Supervised Uncertainty Quantification for Segmentation with Multiple Annotations

The accurate estimation of predictive uncertainty carries importance in medical scenarios such as lung node segmentation. Unfortunately, most existing works on predictive uncertainty do not return calibrated uncertainty estimates, which could be used in practice. In this work we exploit multi-grader annotation variability as a source of 'groundtruth' aleatoric uncertainty, which can be treated as a target in a supervised learning problem. We combine this groundtruth uncertainty with a Probabilistic U-Net and test on the LIDC-IDRI lung nodule CT dataset and MICCAI2012 prostate MRI dataset. We find that we are able to improve predictive uncertainty estimates. We also find that we can improve sample accuracy and sample diversity. In real-world applications, our method could inform doctors about the confidence of the segmentation results.Comment: MICCAI 2019. Fixed a few typo

PatchCamelyon (PCam)

PCam packs the clinically-relevant task of metastasis detection into a straight-forward binary image classification task, akin to CIFAR-10 and MNIST. Models can easily be trained on a single GPU in a couple hours, and achieve competitive scores in the Camelyon16 tasks of tumor detection and whole-slide image diagnosis. Furthermore, the balance between task-difficulty and tractability makes it a prime suspect for fundamental machine learning research on topics as active learning, model uncertainty, and explainability

torchmd/torchmd-net: 0.14.0

<h2>What's Changed</h2> <ul> <li>Refactoring memmapped dataset classes by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/256</li> <li>correct paths for processed files. bugfix for last PR by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/258</li> <li>added comp6v2 dataset by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/257</li> <li>Unique COMP6 GDB molecule IDs by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/262</li> <li>Adding vector feature cutoff to ET by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/260</li> <li>Genentech torsions by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/259</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/torchmd/torchmd-net/compare/0.13.0...0.14.0</p&gt

torchmd/torchmd-net: 0.15.2

<p>Another minor hotfix for CI tests. <strong>Full Changelog</strong>: https://github.com/torchmd/torchmd-net/compare/0.15.1...0.15.2</p&gt

torchmd/torchmd-net: Release 0.2.7

<p>Release before updating Lightning dependency</p> What's Changed <ul> <li>Fix neighbor extension compilation looking for non-existent backwards.cu by @RaulPPelaez in <a href="https://github.com/torchmd/torchmd-net/pull/204">https://github.com/torchmd/torchmd-net/pull/204</a></li> <li>Remove dtype parameter, use previously existing "precision" instead by @RaulPPelaez in <a href="https://github.com/torchmd/torchmd-net/pull/208">https://github.com/torchmd/torchmd-net/pull/208</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/torchmd/torchmd-net/compare/0.2.6...0.2.7">https://github.com/torchmd/torchmd-net/compare/0.2.6...0.2.7</a></p&gt

torchmd/torchmd-net: 0.15.1

<p>Minor fix for test https://github.com/torchmd/torchmd-net/commit/1bbb03aa36ea173e103d155aafb038b7d61db29d .</p> <p><strong>Full Changelog</strong>: https://github.com/torchmd/torchmd-net/compare/0.15.0...0.15.1</p&gt

torchmd/torchmd-net: 0.3.0

This release bumps all dependencies to be up to date with the latest conda-forge versions. Also changes the torch extension compilation so that it happens during installation. What's Changed Updating to Lightning 2.0 by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/210 Compile torch extension in setup.py by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/216 Full Changelog: https://github.com/torchmd/torchmd-net/compare/0.2.7...0.3.

torchmd/torchmd-net: 0.8.1

<h2>What's Changed</h2> <ul> <li>Add option to run External through a CUDA graph by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/222</li> <li>Fix trying to detach a float number in LNNP by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/233</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/torchmd/torchmd-net/compare/0.8.0...0.8.1</p&gt

torchmd/torchmd-net: 2.1.0

<h2>What's Changed</h2> <ul> <li>add arg to MemmappedDataset by @AntonioMirarchi in https://github.com/torchmd/torchmd-net/pull/295</li> <li>Add custom training loop to the docs by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/298</li> <li>Add SPICE 1.1.4, remove leftover remove_ref_energy in some datasets by @RaulPPelaez in https://github.com/torchmd/torchmd-net/pull/303</li> <li>Added support for ensemble models by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/308</li> <li>Support for ensemble model zip files by @stefdoerr in https://github.com/torchmd/torchmd-net/pull/311</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/torchmd/torchmd-net/compare/2.0.0...2.1.0</p&gt

torchmd/torchmd-net: Release 0.2.6

Neural network potentials based on graph neural networks and equivariant transformer