2.0.0-beta12

What's Changed

• fix install to reflect the fact that we're still using beta tags by @akotlar in #503
• Implement geodesic functions and add unit tests with expected results by @IlhaH in #506
• Add POIROT methods, testing file, and pickle file with test data by @IlhaH in #505
• Feature/issue 421 better proteomic filtering by @akotlar in #504
• Random matrix theory methods by @austinTalbot7241993 in #502
• Add adjustable p value thresholds for PRS C+T. by @cristinaetrv in #507
• [api, proteomics] Proxy OpenSearch Requests by @akotlar in #508
• [annotation, proteomics, search] Simple interface for querying Bystro Search Engine by @akotlar in #512
• [annotation, proteomics] Refine annotation api interface, proteomic api join interface by @akotlar in #515

Full Changelog: 2.0.0-beta11...2.0.0-beta12

2.0.0-beta11

What's Changed

• Optimal singular value shrinkage for operator norm by @IlhaH in #492
• [infrastructure] make canopy direct dependency until SomaLogic makes pypi package by @akotlar in #499
• update canopy to somadata by @akotlar in #500
• Add Euclidean and Riemann median calculation functions by @IlhaH in #498

Full Changelog: 2.0.0-beta9...2.0.0-beta11

2.0.0-beta9

What's Changed

• Add nonnegative covariance estimator and tests by @IlhaH in #491
• Add LD maps for hg38 and organize LD maps by build for PRS. by @cristinaetrv in #489
• fix get_user cli and api commands by @akotlar in #494
• [annotation] Remove duplicate entries due to isCanonical by @akotlar in #490
• Optimize PRS C+T preprocess for performance. by @cristinaetrv in #493
• [infrastructure] Improve Python build process by @akotlar in #496

Full Changelog: 2.0.0-beta8...2.0.0-beta9

2.0.0-beta8

What's Changed

• Modified projection method by @austinTalbot7241993 in #473
• [search] Within query slice, paginate by @akotlar in #477
• Incorporated basic shrinkage to adversarial model by @austinTalbot7241993 in #479
• [annotation] Add isCanonical transcript annotation by @akotlar in #478
• Enhance Covariance Matrix Estimation with Symmetry Enforcement and Warnings by @austinTalbot7241993 in #480
• Add shrinkage methods by @IlhaH in #481
• Supervision Augmented PPCA by @austinTalbot7241993 in #485
• Add compressed versions of AD summary stats in hg19 and hg38 by @cristinaetrv in #487
• [search] Improve clnsig analysis by @akotlar in #486

New Contributors

• @IlhaH made their first contribution in #481

Full Changelog: 2.0.0-beta7...2.0.0-beta8

2.0.0-beta7

• Fixes search slicing behavior, so that we are guaranteed to fetch all records, and without having to rely on unbounded number of slices (#477)

2.0.0-beta6

What's Changed

• Soft impute CV by @austinTalbot7241993 in #467
• Feature/ppca regularized adversarial by @austinTalbot7241993 in #469
• Implemented commonly used losses for covariance matrix estimation by @austinTalbot7241993 in #472
• Covariance shrinkage by @austinTalbot7241993 in #471
• Fast dosage matrix filtering by @akotlar in #462
• Feature/no null dosage by @akotlar in #476
• Add back support for nulls in fast dosage matrix calculation by @akotlar in #475

Full Changelog: 2.0.0-beta5...2.0.0-beta6

2.0.0-beta5

• Improve dosage matrix filtering: #462 @akotlar

  • Reduces memory usage during dosage filtering by using B-Tree instead of hashmap to store loci
  • Speeds up sorting loci by sorting each block of 10,000 records fetched in parallel.
  • Reduces memory usage in save handler by writing filtered loci to disk in streaming fashion

• Implement commonly used losses for covariance matrix estimation #472 @austinTalbot7241993

• Ledoit and Wolf covariance shrinkage methods #471 @austinTalbot7241993

2.0.0-beta4

What's Changed

• Competitor SPPCA Methods by @austinTalbot7241993 in #463
• Bugfix marginal likelihood supervision + SVAE by @austinTalbot7241993 in #464
• Covariance Module Improvements by @austinTalbot7241993 in #465
• Feature/streaming proteomics by @dlin30 in #434
• Feature/domain adaptation regularized by @austinTalbot7241993 in #468
• Gaussian mixture fitting of POE by @austinTalbot7241993 in #437
• Improved initialization scheme by @austinTalbot7241993 in #470
• #456: Add SomaScan API support by @akotlar in #466
• Fast dosage matrix filtering in Go by @akotlar in #462

Full Changelog: 2.0.0-beta3...2.0.0-beta4

2.0.0-beta3

What's Changed

• Introduce fast dosage matrix filtering
• Add hg19 version of AD GWAS summary statistics for PRS. by @cristinaetrv in #457
• Implementation Multitask Supervision by @austinTalbot7241993 in #458
• Add preprocess for PRS and C and T PRS calculation. by @cristinaetrv in #414
• GPU Support for PPCA by @austinTalbot7241993 in #461

Full Changelog: 2.0.0-beta2...2.0.0-beta3

2.0.0-beta2

What's Changed

• [search] Fix save handler memory usage by @akotlar in #459

Full Changelog: 2.0.0-beta1...2.0.0-beta2