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.
VAEs help in learning latent variables for cryo-EM applications.
problem Learning latent variables for cryo-EM data.
method Used VAEs for latent variable learning, focusing on the encoder's role.
result The encoder of the VAE in cryo-EM applications resembles traditional latent variable representations.
OptimalFlow uses optimal transport to handle flow cytometry variability.
problem Flow cytometry variability due to biological and technical causes.
method Combines similarity distance and Wasserstein barycenters to cluster and prototype cytometries.
result Supervised learning on new groups performs better than on whole collection.
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Seco…
New test identifies specific biological parameters for personalized CVD detection.
problem Ineffectual pathology tests fail to consider platelet activation and inter-individual variability.
method Stochastic platelet deposition model and approximate Bayesian computation with discriminative summary statistics.
result Inferred parameters help identify specific biological parameters for personalized CVD detection.
Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
problem Complexity and confounders in scRNA-seq data hamper interpretation.
method Extended Gaussian process latent variable model (GPLVM) to handle large datasets.
result Framework reconstructs latent signatures and captures disease-specific gene expression.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
problem Challenges in applying machine learning to biological sequences, including unreliable methods.
method Theoretical analysis and development of modified kernels to ensure reliability and accuracy.
result Developed kernels that are universal, characteristic, and metrize the space of distributions for biological sequences.
This thesis tackles data fusion issues across different biological scales and types.
problem Heterogeneity in data types and scales in systems biology.
method Developed statistical methods to fuse heterogeneous data sets.
result Advantages of proposed methods assessed through simulations and real data analysis.
Automated tests detect interactions in unstructured data.
problem Detecting interactions between latent variables in low-dimensional systems.
method Derive two interaction tests based on pairwise interventions and integrate them into an active learning pipeline.
result Tests can identify more known biological interactions than random search and standard active learning baselines.
High-dimensional data acquired from biological experiments such as next generation sequencing are subject to a number of confounding effects. These effects include both technical effects, such as variation across batches from instrument noise or sample processing, or institution-specific differences in sample acquisiti…
ODBAE detects complex phenotypes in biological data.
problem Challenges in identifying complex phenotypes from high-dimensional biological data.
method ODBAE (Outlier Detection using Balanced Autoencoders) identifies influential and high leverage points in latent relationships among multiple physiological parameters.
result ODBAE reveals novel metabolism-related genes and uncovers coordinated abnormalities across metabolic indicators.
Machine learning predicts biologic therapy outcomes in psoriasis patients.
problem Predicting long-term biologic therapy outcomes in psoriasis patients.
method Machine learning algorithms were used to predict drug discontinuation and treatment duration.
result Machine learning models accurately predict outcomes with high diagnostic accuracy and low MAE.
Statistical learning on biological data can be challenging due to confounding variables in sample collection and processing. Confounders can cause models to generalize poorly and result in inaccurate prediction performance metrics if models are not validated thoroughly. In this paper, we propose methods to control for …
Bayesian Cox model identifies biomarkers from multi-omics data.
problem Produce interpretable survival prognosis from multi-omics data.
method Penalized semiparametric Bayesian Cox model with graph-structured selection priors.
result Model identifies new biomarkers and improves survival prediction.
Automated digital twin discovery from biological data improves drug discovery and personalized medicine.
problem Developing reliable digital twins from noisy, incomplete biological data.
method Symbolic and sparse regression, Bayesian frameworks, deep learning, and large language models.
result Sparse regression generally outperforms symbolic regression, especially with Bayesian frameworks.
Proposes a new neural network architecture inspired by biology to improve learning and information flow.
problem Improving artificial neural networks to match biological neuron properties like multidirectional propagation and probabilistic modeling.
method Extends KAN approach with joint distribution neurons that can propagate values and distributions, including variance and higher-order moments.
result Proposed architecture can predict and propagate distributions, including expected values and variances.
A new theory explains large associative memory with biological plausibility.
problem Large associative memory in neurobiology and machine learning.
method Microscopic theory with hidden neurons and two-body interactions.
result Valid model of large associative memory with biological plausibility.
Study finds minimizers for complex membrane models without symmetry assumptions.
problem Minimizing the Canham-Helfrich functional in multiple phases for heterogeneous biological membranes.
method Reformulated as oriented curvature varifolds, proving existence without symmetry assumptions.
result Existence of minimizers for single- and multiphase models under constraints.
LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.
problem Bayesian optimization for drug design is limited by discrete, high-dimensional decision variables.
method Jointly trains denoising autoencoder with a Gaussian process head for gradient-based optimization in latent space.
result LaMBO outperforms genetic optimizers and requires no large pretraining corpus.
In this publication, we combine two Bayesian non-parametric models: the Gaussian Process (GP) and the Dirichlet Process (DP). Our innovation in the GP model is to introduce a variation on the GP prior which enables us to model structured time-series data, i.e. data containing groups where we wish to model inter- and in…
NegBio-VAE models neural spike counts with negative binomial distribution.
problem Limited biological plausibility of continuous latent variables in VAEs for neural spike modeling.
method Proposes a negative binomial latent-variable model with a dispersion parameter for overdispersed spike count modeling.
result NegBio-VAE outperforms competing models in reconstruction and generation tasks.
A model learns causal graphs from summary statistics of synthetic data.
problem Causal discovery algorithms are brittle with large sets of variables and limited data.
method A supervised model trained on synthetic data predicts causal graphs from summary statistics.
result The model generalizes well beyond its training set and runs on large graphs.
Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Here we use phylogenetic Gaussian process regression to model the evolution of simulated function-valued traits. Given function-valued data only from the tips of an evolutionary tree and utilising independent pri…
Sparse Singular Value Decomposition (SVD) models have been proposed for biclustering high dimensional gene expression data to identify block patterns with similar expressions. However, these models do not take into account prior group effects upon variable selection. To this end, we first propose group-sparse SVD model…
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.
Gaussian graphical models (GGM) have been widely used in many high-dimensional applications ranging from biological and financial data to recommender systems. Sparsity in GGM plays a central role both statistically and computationally. Unfortunately, real-world data often does not fit well to sparse graphical models. I…
SAMS-VAE models cellular perturbations using sparse additive mechanisms.
problem Modeling effects of diverse interventions on cells.
method Sparse Additive Mechanism Shift Variational Autoencoder (SAMS-VAE).
result SAMS-VAE identifies disentangled, perturbation-specific latent subspaces.
The paper examines how timing of observations affects causal discovery methods.
problem The sensitivity of causal discovery methods to mismatched observation timing.
method Empirical and theoretical analysis of classical and recent causal discovery methods.
result Causal discovery methods are sensitive to sampling rate and window length.
ASCEND discovers causal relationships in multi-omics data by leveraging known hierarchical structure.
problem Causal inference in high-dimensional multi-omics data, especially when ignoring the hierarchical structure.
method Two-tiered divide-and-conquer strategy with ancestral conditioning sets.
result Achieves polynomial-time complexity and accurately recovers ancestral relationships.
Optimizes harvesting in biopharmaceutical fermentation with limited data.
problem High variability in fermentation outputs due to model risk with small data.
method Stochastic model, Bayesian approach, Markov decision process.
result Improves fermentation output and reduces variability.
Hierarchical-CPI improves variable importance measurement for medical data.
problem Limited interpretability of complex medical models.
method Hierarchical-CPI measures conditional variable importance with statistical control, handling correlated data.
result Hierarchical-CPI outperforms existing methods in medical datasets.
Unified multitask learning framework for mixed-type outcomes.
problem Difficulty in formulating a unified objective for tasks with different outcomes.
method Multitask transformation framework with shared sparsity, using deep neural networks and rank-based optimization.
result Improved prediction and variable selection across continuous, binary, and mixed outcomes.
Skip connections improve biologically-inspired learning rules.
problem Biologically-inspired learning rules often underperform compared to backpropagation.
method Introduced skip connections between intermediate layers in biologically-motivated learning rules.
result Skip connections can match the performance of backpropagation and are robust to hyper-parameters.
Study counterfactuals in cyclic systems with shifts and scales.
problem Counterfactual inference in cyclic systems with shifts and scales.
method Shift-scale interventions in cyclic SCMs.
result Valid inference in cyclic systems with shifts and scales.
Generalizes causal inference to high-dimensional outcomes.
problem Limited causal inference methods for multivariate outcomes.
method Formulates causal discrepancy tests for nominal variables, uses conditional independence tests.
result Causal CDcorr method improves finite sample validity and power.
We introduce a new approach to variable selection, called Predictive Correlation Screening, for predictor design. Predictive Correlation Screening (PCS) implements false positive control on the selected variables, is well suited to small sample sizes, and is scalable to high dimensions. We establish asymptotic bounds f…
Model captures system input variations in latent space for actionable dynamics.
problem Learning dynamical systems from data without prescribing a mathematical model.
method Structured latent ODE model with stochastic factors of variation for each input.
result Improves generation of time-series data and inference of system inputs over baselines.
New learning algorithm mimics biological neural networks.
problem Biologically implausible backpropagation for directed neural networks.
method Introduces new neuronal dynamics and learning rule for arbitrary architectures, sparsity-inducing pruning method, and dynamical-systems characterization.
result Prunes irrelevant connections and improves learning efficiency.
We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by…
This paper frames causal structure estimation as a machine learning task. The idea is to treat indicators of causal relationships between variables as `labels' and to exploit available data on the variables of interest to provide features for the labelling task. Background scientific knowledge or any available interven…
Spatially positioned neurons in neural networks mimic biological systems.
problem Creating neural networks that can perform multiple tasks efficiently.
method Added spatial positions and proximity penalties to artificial neurons.
result Neurons naturally cluster, each responsible for a specific task.
We consider the inverse Ising problem, i.e. the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form, which allows for simple iterative inference algorithms with…
Researchers identify latent variables and causal structures from nonlinear hierarchical models.
problem Challenging task of identifying latent variables and causal structures from observational data, especially when relationships are nonlinear.
method Investigated nonlinear latent hierarchical causal models, developed identification criterion, and constructed an estimation procedure.
result Identifiability of causal structures and latent variables achieved under mild assumptions.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
problem Interpreting latent causal factors in biological pathways.
method SENA-discrepancy-VAE, a model based on discrepancy-VAE, that produces interpretable latent causal factors.
result Sena-discrepancy-VAE achieves comparable predictive performance with non-interpretable counterparts while providing biologically meaningful causal factors.
Energy trees handle complex data structures with multiple variable types.
problem Handling intricate data structures with various types of covariates.
method Energy trees, a regression and classification model, use energy statistics to accommodate structured covariates of different types.
result Energy trees maintain statistical foundations, interpretability, and robustness to overfitting.
Develops variable-lag Granger causality for more accurate time series analysis.
problem Fixed time delay assumption in Granger causality does not fit many real-world applications.
method Variable-lag Granger causality, inferring with arbitrary time delays.
result Performs better than existing methods in coordinated collective behavior studies.
Deep learning applied to biological data mining.
problem Mining complex biological data from diverse sources.
method Artificial neural networks, deep learning architectures.
result Deep learning techniques improve pattern recognition in biological data.
Bayesian non-parametric model selects latent dimensions automatically.
problem Non-linear, sparse latent variable selection.
method Indian buffet process prior, random Fourier approximation, MCMC sampling.
result Superior performance on synthetic, biological, and text datasets.