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Commits on Dec 12, 2023

• Adding new learning objective: predict all tokens in next visit in one go. (includes token for time to next visit)

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Commits on Dec 11, 2023

• Adding GTP to simulation study pilot

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Commits on Dec 8, 2023

• Initial implementation of GPT

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Commits on Dec 7, 2023

• Merge pull request #8 from OHDSI/sim_eval

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• Fixing another error

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• Fix error when training

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• Adding simple regression model as baseline

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Commits on Dec 6, 2023

• Also grouping results by pretrain_epoch

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Commits on Dec 1, 2023

• Fixing evaluation output file

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• Forgot to pass through checkpoint_every in evaluator.

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• Merge branch 'sim_eval' of https://github.com/OHDSI/Apollo into sim_eval

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• Add checkpoint_every option to save disk space

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• Requiring visit concept tokenizer when using visit concept embedding

  

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Commits on Nov 30, 2023

• Attempting to fix GA build

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• Fix unit tests

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• Defining a pilot simulation study

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Commits on Nov 28, 2023

• Fix typo

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• Adding option to select specific epoch of pretrained model, and limit number of batches in fine-tuned model

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Commits on Nov 23, 2023

• Combining evaluation results across runs into single CSV

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Commits on Nov 21, 2023

• Adding support for MPS

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Commits on Nov 17, 2023

• More work on seperating inputs from learning objectives

  

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Commits on Nov 14, 2023

• Switcing from ini to yaml config files. Implementing meta-evaluation (evaluation across many model settings)

  

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• Not writing configs and tokenizers when evaluating model only.

  

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Commits on Nov 10, 2023

• Removing debug code

  

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• Implemented fine-tuning and testing of single prediction example

  

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• Allowing user to limit number of simulated prediction tasks

  

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• Applying settings pattern to simulator

  

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Commits on Oct 30, 2023

• Switching label prediction to logistic regression. Computing AUC, AUPRC and Brier score

  

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• Work on simulation evaluation

  

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Commits on Oct 27, 2023

• Passing forward settings used to generate model, to avoid mistakes when fine-tuning

  

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Commits on Sep 22, 2023

• Adding (optional) embedding concatenation as alternative to sum

  

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• Fixing typo in name of visit token decoder

  

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Commits on Sep 15, 2023

• Added missing parameter to TimeEmbedding

  

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• Minor changes

  

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• Adding ability to use pre-trained model

  

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