BSBO optimizes constraints for high-throughput experiments.
problem Optimizing high-throughput experiments with combinatorial constraints.
method Stochastic Bayesian optimization with submodular decomposition.
result BSBO outperforms heuristics in real-world protein datasets.
High-throughput 3D control training system achieves 100,000 FPS.
problem Lack of efficient, single-machine reinforcement learning systems.
method Sample Factory combines asynchronous sampling and off-policy correction.
result Achieves 100,000 FPS on 3D control problems without sacrificing sample efficiency.
High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry standard B-score method, work on individual compound plates and do not exploit cross…
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). A new method selects inducing points to optimize high-throughput Bayesian optimisation.
problem Current inducing point selection methods sacrifice high-fidelity modeling of promising regions.
method Information-theoretic criterion to select inducing points maximizing global and maximum value uncertainties.
result Surrogate models support high-precision high-throughput Bayesian optimisation.
Enhances high-throughput imaging of microtubule networks, improving clarity and consistency.
problem Fluorescence noise obscures microtubule structures in high-throughput imaging.
method CycleGAN learning to enhance low-resolution images of microtubule networks.
result CycleGAN effectively identifies microtubules with high accuracy (0.93+ AUC-ROC).
Active learning with Gaussian processes improves crop phenotype data collection.
problem Scalability issue in high throughput phenotyping for crop improvement.
method Active learning algorithm with Gaussian Process model.
result Superior performance compared to current practices on sorghum data.
EB improves asset pricing by mining large strategies without lookahead bias.
problem Lack of unbiased asset pricing models with out-of-sample performance.
method Empirical Bayes applied to 136,000 long-short strategies.
result EB provides unbiased predictions with transparent intuition.
DeepCoDA provides personalized interpretability for complex health data.
problem Interpreting complex health data, especially compositional data, is challenging.
method DeepCoDA framework for high-dimensional compositional data, personalized interpretability through patient-specific weights.
result DeepCoDA maintains state-of-the-art performance and provides coherent, personalized interpretations.
Chemical space is so large that brute force searches for new interesting molecules are infeasible. High-throughput virtual screening via computer cluster simulations can speed up the discovery process by collecting very large amounts of data in parallel, e.g., up to hundreds or thousands of parallel measurements. Bayes…
A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral p…
Automatically computes reference ranges for UK Biobank cardiac data.
problem Improving healthcare by discovering patterns in large-scale population data.
method Fully automatic pipeline for 3D cardiac MR image analysis.
result Statistically significant agreement between manual and automatic indexes.
Many modern data sets are sampled with error from complex high-dimensional surfaces. Methods such as tensor product splines or Gaussian processes are effective/well suited for characterizing a surface in two or three dimensions but may suffer from difficulties when representing higher dimensional surfaces. Motivated by…
CoinTossX is a low-latency, open-source matching engine for financial trading.
problem Efficiently matching orders in financial markets with low latency and high throughput.
method Developed in Java, orders submitted via UDP SBE, low-latency message transport (Aeron Media Driver). Separates order generation and matching.
result Demonstrated low-latency, high-throughput performance in various deployment scenarios.
High throughput sequencing techniques have highly impactedon modern biology, widening the gap between sequenced andannotated data. Automatic annotation tools are thereforeof the foremost importance to guide biologists' experiments. However, most of the state-of-the-art methods rely on annotation transfer, offering reli…
High-speed model accurately simulates neuromorphic devices.
problem Accurately modeling stochastic synapses in large-scale neuromorphic systems.
method Generative vector autoregressive model based on resistive memory cell data.
result Fast, high-throughput model reproduces synaptic parameters and correlations.
Hi-RES framework extracts medical relations from articles and EHRs.
problem Manual annotation bottleneck in relation extraction.
method Labeling sentences, creating improved negative samples, using pretrained language models, and combining EHR embeddings.
result Significant accuracy increases in relation extraction, up to 0.998 for disorder-location relations.
Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here we consider the case that the weight determining the acceptance probability itself is fluctuati…
This paper evaluates quantization techniques for deep learning inference.
problem Reducing the size and improving inference of deep neural networks.
method Review and empirical evaluation of quantization parameters for various neural network models.
result 8-bit quantization maintains accuracy within 1% of floating-point models.
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based neural network architectures have emerged in recent years as the most successful …
New method optimizes Gaussian process allocation for BO.
problem Existing methods for inducing point allocation in BO hinder performance.
method Proposes a new allocation strategy using quality-diversity decomposition.
result Demonstrates improved BO performance through local high-fidelity modeling.
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the consideration of …
It has been recently shown that sparse, nonnegative tensor factorization of multi-modal electronic health record data is a promising approach to high-throughput computational phenotyping. However, such approaches typically do not leverage available domain knowledge while extracting the phenotypes; hence, some of the su…
New method classifies reticulocytes from red blood cells without labels.
problem Classifying reticulocytes from mature red blood cells without fluorescent labels.
method Unsupervised machine learning on morpho-rheological markers.
result Promising results in classifying reticulocytes from mature red blood cells.
Study improves peptide design efficiency using active and meta-learning.
problem Designing novel functional peptides is inefficient due to low throughput and lack of data.
method Investigated active learning and meta-learning for optimizing peptide design experiments.
result Meta-learning improved average accuracy, but neither method outperformed random choice.
New BO methods exploit parallel experiments, reducing search time and improving solution quality.
problem Limitation of Bayesian optimization in exploiting parallel experiments.
method Propose new parallel BO paradigms that exploit the structure of the system to partition the design space.
result Significantly reduce search time and increase probability of finding global solutions.
PIMA autoencoders discover shared features in multimodal scientific data.
problem Discovering shared information in high-throughput scientific datasets.
method Physics-informed multimodal autoencoders (PIMA) with Gaussian mixture prior and product of experts formulation.
result Accurate cross-modal inference between images and mechanical stress-strain response in lattice metamaterials.
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
This study reviews and evaluates clustering methods for single-cell RNA-seq data.
problem Identifying and characterizing novel cell types from single-cell RNA-seq data.
method Review and performance comparison of clustering methods.
result Performance comparison experiments on two datasets.
Paper proposes a deep Gaussian process for predicting formation energy of inorganic compounds.
problem High computational cost of quantum chemistry calculations for material design.
method Develops a deep Gaussian process emulator for quantum calculations using a novel molecular descriptor.
result Demonstrates that the approach can be implemented using a small dataset for prediction of formation energy.
We introduce a new, high-throughput, synchronous, distributed, data-parallel, stochastic-gradient-descent learning algorithm. This algorithm uses amortized inference in a compute-cluster-specific, deep, generative, dynamical model to perform joint posterior predictive inference of the mini-batch gradient computation ti…
BayReL learns molecular interactions across multi-omics data.
problem Inferring meaningful interactions across diverse molecular data types.
method BayReL uses Bayesian representation learning with graph models to integrate multi-omics data.
result BayReL outperforms existing methods in inferring molecular interactions.
Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-con…
The study compares different scRNA sequencing methods using a high-dimensional dataset.
problem To identify unique characteristics of different scRNA sequencing methods.
method Quantitative comparison through clustering analysis of a high-dimensional dataset.
result Identifies unique characteristics associated with different scRNA sequencing methods.
Can one parallelize complex exploration exploitation tradeoffs? As an example, consider the problem of optimal high-throughput experimental design, where we wish to sequentially design batches of experiments in order to simultaneously learn a surrogate function mapping stimulus to response and identify the maximum of t…
Safe autonomous decisions made with machine learning predictions using Conformal Decision Theory.
problem Safe decisions from imperfect machine learning predictions.
method Conformal Decision Theory framework for producing safe decisions.
result Safe decisions with provable statistical guarantees of low risk.
PRETZEL optimizes machine learning prediction serving systems for better performance.
problem Low latency, high throughput, and graceful performance degradation under heavy load in prediction serving systems.
method Introducing a novel white box architecture enabling both end-to-end and multi-model optimizations.
result Average 5.5x reduction in 99th percentile latency, 25x reduction in memory footprint, and 4.7x increase in throughput compared to state-of-the-art approaches.
With the development of high-throughput technologies, principal component analysis (PCA) in the high-dimensional regime is of great interest. Most of the existing theoretical and methodological results for high-dimensional PCA are based on the spiked population model in which all the population eigenvalues are equal ex…
Paper uses DRL for automated power allocation in satellites.
problem Manual resource allocation is impractical for satellites with many power degrees of freedom.
method Continuous state and action spaces, Proximal Policy Optimization (PPO) algorithm.
result DRL shows promising results for minimum Unmet System Demand and power consumption.
Bayesian method discovers local causal relationships among genes from gene expression data.
problem Discovering gene regulatory relationships from gene expression data.
method Bayesian approach scoring covariance structures for triplets of normally distributed variables, incorporating background knowledge as priors.
result Stable and conservative posterior probability estimates of local causal structures.
ORRB enables fast, customizable rendering of robotics environments.
problem Fast and customizable rendering of robotics environments.
method Based on Unity3d and MuJoCo, optimized for cloud deployment.
result Visual domain randomization for improved simulation.
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new view…
The paper proposes a variational autoencoder for discrete data analysis.
problem Sparse, high-dimensional, and overdispersed discrete data analysis.
method Variational autoencoder based on negative-binomial distribution.
result The proposed models achieve significantly better performance on text analysis, collaborative filtering, and multi-label learning compared to state-of-the-art baselines.
We characterize and study variable importance (VIMP) and pairwise variable associations in binary regression trees. A key component involves the node mean squared error for a quantity we refer to as a maximal subtree. The theory naturally extends from single trees to ensembles of trees and applies to methods like rando…
New algorithm predicts geolocation of fungi samples with high accuracy.
problem Identifying the origin of biological material at crime scenes.
method Ensemble of deep neural network classifiers trained on Voronoi partitions.
result More than half of geolocation errors under 100 kilometers for continental analysis and nearly 90% accuracy for global analysis.
Bayesian method infers gene regulatory network structure from data.
problem Discovering local causal relationships in gene regulatory networks.
method Bayesian approach scoring covariance patterns with background priors.
result Stable and conservative posterior estimates of regulatory relationships.
scICML integrates multi-omics data from single cells using co-clustering.
problem High noise and sparsity in multi-omics data from single cells.
method Information-theoretic co-clustering-based multi-view learning.
result Improves clustering performance and provides biological insights.
ShadowSync separates background synchronization for scalable distributed training.
problem Reducing synchronization overhead in distributed training for high scalability.
method Separates synchronization from training and runs it in the background.
result Achieves both high throughput and excellent model quality at scale.