Optimal algorithm selects biological models without prior info.
problem Determining the correct biological model without prior knowledge.
method Systems biology models and likelihood-free inference.
result Improved model selection performance over conventional methods.
In this paper, we provide conditions which ensure that stochastic Lipschitz BSDEs admit Malliavin differentiable solutions. We investigate the problem of existence of densities for the first components of solutions to general path-dependent stochastic Lipschitz BSDEs and obtain results for the second components in part…
These lecture notes in the De Rham-Hodge theory are designed for a 1-semester undergraduate course (in mathematics, physics, engineering, chemistry or biology). This landmark theory of the 20th Century mathematics gives a rigorous foundation to modern field and gauge theories in physics, engineering and physiology. The…
These lecture notes in Lie Groups are designed for a 1--semester third year or graduate course in mathematics, physics, engineering, chemistry or biology. This landmark theory of the 20th Century mathematics and physics gives a rigorous foundation to modern dynamics, as well as field and gauge theories in physics, engi…
Mathematical advances needed for Digital Twins, differing from traditional models.
problem Foundational mathematical advances required for Digital Twins.
method Multi-scale, multi-physics modeling and coupling, different reliability criteria and uncertainty assessments.
result AI/ML methods can perform well in biomedical problems but fail in simple engineering systems.
We describe in this note a new invariant of rooted trees. We argue that the invariant is interesting on it own, and that it has connections to knot theory and homological algebra. However, the real reason that we propose this invariant to readers is that we deal here with an elementary, interesting, new mathematics, an…
Deep learning quantifies butterfly phenotypes, validating evolutionary theory.
problem Capturing comprehensive phenotypic information of butterflies.
method Deep convolutional triplet network for phenotypic distance calculation.
result Euclidean phenotypic distances support classical mimicry theory.
hyperSBINN improves drug cardiosafety assessment by efficiently modeling cardiac action potentials.
problem Complexity and limited data in modeling cardiac effects of drugs.
method Combining meta-learning with SBINNs to solve parameterized cardiac action potential models.
result hyperSBINN outperforms traditional solvers in speed and accuracy for predicting APD90 values.
Novel tests for genetic independence in high-dimensional data.
problem Testing independence in genetics studies with many variables.
method Defining premetric structures on genetic data support spaces.
result Solid theoretical framework and computationally-efficient implementations.
We establish Schauder a priori estimates and regularity for solutions to a class of boundary-degenerate elliptic linear second-order partial differential equations. Furthermore, given a smooth source function, we prove regularity of solutions up to the portion of the boundary where the operator is degenerate. Degenerat…
The aim of this chapter is twofold. In the first part we will provide a brief overview of the mathematical and statistical foundations of graphical models, along with their fundamental properties, estimation and basic inference procedures. In particular we will develop Markov networks (also known as Markov random field…
Review of mathematical representations for biomolecular data.
problem Complexity and high dimensionality of biomolecular datasets hinder ML applications.
method Developed low-dimensional and scalable mathematical representations using algebraic topology, differential geometry, and graph theory.
result Mathematical representations improve protein-ligand binding predictions and other biomolecular applications.
Experimental life sciences like biology or chemistry have seen in the recent decades an explosion of the data available from experiments. Laboratory instruments become more and more complex and report hundreds or thousands measurements for a single experiment and therefore the statistical methods face challenging tasks…
We compute Khovanov homology for tangles using TQFT.
problem Khovanov homology for tangles is not well studied or computed.
method Topological Quantum Field Theory (TQFT) construction.
result A comprehensive method for computing Khovanov homology of tangles.
CHANI learns classification tasks with local transformations inspired by biology.
problem Proving neural networks can learn classification tasks with local transformations.
method CHANI uses spiking neurons modeled by Hawkes processes with expert aggregation for local learning.
result CHANI can learn and encode multiple classes, forming assemblies of neurons.
We introduce a new discriminant analysis method (Empirical Discriminant Analysis or EDA) for binary classification in machine learning. Given a dataset of feature vectors, this method defines an empirical feature map transforming the training and test data into new data with components having Gaussian empirical distrib…
Study Gram determinants in knot theory, focusing on a Möbius band determinant.
problem Closed formula for the Gram determinant of type (Mb)1. method Survey of Gram determinants, focusing on a Möbius band determinant.
result Speculation on closed formula for (Mb)1 Gram determinant. ART automates synthetic biology design with machine learning.
problem Long development times in synthetic biology due to ad-hoc engineering.
method Machine learning and probabilistic modeling for systematic design.
result ART provides optimized strain recommendations and production levels.
DBNs improve accuracy of biological ODE models with missing data.
problem Uncertainty in biological ODE models with missing data.
method Converted ODE models to DBNs and used Particle Filtering for parameter estimation.
result DBNs can accurately infer model variables with missing data.
New method integrates sparse parametric and nonparametric techniques for complex system modeling.
problem Lack of accurate modeling for complex biological systems due to nonlinearities.
method Sparse nonparametric estimation framework combining parametric and nonparametric techniques.
result Accurately captures nonlinearities in complex systems without prior information.
DECAT framework evaluates multimodal models for shared biology, detecting confounders and false positives.
problem Determining if multimodal models learn shared biology or just confounders.
method DECAT framework classifies multimodal representations into four diagnostic scenarios using null-referenced metrics.
result DECAT detects confounders and false positives in multimodal models, improving with larger cohorts and stronger representations.
Two simulation-based methods improve optimal sampling design in systems biology.
problem Optimal selection of sampling points for accurate parameter estimation in dynamical systems.
method E-optimal-ranking (EOR) and LSTM neural network-based methods.
result Simulation studies show the proposed methods outperform random selection and classical E-optimal design.
New model captures complex relationships from experimental data.
problem Capturing intricate feature interactions in empirical data.
method Shape Arithmetic Expressions (SHAREs) combining GAMs and mathematical expressions.
result SHAREs model captures complex feature interactions.
Interacting particle methods are increasingly used to sample from complex and high-dimensional distributions. These stochastic particle integration techniques can be interpreted as an universal acceptance-rejection sequential particle sampler equipped with adaptive and interacting recycling mechanisms. Practically, the…
Regularizes RNNs to handle long-range dependencies and multiple time scales.
problem Identifying nonlinear dynamical systems with varying time scales and long-range dependencies.
method A simple regularization scheme for vanilla RNNs with ReLU activation.
result Regularized RNNs can solve long-range dependency problems and express slow time scales.
Paper solves POMDPs in continuous time and discrete spaces.
problem Optimal decision making in discrete state and action space systems under partial observability.
method Combining optimal filtering theory and deep learning to solve a Hamilton-Jacobi-Bellman equation.
result Derives a mathematical description and solution approach for continuous-time POMDPs.
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
We consider the problem of finding optimal strategies that maximize the average growth-rate of multiplicative stochastic processes. For a geometric Brownian motion the problem is solved through the so-called Kelly criterion, according to which the optimal growth rate is achieved by investing a constant given fraction o…
Quantum computing promises faster bioinformatics, but challenges remain.
problem Efficient bioinformatics processing and drug discovery.
method Quantum algorithms for optimization, simulation, and machine learning.
result Quantum computing can significantly speed up bioinformatics tasks.
A scalable Bayesian inference method for mixed-effects models in systems biology.
problem Scalable Bayesian inference for complex hierarchical mixed-effects models in systems biology.
method Constructing amortized approximations of likelihood and posterior distributions, refined for each individual dataset.
result Our method is both fast and competitive in statistical accuracy compared to exact pseudomarginal Bayesian inference.
ProGen models protein sequences for synthetic biology.
problem Generating proteins without structural annotations.
method Trained a 1.2B-parameter language model on 280M protein sequences.
result ProGen generates proteins with fine-grained control and accuracy.
Method uses network biology to construct gene expression models for cancer.
problem Building models for cancer phenotypes using gene expression data.
method Unsupervised construction of computational graphs based on protein-protein networks.
result The method outperforms other models in cancer phenotype analysis.
FEPS models agents to learn and act in complex environments without deep neural networks.
problem Modeling complex adaptive systems and understanding self-organizing behavior.
method Introducing Free Energy Projective Simulation (FEPS) within the constraints of the free energy principle and active inference.
result FEPS agents resolve ambiguity and infer optimal policies in partially observable environments.
Develops a method to infer cell trajectories from RNA sequencing data.
problem Inferring cell trajectories from single cell RNA-sequencing data.
method Entropy-regularized optimal transport for global optimization.
result Proves and implements a method to recover ground truth trajectories from limited samples.
New framework for online control in evolving populations.
problem Control of evolving populations in real-world conditions.
method Online control framework for linear and non-linear dynamical systems.
result Near-optimal regret bounds for gradient-based controllers.
In the same way as the Hilbert Program was a response to the foundational crisis of mathematics, this article tries to formulate a research program for the socio-economic sciences. The aim of this contribution is to stimulate research in order to close serious knowledge gaps in mainstream economics that the recent fina…
We solve tensor balancing, rescaling an Nth order nonnegative tensor by multiplying N tensors of order N - 1 so that every fiber sums to one. This generalizes a fundamental process of matrix balancing used to compare matrices in a wide range of applications from biology to economics. We present an efficient balancing a…
New method for analyzing complex data spaces.
problem Dimensionality reduction and learning data representations for continuous spaces.
method Manifold factorization based on spectral graph methods.
result Recovering factors yields meaningful lower-dimensional representations.
In this article we develop geometric versions of the classical Langevin equation on regular submanifolds in euclidean space in an easy, natural way and combine them with a bunch of applications. The equations are formulated as Stratonovich stochastic differential equations on manifolds. The first version of the geometr…
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.
Deep neural network generates symbolic equations from data.
problem Lack of insight into underlying mappings from traditional deep learning.
method Combines deep learning flexibility with symbolic solutions.
result Accurately generates governing equations for dynamical systems.
We consider the problem of joint modelling of metabolic signals and gene expression in systems biology applications. We propose an approach based on input-output factorial hidden Markov models and propose a structured variational inference approach to infer the structure and states of the model. We start from the class…
Machine learning integrates diverse biological data to understand complex phenomena.
problem Combining multiple data types to understand biological and medical phenomena.
method Developing effective models to integrate heterogeneous biological data.
result Machine learning can identify important features and predict outcomes from diverse biological data.
Benchmarking graph neural networks for diverse datasets.
problem Quantifying progress in graph neural networks.
method Diverse graph collection, fair model comparison, open-source framework.
result Benchmark framework has spurred interest in graph positional encoding.
X-SHAP assesses multiplicative variable contributions in machine learning models.
problem Understanding multiplicative interactions in machine learning models.
method Model-agnostic method that extends SHAP to assess multiplicative contributions.
result X-SHAP proves useful in capturing multiplicative feature importance.
Transformers approximate mean-field dynamics of indistinguishable particles.
problem Approximating the dynamics of indistinguishable particles in complex systems.
method Using transformers to model the mean-field dynamics of interacting particle systems.
result Theoretical bounds on the distance between true and transformer-obtained mean-field dynamics.
Machine learning methods struggle with geometric data, but shape space analysis provides a framework for studying and analyzing geometric variability.
problem Machine learning methods struggle with geometric data
method Shape space analysis provides a mathematical and computational framework
result Characterizes shape variability, compares geometric objects, and analyzes structural trajectories
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
problem Efficient design of genomic perturbation experiments in drug discovery.
method Integrates Bayesian optimization with multimodal gene embeddings and enrichment analysis.
result Improves labeling efficiency by 25-40% and identifies top-performing perturbations more effectively.