Commits · master · Lannoy, Carlos de / baseLess

20 Jan, 2022 1 commit
- start abf reading functionality · 201ec87f
  Lannoy, Carlos de authored Jan 20, 2022
  
  201ec87f
18 Jan, 2022 1 commit
- update abundance estimation benchmark · b2ff940a
  Carlos de Lannoy authored Jan 18, 2022
  
  b2ff940a
16 Jan, 2022 1 commit
- abundance result analysis · c358f375
  Lannoy, Carlos de authored Jan 16, 2022
  
  c358f375
12 Jan, 2022 2 commits
- multiple samping abundance estimation benchmark · 81a92966
  Carlos de Lannoy authored Jan 12, 2022
  
  81a92966
- multiple samping abundance estimation benchmark · fd6276e3
  Carlos de Lannoy authored Jan 12, 2022
  
  fd6276e3
07 Jan, 2022 1 commit
- model accuracy filtering · 36125033
  Lannoy, Carlos de authored Jan 07, 2022
  
  36125033
28 Dec, 2021 1 commit
- small fixes abundance estimation · 22b33bab
  Lannoy, Carlos de authored Dec 29, 2021
  
  22b33bab
27 Dec, 2021 1 commit
- add abundance estimation mode · 3f6cd45b
  Lannoy, Carlos de authored Dec 28, 2021
  
  3f6cd45b
21 Dec, 2021 1 commit
- batch processing · a1aa952f
  Lannoy, Carlos de authored Dec 22, 2021
  
  a1aa952f
17 Dec, 2021 3 commits
- in 16s validation make training on the fly optional · 6482b41b
  Carlos de Lannoy authored Dec 17, 2021
  
  6482b41b
- ReadTable with queues instead of sqlite · d464a531
  Carlos de Lannoy authored Dec 17, 2021
  
  d464a531
- bug fixes compile_model · 3dc43ac8
  Carlos de Lannoy authored Dec 17, 2021
  
  3dc43ac8
14 Dec, 2021 1 commit
- fix bug in 16S validtion w premade indices · fb465d95
  Carlos de Lannoy authored Dec 14, 2021
  
  fb465d95
11 Dec, 2021 1 commit
- allow using pre-made index files in validate_16S · e49000d7
  Lannoy, Carlos de authored Dec 11, 2021
  
  e49000d7
10 Dec, 2021 1 commit
- update validation routine · d92b49d1
  Carlos de Lannoy authored Dec 10, 2021
  
  d92b49d1
09 Dec, 2021 2 commits
- switch off complicated k-mer selection process for 16S k-mers · 383bdcc0
  Lannoy, Carlos de authored Dec 09, 2021
  
  383bdcc0
- compile all elements of overarching model in single graph · 0faeea48
  Lannoy, Carlos de authored Dec 09, 2021
  
  0faeea48
07 Dec, 2021 2 commits
- express k-mer threshold as fraction of total rather than absolute int · 7b649606
  Carlos de Lannoy authored Dec 07, 2021
  
  7b649606
- reduce number of simultaneously running compile_model to avoid mem issues · 13473cca
  Carlos de Lannoy authored Dec 07, 2021
  
  13473cca
05 Dec, 2021 1 commit
- properly add min-nb-models to compile_model parser · 0e9b2cc7
  Carlos de Lannoy authored Dec 05, 2021
  
  0e9b2cc7
03 Dec, 2021 1 commit
- Merge branch 'master' of git.wur.nl:lanno001/baseless · 71e55f92
  Carlos de Lannoy authored Dec 03, 2021
  
  71e55f92
02 Dec, 2021 1 commit
- make min nb models arg, small fixes · dec89520
  Lannoy, Carlos de authored Dec 02, 2021
  
  dec89520
30 Nov, 2021 2 commits
- overhaul threshold analysis, add precision recall plot · 83e37100
  Lannoy, Carlos de authored Nov 30, 2021
  
  83e37100
- add f1 to summary table · fcdb00a7
  Lannoy, Carlos de authored Nov 30, 2021
  
  fcdb00a7
29 Nov, 2021 1 commit
- fixes for benchmarking and thresholding · 66da9665
  Lannoy, Carlos de authored Nov 29, 2021
  
  66da9665
26 Nov, 2021 6 commits
- on the fly training should only pick k-mers from discernible k-mer list · 7cc65f8a
  Lannoy, Carlos de authored Nov 26, 2021
  
  7cc65f8a
- debugged threshold optimization · d3c668f3
  Lannoy, Carlos de authored Nov 26, 2021
  
  d3c668f3
- small fix · 0b9edbeb
  Lannoy, Carlos de authored Nov 26, 2021
  
  0b9edbeb
- add logit and kmer threshold search code · 254c57a8
  Lannoy, Carlos de authored Nov 26, 2021
  
  254c57a8
- run production pipeline on the fly during compilation · 4f6af55b
  Lannoy, Carlos de authored Nov 26, 2021
  
  4f6af55b
- better k-mer selection for compiled 16S models · d30580b4
  Lannoy, Carlos de authored Nov 26, 2021
  
  d30580b4
24 Nov, 2021 3 commits
- Merge branch 'master' of git.wur.nl:lanno001/baseless · fd3a1006
  Carlos de Lannoy authored Nov 24, 2021
  
  fd3a1006
- Merge branch 'ben_gru_dev' into 'master' · 02097f5a
  Lannoy, Carlos de authored Nov 24, 2021
```
compare_accuracy.py now saves confusion matrices and can be called on the...

See merge request !5
```
  02097f5a
- summarized stats for quick benchmark · 722849c1
  Carlos de Lannoy authored Nov 24, 2021
  
  722849c1
23 Nov, 2021 5 commits
- better timeseries plot · fdfba74c
  Carlos de Lannoy authored Nov 23, 2021
  
  fdfba74c
- Debug script added · 25792824
  Noordijk, Ben authored Nov 23, 2021
  
  25792824
- Set logit cutoff to 5 instead of 0 · 11b1d4c7
  Noordijk, Ben authored Nov 23, 2021
  
  11b1d4c7
- Speedup: directly call model instead of via predict function · b50c353b
  Noordijk, Ben authored Nov 23, 2021
  
  b50c353b
- Hyperparameter output · c8499789
  Noordijk, Ben authored Nov 23, 2021
  
  c8499789
22 Nov, 2021 1 commit
- Updated docstrings and removed unused function · 8abccdda
  Noordijk, Ben authored Nov 05, 2021 and Noordijk, Ben committed Nov 22, 2021
  
  8abccdda