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.
Adjoint SA speeds up bioprocess parameter learning.
problem Challenges in digital twin development for biomanufacturing.
method Adjoint sensitivity analysis on multi-scale enzymatic reaction networks.
result Resilient sensitivities reveal bioprocess regulatory mechanisms.
Paper develops efficient Bayesian inference for enzymatic SRNs with LNA metamodel.
problem Bayesian inference for nonlinear SDE-based mechanistic models with partial observations and measurement errors.
method Interpretable Bayesian updating LNA metamodel and efficient posterior sampling.
result Proposed approach demonstrates promising performance in empirical studies.
Automated method simplifies stochastic chemical reaction network analysis.
problem Analyzing complex stochastic chemical reaction networks is computationally expensive.
method Uses deep learning to create a discrete-time process from a CTMC, optimizing neural network architecture.
result Automated method improves computational efficiency and accuracy for various CRNs.
DeepSKA provides interpretable, reliable neural approximations for SRNs.
problem Estimating expected outputs in SRNs is computationally challenging and unreliable.
method Jointly achieves interpretability, reliability, and computational gains with DeepSKA.
result Delivers accurate predictions and substantial efficiency improvements across SRNs.
Neural models learn continuous-time Markov chain transition rates from data.
problem Learning transition rates for complex stochastic systems.
method Neural networks to model nonlinear transition rates from observed data.
result Neural models outperform traditional methods in accuracy.
Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate…
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.
A novel method reduces dimensionality for filtering SRNs with observed variables.
problem Challenges in estimating hidden state variables in SRNs with limited observations.
method Filtered Markovian Projection (Filtered MP) for dimensionality reduction in filtering.
result Filtered MP guarantees consistency and superior computational efficiency in high dimensions.
Graphs predict reaction conditions for organic chemistry.
problem Predicting specific reaction conditions in organic chemistry.
method Graph Neural Networks (GNNs) for modeling reaction graphs.
result GNNs can identify specific graph features affecting reaction conditions.
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.
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.
DEMOTE uses neural diffusion-reaction processes to capture temporal dynamics in sparse tensor data.
problem Sparse and temporally associated tensor data with limited structural knowledge.
method Develops a neural diffusion-reaction process to estimate dynamic embeddings for tensor modes.
result Captures both commonalities and personalities in evolving tensor entries.
Bayesian inference for biochemical reaction networks using jump-diffusion approximations.
problem Estimating hidden quantities in poorly characterized biochemical processes.
method Developed a Bayesian inference algorithm based on Markov chain Monte Carlo and sequential Monte Carlo methods.
result Numerical evaluation of the algorithm for a partially observed multi-scale birth-death process.
Hopfield networks improve reaction template prediction for few/zero-shot scenarios.
problem Predicting reaction templates for new molecules in CASP.
method Adapted Hopfield networks to associate reaction templates, molecules, and structural information.
result Significantly improved performance for templates with few or zero training examples.
Reaction prediction remains one of the major challenges for organic chemistry, and is a pre-requisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, "learn" from being exposed to examples of the application of the rules of organic chemistry. We explore the use of neural netwo…
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…
New model predicts chemical reactions with conditional graph logic networks.
problem Predicting chemical reactions for synthesizing molecules.
method Conditional Graph Logic Network (CGLN) based on graph neural networks.
result Significant improvement of 8.1% over state-of-the-art methods.
Bounds on chemical reaction network relaxation rates using convex analysis.
problem Understanding relaxation dynamics in chemical reaction networks.
method Convex analysis, generalized gradient flows, singular values of stoichiometric matrix.
result Bounds on Kullback-Leibler divergence to equilibrium for CRNs.
PASTIS selects minimal models from stochastic dynamics data.
problem Overfitting in model selection for stochastic dynamics.
method Combining likelihood-estimation statistics with extreme value theory.
result PASTIS reliably identifies minimal models, even with low sampling rates or error.
This paper considers stochastic bandits with side observations, a model that accounts for both the exploration/exploitation dilemma and relationships between arms. In this setting, after pulling an arm i, the decision maker also observes the rewards for some other actions related to i. We will see that this model is su…
Schrödinger bridge solved with Weyl calculus for quadratic state cost.
problem Optimal control policy to steer joint state statistics.
method Weyl calculus in quantum mechanics for reaction-diffusion PDEs.
result Explicit Markov kernel for quadratic state cost found.
Compact models for NOX formation during methane combustion are created using a new algorithm.
problem Creating accurate models for NOX formation during complex combustion processes.
method Adapted Machine Learning Optimization of Chemical Kinetics (MLOCK) algorithm with Latin Square method for virtual reaction network generation.
result Compact models with high fidelity (>75%) in reproducing industry-defined performance targets are generated.
Reactmine infers chemical reactions from time series data, overcoming sparse model limitations.
problem Inferring chemical reaction networks from time series data, especially when initial conditions are not varied.
method Sequential reaction inference in a search tree, ranking and re-optimizing kinetics.
result Reactmine successfully infers preponderant regulations in real datasets, matching model-based analyses.
A new framework uses stochastic optimal control to estimate rare events more accurately.
problem Estimating rare events like chemical reactions in biomolecules is computationally challenging.
method The approach casts committor estimation as a stochastic optimal control problem, developing direct and off-policy Value Matching losses.
result The framework yields more accurate committor estimates, reaction rates, and equilibrium constants.
Solves probabilistic Lambert problem connecting astrodynamics with optimal mass transport.
problem Determining spacecraft velocity for given positions with probabilistic constraints.
method Generalized optimal mass transport (OMT) and Schrödinger bridge (SBP) connections.
result Existence and uniqueness of solution for probabilistic Lambert problem.
New estimator for SDEs is shown to be an adjoint state method.
problem Estimating gradients for overparameterized SDEs efficiently.
method Demonstrates generator gradient estimator as an adjoint state method.
result Generator gradient estimator is an adjoint state method for SDEs.
GF-Net learns Green's functions for linear reaction-diffusion equations.
problem Learning Green's functions for linear reaction-diffusion equations on arbitrary domains.
method GF-Net, a neural network, learns Green's functions in an unsupervised manner using physics-informed approach and symmetry.
result GF-Net efficiently solves linear reaction-diffusion equations under various boundary conditions and sources.
Study shows neural operators can efficiently solve complex reaction-diffusion systems.
problem Efficiently solving nonlinear reaction-diffusion systems using neural operators.
method Laplacian-based neural operators applied to a generalized Gierer-Meinhardt system.
result Explicit approximation error bounds established for neural operators in terms of network parameters.
Geometric approach to thermodynamics of chemical reaction networks.
problem Thermodynamics of chemical reaction networks with non-ideal behavior.
method Information geometry, Riemannian geometry, Cramer-Rao bound, absolute sensitivity.
result Absolute sensitivity is a projection operator onto the tangent bundle of the equilibrium manifold.
We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that consists of two recurrent neural networks, which has previously shown great success in…
We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a 2−dimensional manifold that can be interpreted as the equilibrium space of the reaction. We first show this i…
Improved chemical reaction prediction using augmented NLP models.
problem Predicting chemical reactions from text representations.
method Data augmentation and Transformer architecture for SMILES representation.
result Significantly improved accuracy in predicting chemical reactions.
Bayesian neural networks improve macroeconomic forecasting and model nonlinearities.
problem Handling small T, big K macroeconomic datasets with temporal dependence.
method Developed Bayesian neural networks with mixture activation functions, shrinkage priors, and stochastic volatility.
result BNNs produce precise density forecasts, often better than other methods.
This work improves chemistry modeling by jointly learning reaction progress variables and look-up models.
problem Jointly modeling turbulent combustion requires solving both chemistry and flow systems simultaneously, which is computationally expensive.
method Developed a deep neural network architecture that jointly learns reaction progress variables and look-up models, improving accuracy.
result Joint learning yields more accurate results in chemistry modeling.
A new method for inferring latent states in Markov jump processes.
problem Intractable exact inference for Markov jump processes.
method Entropic matching within expectation propagation.
result Superior performance in approximating the mean of the posterior process.
Novel deep learning method predicts reaction coordinates and future MD trajectories.
problem Identifying optimal reaction coordinates for chemical reactions.
method Regularized Sparse Autoencoder (RSE) for discovering reaction coordinates and predicting MD trajectory evolution.
result RSE helps in choosing a small but important set of reaction coordinates.
This paper speeds up simulations of hypersonic reentry by combining traditional and neural methods.
problem Accurately simulating hypersonic reentry with chemical reactions is computationally expensive.
method A hybrid simulation code combining a traditional fluid dynamics solver with a neural network approximating chemical reactions.
result Achieved significant acceleration factors (imes10 to imes18.6) while maintaining accuracy. A learning rule for first-spike times in neural networks reduces energy consumption and reaction times.
problem Energy efficiency and reaction time in neuromorphic systems.
method Derivation of a learning rule for first-spike times in leaky integrate-and-fire neurons, using only input and output spike times.
result Demonstrated that the approach can implement error backpropagation in hierarchical spiking networks and is capable of harnessing neuromorphic system's speed and energy characteristics.
Chemical reactions can be described as the stepwise redistribution of electrons in molecules. As such, reactions are often depicted using `arrow-pushing' diagrams which show this movement as a sequence of arrows. We propose an electron path prediction model (ELECTRO) to learn these sequences directly from raw reaction …
RAD estimates gradients with less memory, faster than small batch sizes.
problem Training deep models with stochastic gradient descent requires exact gradients, but they are not needed.
method Developed a framework for randomized automatic differentiation (RAD) to compute unbiased gradient estimates with reduced memory.
result RAD converges in fewer iterations than using a small batch size for feedforward networks and similar number for recurrent networks.
METRO predicts reactions using minimal templates, reducing computational overhead and achieving state-of-the-art results.
problem Predicting possible reaction substrates for complex molecules from simpler precursors.
method METRO (Molecule-Edit Templates for RetrOsynthesis) uses minimal templates to predict reactions efficiently and accurately.
result METRO achieves state-of-the-art results on standard benchmarks, reducing computational overhead.
Machine learning models simulate molecular spectra and reactions in solvents.
problem Accurate simulation of molecular spectra and reactions in solvent environments.
method Introduced FieldSchNet, a deep neural network for modeling molecular interactions with external fields.
result Demonstrated significant lowering of Claisen rearrangement reaction activation barrier using FieldSchNet.
New method infers dynamical systems from population data.
problem Inferring dynamical systems from population data.
method Deducing and estimating Fokker-Planck equation, projecting to test functions, sparse inference.
result Induces driving forces of dynamical systems.
MEP-Net uses MEP to generate solutions from limited data.
problem Generating solutions to scientific problems with incomplete information.
method Combines MEP with neural networks to learn complex distributions from moment constraints.
result Demonstrates MEP-Net's effectiveness in modeling biochemical reaction networks and generating complex distributions.
The problem of retrosynthetic planning can be framed as one player game, in which the chemist (or a computer program) works backwards from a molecular target to simpler starting materials though a series of choices regarding which reactions to perform. This game is challenging as the combinatorial space of possible cho…
Capturing the microscopic interactions that determine molecular reactivity poses a challenge across the physical sciences. Even a basic understanding of the underlying reaction mechanisms can substantially accelerate materials and compound design, including the development of new catalysts or drugs. Given the difficult…
We generalize the reaction-diffusion model A + B -> 0 in order to study the impact of an excess of A (or B) at the reaction front. We provide an exact solution of the model, which shows that linear response breaks down: the average displacement of the reaction front grows as the square-root of the imbalance. We argue t…