All pull requests

Pull requests

• MCS enumeration on CPLEX and Gurobi: SOS1 gates, cost-level sweep, anchor controller, restarts

  #102·VonAlphaBisZulu opened Oct 7, 2026Contributor·

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• Faster preprocessing: sparse kernel edits, bulk GPR detach, FVA probe, parallel reversibility

  #101·VonAlphaBisZulu opened Oct 7, 2026Contributor·

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• Report only proven enumerations as optimal; verify designs at the solver default

  #100·VonAlphaBisZulu opened Oct 7, 2026Contributor·

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• [Prototype] Gene-MCS in gene space (compute_gmcs): gMCSpy-style gene binaries over SD's exact reaction certificate

  #99·VonAlphaBisZulu opened Oct 5, 2026Contributor·5 tasks·

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• SCIP: enumerate each cost level in one tree through a constraint handler

  #98·VonAlphaBisZulu opened Oct 5, 2026Contributor·6 tasks·

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• [Do not merge] Directional-coupling minimality clauses (SD_FCA_CLAUSES): refuted, kept for the record

  #97·VonAlphaBisZulu opened Oct 5, 2026Contributor·2 tasks·

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• MCS enumeration stack: SOS1 gates, cost-level sweep, anchor controller, restarts, honest status, faster preprocessing

  #95·VonAlphaBisZulu opened Oct 5, 2026Contributor·2 tasks·

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• Docs: computing elementary flux modes/vectors as minimal knock-in sets

  #94·VonAlphaBisZulu opened Oct 5, 2026Contributor·1 of 5 tasks·

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• Add flux coupling analysis (flux_coupling_analysis)

  #93·VonAlphaBisZulu opened Oct 5, 2026Contributor·1 of 6 tasks·

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• LP layer: set_lb on every backend, honest SCIP/GLPK LP statuses, cold retry of failed warm solves

  #92·VonAlphaBisZulu opened Oct 5, 2026Contributor·5 tasks·

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• Keep size-1 MCS out of the shortcut when knock-ins are available

  #89·VonAlphaBisZulu opened Aug 23, 2026Contributor·

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• CarveMe module type: network reconstruction

  #83·VonAlphaBisZulu opened Aug 12, 2026Contributor·7 tasks·

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