Bayesian hypergraph inference models disease pathways from EHR data.
problem Modeling rare diseases influenced by shared risk factors.
method Bayesian hypergraph inference framework reframing multi-disease modeling.
result Interpretable disease pathways and well-calibrated uncertainty quantification.
spex-LVM infers interpretable latent factors from biomedical data.
problem Inability to learn sparse and interpretable hidden states.
method Factorial latent variable model with sparse priors and domain-relevant annotations.
result Robustly identifies relevant structure in RNA-seq datasets.
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.
Complex systems may contain heterogeneous types of variables that interact in a multi-level and multi-scale manner. In this context, high-level layers may considered as groups of variables interacting in lower-level layers. This is particularly true in biology, where, for example, genes are grouped in pathways and two …
ISOKANN learns collective variables and effective dynamics for metastable transitions.
problem Understanding metastable transitions in complex molecular systems.
method Integrates Koopman operators with neural networks to extract CVs and effective dynamics.
result Reconstructs coarse-grained kinetics and reproduces transition times across barriers.
When searching for gene pathways leading to specific disease outcomes, additional information on gene characteristics is often available that may facilitate to differentiate genes related to the disease from irrelevant background when connections involving both types of genes are observed and their relationships to the…
Adversarial attacks on probabilistic state-space models affect latent state and policy decisions.
problem Robust reinforcement learning under adversarial observability.
method Analyzing adversarial attacks on linear probabilistic state-space models.
result Demonstrating the influence of adversarial observations on latent state and policy decisions.
Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
problem Understanding pathways essential for c-di-GMP in bacterial cellulose production.
method Applied Lasso and Random Forests for feature selection and modeling gene count data.
result Bacterial chemotaxis is identified as the most essential pathway for c-di-GMP encoding domains.
PKB framework boosts genomic data analysis by integrating pathway knowledge.
problem Boosting discovery power and connecting new findings with biological mechanisms in genomic data.
method Pathway-based Kernel Boosting (PKB) framework integrating clinical and pathway information for prediction of various outcomes.
result PKB substantially outperforms other methods in predicting drug response and cancer survival.
New algorithm extracts shared latent space for cortico-muscular interactions.
problem Challenges of high dimensionality and limited sample sizes in multivariate cortico-muscular analysis.
method Structured and sparse partial least squares coherence (ssPLSC) algorithm.
result ssPLSC achieves competitive or better performance in scenarios with limited sample sizes and high noise levels.
Generative model disentangles dark matter halo properties.
problem Entangling physical factors in generative model latent spaces.
method Auxiliary-variable-guided framework with halo mass and concentration.
result Reveals mass-concentration scaling relation and identifies unusual halo formation.
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have been proposed to leverage prior biological knowledge, such as pathways, to more…
A new method uses LLMs to discover causal pathways that affect fairness in machine learning.
problem Discovering fairness-relevant causal pathways in the presence of noise and confounding.
method Hybrid LLM-guided causal discovery framework combining active learning and dynamic scoring.
result LLM-guided methods, including the proposed active, dynamically scored variant, outperform baselines in recovering fairness-relevant structure under noisy conditions.
Generative models use latent abstractions to create images.
problem Understanding how generative models create high-dimensional data like images.
method Developed a theoretical framework using SDE and information theory.
result Diffusion models can be seen as a non-linear filter driven by latent abstractions.
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.
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small cr…
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.
We analyze large, multi-dimensional, sparse counting data sets, finding unsupervised groups to provide unique insights into genetic data. We create gene and biological pathway groups based on patients' variants to find common risk factors for four common types of cancer (breast, lung, prostate, and colorectal) and auti…
Understanding large-scale patterns in student course enrollment is a problem of great interest to university administrators and educational researchers. Yet important decisions are often made without a good quantitative framework of the process underlying student choices. We propose a probabilistic approach to modellin…
In many scientific studies, it becomes increasingly important to delineate the causal pathways through a large number of mediators, such as genetic and brain mediators. Structural equation modeling (SEM) is a popular technique to estimate the pathway effects, commonly expressed as products of coefficients. However, it …
Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of variou…
Tree-based regularization improves latent variable inference from related datasets.
problem Inferring latent variables from multiple related datasets in causal systems.
method Tree-Based Regularization (TBR) for sparse changes across environments.
result TBR identifies true latent variables up to simple transformations under sparse changes.
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…
Motivated by an important insight from neural science, we propose a new framework for understanding the success of the recently proposed "maxout" networks. The framework is based on encoding information on sparse pathways and recognizing the correct pathway at inference time. Elaborating further on this insight, we pro…
Joint replacement is the most common inpatient surgical treatment in the US. We investigate the clinical pathway optimization for knee replacement, which is a sequential decision process from onset to recovery. Based on episodic claims from previous cases, we view the pathway optimization as an intelligence crowdsourci…
MediEncoder learns nonlinear representations for causal mediation analysis.
problem High-dimensional noisy covariates and mediators in biomedical studies.
method Coupled encoder-decoder architecture with cross-factor network.
result Improves estimation accuracy in high-dimensional causal mediation analysis.
This research improves multitask learning by creating task-specific pathways.
problem Creating task-specific representations for efficient learning.
method Developed generalization bounds for learning multiple tasks over multiple pathways.
result Proves the superiority of multipath representation over traditional shallow supernets.
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than others in term of their multi-omics follows from the analysis of these circuits . T…
Bayesian method estimates causal effects with proxy networks.
problem Estimating causal effects with only proxy measurements of a latent interference network.
method Structural causal model with Block Gibbs sampler and Locally Informed Proposals.
result Accurately estimates causal effects even with noisy proxy networks.
Proposes new method to handle hidden confounders in causal mediation analysis.
problem Break down total effect of treatment on outcome through different causal pathways.
method Combines proxy strategies and deep learning to uncover latent variables and estimate causal effects.
result Validated effectiveness of the proposed method for causal fairness analysis.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
We introduce tools to capture the dynamics of three different pathways, in which the synchronization of human decision-making could lead to turbulent periods and contagion phenomena in financial markets. The first pathway is caused when stock market indices, seen as a set of coupled integrate-and-fire oscillators, sync…
Deep reinforcement learning method finds rare events in complex systems.
problem Computing transition pathways in high-dimensional systems.
method Formulated as a cost minimization problem, solved using DDPG with physical properties.
result Efficiently samples and computes globally optimal transition pathways.
Model infers diffusion networks from heterogeneous cascade data.
problem Understanding and predicting diffusion processes in interconnected populations.
method Double mixture directed graph model with layer-specific constraints.
result Convex formulation allows for statistical and computational guarantees.
New method makes neural networks transparent, revealing learning modes.
problem Lack of interpretability in neural networks.
method Weight pathway analysis (WPA) to decompose neural networks into subnetworks.
result Neural networks store and utilize information holographically, with linear and nonlinear learning modes.
Method learns shared and specific factors in multi-study gene expression data.
problem Understanding shared and specific factors in high-dimensional multi-study data.
method Nonlinear multi-study factor model with sparse variational autoencoder.
result Method recovers meaningful shared and specific factors in platelet gene expression data.
Simulates patient pathways to detect delayed rare disease diagnoses.
problem Delayed rare disease diagnoses in France, causing health system and patient harm.
method Probabilistic modelling of patient pathways to create an alert system.
result Alert system detects and refers wandering patients to CRMRs.
In this work, we developed a network inference method from incomplete data ("PathInf") , as massive and non-uniformly distributed missing values is a common challenge in practical problems. PathInf is a two-stages inference model. In the first stage, it applies a data summarization model based on maximum likelihood to …
Unified method for discovering biclusters and triclusters in longitudinal data.
problem High-dimensional, sparsely sampled, irregularly observed longitudinal data.
method Tri-SfSVD, a unified sparse functional Singular Value Decomposition framework.
result Identified localized structures at the subject, subject-feature, and subject-feature-time levels.
New method analyzes complex multivariate pathways in high-dimensional data.
problem High-dimensional mediation analysis of multivariate exposures, mediators, and outcomes.
method Simultaneous variable selection, indirect effect matrix estimation, and prediction of multivariate outcomes.
result Identifies biologically interpretable genetic-neural-cognitive pathways.
Bayesian method detects mesoscale structures in pathway data networks.
problem Mesoscale structures in pathway data networks are hard to detect due to dependencies between interactions.
method Bayesian approach modeling optimal partitioning and higher-order dynamics.
result Method can recover both proximity-based and role-based groupings of nodes.
ESN model helps understand climate event impacts.
problem Understanding complex climate event impacts.
method Feature importance methods for ESNs on spatio-temporal climate data.
result Characterized relationships between Mount Pinatubo eruption variables.
Improved co-clustering for robust data analysis.
problem Noise and posterior collapse in co-clustering.
method Fully variational Co-clustering framework with Compositional ELBO.
result Enhanced robustness and accuracy in co-clustering.
The paper proposes a method to predict the performance of data-driven algorithms using surrogate models.
problem Improving the performance prediction of data-driven knowledge discovery algorithms.
method Surrogate-assisted performance prediction using evolutionary modeling of clinical pathways.
result The proposed approach provides interpretable prediction of algorithm performance and quality.
Paper proposes methods to handle missing data in online RL, improving efficiency and uncertainty capture.
problem Missing data in online RL poses challenges due to the need to impute and act at each time step.
method Proposes fully online imputation ensembles and multiple imputation pathways to balance uncertainty and efficiency.
result Preliminary evidence suggests multiple imputation pathways can be a useful framework for simple and efficient online missing data RL methods.
RPPs improve deep learning models with soft equivariance constraints.
problem Balancing expressiveness and inductive biases in deep learning.
method Introducing Residual Pathway Priors (RPPs) to convert hard constraints into soft priors.
result RPPs enable models to learn structured solutions while retaining flexibility.
Computer-assisted synthesis planning aims to help chemists find better reaction pathways faster. Finding viable and short pathways from sugar molecules to value-added chemicals can be modeled as a retrosynthesis planning problem with a catalyst allowed. This is a crucial step in efficient biomass conversion. The tradit…
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…