Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.

While spatial proteomics by fluorescence imaging has quickly become an essential discovery tool for researchers, fast and scalable methods to classify and embed single-cell protein distributions in such images are lacking. Here, we present the design and analysis of the results from the competition Human Protein Atlas - Single-Cell Classification hosted on the Kaggle platform. This represents a crowd-sourced competition to develop machine learning models trained on limited annotations to label single-cell protein patterns in fluorescent images. The particular challenges of this competition include class imbalance, weak labels and multi-label classification, prompting competitors to apply a wide range of approaches in their solutions. The winning models serve as the first subcellular omics tools that can annotate single-cell locations, extract single-cell features and capture cellular dynamics.

Author Correction: Analysis of the Human Protein Atlas Image Classification competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Analysis of the Human Protein Atlas Image Classification competition.

Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by ~20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.

Assessing the Performance of Models from the 2022 RSNA Cervical Spine Fracture Detection Competition at a Level I Trauma Center.

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To evaluate the performance of the top models from the RSNA 2022 Cervical Spine Fracture Detection challenge on a clinical test dataset of both noncontrast and contrast-enhanced CT scans acquired at a level I trauma center. Materials and Methods Seven top-performing models in the RSNA 2022 Cervical Spine Fracture Detection challenge were retrospectively evaluated on a clinical test set of 1,828 CT scans (1,829 series: 130 positive for fracture, 1,699 negative for fracture; 1,308 noncontrast, 521 contrast-enhanced) from 1,779 patients (mean age, 55.8 ± 22.1 years; 1,154 male). Scans were acquired without exclusion criteria over one year (January to December 2022) from the emergency department of a neurosurgical and level I trauma center. Model performance was assessed using area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. False positive and false negative cases were further analyzed by a neuroradiologist. Results Although all 7 models showed decreased performance on the clinical test set compared with the challenge dataset, the models maintained high performances. On noncontrast CT scans, the models achieved a mean AUC of 0.89 (range: 0.81-0.92), sensitivity of 67.0% (range: 30.9%-80.0%), and specificity of 92.9% (range: 82.1%-99.0%). On contrast-enhanced CT scans, the models had a mean AUC of 0.88 (range: 0.76-0.94), sensitivity of 81.9% (range: 42.7%-100.0%), and specificity of 72.1% (range: 16.4%-92.8%). The models identified 10 fractures missed by radiologists. False-positives were more common in contrast-enhanced scans and observed in patients with degenerative changes on noncontrast scans, while false-negatives were often associated with degenerative changes and osteopenia. Conclusion The winning models from the 2022 RSNA AI Challenge demonstrated a high performance for cervical spine fracture detection on a clinical test dataset, warranting further evaluation for their use as clinical support tools. ©RSNA, 2024.

Ribonanza: deep learning of RNA structure through dual crowdsourcing.

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 sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.