HazyResearch dd-genomics issues

HazyResearch / dd-genomics

The Genomics DeepDive project

Apache License 2.0

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issues

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Add p[0-9][0-9] genes again; use better supervision for those

#353 Colossus opened 8 years ago
0
Need linear logic for outer/inner factors

#352 Colossus closed 8 years ago
0
Make writing evaluation to results_log optional

#351 Colossus opened 8 years ago
0
Do distinct gp-level precision analysis

#350 Colossus opened 8 years ago
0
Throwing cancer (and in fact, any pheno) messes up joint factors for multiple candidate resolution

#349 Colossus opened 8 years ago
0
We have "NULL" strings in genepheno_relations

#348 Colossus closed 8 years ago
1
Fix onto/make_all.sh

#347 ajratner opened 8 years ago
1
Remove regex DS rules; they might actually be hurting

#346 Colossus closed 8 years ago
13
DS rules targeting specific gene names in the presence of certain words

#345 Colossus closed 8 years ago
0
Features dependent on sequence length

#344 Colossus closed 8 years ago
0
Add full gene names; and remove phenos that are picked up as part of full gene name

#343 Colossus opened 8 years ago
0
Word sequence features: "cause" missing between gene and pheno is an (almost) sure sign of failure

#342 Colossus closed 8 years ago
0
Gene name is gene feature: experiment with throwing out word itself

#341 Colossus opened 8 years ago
0
Fix MindTagger genepheno templates: pheno name in pheno_names table, not postprocess

#340 Colossus closed 8 years ago
0
Fix inferred-to-Charite comparison for phenos and diseases

#339 Colossus closed 8 years ago
0
Try mixing treedlib and ddlib features

#338 Colossus closed 8 years ago
1
Evaluate precision for multi-gp sentences only

#337 Colossus closed 8 years ago
0
Check if OMIM diseases picked up correctly, fix if not

#336 Colossus closed 8 years ago
0
Joint factors for deciding between multiple gp mentions

#335 Colossus closed 8 years ago
3
Find factor weight of gene-to-genepheno factor; experiment with setting to high weight manually

#334 Colossus opened 8 years ago
0
The gp relations extracted should have a high gene expectation

#333 ThomasPalomares opened 8 years ago
6
Charite supervision is messed up with diseases

#332 Colossus closed 8 years ago
0
Remove cancer diseases from OMIM too

#331 Colossus closed 8 years ago
0
Do genepheno-precision specifically on sentences that contain inferred stuff that's not in Charite

#330 Colossus opened 8 years ago
0
added pheno inference + labeling pipeline

#329 shayanzare007 closed 8 years ago
0
Add gene supervised false in the gp candidates (mostly to improve recall)

#328 ThomasPalomares opened 8 years ago
0
Creating evaluation+labeling pipeline for pheno

#327 shayanzare007 opened 8 years ago
0
"Dashboard": report precision in non-charite extracted set

#326 Colossus opened 8 years ago
0
Fix existing labels for updated gene/protein guidelines

#325 Colossus closed 8 years ago
0
Special handling of sentences with multiple candidates

#324 Colossus closed 8 years ago
0
Include HGMD as distant supervision source or at least for comparison

#323 Colossus opened 8 years ago
0
"Dashboard" charite comparison contains bugs

#322 Colossus opened 8 years ago
1
Update "dashboard" with disease numbers

#321 Colossus closed 8 years ago
0
DDLog hates union queries with additional conditions

#320 Colossus opened 8 years ago
1
Make sure to extract walker-warburg syndrome

#319 Colossus opened 8 years ago
0
Add chromosomal regions as separate entity next to genes

#318 Colossus opened 8 years ago
0
Extend evaluation script for precision labels

#317 Colossus closed 8 years ago
0
labels missing from genepheno_holdout database

#316 Colossus closed 8 years ago
2
labeling backups in repo should include holdout set version number

#315 Colossus closed 8 years ago
0
Currently only allowing disease names that are at least two words; relax this in the future

#314 Colossus opened 8 years ago
1
Separate phenotype and disease pipelines

#313 Colossus closed 8 years ago
0
Adapt Mindtagger Instance for Genepheno Precision alone

#312 Colossus closed 8 years ago
1
Join through OMIM diseases and clinical synopsis to explode extracted genephenos

#311 Colossus closed 8 years ago
0
gene mentions sometimes duplicated if gene is both a canonical and noncanonical name

#310 Colossus closed 8 years ago
0
Charite picks up a lot of genephenos by going through disease

#309 Colossus closed 8 years ago
2
Doing recall analysis, only compare our CANONICALIZED phenos against Charite

#308 Colossus closed 8 years ago
1
Even some of Charite's OMIM references are weird

#307 Colossus closed 8 years ago
0
Get rid of MGI in Charite

#306 Colossus closed 8 years ago
5
When having multiple HPO candidates for same word sequence, take only lowest match in HPO DAG

#305 Colossus closed 8 years ago
1
genepheno_relation_ids are not all distinct, fix asap

#304 Colossus closed 8 years ago
13