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.
LHM integrates expert ODEs with neural ODEs for disease progression prediction.
problem Predicting disease progression under medications using limited data.
method Integrating expert-designed ODEs with machine-learned Neural ODEs.
result LHM consistently outperforms previous methods, especially in small sample regimes.
Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, …
Two new minor minimal intrinsically chiral graphs identified.
problem Identifying intrinsically chiral graphs in molecular structures.
method Analyzing graph symmetry and embedding properties.
result Found two new minor minimal intrinsically chiral graphs Γ7 and Γ8. A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning methodology, for de novo molecular design. Various generative autoencoders were used t…
Neuroscience is undergoing faster changes than ever before. Over 100 years our field qualitatively described and invasively manipulated single or few organisms to gain anatomical, physiological, and pharmacological insights. In the last 10 years neuroscience spawned quantitative big-sample datasets on microanatomy, syn…
Develops a new multivariate regression model for complex outcomes.
problem Flexible, heterogeneous, and residual-dependent multivariate regression problems.
method MultiVCBART framework with Graphical Horseshoe priors.
result Empirically outperforms existing models on sparse, high-dimensional datasets.
A new drug embedding method using hierarchical drug relations and chemical structures.
problem Learning accurate drug representations from chemical structures and hierarchies.
method Semi-supervised drug embedding using VAE in hyperbolic space.
result The method accurately places drugs in a hierarchy and predicts side-effects.
Framework designs antiviral drugs using deep learning and RL.
problem Designing effective antiviral drugs for SARS-CoV-2.
method Deep learning framework with conditional molecular generator and RL.
result Framework generates more antiviral ligands than a VAE baseline.
A new RL framework optimizes drug-like molecules synthetically.
problem Optimizing drug-like molecules for specific criteria.
method Deep Reinforcement Learning framework for chemical space optimization.
result Outperforms existing methods in pharmacological optimization.
For most problems in science and engineering we can obtain data sets that describe the observed system from various perspectives and record the behavior of its individual components. Heterogeneous data sets can be collectively mined by data fusion. Fusion can focus on a specific target relation and exploit directly ass…
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
Algorithm selects optimal experiments in Markov chains to learn unknown quantities.
problem Designing efficient experiments in Markov chains to learn about unknown quantities.
method Proposes extsc{markov-design} algorithm for sequential policy selection.
result Algorithm provably converges to optimal measurement allocation.
Without any means of interpretation, neural networks that predict molecular properties and bioactivities are merely black boxes. We will unravel these black boxes and will demonstrate approaches to understand the learned representations which are hidden inside these models. We show how single neurons can be interpreted…
Paper proposes a new method for predicting drug interactions using adversarial autoencoders.
problem Predicting drug interactions to prevent adverse events.
method Introduces adversarial autoencoders based on Wasserstein distances and Gumbel-Softmax relaxation to generate high-quality negative samples.
result Significant improvements in link prediction and DDI classification tasks.
Machine learning is often used in virtual screening to find compounds that are pharmacologically active on a target protein. The weave module is a type of graph convolutional deep neural network that uses not only features focusing on atoms alone (atom features) but also features focusing on atom pairs (pair features);…
The task of drug-target interaction prediction holds significant importance in pharmacology and therapeutic drug design. In this paper, we present FRnet-DTI, an auto encoder and a convolutional classifier for feature manipulation and drug target interaction prediction. Two convolutional neural neworks are proposed wher…
Paper introduces models to discover complex structures in large hypergraphs.
problem Understanding dependency structures in complex systems represented as hypergraphs.
method Probabilistic models treating classes of similar units as nodes in a latent hypergraph, using low-rank representations.
result Improves link prediction and discovers interpretable structures in diverse real-world systems.
Proposes a self-attention-based method for drug-target interaction prediction.
problem Interpreting machine learning models for drug-target interactions.
method Self-attention-based multi-view representation learning approach.
result Competitive prediction performance with biologically interpretable results.
The paper clusters PK curves using ML, finding it useful for identifying similar patterns.
problem Improving drug development and patient outcomes through ML in pharmacogenomics.
method Unsupervised clustering of PK curves using various dissimilarity measures.
result Euclidean distance is most suitable for clustering PK curves, and clustering can validate pharmacogenomic results.
State-space models improve dynamical system predictions efficiently and accurately.
problem Challenges in predicting dynamical systems, including long-time integration and long-range dependencies.
method State-space models implemented in Mamba, addressing limitations of existing architectures.
result Mamba outperforms other models in interpolation and challenging extrapolation tasks.
Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domai…
Bandit algorithms optimize treatment decisions for precision medicine.
problem Optimizing treatment decisions for individual patients based on genetic or molecular profiling.
method Contextual bandit algorithms that consider patient characteristics.
result Bandit algorithms are useful for mobile health and digital phenotyping.
The leverage effect refers to the generally negative correlation between the return of an asset and the changes in its volatility. There is broad agreement in the literature that the effect should be present for theoretical reasons, and it has been consistently found in empirical work. However, a few papers have pointe…
New method for interpreting non-linear models using forward marginal effects.
problem Interpreting non-linear models' feature effects is challenging.
method Introducing forward marginal effects and partitioning feature space for better interpretation.
result Improved interpretation of non-linear prediction functions.
The Kalinin effectivity is studied and applied to compactifications and Hilbert squares.
problem Understanding Kalinin effectivity in compactifications and its applications.
method Definition, construction methods, and analysis of Kalinin effectivity in various compactifications.
result Wonderful compactifications of hyperplane arrangements and configuration spaces are Kalinin effective.
New method estimates treatment effects in network data, accounting for spillover effects.
problem Treatment effect estimation in networks with spillover effects.
method Augmented inverse probability weighting (AIPW) with cross-fitting and machine learning.
result Semiparametric treatment effect estimator converges at parametric rate and follows Gaussian distribution.
Causalfe estimates treatment effects in panel data with fixed effects.
problem Spurious heterogeneity in treatment effect estimates due to fixed effects in panel data.
method CFFE approach with node-level residualization during tree construction.
result Validates the estimator's performance through simulation studies.
The paper clarifies the distinction between CATE and ITE under ignorability assumptions.
problem Confusion between CATE and ITE hinders personalized effect estimation.
method Clarifies the distinction between CATE and ITE under ignorability assumptions.
result CATE and ITE are not necessarily the same under ignorability assumptions.
GADGET framework decomposes global feature effects using recursive partitioning.
problem Misleading global feature effects when feature interactions are present.
method Generalized additive decomposition of global effects (GADGET) based on recursive partitioning.
result Minimizes interaction-related heterogeneity of local feature effects.
A new RL framework evaluates dynamic mediation effects over time.
problem Dynamic mediation effects in sequentially assigned treatments.
method Reinforcement Learning framework for decomposition and estimation of causal effects.
result Superior performance demonstrated through numerical studies and real data analysis.
New memory effect discovered in gravitational wave behavior.
problem Understanding gravitational wave behavior in spacetimes with angular momentum.
method Mathematical analysis of Minkowski spacetime and Kerr black holes.
result Angular momentum memory effect observed at future null infinity.
Effective Yau-Tian-Donaldson conjecture for spherical varieties.
problem Finding effective K-stability criteria for spherical varieties.
method Formulated an effective variant of the Yau-Tian-Donaldson conjecture and reviewed effective K-stability criteria for spherical varieties.
result Effective K-stability criteria can be computed given combinatorial data.
A new method estimates treatment effects in mixed groups, improving accuracy.
problem Estimating treatment effects in mixed groups with heterogeneous responses.
method PCM (pre-cluster and merge) approach for nonparametric estimation.
result Asymptotic consistency and significant improvement in accuracy over existing methods.
Study estimates heterogeneous principal causal effects with binary treatments and intermediate variables.
problem Estimating subgroup effects within strata defined by potential values of an intermediate variable.
method Proposes a framework for estimating and forming confidence intervals for heterogeneous principal causal effects under principal ignorability assumption. Develops several estimators with varying robustness properties.
result Established large-sample theory and analyzed bias contributions of each approach.
Study develops method for estimating causal effects in continuous variables.
problem Lack of methods for estimating causal effects in continuous variables.
method Develops a method independent of data generating models for continuous variable interventions.
result Preserves identifiability of data and applies to any generating models.
ICA accurately estimates treatment effects even with confounders.
problem Estimating treatment effects in the presence of confounding variables.
method Uses Independent Component Analysis (ICA) to identify latent sources and estimate mixing coefficients.
result Linear ICA can consistently estimate multiple treatment effects, even with Gaussian confounders, and is more sample-efficient than Orthogonal Machine Learning (OML).
Method improves treatment effect estimation in randomized experiments.
problem Estimating distributional treatment effects in randomized experiments.
method Distributional regression framework with machine learning for variance reduction.
result The proposed method reduces variance of distributional treatment effect estimators.
New method discovers context effects in choice data.
problem Identifying context effects from choice data is challenging.
method Automatic discovery of context effects from observed choices.
result Automatic discovery of context effects from observed choices.
Dropout introduces both explicit and implicit regularization effects.
problem Understanding the full impact of dropout regularization.
method Disentangled explicit and implicit regularization effects through experiments and analytic simplifications.
result Explicit and implicit regularization effects of dropout are distinct and can be characterized analytically.
New test for binary treatment effects using kernel methods.
problem Testing distributional effects of binary treatments.
method Kernel-based doubly-robust test, avoiding permutations.
result Valid type-I error with computational efficiency.
New Krylov subspace methods speed up mixed-effects models with crossed random effects.
problem Slow computations for high-dimensional crossed random effects in mixed-effects models.
method Krylov subspace-based methods for generalized mixed-effects models with cross effects.
result Speedups by factors of up to 10,000 in computations for mixed-effects models.
The use of drug combinations, termed polypharmacy, is common to treat patients with complex diseases and co-existing conditions. However, a major consequence of polypharmacy is a much higher risk of adverse side effects for the patient. Polypharmacy side effects emerge because of drug-drug interactions, in which activi…
Previous literature has identified an effect, dubbed the Zumbach effect, that is nonzero empirically but conjectured to be zero in any conventional stochastic volatility model. Essentially this effect corresponds to the property that past squared returns forecast future volatilities better than past volatilities foreca…
Identifies causal effects in LiNGAM models with latent variables.
problem Identifying causal effects in LiNGAM models with latent confounders.
method Complete graphical characterization and efficient algorithms for certification. RICA adaptation for estimation.
result Efficient algorithms and RICA adaptation for estimating causal effects.
Develops HCQRF for estimating heterogeneous treatment effects with censored data.
problem Estimating heterogeneous treatment effects on censored responses with high-dimensional variables.
method Hybrid Censored Quantile Regression Forest (HCQRF) combining random forests and censored quantile regression.
result Demonstrates the effectiveness and stability of HCQRF through simulation studies and real-world application.
Study relaxes identification assumptions for natural direct effects in non-randomized settings.
problem Identifying causal direct effects under unmeasured confounding.
method Developed relaxed conditions for identifying natural direct effects in non-randomized settings.
result Identified natural direct effect under unmeasured confounding conditions.
The Sagnac effect is re-examined using Finslerian geometry.
problem Understanding the Sagnac effect in general relativity.
method Reviewing the geometry of the Sagnac effect with a focus on Finslerian metrics.
result An asymmetry in Finslerian metrics affects the Sagnac effect for both future-pointing null and timelike geodesics.