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a0dce372b6
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ranking: Compute percentiles
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2022-01-09 19:54:05 +01:00 |
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48ff555e88
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ranking: Cache optimizations
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2022-01-09 19:54:05 +01:00 |
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e2b93babe5
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Restructure classes and their responsibilities
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2022-01-09 19:54:05 +01:00 |
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01ec301d6d
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data: Remove absolute positions
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2022-01-04 14:58:49 +01:00 |
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d98c70a205
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Use inherits() for class checking
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2022-01-04 14:58:49 +01:00 |
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207fc753a7
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adjacency: Fix bug in density computation
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2022-01-04 14:58:49 +01:00 |
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8aafcb7555
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clusteriness: Let weights decrease exponentially
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2022-01-04 14:58:49 +01:00 |
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d6ee59af4b
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neural: Increase training time
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2022-01-04 14:58:49 +01:00 |
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1f5909cc02
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plots: Improve scores plot performance
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2022-01-04 14:58:49 +01:00 |
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35fb5e3884
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Add cross-validation function
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2022-01-04 14:58:49 +01:00 |
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83fedfe9be
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neural: Use mean absolute error
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2022-01-04 14:58:49 +01:00 |
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397340cc64
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neural: Use optimizer adam
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2022-01-04 14:58:49 +01:00 |
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f940d7d9b0
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plots: Simplify positions plot
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2021-12-03 11:33:51 +01:00 |
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a347bf0ad4
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plots: Refactor and improve
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2021-12-02 17:23:18 +01:00 |
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f997b5fdd7
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plots: Add rankings plot
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2021-12-02 15:28:03 +01:00 |
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2c15ba55c1
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preset: Actually filter input genes
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2021-11-27 12:09:52 +01:00 |
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c6a5c2b59c
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neural: Store the serialized model
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2021-11-27 12:09:52 +01:00 |
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88b1a9ab6a
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Add new method adjacency
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2021-11-27 12:09:52 +01:00 |
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c0e2dfced2
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neural: Validate models and store training data
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2021-11-23 16:26:04 +01:00 |
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7c87788cad
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neural: Use tensorflow seed
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2021-11-23 11:08:21 +01:00 |
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51e7176a1a
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Store more method results
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2021-11-23 09:56:02 +01:00 |
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f2bc4318a2
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Fix some package issues
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2021-11-23 09:42:21 +01:00 |
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599f09a52f
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Remove position analysis
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2021-11-22 15:16:05 +01:00 |
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2f3dc80a2f
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plots: Add chromosome plot
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2021-11-22 14:10:08 +01:00 |
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1058dfaa17
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neural: Add progress information
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2021-11-22 13:32:50 +01:00 |
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7d3bedb436
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ranking: Add optimization for median
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2021-11-21 23:56:15 +01:00 |
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61422a6a06
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neural: Reimplement merging positions and distances
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2021-11-21 23:55:56 +01:00 |
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5a58f457a4
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analyze: Add optimization
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2021-11-19 15:07:15 +01:00 |
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b018838d37
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analysis: Cache the analysis object itself
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2021-11-18 15:18:07 +01:00 |
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de1c1ed40e
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preset: Remove min_n_species customization
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2021-11-18 14:03:11 +01:00 |
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33056bfa40
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Move species count to analysis
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2021-11-18 14:03:11 +01:00 |
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f84d37dd30
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neural: Readd distances as input data
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2021-11-18 14:03:11 +01:00 |
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88d6837fee
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ranking: Allow negative weights
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2021-11-18 14:03:11 +01:00 |
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47a26da94a
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neural: Exclude genes from training for themselves
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2021-11-18 14:03:11 +01:00 |
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e28bcaafed
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plots: Add position plot
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2021-11-15 15:12:13 +01:00 |
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19bae34a96
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plots: Add max_rank to score plot
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2021-11-15 09:21:37 +01:00 |
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1af138bf6f
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neural: Always use position data
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2021-11-14 19:27:11 +01:00 |
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4b1ab9fc9a
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correlation: Fix data preparation
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2021-11-14 17:49:16 +01:00 |
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7bd63aa6d3
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proximity: Remove use_positions
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2021-11-14 17:21:39 +01:00 |
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cfc5e7a6bf
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Implement all methods using positions additionally
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2021-11-14 16:35:59 +01:00 |
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9cbc127177
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Fix some analysis bugs
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2021-11-12 18:22:22 +01:00 |
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0e641e4dd2
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ranking: Fix error copying the input
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2021-11-12 10:33:33 +01:00 |
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4dda7fa49e
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ranking: Filter out species with too few species
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2021-11-12 10:25:07 +01:00 |
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910eb06fe9
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analyze: Include preset in result
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2021-11-12 10:16:11 +01:00 |
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6d9511fa2e
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Fix some package issues
|
2021-11-06 13:22:57 +01:00 |
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28f9834984
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plots: Move rank plot and add boxplot
|
2021-11-06 13:03:36 +01:00 |
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d075380559
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ranking: Add plot method
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2021-11-05 23:05:40 +01:00 |
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f98800f1e0
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Add comparison feature
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2021-11-05 19:08:50 +01:00 |
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4992bb2930
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ranking: Use S3 classes and rename optimize method
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2021-11-05 14:47:33 +01:00 |
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4792bbaefd
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analyze: Turn analysis into S3 class
|
2021-11-05 14:33:39 +01:00 |
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