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.
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48 results for “biochemical modeling”
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.
New model uses pretrained biochemical language models to generate drug compounds.
problem Developing novel compounds targeting specific proteins.
method Exploits pretrained language models to initialize and fine-tune targeted molecule generation models.
result Warm-started models outperform baseline models, with one-stage strategy showing better generalization.
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated …
Neural network model improves leaf spectral reflectance prediction for grapevines.
problem Inaccurate modeling of grapevine leaf spectral reflectance from traits.
method Multi-head attention neural network trained on grapevine-specific data.
result Model achieved high accuracy (R^2=0.84, NRMSE=1.52%) and outperformed PROSPECT-PRO.
Jet-Ricci Geometry of Time-Dependent Human Biomechanicsphysics.bio-ph
We propose the time-dependent generalization of an `ordinary' autonomous human biomechanics, in which total mechanical + biochemical energy is not conserved. We introduce a general framework for time-dependent biomechanics in terms of jet manifolds derived from the extended musculo-skeletal configuration manifold. The …
We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the vector to handle the spatial information from molecular topology. The 3DGCN model ex…
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.
A new GNN module learns geometric scattering features for better graph classification and feature exploration.
problem Learning long-range graph relations and extracting meaningful features from graphs.
method Proposes a learnable geometric scattering (LEGS) module in graph neural networks (GNNs), incorporating wavelet filters.
result LEGS-based GNNs outperform existing methods in graph classification and feature extraction tasks.
nUDEs use neural networks to model biology without negative values.
problem Unrealistic negative values in hybrid models of biology.
method Developed non-negative UDEs (nUDEs) with regularization techniques.
result nUDEs provide realistic solutions for biological models.
In many high-throughput experimental design settings, such as those common in biochemical engineering, batched queries are more cost effective than one-by-one sequential queries. Furthermore, it is often not possible to directly choose items to query. Instead, the experimenter specifies a set of constraints that genera…
SparseChem speeds up ML for small molecules.
problem Training fast and accurate ML models for high-dimensional data.
method Supports millions of features and compounds, trains various models.
result Fast and accurate machine learning models for biochemical applications.
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.
Standard ChIP-seq peak calling pipelines seek to differentiate biochemically reproducible signals of individual genomic elements from background noise. However, reproducibility alone does not imply functional regulation (e.g., enhancer activation, alternative splicing). Here we present a general-purpose, interpretable …
Text-based representations of chemicals and proteins can be thought of as unstructured languages codified by humans to describe domain-specific knowledge. Advances in natural language processing (NLP) methodologies in the processing of spoken languages accelerated the application of NLP to elucidate hidden knowledge in…
Complex biological systems have been successfully modeled by biochemical and genetic interaction networks, typically gathered from high-throughput (HTP) data. These networks can be used to infer functional relationships between genes or proteins. Using the intuition that the topological role of a gene in a network rela…
Hierarchical Graph-to-Graph Translation for Moleculesphysics.chem-ph
The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize …
We propose a method for learning cyclic causal models from a combination of observational and interventional equilibrium data. Novel aspects of the proposed method are its ability to work with continuous data (without assuming linearity) and to deal with feedback loops. Within the context of biochemical reactions, we a…
Novel parallel GNN predicts protein-ligand interactions with high accuracy.
problem Accurate prediction of protein-ligand interactions for drug design.
method Parallel Graph Neural Networks (GNN) integrating 3D structural data.
result GNN achieves high accuracy in predicting binary interactions and activity.
Design of experiments improves validation of biomolecular networks.
problem Efficiently validate non-machine learning designed biomolecular networks.
method Use Gaussian processes and Bayesian optimization to select experimental points.
result Developed a stopping criterion based on discrepancy metric and uncertainty.
Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurement…
Infrared spectra obtained from cell or tissue specimen have commonly been observed to involve a significant degree of (resonant) Mie scattering, which often overshadows biochemically relevant spectral information by a non-linear, non-additive spectral component in Fourier transformed infrared (FTIR) spectroscopic measu…
Graph Neural Network (GNN) is a popular architecture for the analysis of chemical molecules, and it has numerous applications in material and medicinal science. Current lines of GNNs developed for molecular analysis, however, do not fit well on the training set, and their performance does not scale well with the comple…
New algorithm improves model generalization in structured biomedical domains.
problem Improving model generalization in structured biomedical domains.
method Proposes a new regret minimization (RGM) algorithm and its structured extension for better performance in diverse environments.
result Significantly outperforms previous state-of-the-art baselines on molecular property prediction, protein homology, and stability prediction.
Machine learning algorithms for generating molecular structures offer a promising new approach to drug discovery. We cast molecular optimization as a translation problem, where the goal is to map an input compound to a target compound with improved biochemical properties. Remarkably, we observe that when generated mole…
Graph Beta Diffusion (GBD) generates graphs with mixed discrete and continuous components.
problem Generating graphs with mixed discrete and continuous components.
method Introduces Graph Beta Diffusion (GBD) using a beta diffusion process.
result Competes strongly with existing models across graph benchmarks.
Study shows annealing with adaptive schedule reduces mode collapse in NFs for parameter estimation.
problem Mode collapse in normalizing flows for multimodal distributions.
method Annealing with an adaptive schedule based on effective sample size (ESS).
result Our approach reduces mode collapse and converges marginal likelihood faster than MCMC methods.
Method learns drug-disease representations for repositioning opportunities.
problem Identifying new uses for existing drugs.
method Multi-relation unsupervised graph embedding model.
result Superior prediction performance in repositioning opportunities.
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Languageq-bio.BM
Enhances drug discovery models by understanding human language.
problem Low predictive quality of activity prediction models in drug discovery.
method Proposes a novel architecture with separate chemical and natural language input modules and a contrastive pre-training objective.
result Improves predictive performance on few-shot and zero-shot learning benchmarks.
Fusing heterogeneous data setsq-bio.GN
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses two types of heterogeneity. The first one is the type of data, such as metabolomic…
MoleculeSTM learns from molecule structures and texts for better drug design.
problem Lack of integration between chemical structures and textual knowledge in AI drug discovery.
method Jointly learns chemical structures and texts via contrastive learning, using a large dataset.
result MoleculeSTM achieves state-of-the-art performance in zero-shot tasks like structure-text retrieval and molecule editing.
Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary to facilitate efficient protein design. However, accuracy of predic…
Proposes using entity embedding vectors to improve Gaussian Process models for knowledge transfer across cell lines.
problem Lack of reuse of experimental data for predicting novel processes.
method Hybrid Gaussian Process models with entity embedding vectors to represent product identity.
result Improved performance in predicting novel processes compared to traditional methods.
EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representationq-bio.QM
During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank has increased more than 15 fold since 1999, which …
Framework predicts mortality risk in MAFLD subjects.
problem Lack of mortality prediction methods for MAFLD subjects.
method Artificial Intelligence-based framework MAFUS using ML algorithms.
result Support Vector Machines (SVM) is the best model for mortality prediction.
Deviance-style normalization for sparse, jointly overdispersed count matrices
problem Jointly overdispersed count matrices
method Dirichlet-multinomial deviance residualization
result Preserves exact sparsity, evaluates in constant time, recovers multinomial residual
Adaptive teacher improves sample efficiency and mode coverage in sampling tasks.
problem Efficient exploration and mode coverage in sampling tasks with amortized inference.
method An adaptive training distribution (teacher) guides the training of the primary sampler (student).
result Improves sample efficiency and mode coverage across various tasks.
Local search improves GFlowNets' ability to generate high-reward samples.
problem GFlowNets struggle with over-exploration in high-reward space.
method Local search focusing on high-reward samples via backtracking and reconstruction.
result Significant performance improvement in biochemical tasks.
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques f…
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.
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…
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into groups that further subdivide into groups of groups, and so forth over multiple…
Understanding the adaptation process of plants to drought stress is essential in improving management practices, breeding strategies as well as engineering viable crops for a sustainable agriculture in the coming decades. Hyper-spectral imaging provides a particularly promising approach to gain such understanding since…
Jet Methods in Time-Dependent Lagrangian Biomechanicsphysics.bio-ph
In this paper we propose the time-dependent generalization of an `ordinary' autonomous human biomechanics, in which total mechanical + biochemical energy is not conserved. We introduce a general framework for time-dependent biomechanics in terms of jet manifolds associated to the extended musculo-skeletal configuration…
Reactmine: a statistical search algorithm for inferring chemical reactions from time series dataq-bio.QM
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.
New method optimises learning via surrogate PAC-Bayes bounds.
problem Computational intractability of optimising generalisation bounds.
method Iteratively optimising surrogate training objectives derived from PAC-Bayes bounds.
result Iteratively optimising surrogates implies optimising original generalisation bounds.
Bayesian approach infers signaling pathways from data.
problem Accurately understand cellular regulation processes.
method Dynamic Bayesian Network structure estimation using Markov Chain Monte Carlo.
result Efficient sampling of sparse graphs improves inference.
Autonomous Discovery of Unknown Reaction Pathways from Data by Chemical Reaction Neural Networkq-bio.MN
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet, revealing the reaction pathways for complex systems and processes is still challen…