# Latest

**URL:** https://discourse.cogstack.org/latest.md

[Latest](https://discourse.cogstack.org/latest.md) · [Categories](https://discourse.cogstack.org/categories.md) · [Tags](https://discourse.cogstack.org/tags.md)

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## [Welcome to Discourse](https://discourse.cogstack.org/t/welcome-to-discourse/7)

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**Author:** [@system](https://discourse.cogstack.org/u/system)\
**Replies:** 0\
**Last updated:** [October 27, 2021, 12:23pm UTC](https://discourse.cogstack.org/t/welcome-to-discourse/7 "2021-10-27T12:23:51Z")

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This is an Open Source Project so please be mindful that like in any other project of this kind there is no obligation to answer all requests for help. However, we want to encourage you to ask for help whenever you thin…

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## [Model download links broken — "Application Not Authorized" and "Bad Gateway" (502)](https://discourse.cogstack.org/t/model-download-links-broken-application-not-authorized-and-bad-gateway-502/407)

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**Author:** [@Ptoski31](https://discourse.cogstack.org/u/Ptoski31)\
**Replies:** 2\
**Last updated:** [July 9, 2026, 9:16am UTC](https://discourse.cogstack.org/t/model-download-links-broken-application-not-authorized-and-bad-gateway-502/407 "2026-07-09T09:16:10Z")

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Hi all, I’m trying to download a pre-built MedCAT model pack (SNOMED / UMLS) using my UMLS licence, but both download links in the GitHub README appear to be broken: The interactive login link ( UMLS Metathesaurus Br…

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## [TestTrainSplitter silently drops documents instead of adding to train set](https://discourse.cogstack.org/t/testtrainsplitter-silently-drops-documents-instead-of-adding-to-train-set/404)

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**Author:** [@ollielloyd](https://discourse.cogstack.org/u/ollielloyd)\
**Replies:** 1\
**Last updated:** [July 9, 2026, 7:51am UTC](https://discourse.cogstack.org/t/testtrainsplitter-silently-drops-documents-instead-of-adding-to-train-set/404 "2026-07-09T07:51:33Z")

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Description When using make\_mc\_train\_test (or test\_size \> 0 in train\_supervised\_raw), the TestTrainSplitter.split() method seems to silently drops the majority of documents rather than assigning them to the train set. T…

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## [Manual meta-task selection overwritten when using model pack without MetaCAT models](https://discourse.cogstack.org/t/manual-meta-task-selection-overwritten-when-using-model-pack-without-metacat-models/403)

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**Author:** [@ollielloyd](https://discourse.cogstack.org/u/ollielloyd)\
**Replies:** 4\
**Last updated:** [June 27, 2026, 2:53pm UTC](https://discourse.cogstack.org/t/manual-meta-task-selection-overwritten-when-using-model-pack-without-metacat-models/403 "2026-06-27T14:53:51Z")

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\### Summary In MedCAT Trainer 3.6.1, manually selected meta-annotation tasks are automatically cleared when a project uses a model pack that does not contain MetaCAT models. This prevents users from setting up manual me…

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## [New Synonyms and train count not updating + general query](https://discourse.cogstack.org/t/new-synonyms-and-train-count-not-updating-general-query/384)

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**Author:** [@KenMMUH](https://discourse.cogstack.org/u/KenMMUH)\
**Replies:** 7\
**Last updated:** [May 12, 2026, 10:54am UTC](https://discourse.cogstack.org/t/new-synonyms-and-train-count-not-updating-general-query/384 "2026-05-12T10:54:14Z")

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Summary: version 2.5.3 of medcat. Added a synonym for the CUI for acute kidney injury in medcattrainer. Trained model, saved new version. aki added was added as synonym but it has a train count of 0 (even though it was i…

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## [Adding custom concepts / synonyms to cat](https://discourse.cogstack.org/t/adding-custom-concepts-synonyms-to-cat/377)

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**Author:** [@cleu0310](https://discourse.cogstack.org/u/cleu0310)\
**Replies:** 8\
**Last updated:** [May 11, 2026, 8:41am UTC](https://discourse.cogstack.org/t/adding-custom-concepts-synonyms-to-cat/377 "2026-05-11T08:41:34Z")

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I am working in an area where a lot of slang and jargon are used. I am trying to add these terms to an existing MedCAT model using add\_and\_train\_concepts() without providing a spacy\_doc, since I don’t have annotated trai…

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## [MedCAT Trainer -- cannot export JSON CUI filter](https://discourse.cogstack.org/t/medcat-trainer-cannot-export-json-cui-filter/382)

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**Author:** [@ollielloyd](https://discourse.cogstack.org/u/ollielloyd)\
**Replies:** 1\
**Last updated:** [May 11, 2026, 8:36am UTC](https://discourse.cogstack.org/t/medcat-trainer-cannot-export-json-cui-filter/382 "2026-05-11T08:36:15Z")

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When trying to download a concerpt filter JSON from the concepts tab I get this error: \[medcattrainer\] Internal Server Error: /api/generate-concept-filter-json/ \[medcattrainer\] Traceback (most recent call last): \[medcat…

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## [MedCAT Trainer issues -- can't submit annotations as irrelevant](https://discourse.cogstack.org/t/medcat-trainer-issues-cant-submit-annotations-as-irrelevant/381)

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**Author:** [@ollielloyd](https://discourse.cogstack.org/u/ollielloyd)\
**Replies:** 1\
**Last updated:** [May 11, 2026, 8:30am UTC](https://discourse.cogstack.org/t/medcat-trainer-issues-cant-submit-annotations-as-irrelevant/381 "2026-05-11T08:30:51Z")

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Hi, for background I mainly use R for doing audit work but am using MedCAT to perform NER+L to SNOMED concepts on a list of free text diagnosis strings, which form a subsection of our infectious diseases consult notes, t…

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## [Unable to save model from trainer](https://discourse.cogstack.org/t/unable-to-save-model-from-trainer/378)

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**Author:** [@TKaplan](https://discourse.cogstack.org/u/TKaplan)\
**Replies:** 3\
**Last updated:** [April 7, 2026, 2:49pm UTC](https://discourse.cogstack.org/t/unable-to-save-model-from-trainer/378 "2026-04-07T14:49:24Z")

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I’m getting the below error (AttributeError: 'NoneType' object has no attribute 'cdb\_file') when attemping to save a model from “Save Model” button on the MedCAT trainer landing page, following a bunch of submitted annot…

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## [Using MedCAT Trainer without internet access](https://discourse.cogstack.org/t/using-medcat-trainer-without-internet-access/376)

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**Author:** [@cleu0310](https://discourse.cogstack.org/u/cleu0310)\
**Replies:** 2\
**Last updated:** [March 23, 2026, 12:48am UTC](https://discourse.cogstack.org/t/using-medcat-trainer-without-internet-access/376 "2026-03-23T00:48:42Z")

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Hi, I am building a MedCAT pipeline in a safe e-research environment that blocks any access to the internet. Is there any way I can use the MedCAT trainer in an enclosed environment? My understanding is that it requires…

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## [Cogstack-NiFi documentation](https://discourse.cogstack.org/t/cogstack-nifi-documentation/374)

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**Author:** [@jmw](https://discourse.cogstack.org/u/jmw)\
**Replies:** 1\
**Last updated:** [December 9, 2025, 10:58am UTC](https://discourse.cogstack.org/t/cogstack-nifi-documentation/374 "2025-12-09T10:58:25Z")

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I’ve just deployed cogstack. I had some problems with the documentation, though: In the prerequisites, it says to run cd deploy && git-update-submodules. git-update-submodules isn’t a command. I wonder if the author h…

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## [New publicly available MedCAT models](https://discourse.cogstack.org/t/new-publicly-available-medcat-models/373)

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**Author:** [@mart.ratas](https://discourse.cogstack.org/u/mart.ratas)\
**Replies:** 2\
**Last updated:** [October 20, 2025, 8:40am UTC](https://discourse.cogstack.org/t/new-publicly-available-medcat-models/373 "2025-10-20T08:40:11Z")

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Hello everyone, With the semi recent release of MedCAT v2 we figured it’s finally time to release a few newer publicly available Snomed models. These are available through the download link in the README. Or just here d…

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## [How to map SNOMED IDs to UMLS Semantic Types](https://discourse.cogstack.org/t/how-to-map-snomed-ids-to-umls-semantic-types/340)

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**Author:** [@SunshineAndRain](https://discourse.cogstack.org/u/SunshineAndRain)\
**Replies:** 3\
**Last updated:** [October 7, 2025, 11:20am UTC](https://discourse.cogstack.org/t/how-to-map-snomed-ids-to-umls-semantic-types/340 "2025-10-07T11:20:03Z")

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I am currently using MedCAT with the SNOMED International (Full SNOMED modelpack trained on MIMIC-III) model. The extracted entities are of the following form: 'pretty\_name': 'Diverticulitis', 'cui': '18126004', 'ty…

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## [Config.general.show\_nested\_entities is not working (with fix proposed)](https://discourse.cogstack.org/t/config-general-show-nested-entities-is-not-working-with-fix-proposed/371)

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**Author:** [@pisong](https://discourse.cogstack.org/u/pisong)\
**Replies:** 4\
**Last updated:** [October 2, 2025, 11:41am UTC](https://discourse.cogstack.org/t/config-general-show-nested-entities-is-not-working-with-fix-proposed/371 "2025-10-02T11:41:00Z")

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Hi there. My name is Dr Pi Songsiritat. I am a GP from Australia. I am trying to make use of this wonderful project in my day-to-day work (so much thanks for making it open source). I have just come across an issue that …

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## [Error Report: Training Meta Annotations with CogStack Scripts + MedCAT](https://discourse.cogstack.org/t/error-report-training-meta-annotations-with-cogstack-scripts-medcat/370)

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**Author:** [@Samora](https://discourse.cogstack.org/u/Samora)\
**Replies:** 2\
**Last updated:** [September 17, 2025, 9:10am UTC](https://discourse.cogstack.org/t/error-report-training-meta-annotations-with-cogstack-scripts-medcat/370 "2025-09-17T09:10:19Z")

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Error Report: Training Meta Annotations with CogStack Scripts + MedCAT Environment MedCAT version: 1.16.0 Python version: 3.10 Workflow: Training meta\_model using Cogstack scripts and project-exported annotations…

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## [Downloading SNOMED model for MedCAT 1.16.0](https://discourse.cogstack.org/t/downloading-snomed-model-for-medcat-1-16-0/368)

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**Author:** [@Lpasquarelli](https://discourse.cogstack.org/u/Lpasquarelli)\
**Replies:** 2\
**Last updated:** [August 13, 2025, 2:33pm UTC](https://discourse.cogstack.org/t/downloading-snomed-model-for-medcat-1-16-0/368 "2025-08-13T14:33:07Z")

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I am using medcat 1.16.0, but the only snomed model I could find is 1.2.dev361 version. I was wondering if anyone knows how to get the latest snomed model for medcat 1.16.0? Context: This link is where I found the snome…

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## [Downloading UMLS Full Model](https://discourse.cogstack.org/t/downloading-umls-full-model/363)

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**Author:** [@Angrymuffin](https://discourse.cogstack.org/u/Angrymuffin)\
**Replies:** 5\
**Last updated:** [June 23, 2025, 3:01am UTC](https://discourse.cogstack.org/t/downloading-umls-full-model/363 "2025-06-23T03:01:43Z")

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I’m trying to download the UMLS Full model from here CogStack/MedCAT: Medical Concept Annotation Tool. I tried clicking on the link UMLS Metathesaurus Browser and signing in with my UMLS license to download the Full mode…

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## [Medcat KCL website down](https://discourse.cogstack.org/t/medcat-kcl-website-down/350)

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**Author:** [@jxz](https://discourse.cogstack.org/u/jxz)\
**Replies:** 5\
**Last updated:** [June 20, 2025, 2:54pm UTC](https://discourse.cogstack.org/t/medcat-kcl-website-down/350 "2025-06-20T14:54:12Z")

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I tried to download the SNOMED-CT model after authenticating through the NIH but https://medcat.rosalind.kcl.ac.uk/ is down (I got a Service Unavailable error). Were the downloads moved somewhere else or is the site temp…

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## [MedCAT French model only matches exact terms - accuracy similarity always 1](https://discourse.cogstack.org/t/medcat-french-model-only-matches-exact-terms-accuracy-similarity-always-1/353)

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**Author:** [@thdiot](https://discourse.cogstack.org/u/thdiot)\
**Replies:** 7\
**Last updated:** [June 8, 2025, 3:21pm UTC](https://discourse.cogstack.org/t/medcat-french-model-only-matches-exact-terms-accuracy-similarity-always-1/353 "2025-06-08T15:21:46Z")

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Hello, I recently discovered MedCAT with great interest, and I would like to use it for a research project involving a French psychiatric EHR. I managed to create a model that extracts concepts with reasonably good rele…

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## [Overlap between datasets for training and evaluation](https://discourse.cogstack.org/t/overlap-between-datasets-for-training-and-evaluation/357)

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**Author:** [@jxz](https://discourse.cogstack.org/u/jxz)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 10:00am UTC](https://discourse.cogstack.org/t/overlap-between-datasets-for-training-and-evaluation/357 "2025-05-22T10:00:11Z")

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I’m in the process of evaluating the performance of our own MedCAT model and I’m trying to understand how I should split my dataset for evaluating the performance of my model after both unsupervised and supervised learni…

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## [Snomed relationships](https://discourse.cogstack.org/t/snomed-relationships/301)

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**Author:** [@Jakub\_mitura](https://discourse.cogstack.org/u/Jakub_mitura)\
**Replies:** 7\
**Last updated:** [May 22, 2025, 7:41am UTC](https://discourse.cogstack.org/t/snomed-relationships/301 "2025-05-22T07:41:41Z")

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Hello MedCat is excellent in snomed entity recognition but is there a way to use it (or some other tool) in order to extract snomed entity relationships between entities?

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## [Re using Vocabulary files](https://discourse.cogstack.org/t/re-using-vocabulary-files/354)

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**Author:** [@jxz](https://discourse.cogstack.org/u/jxz)\
**Replies:** 1\
**Last updated:** [May 7, 2025, 9:08am UTC](https://discourse.cogstack.org/t/re-using-vocabulary-files/354 "2025-05-07T09:08:49Z")

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I got access to your “SNOMED INT enriched with UMLS and trained unsupervised on MIMIC-III” model. Just to be sure, I want to confirm that it is alright to use its vocabulary to build a new model alongside our existing …

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## [MetaCAT - Issue with training when there's more than 2 output classes](https://discourse.cogstack.org/t/metacat-issue-with-training-when-theres-more-than-2-output-classes/351)

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**Author:** [@Yoshi](https://discourse.cogstack.org/u/Yoshi)\
**Replies:** 5\
**Last updated:** [May 1, 2025, 7:59am UTC](https://discourse.cogstack.org/t/metacat-issue-with-training-when-theres-more-than-2-output-classes/351 "2025-05-01T07:59:43Z")

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As above, I keep getting the error ‘Target 2 is out of bounds’ when trying to train a MetaCAT model with 3 possible outputs. From this thread, IndexError: Target 2 is out of bounds - #12 by Vijaya\_kumar - vision - PyT…

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## [MetaCAT with grid search](https://discourse.cogstack.org/t/metacat-with-grid-search/71)

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**Author:** [@Yoshi](https://discourse.cogstack.org/u/Yoshi)\
**Replies:** 6\
**Last updated:** [April 25, 2025, 1:56pm UTC](https://discourse.cogstack.org/t/metacat-with-grid-search/71 "2025-04-25T13:56:21Z")

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Does anyone have experience of using a grid search for hyperparameter tuning of a MetaCAT model?

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## [Public models for meta annotations](https://discourse.cogstack.org/t/public-models-for-meta-annotations/42)

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**Author:** [@sangeetabose](https://discourse.cogstack.org/u/sangeetabose)\
**Replies:** 5\
**Last updated:** [April 16, 2025, 1:15pm UTC](https://discourse.cogstack.org/t/public-models-for-meta-annotations/42 "2025-04-16T13:15:28Z")

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Hi We have used the published model for ‘status’ meta annotation. Are public models available for the other contexts like experiencer and temporality as well. Thanks Sangeeta

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## [MedCATtrainer installation brings up medcattrainer\_medcattrainer-bg-process\_1 with errors](https://discourse.cogstack.org/t/medcattrainer-installation-brings-up-medcattrainer-medcattrainer-bg-process-1-with-errors/334)

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**Author:** [@elenaP](https://discourse.cogstack.org/u/elenaP)\
**Replies:** 3\
**Last updated:** [January 14, 2025, 11:09am UTC](https://discourse.cogstack.org/t/medcattrainer-installation-brings-up-medcattrainer-medcattrainer-bg-process-1-with-errors/334 "2025-01-14T11:09:17Z")

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I have just pulled the latest Trainer version from Github. (The same error was encoutered before the most recent github upgrade - 2.17.4). Gettign the container up returns the following error. (base) elenapurcaru@rhmmed…

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## [Error messages when uploading current UMLS full model to MedCATrainer](https://discourse.cogstack.org/t/error-messages-when-uploading-current-umls-full-model-to-medcatrainer/338)

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**Author:** [@Samuellim](https://discourse.cogstack.org/u/Samuellim)\
**Replies:** 5\
**Last updated:** [January 13, 2025, 9:45am UTC](https://discourse.cogstack.org/t/error-messages-when-uploading-current-umls-full-model-to-medcatrainer/338 "2025-01-13T09:45:42Z")

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Hello, I am facing this problem with uploading the current UMLS full model to MedCATrainer. I have been trying to upload the model pack to the admin Django app, but to no avail and have encountered the errors below. The…

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## [Could Someone Give me Advice for Implementing CogStack in a Large Healthcare System?](https://discourse.cogstack.org/t/could-someone-give-me-advice-for-implementing-cogstack-in-a-large-healthcare-system/327)

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**Author:** [@Elizashahh](https://discourse.cogstack.org/u/Elizashahh)\
**Replies:** 1\
**Last updated:** [January 6, 2025, 5:34pm UTC](https://discourse.cogstack.org/t/could-someone-give-me-advice-for-implementing-cogstack-in-a-large-healthcare-system/327 "2025-01-06T17:34:21Z")

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Hello there, I am involved in a project where we are planning to implement CogStack within a large healthcare system that serves multiple hospitals and clinics. Our goal is to enhance our clinical data processing capabi…

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## [Cat.train\_supervised\_from\_json suggested setup](https://discourse.cogstack.org/t/cat-train-supervised-from-json-suggested-setup/325)

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**Author:** [@lw\_serenic](https://discourse.cogstack.org/u/lw_serenic)\
**Replies:** 1\
**Last updated:** [August 22, 2024, 3:04pm UTC](https://discourse.cogstack.org/t/cat-train-supervised-from-json-suggested-setup/325 "2024-08-22T15:04:51Z")

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Hello, after reading both the tutorials and the paper I noticed that the train setup in the MedCATtutorials set the train\_from\_false\_positives as False so do the devalue\_others variable (which I try to find add\_name to n…

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## [Why my post has been hidden?](https://discourse.cogstack.org/t/why-my-post-has-been-hidden/329)

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**Author:** [@Elizashahh](https://discourse.cogstack.org/u/Elizashahh)\
**Replies:** 1\
**Last updated:** [August 30, 2024, 8:34am UTC](https://discourse.cogstack.org/t/why-my-post-has-been-hidden/329 "2024-08-30T08:34:37Z")

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Hello there, Recently I posted a query on this website- https://discourse.cogstack.org/t/akismet-has-temporarily-hidden-your-post/328 After few minutes, I got a notification that left me disappointed as it shows my …

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