fastrg
A fast random-graph sampler that spent 0.3.1 fixing what its parameters actually mean.
Comparison · Analytics
GeneNMF vs vahtian
A side-by-side editorial comparison of GeneNMF and vahtian — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs vahtian: at a glance
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.
What is vahtian?
A provenance-first corpus tool hands its verification core to agents over MCP
vahtian freezes a set of research records into a content-hashed, date-locked corpus, verifies it is untampered, and keeps a hash-chained audit ledger. It ships in Python and R with byte-identical content hashes enforced by a golden-hash test in both suites. In five weeks it went from first release to exposing its five core operations through a local stdio MCP server and registering in the MCP Registry.
GeneNMF vs vahtian: editorial side-by-side
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.
vahtian
3.8ANALYTICS
A provenance-first corpus tool hands its verification core to agents over MCP
◆ Current state
vahtian freezes a set of research records into a content-hashed, date-locked corpus, verifies it is untampered, and keeps a hash-chained audit ledger. It ships in Python and R with byte-identical content hashes enforced by a golden-hash test in both suites. In five weeks it went from first release to exposing its five core operations through a local stdio MCP server and registering in the MCP Registry.
◆ Where it's heading
The direction is explicit in the project's own framing — human-first, AI-second, auditable — and the MCP server is what makes that framing operational rather than rhetorical. Rather than adding judgement, the tool is being positioned as the thing an agent calls to prove a corpus has not moved. The CiteVahti claim-source comparator, mirrored across both languages under a parity gate, extends the same idea to per-claim checking. Everything stays on the user's machine: no accounts, no telemetry.
◆ Prediction
The comparator's per-field epistemic states are the newest and least settled piece; expect the next release to extend those states or to widen the R package's distribution, which is still described as coming.
Alternatives to GeneNMF and vahtian
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 GeneNMF or vahtian.
maths.genealogy
A young Mathematics Genealogy client spending its first four releases satisfying CRAN.
nat.templatebrains
The natverse package that taught neuron data to remember which brain space it lives in.
nat.nblast
The NBLAST neuron-similarity engine is stable code on life support, shipping once every few years.
RandomWalker
A random-walk generator that outgrew one dimension and renamed its core column to prove it.
tbrf
Time-based rolling statistics for water-quality data, finally getting plotting and padding built in.
See all GeneNMF alternatives → · See all vahtian alternatives →
Recent activity from GeneNMF and vahtian
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 18d agovahtianvahtian 0.2.0 ⚡
- 1mo agovahtianvahtian v0.1.1 — citation metadata release
- 1mo agovahtianvahtian v.0.1.0 ⚡
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 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 GeneNMF and vahtian?
They serve adjacent needs but don't currently overlap on shipped themes. vahtian is currently shipping more aggressively (velocity 3.8 vs 0.0), with 1 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is GeneNMF better than vahtian?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. vahtian is currently shipping more aggressively (velocity 3.8 vs 0.0), with 1 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
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.
What are the best alternatives to vahtian?
Top vahtian alternatives in Analytics are ranked by recent ship velocity. Browse the "vahtian alternatives" section above for the current picks, or visit /alternatives/vahtian for the full list with editorial commentary on each.