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 …
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48 results for “chemical diversity”
GLAMOUR learns from macromolecules, overcoming diversity challenges.
problem Challenges in machine learning with macromolecules due to their vast diversity.
method Developed GLAMOUR, a framework for chemistry-informed graph representation of macromolecules.
result Quantifies structural similarity and enables supervised learning for macromolecules.
MEGAN models chemical reactions as graph edits, improving synthesis planning.
problem Generating and predicting chemical reactions under constraints.
method End-to-end encoder-decoder neural model inspired by arrow pushing formalism.
result State-of-the-art accuracy in standard benchmarks for retrosynthesis prediction.
Proposes qPO, a new acquisition strategy for batched Bayesian optimization that maximizes the probability of including the optimum.
problem Efficiently identifying top-performing compounds from a large chemical library.
method qPO (multipoint Probability of Optimality) acquisition strategy that maximizes the probability of including the true optimum.
result Empirical evidence shows that qPO is competitive with and complements other state-of-the-art methods in batched Bayesian optimization.
Generates natural product-like compounds using GPT models.
problem Challenges in generating and evaluating natural product-like compounds.
method Trained GPT-based chemical language models on natural product dataset.
result Generated compounds have similar distribution to natural products.
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…
Rank-based Bayesian Optimization improves molecule selection in chemical systems.
problem Optimizing chemical compounds using traditional regression models.
method Introducing Rank-based Bayesian Optimization (RBO) using ranking models.
result RBO outperforms regression-based BO, especially for rough landscapes and activity cliffs.
We propose a new model for making generalizable and diverse retrosynthetic reaction predictions. Given a target compound, the task is to predict the likely chemical reactants to produce the target. This generative task can be framed as a sequence-to-sequence problem by using the SMILES representations of the molecules.…
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of objects--such as a gene and a disease--can be related in different ways, for example…
The new wave of successful generative models in machine learning has increased the interest in deep learning driven de novo drug design. However, assessing the performance of such generative models is notoriously difficult. Metrics that are typically used to assess the performance of such generative models are the perc…
ChemCrow enhances LLMs for chemistry tasks, automating complex chemical processes.
problem Limited access to computational chemistry tools for large-language models.
method Integrating 18 expert-designed chemistry tools into an LLM (ChemCrow).
result ChemCrow autonomously plans and executes chemical syntheses and discoveries.
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
A new machine-learned CG model predicts protein structures efficiently.
problem Developing a universal, computationally efficient protein simulation model.
method Combining deep learning with all-atom protein simulations to create a transferable CG force field.
result The model predicts protein structures, intermediates, and fluctuations efficiently.
The paper develops a Gaussian process model for predicting chemical efficacy.
problem Statistical methodologies for analyzing chemical databases are limited.
method Conditional Gaussian process models with Tanimoto distance and a scaling parameter.
result Predictive performance improves when accounting for chemical space correlation.
Generative model learns to create molecules with multiple properties using interpretable substructures.
problem Creating molecules with multiple chemical properties is challenging.
method Compose molecules from substructures identified as responsible for each property, using graph generative models.
result Significant improvements in accuracy, diversity, and novelty of generated compounds over state-of-the-art baselines.
Range-Aware Bayesian Optimization for Discovering Diverse Designs within Target Property Windowscs.LG
Developing a range-aware Bayesian optimization framework for discovering diverse designs within target property windows.
problem Discovering multiple, distinct solutions within target property windows.
method Range-aware Bayesian optimization framework.
result Consistently recovers larger and more diverse sets of valid designs.
This review discusses challenges and solutions for AI in chemical engineering.
problem Challenges in applying classical machine learning to chemical engineering data.
method Identifying four data characteristics and discussing their applications and solutions.
result Current research extends data science and machine learning to handle chemical engineering data challenges.
Novel ML model predicts solvation free energies from atom interactions.
problem Predicting solvation free energies from atomistic interactions.
method Two encoding functions extract atomic feature vectors, interactions calculated by inner product.
result Outstanding performance and transferability on 6,493 experimental measurements.
Chemical structure elucidation is a serious bottleneck in analytical chemistry today. We address the problem of identifying an unknown chemical threat given its mass spectrum and its chemical formula, a task which might take well trained chemists several days to complete. Given a chemical formula, there could be over a…
GraphAF generates chemically valid molecules efficiently and accurately.
problem Generating chemically valid molecular structures while optimizing chemical properties.
method Flow-based autoregressive model combining autoregressive and flow-based approaches.
result GraphAF generates 68% chemically valid molecules without chemical knowledge rules and 100% with rules, achieving state-of-the-art performance.
Analyzes Indian chemical industry post-Covid.
problem Global uncertainty impacts chemical industry performance.
method Fundamental analysis of key players and trends.
result Various geopolitical and macroeconomic trends shape industry performance.
Autonomous Discovery of Unknown Reaction Pathways from Data by Chemical Reaction Neural Networkq-bio.MN
CRNN discovers chemical reaction pathways from data.
problem Challenging to infer reaction pathways for complex systems.
method Neural network approach that satisfies fundamental physics laws.
result CRNN autonomously discovers reaction pathways from species concentration data.
SMILES2Vec: An Interpretable General-Purpose Deep Neural Network for Predicting Chemical Propertiesstat.ML
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…
Chemical networks outperform spiking neural networks in classification tasks.
problem Learning tasks with spiking neural networks require hidden layers, which are computationally expensive.
method Used deterministic mass-action kinetics to prove chemical reaction networks without hidden layers can solve tasks previously solved by spiking neural networks.
result A chemical reaction network without hidden layers outperforms a spiking neural network with hidden layers in a handwritten digit classification task.
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 …
MoFlow generates chemically valid molecular graphs from latent representations.
problem Generating chemically valid molecular graphs from latent representations is challenging.
method MoFlow uses a flow-based approach with Glow for bond generation and a novel graph conditional flow for atom generation, ensuring chemical validity and efficiency.
result MoFlow achieves state-of-the-art performance in molecular graph generation and optimization.
Researchers derive the chemical potential equation for ideal agent systems.
problem Missing equation of state for chemical potential in ideal agent systems.
method Derived from econophysical model assumptions of ideal agent systems.
result Equation of state for chemical potential derived for ideal agent systems.
Orders-of-magnitude speedup in atmospheric chemistry modeling through neural network-based emulationphysics.ao-ph
Chemical transport models (CTMs), which simulate air pollution transport, transformation, and removal, are computationally expensive, largely because of the computational intensity of the chemical mechanisms: systems of coupled differential equations representing atmospheric chemistry. Here we investigate the potential…
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
Mapping chemical performance on molecular structures using locally interpretable explanationsstat.ML
In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. T…
A major challenge in materials design is how to efficiently search the vast chemical design space to find the materials with desired properties. One effective strategy is to develop sampling algorithms that can exploit both explicit chemical knowledge and implicit composition rules embodied in the large materials datab…
Site-specific graph neural network for predicting protonation energy of oxygenate moleculesphysics.chem-ph
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…
PerturBench benchmarks ML models for cellular perturbation analysis.
problem Standardizing benchmarking in modeling single cell transcriptomic responses to perturbations.
method Modular platform, diverse datasets, metrics, extensive evaluation, rank metrics.
result Simpler models are competitive and scale well with larger datasets.
A new algorithm optimizes multiple molecular properties efficiently.
problem Designing molecules with conflicting objectives and costly evaluations.
method Multi-objective Bayesian optimization with GFlowNets.
result HN-GFN samples diverse molecules from an approximate Pareto front.
Hyperbolic volume correlates with chemical properties of fullerenes.
problem Understanding the relationship between fullerene structure and chemical properties.
method Calculated hyperbolic volumes of fullerenes and correlated them with topological indices.
result Hyperbolic volume correlates with Wiener index and other topological indices of fullerenes.
During reactive transport modeling, the computational cost associated with chemical reaction calculations is often 10-100 times higher than that of transport calculations. Most of these costs results from chemical equilibrium calculations that are performed at least once in every mesh cell and at every time step of the…
An active learning approach for improving the performance of equilibrium based chemical simulationsstat.ML
A new method uses active learning to improve chemical simulation efficiency.
problem Efficiently estimating equilibrium-based chemical simulations.
method Sequential data-driven approach using Gaussian process uncertainty.
result Significantly reduced number of function evaluations.
NLP techniques improve drug discovery by analyzing chemical and protein text.
problem Improving drug discovery through better analysis of chemical and protein text.
method Natural language processing techniques applied to biochemical entities.
result Enhanced prediction of molecular properties and design of novel molecules.
Framework separates chemical and structural contributions to aqueous solubility.
problem Merging chemical and structural information in solubility models obscures their relative importance.
method Additive MLP-GNN framework with separate chemical and structural branches.
result Framework reveals distinct roles of chemical and structural information in solubility.
A framework separates chemical and structural contributions to aqueous solubility.
problem Merging chemical and structural information in solubility models obscures their relative contributions.
method Additive MLP-GNN framework with separate chemical and structural branches.
result Framework reveals distinct roles of chemical and structural information in solubility.
ChemGrapher uses deep learning to automatically convert chemical compound images into accurate graphs.
problem Automatically converting chemical compound images into accurate graphs with correct bond multiplicity and stereochemical information.
method Developed a deep neural network model for optical compound recognition, including segmentation and classification models.
result Significant error reductions in bond multiplicity and stereochemical information compared to existing tools.
Geometric modeling for human food and chemical sensitivities.
problem Modeling biochemical processes in humans with sensitivities.
method Geometric approach to biochemical modeling.
result Geometric models improve understanding of sensitivities.
Chemical plants are complex and dynamical systems consisting of many components for manipulation and sensing, whose state transitions depend on various factors such as time, disturbance, and operation procedures. For the purpose of supporting human operators of chemical plants, we are developing an AI system that can s…
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…
Upper bound on CRN reaction rates derived using information geometry.
problem Challenging task of deriving an upper bound on reaction rates of nonlinear, discrete CRNs.
method Information geometric approach using natural gradient.
result Validated through numerical simulations, demonstrating faster convergence in specific CRNs.
Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences. However, structures are available only for a small subset of biomolecules and sequence similarity is not always correlated with functional similar…
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…