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Put transcriptome in first message #6

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@moritzschaefer moritzschaefer commented Apr 3, 2024

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moritzschaefer and others added 30 commits December 23, 2023 22:10
@moritzschaefer
Use shared LLM-embedding model to describe/annotate cells
545ffc3 
* Deactivate github hooks etc.

* Add BottomSideBar inculding necessary UI elements

* Add installation notes and relevant starting pointer to readme

* add editor config to adhere to repositories coding convention

* LLMEmbeddings Reducer and API calls

Already connected to UI elements

* Implement server API endpoints with full boilerplate to enable immediate interaction with LLMs

* Displaying continuous annotations queried via API
@moritzschaefer
Implement LLM-embedding-based continuous cell visualization
bdfffda
@moritzschaefer
Loading of pytorch lightning model for LLM embeddings
b7dc078
@tomazou-lab @moritzschaefer
Adapted llm_obs_to_text() to use the single_cellm.validation.zero_sho…
80ce9fd 
…t.transcriptomes_to_scored_keywords implementation
@moritzschaefer
Fix/Refactor llm_obs_to_text to fit to the single-cellm repo
6644e87
@moritzschaefer
Fix Cell->Text. With baseline unittest. Also don't load model (to sav…
b9d3486 
…e time debugging)
@moritzschaefer
refactor imports
87c1c93
@moritzschaefer
load_from_checkpoint with correct args
4902e6a
@moritzschaefer
Adapt LLM calling to up to date single-cellm state
eca0097
@moritzschaefer
remove superfluous werkzeug dependency
0035372
@moritzschaefer
rename llm_embeddings to single_cellm_wrapper
a1fdb64
@moritzschaefer
More renaming and refactoring of single-cellm functions into a class
0467d11
@moritzschaefer
Automatically show newly created annotation
b1ee22b
@moritzschaefer
Use 'best' model from our sweep
95de5ee
@moritzschaefer
Run single-cellm model based on transient selection (rather than DEG …
009ef93 
…selection1)
@moritzschaefer
Render generated text (GO keywords) in a structured format
86c09be
@moritzschaefer
Provide scLLM model via appropriate config file
83a90ae
@moritzschaefer
Improve formatting of LLM output (allowing error values)
ec9d6fd
@moritzschaefer
Minifix with single ceLLM API and prepare for more performant dataloa…
a593ad2 
…ding (#14)
@moritzschaefer
Use of precomputed CLIP embeddings to accelerate web UI
988ae47 
- ...
- replace `obs_cols` with `additional_text_dict`
@moritzschaefer
Use full tabula_sapiens dataset by default
64ea816
@moritzschaefer
Use new 609 model
5443d5d
@moritzschaefer
Update used model. Use correct dataset-preloading-file now
bfe9822
@moritzschaefer
Move LLM-interface to the right (and more)
7e22cd0 
- rename to chatsidebar
- minifixing lack of model_processed_data
- deactivate Undo
- sorting of keyword groups
@moritzschaefer
Refactor CellWhisperer wrapper for more flexible data input
e0f839b 
- use precomputed data from anndata object
  - includes 'terms' dict
- pass model via CLI arg
@moritzschaefer
Change placeholder in chat input
4493037
@moritzschaefer
Hack/Easter egg to support subtraction of two prompts
991e732
@moritzschaefer
Fix preprocessing (especially for keywords).
4163672 
Most importantly, cache storing was lacking before
@moritzschaefer
rename to cellwhisperer
708e8f1
@moritzschaefer
Rename and change API within cellxgene
0281886
moritzschaefer and others added 15 commits February 15, 2024 09:54
@moritzschaefer
Adopt single cellm wrapper to use API service to call model
69364c4
@moritzschaefer
Rename, fixes and implementation of llm_obs_to_text
7bfef81
@moritzschaefer
Use cellwhisperer API to compute text embeddings, rather than the ful…
7ac1a9e 
…l scoring
@moritzschaefer
Add CellWhisperer logo and fix wrong asset path in npm building
ee9de45
@moritzschaefer
Fix broken call to CellWhisperer API
7f619f6
@moritzschaefer
Extend API to allow JSON as return type
4c01490
@moritzschaefer
working implementation for LLM access (#4)
15b38ec 
* working implementation for LLM access
* fix streaming from llava to frontend (by disabling http compression)
@moritzschaefer
Full continuous chat support with improved style
006b85e
@moritzschaefer
Hallucination inializaiton method
9eb98ff
@moritzschaefer
Fix button and enter behavior in chat
dccf6b7
@moritzschaefer
Use the cellwhisperer icon
4c8c3a7
@moritzschaefer
Provide gene names to LLM via conversation
1498dfc
@moritzschaefer
fix missing f-string indicator
69d0908
@moritzschaefer
Revert breaking code
870e108
@moritzschaefer
Implement
8132870 
- This reverts commit 870e108.
- But it breaks the LLM for some weird reason...
@moritzschaefer moritzschaefer force-pushed the main branch 2 times, most recently from eaeca62 to 2097ca7 Compare September 11, 2024 11:45
@moritzschaefer moritzschaefer force-pushed the main branch 2 times, most recently from 5611a0f to 375b5bd Compare September 26, 2024 15:21
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3 participants

@moritzschaefer @tomazou-lab