
MACE architecture outperforms alternatives in various molecular and materials science tasks.
BERT learns molecular substructures for chemistry problems.
Transformer adapts to graphs with adaptive attention and auto-regressive decoding.
The development of accurate and transferable machine learning (ML) potentials for predicting molecular energetics is a challenging task. The process of data generation to train such ML potentials is a task neither well understood nor researched in detail. In this work, we present a fully automated approach for the gene…
Automating molecular design using deep reinforcement learning (RL) holds the promise of accelerating the discovery of new chemical compounds. Existing approaches work with molecular graphs and thus ignore the location of atoms in space, which restricts them to 1) generating single organic molecules and 2) heuristic rew…
We have numerically simulated the ideal-gas models of trading markets, where each agent is identified with a gas molecule and each trading as an elastic or money-conserving two-body collision. Unlike in the ideal gas, we introduce (quenched) saving propensity of the agents, distributed widely between the agents ($0 \le…
Emission from a class of benzene-based molecules known as Polycyclic Aromatic Hydrocarbons (PAHs) dominates the infrared spectrum of star-forming regions. The observed emission appears to arise from the combined emission of numerous PAH species, each with its unique spectrum. Linear superposition of the PAH spectra ide…
In the majority of molecular optimization tasks, predictive machine learning (ML) models are limited due to the unavailability and cost of generating big experimental datasets on the specific task. To circumvent this limitation, ML models are trained on big theoretical datasets or experimental indicators of molecular s…
A new drug embedding method using hierarchical drug relations and chemical structures.
Deep neural network predicts molecular wave functions in minimal basis.
Sparse molecular representations improve interpretability in graph neural networks.
Graph generation is an extremely important task, as graphs are found throughout different areas of science and engineering. In this work, we focus on the modern equivalent of the Erdos-Renyi random graph model: the graph variational autoencoder (GVAE). This model assumes edges and nodes are independent in order to gene…
A fundamental problem in applying machine learning techniques for chemical problems is to find suitable representations for molecular and crystal structures. While the structure representations based on atom connectivities are prevalent for molecules, two-dimensional descriptors are not suitable for describing molecula…
Bayesian algorithm discovers synthetic routes from target molecules.
Paper proposes a method to design molecules with specific properties.
This work improves molecular design by efficiently selecting diverse candidate molecules.
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…
In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language process…
A new model designs molecules with desired properties.
SILVR generates new molecules fitting protein binding sites.
GCDM generates valid large 3D molecules and optimizes existing molecules.
Modof-pipe optimizes molecules by modifying a single site, outperforming state-of-the-art methods.
Improved RL model for fragment-based molecule generation.
A new deep model generates molecules by fragments, improving validity and uniqueness.
We present a framework, which we call Molecule Deep -Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double -learning and randomized value functions). We directly define modifications on molecules, thereby ensuring 100…
In unsupervised data generation tasks, besides the generation of a sample based on previous observations, one would often like to give hints to the model in order to bias the generation towards desirable metrics. We propose a method that combines Generative Adversarial Networks (GANs) and reinforcement learning (RL) in…
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which can be of medical and biological importance. Graphs are are useful in this prob…
A general machine learning architecture is introduced that uses wavelet scattering coefficients of an inputted three dimensional signal as features. Solid harmonic wavelet scattering transforms of three dimensional signals were previously introduced in a machine learning framework for the regression of properties of sm…
Molecule optimization is about generating molecule with more desirable properties based on an input molecule . The state-of-the-art approaches partition the molecules into a large set of substructures and grow the new molecule structure by iteratively predicting which substructure from to add. However, s…