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Comparison · Analytics
fastml vs GeneNMF
A side-by-side editorial comparison of fastml and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
fastml vs GeneNMF: at a glance
What is fastml?
fastml added survival modelling and leakage-proof resampling, moving past classification and regression.
A tidymodels-based AutoML wrapper that trains, tunes and compares many engines from one call. The 0.6.x line added engine-specific tuning parameters, class-imbalance handling, early stopping and DALEX-based explainability. The 0.7.5 release is far larger: a full survival analysis task with its own engines, MICE imputation and integrated Brier scoring, plus unbiased nested cross-validation, grouped, blocked and rolling resampling helpers, fold-wise imputation, recipe leakage checks, and a sandbox for user-supplied preprocessing.
What is GeneNMF?
GeneNMF rebuilt how it derives meta-programs, changing every result it had produced.
GeneNMF applies non-negative matrix factorization to single-cell expression data to find gene programs, then consolidates programs recurring across samples into meta-programs. Version 0.6.0 replaced the consolidation method: instead of reducing each program to a gene set and taking a consensus, it retains full gene weight vectors and compares them by cosine similarity. Later releases have built reporting and control around that core — a metaprogram composition matrix showing which samples contributed, custom signature databases for enrichment testing, and the ability to drop meta-programs from results.
fastml vs GeneNMF: editorial side-by-side
fastml
0.0ANALYTICS
fastml added survival modelling and leakage-proof resampling, moving past classification and regression.
◆ Current state
A tidymodels-based AutoML wrapper that trains, tunes and compares many engines from one call. The 0.6.x line added engine-specific tuning parameters, class-imbalance handling, early stopping and DALEX-based explainability. The 0.7.5 release is far larger: a full survival analysis task with its own engines, MICE imputation and integrated Brier scoring, plus unbiased nested cross-validation, grouped, blocked and rolling resampling helpers, fold-wise imputation, recipe leakage checks, and a sandbox for user-supplied preprocessing.
◆ Where it's heading
The package is moving from convenience wrapper to something that has to be defensible statistically. Nested cross-validation, fold-wise rather than up-front imputation, and explicit leakage checks are all corrections to the shortcuts that make AutoML easy and its scores optimistic. Survival adds a third task type alongside classification and regression, and it arrived with its own metrics rather than being bolted onto the existing ones. Note the entry body is cut off at 8,000 characters, so the release is larger than what is shown.
◆ Prediction
Expect the remaining survival engines to fill in and the sandboxing of custom preprocessing to tighten, since both were still being iterated on within this same release's commit list.
GeneNMF
0.0ANALYTICS
GeneNMF rebuilt how it derives meta-programs, changing every result it had produced.
◆ Current state
GeneNMF applies non-negative matrix factorization to single-cell expression data to find gene programs, then consolidates programs recurring across samples into meta-programs. Version 0.6.0 replaced the consolidation method: instead of reducing each program to a gene set and taking a consensus, it retains full gene weight vectors and compares them by cosine similarity. Later releases have built reporting and control around that core — a metaprogram composition matrix showing which samples contributed, custom signature databases for enrichment testing, and the ability to drop meta-programs from results.
◆ Where it's heading
The package is moving from producing meta-programs to letting users interrogate and constrain how they were formed. Composition matrices, the drop function and downsampled similarity heatmaps all serve inspection rather than derivation. The parameters added alongside the 0.6.0 rewrite — specificity weighting, cumulative weight thresholds, confidence defined as the fraction of programs containing a gene — turn what were fixed internal choices into stated, tunable ones.
◆ Prediction
Recent releases have been fixes and compatibility work rather than method changes, so the core approach appears settled. The dependency on an RcppML version not on CRAN is the loose end most likely to force the next release.
Alternatives to fastml and GeneNMF
Other Analytics products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either fastml or GeneNMF.
cfbfastr
College football's open data client hit v2 — and now reports how many API calls you have left.
rnpn
The USA phenology data client rebuilt its entire stack and stopped handing users -9999 as a number.
rempsyc
Publication-ready psychology tables and plots, tracking APA style as closely as the software allows.
sdsfun
A spatial-statistics utility package exists to be depended on, and is built accordingly.
eulerr
The area-proportional Euler diagram package is finished software, and maintained like it.
See all fastml alternatives → · See all GeneNMF alternatives →
Recent activity from fastml and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 8mo agofastmlVersion 0.7.5 ⚡
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agofastmlEngine-specific tuning, imbalance handling and explainability
- 1y agofastmlSingle-workflow evaluation fix
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agofastmlVersion 0.5.0
- 1y agoGeneNMFSimilarity heatmap downsampling and meta-program removal
- 2y agoGeneNMFMeta-programs rebuilt on gene weight vectors and cosine similarity ⚡
- 2y agoGeneNMFFirst stable release published to CRAN
Frequently asked questions
What is the difference between fastml and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. fastml and GeneNMF are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is fastml better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. fastml and GeneNMF are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to fastml?
Top fastml alternatives in Analytics are ranked by recent ship velocity. Browse the "fastml alternatives" section above for the current picks, or visit /alternatives/fastml for the full list with editorial commentary on each.
What are the best alternatives to GeneNMF?
Top GeneNMF alternatives in Analytics are ranked by recent ship velocity. Browse the "GeneNMF alternatives" section above for the current picks, or visit /alternatives/genenmf for the full list with editorial commentary on each.