georgeamccarthy protein_search issues

georgeamccarthy / protein_search

The neural search engine for proteins.

GNU Affero General Public License v3.0

15 stars 6 forks source link

issues

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Results quality?

#61 alexcg1 opened 2 years ago
3
Fix 2022 update

#60 alexcg1 closed 2 years ago
4
[FEAT] Adding Deep Learning models for similarity search

#59 fissoreg opened 3 years ago
0
Integrate the Annoy indexer

#58 fissoreg opened 3 years ago
1
[FEAT] Sequence alignment widget

#57 fissoreg opened 3 years ago
0
Rubix982/make deps

#56 Rubix982 closed 2 years ago
5
[WIP] Load or download the model.

#55 georgeamccarthy opened 3 years ago
2
Shuffle protein data on first load and then store in memmap (on disk) instead of in memory.

#54 georgeamccarthy opened 3 years ago
3
[WIP] Merging.

#53 fissoreg closed 3 years ago
1
[Documentation] `make deps` should be updated for the new structure

#52 Rubix982 closed 1 year ago
2
Add license, contributing terms and update PR to include checkbox.

#51 georgeamccarthy closed 3 years ago
4
Using `gRPC` for the indexing step.

#50 fissoreg closed 3 years ago
0
Feature: Reimplement Indexer using built in Jina docs.matches

#48 georgeamccarthy closed 3 years ago
2
feat: use another indexing protocol to http

#47 georgeamccarthy closed 3 years ago
3
More informative search results for usability and evaluation purposes.

#46 fissoreg opened 3 years ago
0
bug: application times out if indexing goes on for longer than 5 mins

#45 georgeamccarthy closed 3 years ago
1
feat: Show RCSB metadata on frontend.

#44 fissoreg closed 3 years ago
9
feat: improve indexing flow

#43 georgeamccarthy closed 3 years ago
2
Cull duplicate proteins.

#42 georgeamccarthy closed 3 years ago
1
bug: search bar accepts inputs other than amino strings

#40 georgeamccarthy opened 3 years ago
1
bug: duplicates in the search results

#39 georgeamccarthy closed 3 years ago
0
bug: tries to access /results but doesn't exist (error)

#38 georgeamccarthy closed 3 years ago
0
logs: batch total is incorrect

#37 georgeamccarthy closed 3 years ago
0
Show similarity metrics

#36 georgeamccarthy closed 3 years ago
0
Add contact info to frontend

#35 georgeamccarthy opened 3 years ago
3
Explain what the app does on the frontend

#34 georgeamccarthy opened 3 years ago
3
Deploy the application on Google Cloud Platform

#33 georgeamccarthy closed 3 years ago
1
Include similarity metric in results

#32 georgeamccarthy closed 3 years ago
0
Loading ProtBert model takes too long, times out.

#31 georgeamccarthy closed 3 years ago
10
[Structure] Dockerizing the project

#30 Rubix982 closed 3 years ago
50
[WIP] Dockerize the application

#29 georgeamccarthy closed 3 years ago
1
Extend indexing to more proteins

#28 georgeamccarthy closed 3 years ago
5
Computing embeddings during indexing takes exceptionally long on Apple Silicon

#27 georgeamccarthy closed 3 years ago
2
Simple logging

#26 georgeamccarthy closed 3 years ago
1
Frontend integration.

#25 fissoreg closed 3 years ago
0
Fixing HTTP request processing, frontend seems to work now.

#24 fissoreg closed 3 years ago
0
Improve logging

#23 fissoreg opened 3 years ago
3
Dataset

#22 fissoreg closed 3 years ago
7
MyIndexer tests are failing because a flow has not been opened.

#21 georgeamccarthy closed 3 years ago
1
Frontend

#20 fissoreg closed 3 years ago
2
Implement query flow. top_k proteins saved to results/results.json

#19 georgeamccarthy closed 3 years ago
1
Include YAML config file

#18 fissoreg opened 3 years ago
5
Got rid of `workspace` variable and implemented indexer test.

#17 fissoreg closed 3 years ago
1
Link frontend search bar to query flow

#16 georgeamccarthy closed 3 years ago
1
Frontend site including search bar

#15 georgeamccarthy closed 3 years ago
1
Query executor

#14 georgeamccarthy closed 3 years ago
0
Implement query flow

#13 georgeamccarthy closed 3 years ago
1
Create pull request

#12 georgeamccarthy closed 3 years ago
2
File paths are not using workspace variable.

#11 georgeamccarthy closed 3 years ago
1
ProtBertExecutor cannot handle proteins of different lengths.

#10 georgeamccarthy closed 3 years ago
1