PropEn uses matching to create a larger dataset for efficient design optimization.
problem Limited data and complex landscapes in scientific applications.
method PropEn uses a matching approach to implicitly guide design without a discriminator.
result PropEn efficiently approximates the gradient of property improvement within the data distribution.
Paper proposes a framework to predict therapeutic properties of compounds.
problem Predict therapeutic properties of compounds with heterogeneous data.
method Domain-adversarial multi-task framework using adversarial learning.
result Framework improves performance over competitive baselines.
FRnet-DTI predicts drug-target interactions using deep learning.
problem Predicting drug-target interactions for therapeutic drug design.
method Auto encoder and convolutional classifier with feature manipulation and classification.
result Significantly improved on drug-target interaction prediction metrics.
Improved RL model for fragment-based molecule generation.
problem Generating molecules with high docking scores.
method Thorough reproduction, scrutiny, and improvement of the FREED model.
result The improved model produces molecules with superior docking scores.
Bayesian model for understanding gut bacteria interactions.
problem Understanding complex interactions in gut microbiome dynamics.
method Bayesian nonparametric model with interaction modules, efficient inference algorithm.
result Efficiently learned clusters of latent variables with reduced interaction coefficients.
New method refines model predictions as design evolves.
problem Designing objects with desired properties using data-driven methods.
method Formalized as a game, developed autofocusing strategy for model retraining.
result Autofocusing improves model predictions in design space.
BoGA combines evolutionary search with Bayesian optimization for efficient protein design.
problem Designing novel proteins with specific characteristics is challenging due to sequence space complexity.
method BoGA integrates a genetic algorithm with Bayesian optimization to efficiently explore sequence space.
result BoGA accelerates discovery of high-confidence binders for diverse protein design objectives.
NucleusDiff models atomic nuclei interactions to prevent separation violations in drug design.
problem Maintaining minimum pairwise distance between atoms to avoid separation violations in drug design.
method Enforces distance constraint between atomic nuclei and manifolds in a diffusion model.
result Reduces separation violations by up to 100.00% and enhances binding affinity by up to 22.16%.
The paper proposes a method to reliably select design algorithms for machine learning-guided design tasks.
problem Choosing the right design algorithm for machine learning-guided design tasks.
method Combining designs' predicted property values with held-out labeled data to reliably forecast characteristics of the label distributions produced by different design algorithms.
result The method is guaranteed to return design algorithms that yield successful label distributions.
Clusters of ACS patients identified for better therapeutic stratification.
problem Data-driven classification and subtyping of ACS patients for improved treatment.
method Outcome-driven clustering using a multi-task neural network with attention.
result Seven patient clusters with distinct characteristics and risk profiles identified.
New method designs antimicrobial peptides with high potency and low toxicity.
problem Designing potent antimicrobial drugs with low toxicity.
method CLaSS method using deep generative autoencoder and atomistic simulations.
result Design and synthesis of two novel AMPs with high potency and low toxicity.
CGD improves diffusion models' out-of-distribution generalization.
problem Reliable sampling from high-value regions beyond training data.
method Context-guided diffusion (CGD) using unlabeled data and smoothness constraints.
result Substantial performance gains across various diffusion processes.
Study repurposes open data to find potential COVID-19 drugs.
problem Developing effective treatments for COVID-19.
method Deep learning network-based approach using large scientific corpus.
result Identified 41 repurposable drugs for COVID-19.
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.
Study shows peers' graduation improves residents' success in TCs.
problem Identifying peer influence in therapeutic communities adjusting for latent homophily.
method Used data on affirmations and exit dates to form peer networks, modeled latent homophily, and proposed bias correction methods.
result Positive effect of peers' graduation on residents' graduation, varying by gender, race, and role model definition.
AntBO optimizes antibody design using Bayesian optimization for efficient and effective CDRH3 sequence generation.
problem Designing optimal antigen-specific CDRH3 regions in antibody design due to combinatorial sequence space.
method Combinatorial Bayesian optimization framework with trust region for developability.
result AntBO designs CDRH3 regions with diverse biophysical properties and outperforms existing methods.
Novel algorithms improve warfarin dose prediction accuracy.
problem Challenges in estimating warfarin dose due to narrow therapeutic index and individual variability.
method Stacked generalization frameworks combining different machine learning algorithms.
result Stacked algorithms outperform the IWPC MLR algorithm, especially in subgroups.
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.
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.
Bayesian optimization of antibodies learns from immune system evolution.
problem Efficiently optimizing antibody sequences in a large space of possibilities.
method Bayesian optimization guided by a generative model of evolving antibody sequences.
result CloneBO optimizes antibodies more efficiently than previous methods.
PerturBench benchmarks ML models for cellular perturbation analysis.
problem Standardizing benchmarking in modeling single cell transcriptomic responses to perturbations.
method Modular platform, diverse datasets, metrics, extensive evaluation, rank metrics.
result Simpler models are competitive and scale well with larger datasets.
Deep learning predicts RNA degradation from crowdsourced data.
problem Predicting RNA degradation to improve thermostability.
method Crowdsourced machine learning competition on Kaggle.
result 41% of predictions matched experimental data, and models generalized to longer RNA molecules.
Two ML frameworks predict antibody properties using structural data.
problem Predicting antibody properties using sequence and structural data.
method ANTIPASTI and INFUSSE models using graph representations and neural networks.
result ANTIPASTI predicts binding affinity; INFUSSE predicts residue flexibility.
Intratumor heterogeneity is often manifested by vascular compartments with distinct pharmacokinetics that cannot be resolved directly by in vivo dynamic imaging. We developed tissue-specific compartment modeling (TSCM), an unsupervised computational method of deconvolving dynamic imaging series from heterogeneous tumor…
Machine learning identifies potential drugs for COVID-19.
problem Finding effective treatments for COVID-19.
method Trained neural network models on virus protein sequences and antiviral drugs.
result Identified potential drug candidates for treating COVID-19.
New models suggest molecules that are often unfeasible to synthesize.
problem Models suggest molecules that are difficult to synthesize.
method Used a computer-aided synthesis planning program to analyze synthesizability of molecules generated by state-of-the-art models.
result State-of-the-art models generate molecules that are often unfeasible to synthesize.
BioFinBERT analyzes sentiment of biotech press releases and financial text around inflection points.
problem Analyzing sentiment of biotech press releases and financial text around inflection points.
method Finetuning BioBERT on financial datasets to create BioFinBERT for sentiment analysis.
result BioFinBERT accurately analyzes sentiment of biotech press releases and financial text around inflection points.
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our cluste…
A model predicts which patients can safely use a warfarin dosing algorithm.
problem Determining the optimal initial dose for warfarin patients.
method Support Vector Machines with a polynomial kernel function.
result The model increases dosing accuracy by 15% in RMSE and 17% in MAE.
AUTOPROGNOSIS automates clinical prognosis models using Bayesian optimization.
problem Developing accurate clinical prognostic models from large healthcare data.
method AUTOPROGNOSIS uses Bayesian optimization with structured kernel learning to optimize pipeline configurations.
result AUTOPROGNOSIS automates the design of predictive modeling pipelines for clinical prognosis.
This abstract reviews recent methods for predicting protein-ligand binding affinity.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
Model uses smartphone data to assess MS trajectories.
problem Personalized longitudinal MS assessment.
method Imputation, generalized estimation equation, ensemble learning, fine-tuning.
result Promising model for predicting MS over time.
Adapts causal inference for high-dimensional treatments like text strings.
problem Predicting effects of interventions with many possible variations.
method Adapts classical causal estimators to high-dimensional treatment spaces, balancing moment errors.
result Shows high-dimensional treatment spaces can be addressed with a single model.
This study quantifies uncertainty in comparing treatments using RCTs with before-and-after measures.
problem Uncertainty in comparing treatments using RCTs with before-and-after measures.
method New statistical modeling principle called ETZ enables counterfactual uncertainty quantification (CUQ) in RCTs with Before-and-After Repeated Measures.
result CUQ typically has lower variability than factual uncertainty quantification and can be achieved in RCTs.
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.
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.
CSLVAE generates large chemical libraries efficiently.
problem Navigating ultra-large combinatorial synthesis libraries.
method Hierarchically-organized database with molecular encoder and decoder.
result Generates valid molecular graphs without autoregression.
Generative ODE model learns unknown variables in medical systems.
problem Estimating unknown variables in complex medical systems.
method Variational autoencoder incorporating known ODE functions.
result Modeling known-unknowns improves system parameter discovery and extrapolation.
Novel parallel GNN predicts protein-ligand interactions with high accuracy.
problem Accurate prediction of protein-ligand interactions for drug design.
method Parallel Graph Neural Networks (GNN) integrating 3D structural data.
result GNN achieves high accuracy in predicting binary interactions and activity.
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.
PANDA predicts protein binding affinity changes from sequences, outperforming existing methods.
problem Accurately predicting changes in protein binding affinity due to mutations.
method Sequence-based machine learning approach using protein sequence information.
result PANDA achieves higher Pearson correlation coefficients than existing methods.
RL algorithms with medical integration improve personalized treatment recommendations.
problem Developing effective personalized treatment strategies for chronic diseases.
method Integrating medical knowledge into RL algorithms for DTR.
result Enhanced treatment recommendations with increased confidence.
Improved GCNNs tackle noisy knowledge graphs for better link prediction.
problem Link prediction on noisy biomedical knowledge graphs.
method Regularized attention mechanism for GCNNs, interpretable visualization methods.
result Improved performance on noisy datasets, automated denoising potential.
Model predicts VKA dosage for Indian patients, aiding in safe medication.
problem Safe and accurate dosing of VKA drugs for Indian patients.
method Support Vector Machine (SVM) Regression model trained on patient data.
result Predicted dosages closely match actual dosages.
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
AI enhances microbiology and microbiome research through machine learning.
problem Understanding microbial life and its impact on health and the environment.
method AI-driven approaches including machine learning and deep learning.
result Transformative role in enhancing microbial life understanding.
DeepNovoV2 improves de novo peptide sequencing from mass spectrometry data.
problem De novo peptide sequencing from mass spectrometry data for personalized cancer vaccines.
method DeepNovoV2 combines T-Net and recurrent neural networks for end-to-end training and prediction.
result DeepNovoV2 achieves 13.01-23.95\% higher accuracy than previous methods.
Broad learning integrates diverse healthcare data for diagnostics and precision medicine.
problem Integrating various types of healthcare data for better diagnostics and personalized medicine.
method Fusing multi-view data including scalar, tensor, graph, and sequence data for knowledge discovery and machine learning tasks.
result Accurate user profiles and brain connectivity patterns can be created for improved diagnostics and personalized medicine.