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.
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.
Warfarin dosing remains challenging due to narrow therapeutic index and highly individual variability. Incorrect warfarin dosing is associated with devastating adverse events. Remarkable efforts have been made to develop the machine learning based warfarin dosing algorithms incorporating clinical factors and genetic va…
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.
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.
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.
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.
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.
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.
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.
Paper uses AI to predict medications from medical codes, improving accuracy in healthcare.
problem Predicting medications from incomplete or incorrect medical codes is challenging.
method Robust Recurrent Neural Networks (RNNs) with decay mechanism and noise injection.
result The method accurately predicts medication orders from contaminated medical codes.
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.
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.
Improved antibody humanness prediction using patent data.
problem Predicting the immunogenic response of antibody therapeutics.
method Multi-stage, multi-loss training process with contrastive learning and cross-entropy loss.
result The model outperforms baselines on five out of six inference tasks, improving humanness prediction.
Clinical prognostic models derived from largescale healthcare data can inform critical diagnostic and therapeutic decisions. To enable off-theshelf usage of machine learning (ML) in prognostic research, we developed AUTOPROGNOSIS: a system for automating the design of predictive modeling pipelines tailored for clinical…
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…
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.
VGAE learns gene-disease associations from networks, predicting disease-genes.
problem Predicting gene-disease associations from disease-gene networks.
method Introducing VGAE, a variational graph auto-encoder for disease-gene prediction.
result VGAE and C-VGAE outperform baseline methods in disease-gene prediction.
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here we present OhmNet, a hierarchy-aware unsupervised node feature le…
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.
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.
Paper addresses data heterogeneity in federated learning for CoxPH models in healthcare.
problem Data heterogeneity in federated learning of CoxPH models for healthcare.
method Feature-based clustering and event-based reporting strategy.
result Enhanced model accuracy and performance in federated survival analysis.
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.
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.
Models predict Alzheimer's Dementia from spontaneous speech with high accuracy.
problem Early diagnosis of Alzheimer's Dementia (AD) through spontaneous speech analysis.
method Compared natural language processing techniques including SVM, GBDT, CRFs, and Transformer-based models.
result Top models achieve 0.81-0.82 test set scores for AD vs controls and 4.58 RMSE for Mental Mini State Exam scores.
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.
A broad spectrum of data from different modalities are generated in the healthcare domain every day, including scalar data (e.g., clinical measures collected at hospitals), tensor data (e.g., neuroimages analyzed by research institutes), graph data (e.g., brain connectivity networks), and sequence data (e.g., digital f…
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.
Study improves neural network calibration for drug discovery.
problem Improper calibration of neural network predictions in drug discovery.
method Compared different metrics for model hyperparameter tuning and proposed Bayesian Linear Probing (BLP) method.
result Bayesian Linear Probing (BLP) improves model calibration and accuracy.
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However,…
Paper presents a machine learning method to predict cancer sub-clones.
problem Predicting the growth of sub-clones in cancer tumors.
method Data-driven machine learning approach to capture sub-clonal characteristics.
result Machine learning can predict which sub-clones are more likely to grow.
A new model uses GPs and latent force models to predict patient responses to drugs.
problem Challenges in modeling short-term effects of drugs on patient physiology.
method Hybrid Gaussian process with latent force model for joint modeling of patient physiology and drug effects.
result The model accurately predicts patient responses to three common drugs, showing competitive performance.
Project predicts Alzheimer's progression using neural networks and novel data processing.
problem Difficulty in early identification of Alzheimer's patients.
method Used machine learning, specifically neural networks, and a novel pre-processing technique.
result Neural network model accurately predicts AD progression with high accuracy.
A new meta-learner improves prediction of individualized outcomes in sequential decisions.
problem Predicting individualized outcomes over long horizons in sequential decision-making.
method Developed a novel meta-learner called DRQ-learner with theoretical guarantees of orthogonality and quasi-oracle efficiency.
result DRQ-learner achieves quasi-oracle efficiency, doubly robustness, and Neyman-orthogonality.
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.
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.
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.
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.
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs," which are communities of bacteria administered to patients for specific therapeuti…
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.
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.
New edge features improve GNN performance in biological datasets.
problem Inefficient use of edge features in GNNs.
method Self-supervised and unsupervised learning for new edge features, incorporating Forman-Ricci curvature.
result Improved node classification performance over baseline GNN models.
Q-SAVI model improves drug discovery accuracy with prior knowledge of chemical space.
problem Challenges in drug discovery due to covariate shift and limited labeled data.
method Probabilistic model with domain-informed prior distributions over functions.
result Q-SAVI outperforms state-of-the-art techniques in predictive accuracy and calibration.
Study identifies personality traits from dance movements in music.
problem Predicting individual differences from music-induced movement.
method Identified Big Five personality traits and EQ/SQ scores from dance movements.
result Successfully explored unseen space for personality and EQ/SQ.
Predicts clinical events using a landmark approach with machine learning for large biomarker histories.
problem Dynamic prediction of clinical events from large biomarker histories.
method Landmark approach extended to endogenous markers history combined with machine learning methods for survival data.
result Superlearner combining regularized regressions and random survival forests outperforms standard survival models.
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.
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.