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.
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.
Bayesian model identifies cancer pathways using genomic data.
problem Identifying altered pathways associated with specific cancer types.
method Bayesian semi-nonnegative tri-matrix factorization incorporating biological prior knowledge.
result Pathways identified can be used as prognostic biomarkers.
Method infers multi-layer networks from gene expression data.
problem Inference of multi-level networks from gene expression data.
method Extension of latent graphical lasso method leveraging group structure.
result Efficacy in retrieving multi-layer network structure from synthetic data.
PKB method uses pathway information for cancer sample classification.
problem Cancer genomic data's high dimensionality and limited sample sizes.
method Pathway-based Kernel Boosting (PKB) method integrating gene pathway information for sample classification.
result PKB method outperforms other methods and identifies relevant pathways.
PIMKL uses pathway knowledge to improve sample classification and provide interpretable molecular signatures.
problem Lack of reliable molecular biomarkers and poor generalization in machine learning for health care.
method Pathway Induced Multiple Kernel Learning (PIMKL) using a mixture of pathway-induced kernels optimized via Multiple Kernel Learning.
result PIMKL provides interpretable molecular signatures and stable predictions.
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.
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.
Deep RL finds efficient pathways for sugar to chemicals.
problem Finding efficient pathways from sugar to value-added chemicals.
method Markov decision process with deep reinforcement learning.
result Promising preliminary results in efficient biomass conversion.
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…
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.
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.
A deep neural network learns to balance memory formation and network activity with context sensitivity.
problem Improving neural network performance with limited resources.
method Integrates biological hippocampal pathways into a deep convolutional network with context-sensitive bias.
result Demonstrates a significant performance increase in a constrained network architecture.
PUMA interprets metabolomics data to predict pathway activity and assign chemical identities.
problem Interpreting metabolomics data to determine biochemical pathway activities.
method Generative probabilistic modeling using stochastic sampling.
result PUMA predicts pathway activity and assigns chemical identities to metabolites.
Machine learning identifies key metabolic control circuits in bacterial pathways.
problem Identifying regulated metabolic pathways in bacteria.
method Machine learning approach analyzing multi-omics data.
result Identification of E. coli Glycolysis regulatory circuits.
Crowdsourced reinforcement learning optimizes knee replacement pathway, reducing costs.
problem Optimizing the sequential decision process for knee replacement surgery.
method Reinforcement learning, value iteration, state compression, kernel representation, cross validation.
result Optimized policy reduces overall cost by 7% and excessive cost premium by 33%.
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…
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.
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 …
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…
NetBiTE predicts drug sensitivity and identifies biomarkers in cancer.
problem Predicting drug sensitivity and identifying biomarkers in cancer.
method NetBiTE combines prior knowledge and gene expression data using a biased tree ensemble approach.
result NetBiTE outperforms RF in predicting IC50 drug sensitivity for drugs targeting membrane receptor pathways.
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.
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.
Developed PathInf for network inference from incomplete data.
problem Massive and non-uniformly distributed missing values in data.
method Two-stage inference model: data summarization and graph inference.
result Consistently superior performance compared to state-of-the-art methods.
Bayesian networks for gene regulatory pathways using hybrid quantum-classical ML.
problem Elucidate gene regulatory pathways from proteomics data.
method Hybrid quantum-classical machine learning framework to build Bayesian networks.
result Scalable framework for learning gene regulatory networks from proteomics data.
The paper develops methods to optimize personalized policies in complex causal pathways.
problem Optimizing policies in healthcare settings with entangled causal effects.
method Combining mediation analysis and dynamic treatment regime ideas for longitudinal data.
result Derived methods for learning high-quality policies from observational data.
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.
Fair decision-making method avoids ignoring fair pathways.
problem Learning fair decision systems in complex scenarios with sensitive attributes.
method Causal approach to disregard unfair pathways, corrects affected observations, uses for decision-making.
result Avoids ignoring fair information, widely applicable to complex scenarios.
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.
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.
TrueLearn uses Bayesian algorithms to match learners with educational resources.
problem Matching lifelong learners to open educational resources efficiently and effectively.
method TrueLearn uses a text ontology and Bayesian strategies to match learners with educational resources based on their background knowledge and material novelty.
result TrueLearn algorithms show promise in building an effective educational recommendation system.
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic loci. While several methods for multi-locus mapping have been proposed, it is often…
Three ways synchronization in financial markets can cause contagion, using models of decision-making and oscillators.
problem Contagion in financial markets caused by synchronization of decision-making.
method Agent-based modeling, integrate-and-fire oscillators, and communication models.
result Synchronization in financial markets can lead to turbulent periods and contagion.
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.
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.
engGNN combines external and generated graphs to improve disease classification and biomarker discovery.
problem Challenges in integrating omics data due to high dimensionality and small sample sizes.
method Dual-graph framework that integrates external biological networks with data-driven generated graphs.
result engGNN outperforms state-of-the-art methods in disease classification and biomarker discovery.
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.
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.
HOPE uses Hilbert space to deconstruct deep network representations.
problem Deconstructing learned representations in deep networks is challenging.
method Introduces Hilbert Operator for Progressive Encoding (HOPE) to deconstruct network weights.
result HOPE provides an unbiased approach to network compression and fine-tuning.
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.
Study tackles high-dimensional datasets in molecular biology by reducing intrinsic variability.
problem High-dimensional datasets in molecular biology pose a challenge for thorough analysis.
method Intrinsic dimensionality analysis, including dimension reduction techniques and nonlinear time series analysis.
result Dimension reduction techniques help identify irrelevant variability and understand critical processes.
Study optimizes climate adaptation strategies for NYC.
problem Catastrophic damages from extreme weather in NYC.
method Real options analysis and extreme value theory.
result Optimal adaptation pathways identified for NYC.
Neural networks improve geoscience by enabling interpretable decision pathways.
problem Lack of methods to interpret neural networks' learning and decision-making.
method Backwards optimization and layerwise relevance propagation.
result Interpretation techniques reveal meaningful connections in geoscientific data.
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.
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
problem Lack of methods to model pleiotropy in multi-phenotype GWAS.
method Bayesian inference model using summary statistics, fast computation, and biologically informed priors.
result Demonstrates utility in metabolite GWAS with interpretable pathway-level inference.
Deep learning excels in AI but struggles with causal physics.
problem Deep learning struggles with causal relationships in physical sciences.
method Combining Bayesian methods, physical constraints, and causal models.
result Deep learning can mislead in systems with unclear causal relationships.
Paper tackles anomaly detection with missing causal knowledge.
problem Detect anomalies with missing structural knowledge.
method Simple, efficient methods for polytree causal graphs.
result Heuristic identifies root causes based on anomaly scores.