Feature/fast clustering - #31

Open

Janne98 wants to merge 72 commits into

mainfrom

feature/fast-clustering

Commits on Oct 23, 2024

add spectral averaging as consensus spectrum method
Janne98
committed
55e09cc
remove hard-coded parameters
Janne98
committed
e652237
add bin_size parameter to config
Janne98
committed
75d13db

Commits on Oct 24, 2024

bugfix in sigma clipping
Janne98
committed
624c5c9
separate parameters for upper and lower bound in outlier rejection
Janne98
committed
db49a38
fix bin_size at 2 * fragment_tol
Janne98
committed
213acc4

Commits on Oct 25, 2024

scale peaks to [0, 1000] before exporting to mgf
Janne98
committed
5687fb9
Merge branch 'main' into feature/spectral-averaging
Janne98
committed
b550c56

Commits on Oct 31, 2024

fix empty bins resulting in zero intensities after spectra averaging
Janne98
committed
9e62147

Commits on Nov 3, 2024

add more info to export spectra
Janne98
committed
27a7610

Commits on Nov 5, 2024

Merge branch 'main' into feature/spectral-averaging
Janne98
authored
469c747
fix errors
Janne98
committed
5596d5f

Commits on Nov 14, 2024

switch to greedy cosine similarity
Janne98
committed
1219aca

Commits on Nov 19, 2024

clustering: use processes instead of threads
Janne98
committed
54fb0bb
imap instead of starmap (for progress bars)
Janne98
committed
1521863

Commits on Dec 16, 2024

cost-based chunking + improved logging
Janne98
committed
3bc751a

Commits on Dec 17, 2024

remove peaks in less than 70% of spectra
Janne98
committed
6ec9d90

Commits on Dec 20, 2024

Commits on Jan 3, 2025

apply sigma clipping to whole array in one go
Janne98
committed
41f9ac1

Commits on Jan 6, 2025

put averaged peaks at average mz
Janne98
committed
f83547c

Commits on Jan 9, 2025

fix cluster labeling + cluster count
Janne98
committed
79dc7c9

Commits on Jan 10, 2025

memmap distance matrix
Janne98
committed
e887de5
refine noise peak labeling in spectral averaging + bug fix
Janne98
committed
0568e68

Commits on Jan 13, 2025

bug fix: order of cluster labels
Janne98
committed
b06e613

Commits on Jan 14, 2025

Merge branch 'main' into feature/spectral-averaging
Janne98
committed
e211f2b
fix bug in noise peak labeling
Janne98
committed
f747c0a

Commits on Jan 28, 2025

reduce memory usage with lazy loads, no multithreading (cosine) and fork instead of spawn
Janne98
committed
aa2f6df

Commits on Jan 29, 2025

Merge branch 'feature/spectral-averaging' into feature/fast-clustering
Janne98
committed
2e08465

Commits on Feb 12, 2025

Commits on Feb 24, 2025

joblib loky multiprocessing + fix cluster labeling issue
Janne98
committed
61ba1e3

Commits on Feb 25, 2025

fix weird cluster labels by filling labels array with -1
Janne98
committed
1de0f60
for debugging: plug in dbscan
Janne98
committed
4333b30

Commits on Mar 7, 2025

bring back USI inspired identifiers
Janne98
committed
a6c1311

Commits on Mar 12, 2025

sort metadata for cluster label assignment (bugfix hopefully) - code cleanup needed
Janne98
committed
1c33135
tiny fix
Janne98
committed
9ce0456

Commits on May 19, 2025

add identifier to consensus spectra + give singletons unique label
Janne98
committed
eef8502

Commits on Aug 5, 2025

bug fix: consensus spectra for clusters of size 2
Janne98
committed
81b528b

Commits on Aug 13, 2025

singleton medoid bug fix + some code clean up
Janne98
committed
d1b8399

Commits on Oct 10, 2025

bug fix?
Janne98
committed
9289412

Commits on Feb 12, 2026

Commits on Jun 8, 2026

fix minor bug and make lazy loading default
Janne98
committed
14ca495
code clean up
Janne98
committed
6b87dd0
update doc strings
Janne98
committed
90ae0f1
add tests
Janne98
committed
be5cedb
add more tests
Janne98
committed
0fdbac2

Commits on Jun 9, 2026

cluster by charge bucket instead of single charge
Janne98
committed
56bd82e
bug fix: cluster unknow charge with known charges
Janne98
committed
a4aac63
bug fix: lance dataset of missing charges
Janne98
committed
578cd89
add tests for charge buckets
Janne98
committed
7d672da
update readme and overview figure
Janne98
committed
63a48f5
Potential fix for pull request finding

Janne98
and
Copilot
authored
859a4b3
Apply suggestions from code review

Janne98
and
Copilot
authored
ba097f9
Apply suggestions from code review
Janne98
committed
c3685f4
Apply suggestions from code review
Janne98
committed
2225511
Refactor precursor mz splits logic
Janne98
committed
7f73715
code clean up
Janne98
committed
eff3448
Ensure cluster assignments are of type int32 in _postprocess_cluster
Janne98
committed
ec9c32a
set default charge buckets to none -> cluster each charge separately
Janne98
committed
3cda72f

Commits on Jun 11, 2026

fix temp file leak
Janne98
committed
8f1fbbd
Parallelize clustering across charge buckets in one shared pool to optimize CPU usage
Janne98
committed
0185bdf

Commits on Jun 12, 2026

split giant distance matrices into smaller jobs and distribute across CPUs
Janne98
committed
2eb1c13
code clean up
Janne98
committed
b53f4f2
code clean up
Janne98
committed
2ee8fa4
validate config
Janne98
committed
b85e97a

Commits on Jun 13, 2026

code clean up
Janne98
committed
1f7806f