Walter Reade
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View article: Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography
Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography Open
The difficulty of particle picking in cryo-electron tomography remains a barrier to routine in situ structure determination. Machine learning is well-suited to overcome this bottleneck with efficient algorithms that generalize across molec…
View article: Learning to detect continuous gravitational waves: an open data-analysis competition
Learning to detect continuous gravitational waves: an open data-analysis competition Open
We report results of a public data-analysis challenge, hosted on the open data-science platform Kaggle, to detect simulated continuous gravitational-wave signals. These are weak signals from rapidly spinning neutron stars that remain undet…
View article: MotorBench: A Cryo-Electron Tomography Dataset of Bacterial Flagellar Motors for Testing Detection Algorithms
MotorBench: A Cryo-Electron Tomography Dataset of Bacterial Flagellar Motors for Testing Detection Algorithms Open
Understanding bacterial nanomachines like flagellar motors, which are crucial for pathogenic bacteria motility, is vital for microbiological and therapeutic research. Cryogenic electron tomography (cryo-ET) enables visualization of these s…
View article: Image segmentations produced by BAMF under the AIMI Annotations initiative
Image segmentations produced by BAMF under the AIMI Annotations initiative Open
The Imaging Data Commons (IDC)(https://imaging.datacommons.cancer.gov/) [1] connects researchers with publicly available cancer imaging data, often linked with other types of cancer data. Many of the collections have limited annotations du…
View article: Ribonanza: deep learning of RNA structure through dual crowdsourcing
Ribonanza: deep learning of RNA structure through dual crowdsourcing Open
Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequen…
View article: Challenge design roadmap
Challenge design roadmap Open
Challenges can be seen as a type of game that motivates participants to solve serious tasks. As a result, competition organizers must develop effective game rules. However, these rules have multiple objectives beyond making the game enjoya…
View article: CAFA-evaluator: a Python tool for benchmarking ontological classification methods
CAFA-evaluator: a Python tool for benchmarking ontological classification methods Open
We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the predict…
View article: CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods
CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods Open
We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the predict…
View article: A deep learning approach to photo–identification demonstrates high performance on two dozen cetacean species
A deep learning approach to photo–identification demonstrates high performance on two dozen cetacean species Open
Researchers can investigate many aspects of animal ecology through noninvasive photo–identification. Photo–identification is becoming more efficient as matching individuals between photos is increasingly automated. However, the convolution…
View article: Deep learning models for predicting RNA degradation via dual crowdsourcing
Deep learning models for predicting RNA degradation via dual crowdsourcing Open
View article: Deep learning models for predicting RNA degradation via dual crowdsourcing.
Deep learning models for predicting RNA degradation via dual crowdsourcing. Open
Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited …
View article: Deep learning models for predicting RNA degradation via dual crowdsourcing
Deep learning models for predicting RNA degradation via dual crowdsourcing Open
Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited …
View article: A community-powered search of machine learning strategy space to find NMR property prediction models
A community-powered search of machine learning strategy space to find NMR property prediction models Open
The rise of machine learning (ML) has created an explosion in the potential strategies for using data to make scientific predictions. For physical scientists wishing to apply ML strategies to a particular domain, it can be difficult to ass…
View article: The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification
The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification Open
The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Int…
View article: Laboratory earthquake forecasting: A machine learning competition
Laboratory earthquake forecasting: A machine learning competition Open
Earthquake prediction, the long-sought holy grail of earthquake science, continues to confound Earth scientists. Could we make advances by crowdsourcing, drawing from the vast knowledge and creativity of the machine learning (ML) community…
View article: A Criticism of Einstein and His Problem
A Criticism of Einstein and His Problem Open