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Add BioPreDyn-bench B1, B2, B4, B5 benchmarks#1496

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Add BioPreDyn-bench B1, B2, B4, B5 benchmarks#1496
ChrisRackauckas-Claude wants to merge 5 commits intoSciML:masterfrom
ChrisRackauckas-Claude:biopredyn-benchmarks

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Summary

  • Adds 4 of 6 BioPreDyn-bench work-precision benchmarks for systems biology ODE solver comparison
  • B1: S. cerevisiae genome-wide kinetics (285 ODEs, 1759 params) - uses SBMLImporter + JLD2 parameter file
  • B2: E. coli central carbon metabolism (18 ODEs, 116 params) - uses SBMLImporter + JLD2 parameter file
  • B4: CHO cell metabolism (35 ODEs, 117 params) - manually translated from Matlab (SBML uses rate rules)
  • B5: EGF/TNFa signal transduction logic network (26 ODEs, 124 params) - manually translated from C source
  • Updates Bio/Project.toml: adds SBMLImporter dependency, widens Catalyst/MTK compat bounds
  • B3 (E. coli gene regulation, 47 ODEs with diauxic shift events) deferred due to SBMLImporter callback _to_float bug and parameter mapping issues
  • B6 (spatial PDE) skipped as not suitable for standard ODE benchmarks

Each benchmark includes: model loading, solution visualization, reference solution generation, and work-precision diagrams at high/low tolerances with SDIRK methods and a summary comparison.

Closes #555

Test plan

  • B1 solves with CVODE_BDF at 1e-5 and 1e-12 tolerance
  • B2 solves with CVODE_BDF, reference solution works, WorkPrecisionSet verified
  • B4 solves with Rodas5P at 1e-8 and 1e-14 tolerance
  • B5 solves with Rodas5P at 1e-8 and 1e-14 tolerance
  • CI weave of all 4 benchmarks

🤖 Generated with Claude Code

@ChrisRackauckas-Claude
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Build Artifact Review

Reviewed the CI build artifacts for B4 and B5 benchmarks:

B4 (BioPreDynB4.jmd) - All Good

  • Solution plot renders (35 ODEs, one dominant variable at ~10^5 scale)
  • All 4 work-precision diagrams (High Tol, Low Tol, SDIRK, Summary) render correctly
  • No errors

B5 (BioPreDynB5.jmd) - Fixed one issue

  • Solution plot had DimensionMismatch error: Plots.jl's ODE recipe tried to arrange 26 variables into subplot grid with uneven rows (10, 10, 6), causing DimensionMismatch: number of columns of each array must match (got (10, 10, 6)). Fixed by plotting Array(sol)' directly against sol.t instead of using the ODE plot recipe.
  • All 4 work-precision diagrams rendered correctly with no issues
  • Reference solution generates fine (0.3s)

Julia Tests CI failure - Not related to this PR

The "Julia Tests" check failed with No space left on device during Julia setup - infrastructure issue on the CI runner, not related to PR changes.

Fix pushed

Commit 453933d fixes the B5 solution plot error.

ChrisRackauckas and others added 5 commits March 21, 2026 07:20
Add four benchmarks from the BioPreDyn-bench suite for systems biology
ODE solver comparison:

- B1: S. cerevisiae genome-wide kinetics (285 ODEs, 1759 parameters)
- B2: E. coli central carbon metabolism (18 ODEs, 116 parameters)
- B4: CHO cell metabolism (35 ODEs, 117 parameters, log-linear kinetics)
- B5: EGF/TNFa signal transduction logic network (26 ODEs, 124 parameters)

B1 and B2 use SBMLImporter to load SBML models with parameter values
extracted from the original BioPreDyn-bench Matlab files. B4 and B5 are
manually translated from Matlab/C sources since their SBML representations
use rate rules and SBML-qual respectively.

B3 (E. coli gene regulation, 47 ODEs with events) is deferred due to
SBMLImporter callback compatibility issues.

Closes SciML#555

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Ser (serine) and inh (inhibitor) are standard abbreviations in
systems biology models, not typos.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
rodas() and radau() from ODEInterfaceDiffEq require compiled Fortran
libraries that may not be available in CI. Replace with Rodas5() and
RadauIIA5() from OrdinaryDiffEq. Also remove ODEInterfaceDiffEq import
from B2, B4, B5 since it's no longer used.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…rade

B1 and B2 require SBMLImporter v3 which needs Catalyst v15+, but the
existing Bio benchmarks (BCR, Bidkhori2012, etc.) are written for
Catalyst v14. Widening compat caused CI to resolve Catalyst v15 and
break existing benchmarks.

Revert Project.toml and Manifest.toml to master's versions. B4 and B5
are self-contained (manually coded ODE functions) and don't need
SBMLImporter or Catalyst. B1/B2 will be added in a follow-up PR once
SBMLImporter compatibility is resolved.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The default ODE plot recipe creates subplots with uneven grid layout
(10, 10, 6) for 26 variables, causing a DimensionMismatch. Plot the
solution matrix directly instead to render all variables on one axis.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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BioPreDyn-bench Benchmarks

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