beam

beam is a benchmark evaluation and metrics suite. For benchmarks as in method comparisons, mainly in bioinformatics.

Documentation: how-tos, vignettes, and explanations.

Install

Python package:

python3.12 -m venv .venv
source .venv/bin/activate
pip install -e ".[dev,docs]"

[docs] pulls in Jupyter and matplotlib so Quarto can execute the Python code chunks in the vignettes. [io] pulls in pandas for the CSV adapter. [dev] covers the test suite.

R package:

library("remotes")
remotes::install_github("imallona/beam", subdir = "r/beam")
rbeam::install_beam_python()

Heterogeneity diagnostics (optional, needs R)

The MCDA ranking is pure Python. The heterogeneity diagnostics (Bradley-Terry trees, mixed-effects, Plackett-Luce, variance decomposition, network meta-analysis) call Rscript and need lme4, glmmTMB, psychotree, partykit, PlackettLuce, qvcalc, meta, netmeta and jsonlite. The conda recipe puts Python and R in one environment so the wrapper finds Rscript:

mamba env create -f envs/heterogeneity.yml
conda activate beam-heterogeneity
pip install -e ".[dev]"

From R, install them once with rbeam::install_beam_heterogeneity_deps(). The availability checks (beam.heterogeneity.r_available() and friends) report whether the toolchain is in place.

Usage

From a CSV to an HTML report:

On a shell:

beam validate scores.csv
beam rank scores.csv --weights entropy --method topsis --out result.json --report report.html
beam report result.json --out report.html
beam metric show ari
beam heterogeneity scores.csv --model bradley-terry-tree --features features.csv --out tree.json
beam run beam.yaml

In python:

import beam
from beam.cards import Registry
from beam.config import run_config

beam.load_scores("scores.csv")
result = beam.rank("scores.csv", weights="entropy", method="topsis")
beam.report(result, "report.html")
print(Registry().get("ari"))
run_config("beam.yaml")

In R

library(rbeam)

result <- beam_rank("scores.csv", weights = "entropy", method = "topsis")
beam_validate("scores.csv")
beam_report(result, "report.html")
beam_metric_show("ari")
beam_run("beam.yaml")

Build artefacts

• Documentation site: vignettes, how-tos, explanations, and the Python API reference.
• Ontology release: docs/beam.owl.ttl (OWL) and docs/beam.skos.ttl (SKOS), regenerated from the cards on each release.

Licence

• Code: GPL-3.0-or-later (LICENSE).
• Metric cards under src/beam/metrics/: CC-BY-4.0 (src/beam/metrics/LICENSE.md).

Citation

Mallona, Izaskun (2026). beam: Benchmark Evaluation And Metrics. Version 0.2.0. https://github.com/imallona/beam. ORCID 0000-0002-2853-7526.

@software{mallona_beam_2026,
  author  = {Mallona, Izaskun},
  title   = {beam: Benchmark Evaluation And Metrics},
  version = {0.2.0},
  year    = {2026},
  url     = {https://github.com/imallona/beam},
  license = {GPL-3.0-or-later}
}

Contact

Izaskun Mallona, izaskun.mallona.work@gmail.com.

Inspiration

• Commonly used software tools produce conflicting and overly-optimistic AUPRC values
• Performance Evaluation in Machine Learning: The Good, The Bad, The Ugly and The Way Forward
• Measurement theory and paleobiology

Started

21st Feb 2025