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.
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.
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.
BOAT optimizes multiple antibody properties efficiently.
problem Balancing multiple drug-like properties in antibody design.
method Bayesian optimization framework coupling surrogate modeling and genetic algorithm.
result Competitive performance with state-of-the-art multi-objective protein optimization methods.
AbDiffuser generates full-atom antibodies with sequence and structure fidelity.
problem Generating high-fidelity antibodies with both structure and sequence information.
method Equivariant and physics-informed diffusion model with novel protein structure representation.
result AbDiffuser generates antibodies with sequence and structural properties matching a reference set.
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.
Active learning speeds up antibody affinity prediction.
problem Challenging to identify mutations enhancing antibody affinity.
method Iterative proposal of promising sequences for simulation.
result Accelerates search for improved binders.
Antibodies are a critical part of the immune system, having the function of directly neutralising or tagging undesirable objects (the antigens) for future destruction. Being able to predict which amino acids belong to the paratope, the region on the antibody which binds to the antigen, can facilitate antibody design an…
K-Models clusters functional data with ordinal constraints for better interpretability.
problem Challenges in extracting meaningful insights from functional data due to lack of interpretability.
method Integrates ordinal constraints into clustering to improve interpretability and structure identification.
result Enhances interpretability of clustering results while maintaining performance.
New method combines regional HIV prevention trial data without sharing individual patient info.
problem Regional differences in HIV prevention efficacy, privacy concerns, and data sharing limitations.
method Federated learning approach that combines site-specific estimators via L1-regularization.
result Improved precision in estimating region-specific survival curves.
Method scales up ML science by measuring multiple molecules at once.
problem Scaling up ML-driven science with wet lab experiments.
method Neural extension of compressed sensing for function space.
result Proves orders-of-magnitude gains in information density.
Improved GAN performance using higher-order Wasserstein moments.
problem Stabilizing and enhancing GANs for better mode coverage and stability.
method Deriving and training a GAN with a modified Wasserstein distance using higher-order moments.
result Training a GAN with higher-order Wasserstein moments improves performance, even with increased computational cost.
Super learner uses diverse screeners to improve prediction performance.
problem Performance issues with lasso screening in super learner.
method Used a diverse set of candidate screeners within the super learner ensemble.
result Diverse screeners protect against poor performance of any one screener.
New algorithms speed up learning from large screens of proteins.
problem Lack of scaled data hampers biological machine learning.
method Optimized high throughput screens and generative models.
result Maximized information gain with consistent estimates of p(y∣x). Proposes a framework to assess feature importance without algorithm constraints.
problem Lack of a general framework for assessing feature importance across different algorithms.
method Develops a nonparametric framework for algorithm-agnostic variable importance assessment.
result Valid confidence intervals and testing strategies for variable importance.
Estimates vaccine effectiveness and immune correlates in TND studies with missing data.
problem Confounding and missing data in TND studies of vaccine effectiveness and immune correlates.
method Targeted maximum likelihood estimation using a semiparametric logistic regression model.
result Valid causal inference of vaccine effectiveness and immune correlates in TND studies with missing exposure data.
Branching Flows generates sequences of varying lengths using binary trees.
problem Generating sequences of unknown lengths or fixed elements.
method A generative modeling framework that evolves states over binary trees, controlling sequence length.
result Branching Flows can generate sequences of varying lengths and mix different types of state spaces.