# AutoZyme

> AutoZyme is an autonomous optimization layer for bioinformatics and scientific-computing tools. It builds verified drop-in R and Python patches that keep the same public APIs and preserve scientific outputs while reducing CPU runtime.

## Core Facts

- Finalized optimized tasks: 45
- Scientific domains covered: 9
- Primary user paths: install a published accelerator, inspect benchmark evidence, or suggest the next slow package to optimize.
- Verification model: frozen inputs, upstream baseline comparisons, output concordance gates, timing, and peak memory checks.
- Public release status: source is open at https://github.com/ElliotXie/autozyme; the Python package is published on PyPI (pip install autozyme), the R package installs from GitHub (CRAN release pending).

## Primary Pages

- [Make scientific software faster](https://autozyme.com/): AutoZyme autonomously finds safe CPU-side speedups in bioinformatics and scientific-computing tools, packaged as drop-in R and Python patches with verified outputs.
- [AutoZyme benchmarks](https://autozyme.com/benchmarks/): Benchmark catalog for 45 finalized AutoZyme tasks across 9 scientific domains.
- [Suggest and vote on AutoZyme targets](https://autozyme.com/suggest/): Nominate slow scientific-computing packages and vote on what AutoZyme should accelerate next.
- [Single-cell genomics AutoZyme benchmarks](https://autozyme.com/benchmarks/field/single-cell/): scRNA-seq, deconvolution, trajectory, cell-cell communication. 28 optimized tasks. 17-fold median speedup. 1.5k-fold peak speedup.
- [Bulk genomics & enrichment AutoZyme benchmarks](https://autozyme.com/benchmarks/field/genomics/): pathway enrichment, networks. 6 optimized tasks. 66-fold median speedup. 91-fold peak speedup.
- [Molecular & structural biology AutoZyme benchmarks](https://autozyme.com/benchmarks/field/molecular/): molecular dynamics, protein structure. 2 optimized tasks. 181-fold median speedup. 181-fold peak speedup.
- [Statistics & survival AutoZyme benchmarks](https://autozyme.com/benchmarks/field/statistics/): regression, survival analysis, mixed models. 2 optimized tasks. 25-fold median speedup. 25-fold peak speedup.
- [Biomedical imaging AutoZyme benchmarks](https://autozyme.com/benchmarks/field/imaging/): cell phenotyping, diffusion MRI. 1 optimized task. 6.6-fold median speedup. 6.6-fold peak speedup.
- [Ecology AutoZyme benchmarks](https://autozyme.com/benchmarks/field/ecology/): community ecology, PERMANOVA. 1 optimized task. 239-fold median speedup. 239-fold peak speedup.
- [Earth & atmospheric sciences AutoZyme benchmarks](https://autozyme.com/benchmarks/field/earth/): climate, seismology, radar. 3 optimized tasks. 27-fold median speedup. 918-fold peak speedup.
- [Astronomy AutoZyme benchmarks](https://autozyme.com/benchmarks/field/astronomy/): transit-search periodograms. 1 optimized task. 6.7-fold median speedup. 6.7-fold peak speedup.
- [Physics & chemistry AutoZyme benchmarks](https://autozyme.com/benchmarks/field/physchem/): PDE solvers. 1 optimized task. 35-fold median speedup. 35-fold peak speedup.

## Benchmark Domains

- [Single-cell genomics](https://autozyme.com/benchmarks/field/single-cell/): scRNA-seq, deconvolution, trajectory, cell-cell communication; 28 optimized tasks.
- [Bulk genomics & enrichment](https://autozyme.com/benchmarks/field/genomics/): pathway enrichment, networks; 6 optimized tasks.
- [Molecular & structural biology](https://autozyme.com/benchmarks/field/molecular/): molecular dynamics, protein structure; 2 optimized tasks.
- [Statistics & survival](https://autozyme.com/benchmarks/field/statistics/): regression, survival analysis, mixed models; 2 optimized tasks.
- [Biomedical imaging](https://autozyme.com/benchmarks/field/imaging/): cell phenotyping, diffusion MRI; 1 optimized task.
- [Ecology](https://autozyme.com/benchmarks/field/ecology/): community ecology, PERMANOVA; 1 optimized task.
- [Earth & atmospheric sciences](https://autozyme.com/benchmarks/field/earth/): climate, seismology, radar; 3 optimized tasks.
- [Astronomy](https://autozyme.com/benchmarks/field/astronomy/): transit-search periodograms; 1 optimized task.
- [Physics & chemistry](https://autozyme.com/benchmarks/field/physchem/): PDE solvers; 1 optimized task.

## Machine-Readable Files

- [Full LLM summary](https://autozyme.com/llms-full.txt)
- [AI summary JSON](https://autozyme.com/ai-summary.json)
- [Benchmark data JSON](https://autozyme.com/assets/data/benchmarks.json)