Commits · 76b9b0bf53fc05d9dead58683561a3a8ccf97b4a · iago-lito / aphid · GitLab

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Sep 02, 2024
- Move most stdout output to `detail.json`. · 76b9b0bf
  iago-lito authored 7 months ago
  76b9b0bf
Aug 29, 2024
- Expose `main/linsearch` csv trace files. · c0965091
  iago-lito authored 8 months ago
  
  c0965091
- Small proofreading of the main function. · 1f6b4433
  iago-lito authored 8 months ago
  1f6b4433
- Full config detail export is proper json. · ae33f18c
  iago-lito authored 8 months ago
  
  ae33f18c
Jul 24, 2024
- Export full config detail as an output warmup. · 719e496a
  iago-lito authored 9 months ago
  
  719e496a
- Guard against missing fields in debug display. · b509da3d
  iago-lito authored 9 months ago
  
  b509da3d
- Resolve file paths relatively to the config file. · 3b1106c6
  iago-lito authored 9 months ago
  
  3b1106c6
Jul 22, 2024
- Implement Nocedal & Wright 2006 BFGS algorithm. · c0b0be69
  iago-lito authored 1 year ago
  
  c0b0be69
Mar 11, 2024
- Switch to AdamW optimizer, expose search parms. · e6a95e85
  iago-lito authored 1 year ago
  
  e6a95e85
- Stop requesting cuda device. · e83726bb
  iago-lito authored 1 year ago
  
  e83726bb
Mar 07, 2024
- Weak consistency check for two likelihood calcs. · 78c782a6
  iago-lito authored 1 year ago
  
  78c782a6
- Fix the semantics of `unresolved_length`. · 1f2a63c6
  iago-lito authored 1 year ago
  1f2a63c6
- Temporary fix, work around Glog subdep upgrade. · b2dfbc93
  iago-lito authored 1 year ago
  
  b2dfbc93
Feb 15, 2024
- Fix/Update README.md. · e44f6d33
  iago-lito authored 1 year ago
  
  e44f6d33
- Update container with pytorch (no CUDA yet). · 57718870
  iago-lito authored 1 year ago
  
  57718870
- Forbid that tau_1 == tau_2. · 321bbddb
  iago-lito authored 1 year ago
  
  321bbddb
- Bump dependencies. · 00974711
  iago-lito authored 1 year ago
  00974711
- Optimize likelihood with torch. · 170d54ae
  iago-lito authored 1 year ago
  170d54ae
- Satisfy clippy. · 16533383
  iago-lito authored 1 year ago
  
  16533383
- Fix `max_clock_ratio` meaning: Geometry Filter. · c1b52965
  iago-lito authored 1 year ago
  
  c1b52965
- Implement unresolved_length. Clarify length units. · 5f8bc8da
  iago-lito authored 1 year ago
  
  5f8bc8da
- Implement max_clock_ratio filter. · 48a7e5ed
  iago-lito authored 1 year ago
  
  48a7e5ed
- Satisfy clippy. · 1cc19c87
  iago-lito authored 1 year ago
  
  1cc19c87
- Implement triplet_other_monophyly filter. · ee09a8b2
  iago-lito authored 1 year ago
  
  ee09a8b2
- Start accumulating iterators from non-root nodes. · 83570784
  iago-lito authored 1 year ago
  
  83570784
- Orient children in downwards tree accumulators. · 8008fad7
  iago-lito authored 1 year ago
  
  8008fad7
- Retrieve left-descendance ancestor information. · 0917bbeb
  iago-lito authored 1 year ago
  
  0917bbeb
- Iterate up from node to root. · 10f264f5
  iago-lito authored 1 year ago
  
  10f264f5
- Test internal/external top species sorting. · 2c3624f1
  iago-lito authored 1 year ago
  
  2c3624f1
- Read three new parameters from config. · 9083db9f
  iago-lito authored 1 year ago
  9083db9f
- Receive init parameters from config + display lnL. · 7e46fe06
  iago-lito authored 1 year ago
  
  7e46fe06
- Calculate likelihood of the gene forest. · aaa6dd6b
  iago-lito authored 1 year ago
  
  aaa6dd6b
- Retrieve prior vs. actual branches lengths. · d1952a59
  iago-lito authored 1 year ago
  
  d1952a59
- Sketch model with various ILS/GF scenarios.. · 01885f60
  iago-lito authored 1 year ago
  01885f60
- Bump strip-ansi-escapes. · 74834be1
  iago-lito authored 1 year ago
  
  74834be1
- Use standard cargo layout for `src/bin/` folder. · 0da612d3
  iago-lito authored 1 year ago
  
  0da612d3
- Intern names into integer symbols. · 082a8959
  iago-lito authored 1 year ago
  082a8959
- Tree becomes generic over node 'payload' types. · a8a1ee2e
  iago-lito authored 1 year ago
  a8a1ee2e
- Filter out LCA(triplet, outgroup) ≠ root. · 829aaf8e
  iago-lito authored 2 years ago
  829aaf8e
- Iterate on all children *leaves* of given node. · 203a2b96
  iago-lito authored 1 year ago
  
  203a2b96