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Commits on Apr 11, 2019

• Create README.md

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• add ingest

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• Pulls over my BigQuery-based tabfile parser / CVDI disease phenotyper.

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Commits on Apr 15, 2019

• When exclusions occur after enrollment but prior to disease occurrence,

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Commits on Apr 17, 2019

• Adding 2 notes:

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Commits on Apr 20, 2019

• Treat disease censoring like how phenotype censoring is treated,

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• Separate billing account from the database incantation.

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• When censoring, if the UK Biobank has used a nonsensical or unparseable

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Commits on Apr 22, 2019

• init

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Commits on Apr 23, 2019

• function to creatre a dev dataset for experimentation.

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• reads phenotype from database, converts to (sample_id, [list of sample_id dicts])

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• dataflow.py

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• Have Dataflow workers install our PyPI packages

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• Updating censor code to account for lost to follow up, updating the

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• Directory shuffling for packaging

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• Dataflow working with tensorize packaged. README added with how-to-run info.

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• Add more info to README

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Commits on Apr 24, 2019

• clean up

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• sampleid -> list(dict) for phenotypes on directrunner

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• sampleid -> list(dict) for 500 phenotype rows on dataflowrunner

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• sampleid -> list(dict) for 600k phenotype rows on dataflowrunner

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• sampleid -> list(dict) for 520M phenotype rows on dataflowrunner

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Commits on Apr 25, 2019

• only looking at limited fieldids in tensorization

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• tensorization for categorical fields part 1

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• Import hd5 constants

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Commits on Apr 26, 2019

• Move ML4CVD over (#1)

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• Update README.md

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• Update README.md

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• Categorical tensorization with DirectRunner

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• Categorical tensorization with DataflowRunner

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Commits on Apr 29, 2019

• Mini refactoring to also avoid explicit pickling of storage client

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• Fuse the last pipeline steps for efficiency

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• continuous tensor maps made from big query (#2)

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Commits on Apr 30, 2019

• Add continuous field tensorization

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Commits on May 1, 2019

• Fix bug in continuous field query. Make it easier to run for cat vs cont.

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• Script to merge hd5 file contents

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Commits on May 2, 2019

• env

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• arg parsing for merge_hd5s

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• PR clean up

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• Enable merge_hd5s.py script to take multiple group/source pairs

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• Merge remote-tracking branch 'origin/master' into tensorize_with_dataflow

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Commits on May 3, 2019

• Move dataflow pipeline option values to defines.py

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• Arrays of continuous variables (#4)

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• MRI pixel size (#3)

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Commits on May 5, 2019

• address PR feedback part-1

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• address PR feedback part-2

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Commits on May 6, 2019

• address PR feedback part-3

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• Merge remote-tracking branch 'origin/master' into tensorize_with_dataflow

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• Update README

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• Fix Dataflow breakage introduce with commandline arg parsing changes

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• Merge pull request #5 from broadinstitute/tensorize_with_dataflow

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• trying to unbury files (#7)

  

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• load, apply phecode mappings (#8)

  

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Commits on May 7, 2019

• Jupyter notebook script fixes (#18)

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Commits on May 8, 2019

• ml4cvd package (#20)

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Commits on May 9, 2019

• Saliency Maps for MRI models (#21)

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Commits on May 14, 2019

• Updates to VM boot image creation and documentation (#22)

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• Update README.md

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Commits on May 15, 2019

• Concats continuous tensor maps into one tensor map (#23)

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Commits on May 23, 2019

• Tensorization updates (#26)

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Commits on May 28, 2019

• Plot histograms of continuous field values from tensors (#27)

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Commits on May 31, 2019

• Comparison plot improvements (#28)

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Commits on Jun 4, 2019

• More stats on continuous tensor plots (#29)

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Commits on Jun 10, 2019

• Merge branch 'master' into jpp/feature-cvdi-disease

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• Adds SQL to materialize the HESIN and specially extracted date fields

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Commits on Jun 11, 2019

• Correlation tabulation (#31)

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• t-SNE Plots from models and scalar evaluators to avoid out of memory errors (#30)

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• Update analysis/phenotyping/cvdi/disease/DATES.md

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• Documenting the special case conditions+dates encompassed by

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• Removing errant comment.

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• Adds a bunch of comments to explain the meaning of various parts of the

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• Moving as per #33 (comment)

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Commits on Jun 14, 2019

• Adds arguments for missingness and a new categorical TensorMap (#34)

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Commits on Jun 16, 2019

• Merge branch 'master' into jpp/feature-cvdi-disease

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• Merge branch 'jpp/feature-cvdi-disease'

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Commits on Jun 21, 2019

• Update README.md

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Commits on Jun 25, 2019

• Continuous tensor heatmap (#35)

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Commits on Jun 26, 2019

• updating readme's, moving them around. CPU v of README working. (#32)

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Commits on Jul 17, 2019

• Update readme

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Commits on Jul 30, 2019

• Better t-SNE support & tensor editting (#36)

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• notebook for cleaning, plotting 12-lead ecgs (#38)

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Commits on Aug 6, 2019

• Add brain tensors (#40)

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Commits on Aug 9, 2019

• Brain DICOM tensorization (#39)

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Commits on Aug 20, 2019

• ECG coarse rhythms and long axis MRI (#41)

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Commits on Aug 21, 2019

• Handmade brain tmaps (#42)

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• Pb nd ecg building (#43)

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Commits on Aug 22, 2019

• Updates the ukbb bulk file downloader tool (#37)

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Commits on Aug 29, 2019

• Flair and susceptibility tensorization (#46)

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• Tensor from file function! (#49)

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Commits on Aug 30, 2019

• fix recovery tmap

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Commits on Sep 3, 2019

• Add optimizer option to make_multimodal_to_multilabel_model (#51)

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Commits on Sep 4, 2019

• Retensorize bike ecg (#48)

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Commits on Sep 6, 2019

• Sf mixup (#45)

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Commits on Sep 9, 2019

• ROC curves show counts (#52)

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Commits on Sep 16, 2019

• New Model Factory (#55)

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• Retensorize exercise ecg part 2 (#54)

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Commits on Sep 17, 2019

• small fix (#56)

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• Add Brain volume tensor maps (#53)

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Commits on Sep 18, 2019

• Pool layer cycle fix (#59)

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Commits on Sep 20, 2019

• Add optimizer option to make_multimodal_multi_task_new (#60)

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• tensor_from_file (#57)

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Commits on Sep 24, 2019

• Small bug fix (#61)

  

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Commits on Sep 27, 2019

• Variational auto encoder notebook fix (#58)

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Commits on Oct 7, 2019

• Latent space inference, more tensor maps (#62)

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Commits on Oct 17, 2019

• Fix the broken exercise ECG parsing (#63)

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• Suppress errors in training and testing (#64)

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Commits on Oct 22, 2019

• Nd hyperopt update (#65)

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Commits on Oct 23, 2019

• External holdout sets and Brain tensor map updates (#66)

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Commits on Oct 29, 2019

• Siamese networks (#69)

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Commits on Nov 5, 2019

• Tensormaps for LVH criteria and ECG resting plots (#67)

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Commits on Nov 6, 2019

• Bug fixes (#72)

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Commits on Nov 8, 2019

• Faster training! (#70)

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Commits on Nov 14, 2019

• Ingest readme updates (#74)

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Commits on Nov 19, 2019

• Nd breakup multitask worker (#77)

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• Notebook cleanup (#75)

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Commits on Nov 20, 2019

• update tests (#76)

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Commits on Nov 25, 2019

• changed how loading frozen model weights works (#78)

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• Nd fix infer which i broke (#79)

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Commits on Dec 4, 2019

• Add long axis MRI notebook (#82)

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• Nifty brainz (#80)

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Commits on Dec 6, 2019

• disk fix

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Commits on Dec 16, 2019

• notebook to inspect tmaps satisfying predicates (#83)

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Commits on Jan 7, 2020

• Nd inference tensor from file (#84)

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• Initial commit of Terra docker image. (#85)

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Commits on Jan 13, 2020

• removed extra line

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Commits on Jan 14, 2020

• Saliency map recipes for MRI and ECG (#89)

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Commits on Jan 22, 2020

• Initial commit of dicom plotting code. (#91)

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• 3-D MRI Orientation (#81)

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• Daisy chain TensorMap parents to learn trees (#98)

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• added to plot_scatter (#97)

  

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• Tensorize annotated PNGs (#96)

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• parent fix (#99)

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Commits on Jan 27, 2020

• Nd simple variational (#102)

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Commits on Jan 28, 2020

• Make inference recipes work for VAEs (#105)

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Commits on Jan 30, 2020

• vae visualization (#109)

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• Adding BSDv3 License (#106)

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• Expanding project description in README. (#107)

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Commits on Feb 3, 2020

• Nd inference update (#115)

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Commits on Feb 4, 2020

• TensorMap interpretation field (#101)

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Commits on Feb 5, 2020

• Add brain MRI visualization. (#108)

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Commits on Feb 7, 2020

• Pd small fix for tensor_writer_ukbb to work on GPU-less machines (#118)

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Commits on Feb 10, 2020

• test time warning and _build_tensor_from_file bug fix (#122)

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• Effectless model refactor (#117)

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Commits on Feb 11, 2020

• model tests (#119)

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Commits on Feb 13, 2020

• minimal git secrets provider for google cloud keys (#130)

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Commits on Feb 20, 2020

• Cr discretization interpretation (#124)

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Commits on Feb 21, 2020

• fixes shuffling bug (#137)

  

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Commits on Feb 24, 2020

• Terra exercise ecg (#128)

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• ECG demo notebook - annotate samples using widgets (#132)

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Commits on Feb 25, 2020

• augmentations field for TensorMap (#125)

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Commits on Feb 28, 2020

• TensorFlow 2.0! (#94)

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Commits on Mar 4, 2020

• Explore mode for recipes (#135)

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Commits on Mar 5, 2020

• Sf ecg segment (#145)

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• hot fix

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• Normalizer class added (#148)

  ndiamant

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• BroadE Notebook for ML Workshop (#133)

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Commits on Mar 11, 2020

• skip paths (#154)

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  ndiamant

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Commits on Mar 12, 2020

• Type annotation fix (#162)

  ndiamant

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Commits on Mar 16, 2020

• Bounding boxes as the beginning of TensorMap Meshes (#131)

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Commits on Mar 18, 2020

• Small fix of normalization (#172)

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• bug fixes (#173)

  ndiamant

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Commits on Mar 19, 2020

• Update issue templates

  

  Erik Reinertsen

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Commits on Mar 20, 2020

• bugs fixed (#179)

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  ndiamant

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Commits on Mar 23, 2020

• Tensor Maps on Partners data (#171)

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• Use tensor_flow_addons (#170)

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Commits on Mar 24, 2020

• pre-commit hooks (#129)

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Commits on Mar 25, 2020

• always plot find learning rate (#193)

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Commits on Apr 3, 2020

• sample weight (#198)

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• tensorize Partners ECG XMLs → HD5, and relevant documentation (#175)

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Commits on Apr 6, 2020

• bug fixed for multitask models (#205)

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Commits on Apr 7, 2020

• retensorize partners (#196)

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Commits on Apr 9, 2020

• More Survival Models (#206)

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Commits on Apr 10, 2020

• TMaps for learning STS cardiac surgery outcomes from Partners ECGs (#203)

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Commits on Apr 14, 2020

• tweaks to partners tensorize and ingest scripts (#210)

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Commits on Apr 20, 2020

• Terra notebooks can also run in the ml4cvd environment. (#177)

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Commits on Apr 22, 2020

• fix infer bug (#215)

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Commits on Apr 23, 2020

• update partners tmaps to use new hd5 structure (#212)

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Commits on Apr 24, 2020

• quick fix for _newest (#228)

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Commits on Apr 25, 2020

• remove empty line at bottom of issue template

  

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Commits on Apr 27, 2020

• calls build_cardiac_surgery_tensor_maps in arguments to load the correct TMaps (#223)

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• adds _outcome_channels() func and constant CARDIAC_SURGERY_OUTCOMES_CSV (#239)

  

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Commits on Apr 28, 2020

• Update Tensor maps for partners with dynamic ECGs (#238)

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• Output TSVs compatible with genetic association software (#227)

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Commits on May 1, 2020

• Surgery cohort ECGs near event (#247)

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• clinical and full ECG view from partners ecg (#211)

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  StevenSong

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• True epoch stats (#248)

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• ignore build folder from pip 20.1 (#249)

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• comment out in progress language tmaps work (#250)

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Commits on May 2, 2020

• rounds df to two decimals; report % not fraction (#240)

  

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Commits on May 7, 2020

• cross reference mode (#235)

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Commits on May 13, 2020

• model factory refactor (#146)

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• get_train_valid_test_paths refactor (#255)

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Commits on May 20, 2020

• STS TMaps and time_series_lookup (#275)

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Commits on May 21, 2020

• _tensors_to_df overhaul and voltage QC categorical TMaps (#274)

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Commits on May 22, 2020

• ref_start -> ref_time in explore (#285)

  

  Erik Reinertsen

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Commits on May 28, 2020

• enhancement to date formatting function. Ref #288 (#300)

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• --embed_visualization arg to control t-SNE or UMAP plots. Fixes #268. (#298)

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  Erik Reinertsen

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• Infer MRN column from sample_csv. Fixes #287. (#301)

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  Erik Reinertsen

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• fix typo (#303)

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  StevenSong

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Commits on May 29, 2020

• Remove unused res_layers argument (#304)

  ndiamant

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Commits on May 30, 2020

• removes sort_csv & error cols from explore. Fixes #236. Fixes #284 (#295)

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Commits on May 31, 2020

• partners ecg sampling frequency metadata and tmaps (#292)

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Commits on Jun 1, 2020

• Small fix to run jupyter notebooks on cpu only (#310)

  paolodi

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• Use TMAPS for ECG visualization input (#281)

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Commits on Jun 3, 2020

• Better generator stats (#302)

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• Plots histograms of continuous tensors in explore mode (#311)

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• cross reference multiple time windows (#307)

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Commits on Jun 4, 2020

• Reuse the ml4cvd dependencies file to build the custom Terra image. (#312)

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Commits on Jun 18, 2020

• partners tmaps time selection and cardiac surgery tmap rework (#309)

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  StevenSong

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  Erik Reinertsen

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• fixes in tensor generator (#327)

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  StevenSong

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Commits on Jun 19, 2020

• ML4CVD on MNIST (#294)

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Commits on Jun 24, 2020

• do not crash if sts data not found (#336)

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  StevenSong

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• define specific filter sizes per convolutional layer (#322)

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Commits on Jun 25, 2020

• switch explore from multiprocess to multiprocessing (#335)

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Commits on Jun 29, 2020

• Fix UKB resting ECG plots (#338)

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Commits on Jul 1, 2020

• infer metrics when dynamically reshaping time series tensor maps (#343)

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• explore can check multidimensional TensorMaps for failure (#337)

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  ndiamant

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• infer mrn column header. Closes #331 (#351)

  

  Erik Reinertsen

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Commits on Jul 2, 2020

• generated output is owned by ${USER} instead of root (#344)

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Commits on Jul 4, 2020

• Rehaul Partners Plotting (#315)

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Commits on Jul 6, 2020

• explore multi works with validators now

  

  ndiamant

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• bug fix. What happens for None shapes still to be addressed

  

  ndiamant

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• intersection bug fix

  

  ndiamant

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