biocore/mmvec

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Neural networks for microbe-metabolite interaction analysis

Stars: 133
Forks: 54
Open beginner issues: 0
Indexed issues: 43

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Nov 4, 2022
Latest indexed: Sep 14, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue help wanted
PR merge metrics: No merged PRs in 30d

Open All

43 open issues indexed

Switch to pytests Open

biocore/mmvec#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
better defaults Open

biocore/mmvec#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Parameter recovery tutorial Open

biocore/mmvec#19 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Low level optimizations Open

good first issue

biocore/mmvec#22 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Simplify the standalone CLI interface Open

biocore/mmvec#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Switch to pytorch Open

biocore/mmvec#40 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Upcoming commands Open

question

biocore/mmvec#41 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Automatic hyperparameter tuning Open

biocore/mmvec#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
train/test split is inefficient Open

biocore/mmvec#44 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
scramble input Open

biocore/mmvec#54 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
naming summary directories Open

biocore/mmvec#55 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Ordination results as a separate command Open

biocore/mmvec#56 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Early stopping Open

enhancement good first issue help wanted

biocore/mmvec#59 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
GPU Memory Allocation Limits Open

biocore/mmvec#67 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Docker containers for Rhapsody Open

biocore/mmvec#73 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Nailing down terminology Open

question

biocore/mmvec#74 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Linked scatter plots through vega? Open

biocore/mmvec#76 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Better summaries Open

biocore/mmvec#77 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Error running on GPU: device renaming issue? Open

biocore/mmvec#79 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Version 1 action items Open

biocore/mmvec#81 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update qiime2/GNPS tutorials Open

biocore/mmvec#83 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Clean up branches Open

biocore/mmvec#87 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Enable simple hypothesis tests Open

biocore/mmvec#94 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Make filtering consistent between tables Open

biocore/mmvec#95 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Need warning for cross validation Open

biocore/mmvec#96 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Adding --p-logging-dir option Open

biocore/mmvec#101 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
bug: paired-heatmap top-k-microbes fails when top microbes are not found in ranks Open

biocore/mmvec#108 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Raise error when passing in wrong files Open

biocore/mmvec#109 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Simplify delivery and interfacing Open

bug

biocore/mmvec#111 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update min-feature-count argument Open

biocore/mmvec#113 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
BUG: paired-heatmap keep_top_samples option is broken Open

biocore/mmvec#121 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Throw error when iterations is too small Open

biocore/mmvec#129 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
mmvec metagenomic full abundance table or sub-selected table Open

biocore/mmvec#136 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Tensorboard only shows a single point Open

biocore/mmvec#144 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Upgrade pandas Open

biocore/mmvec#145 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Tips and Tricks to speed up training Open

biocore/mmvec#165 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
MMvec refactor Open

biocore/mmvec#166 · 6 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Plugin error from mmvec: index 0 is out of bounds for axis 0 with size 0 Open

biocore/mmvec#170 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Compatibility issues on macbook pro with M1 chip Open

biocore/mmvec#175 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Tensorflow-gpu is not found upon installation Open

biocore/mmvec#177 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
visualization the result of mmvec Open

biocore/mmvec#181 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Multiple group comparisons within one sole mmvec analysis Open

biocore/mmvec#182 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Missing file in output folder of mmvec paired-omics command Open

biocore/mmvec#183 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

biocore/mmvec

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