{ "evaluated_at_unix": 1778738056.609411, "task_id": "transcript-quant", "runs_root": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs", "dataset_root": "/225040511/project/bioagent-bench/dataset", "manifest": { "mcp_root": "/225040511/project/Biomni/mcp_generated", "execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python", "available_server_count": 793, "available_tool_count": 3189, "targets": { "100": { "config": "/225040511/project/Biomni/experiments/mcp_tool_scaling/configs/mcp_scale_100.yaml", "server_count": 10, "tool_count": 107, "servers": [ "mcp_kallisto", "mcp_kraken2", "mcp_csvtk", "mcp_megahit", "mcp_kaiju", "mcp_fastp", "mcp_spades", "mcp_scanpy", "mcp_scanpy-cli", "mcp_scanpy-scripts" ] }, "500": { "config": "/225040511/project/Biomni/experiments/mcp_tool_scaling/configs/mcp_scale_500.yaml", "server_count": 96, "tool_count": 504, "servers": [ "mcp_kallisto", "mcp_kraken2", "mcp_csvtk", "mcp_megahit", "mcp_kaiju", "mcp_fastp", "mcp_spades", "mcp_scanpy", "mcp_scanpy-cli", "mcp_scanpy-scripts", "mcp_seurat-scripts", "mcp_bioconductor-deseq2", "mcp_bioconductor-edger", "mcp_bioconductor-limma", "mcp_bioconductor-clusterprofiler", "mcp_star", "mcp_hisat2", "mcp_subread", "mcp_bcftools", "mcp_bwa", "mcp_gatk4", "mcp_gatk", "mcp_snpeff", "mcp_freebayes", "mcp_orthofinder", "mcp_blast", "mcp_blast-legacy", "mcp_diamond", "mcp_gffread", "mcp_seqkit", "mcp_multiqc", "mcp_fastqc", "mcp_trimmomatic", "mcp_abnumber", "mcp_abricate", "mcp_abundancebin", "mcp_abyss", "mcp_adapterremoval", "mcp_alfred", "mcp_anansescanpy", "mcp_anarci", "mcp_aragorn", "mcp_aria2", "mcp_ariba", "mcp_arriba", "mcp_art", "mcp_arvados-cwl-runner", "mcp_arvados-python-client", "mcp_atropos", "mcp_augustus", "mcp_auspice", "mcp_bactopia", "mcp_bamtools", "mcp_barrnap", "mcp_bbmap", "mcp_bcbio-gff", "mcp_bcbio-nextgen", "mcp_bedops", "mcp_bedtools", "mcp_bin2cell", "mcp_bioawk", "mcp_biobambam", "mcp_bioconductor-affy", "mcp_bioconductor-affyio", "mcp_bioconductor-alabaster", "mcp_bioconductor-alabaster.sfe", "mcp_bioconductor-alabaster.spatial", "mcp_bioconductor-annotate", "mcp_bioconductor-annotationdbi", "mcp_bioconductor-annotationfilter", "mcp_bioconductor-apeglm", "mcp_bioconductor-apl", "mcp_bioconductor-awaggregator", "mcp_bioconductor-banksy", "mcp_bioconductor-beachmat", "mcp_bioconductor-benchdamic", "mcp_bioconductor-biobase", "mcp_bioconductor-biocbaseutils", "mcp_bioconductor-biocfilecache", "mcp_bioconductor-biocgenerics", "mcp_bioconductor-biocio", "mcp_bioconductor-biocneighbors", "mcp_bioconductor-biocparallel", "mcp_bioconductor-biocsingular", "mcp_bioconductor-biomart", "mcp_bioconductor-biomformat", "mcp_bioconductor-biostrings", "mcp_bioconductor-biovizbase", "mcp_bioconductor-blase", "mcp_bioconductor-bluster", "mcp_bioconductor-bulksignalr", "mcp_bioconductor-cardspa", "mcp_bioconductor-catscradle", "mcp_bioconductor-cdi", "mcp_bioconductor-cellhashr", "mcp_bioconductor-cellid" ] }, "1000": { "config": "/225040511/project/Biomni/experiments/mcp_tool_scaling/configs/mcp_scale_1000.yaml", "server_count": 275, "tool_count": 1002, "servers": [ "mcp_kallisto", "mcp_kraken2", "mcp_csvtk", "mcp_megahit", "mcp_kaiju", "mcp_fastp", "mcp_spades", "mcp_scanpy", "mcp_scanpy-cli", "mcp_scanpy-scripts", "mcp_seurat-scripts", "mcp_bioconductor-deseq2", "mcp_bioconductor-edger", "mcp_bioconductor-limma", "mcp_bioconductor-clusterprofiler", "mcp_star", "mcp_hisat2", "mcp_subread", "mcp_bcftools", "mcp_bwa", "mcp_gatk4", "mcp_gatk", "mcp_snpeff", "mcp_freebayes", "mcp_orthofinder", "mcp_blast", "mcp_blast-legacy", "mcp_diamond", "mcp_gffread", "mcp_seqkit", "mcp_multiqc", "mcp_fastqc", "mcp_trimmomatic", "mcp_abnumber", "mcp_abricate", "mcp_abundancebin", "mcp_abyss", "mcp_adapterremoval", "mcp_alfred", "mcp_anansescanpy", "mcp_anarci", "mcp_aragorn", "mcp_aria2", "mcp_ariba", "mcp_arriba", "mcp_art", "mcp_arvados-cwl-runner", "mcp_arvados-python-client", "mcp_atropos", "mcp_augustus", "mcp_auspice", "mcp_bactopia", "mcp_bamtools", "mcp_barrnap", "mcp_bbmap", "mcp_bcbio-gff", "mcp_bcbio-nextgen", "mcp_bedops", "mcp_bedtools", "mcp_bin2cell", "mcp_bioawk", "mcp_biobambam", "mcp_bioconductor-affy", "mcp_bioconductor-affyio", "mcp_bioconductor-alabaster", "mcp_bioconductor-alabaster.sfe", "mcp_bioconductor-alabaster.spatial", "mcp_bioconductor-annotate", "mcp_bioconductor-annotationdbi", "mcp_bioconductor-annotationfilter", "mcp_bioconductor-apeglm", "mcp_bioconductor-apl", "mcp_bioconductor-awaggregator", "mcp_bioconductor-banksy", "mcp_bioconductor-beachmat", "mcp_bioconductor-benchdamic", "mcp_bioconductor-biobase", "mcp_bioconductor-biocbaseutils", "mcp_bioconductor-biocfilecache", "mcp_bioconductor-biocgenerics", "mcp_bioconductor-biocio", "mcp_bioconductor-biocneighbors", "mcp_bioconductor-biocparallel", "mcp_bioconductor-biocsingular", "mcp_bioconductor-biomart", "mcp_bioconductor-biomformat", "mcp_bioconductor-biostrings", "mcp_bioconductor-biovizbase", "mcp_bioconductor-blase", "mcp_bioconductor-bluster", "mcp_bioconductor-bulksignalr", "mcp_bioconductor-cardspa", "mcp_bioconductor-catscradle", "mcp_bioconductor-cdi", "mcp_bioconductor-cellhashr", "mcp_bioconductor-cellid", "mcp_bioconductor-cellmigration", "mcp_bioconductor-clusterfoldsimilarity", "mcp_bioconductor-clustifyr", "mcp_bioconductor-clustsignal", "mcp_bioconductor-complexheatmap", "mcp_bioconductor-concordexr", "mcp_bioconductor-cotan", "mcp_bioconductor-csoa", "mcp_bioconductor-ctsv", "mcp_bioconductor-curatedatlasqueryr", "mcp_bioconductor-cytomapper", "mcp_bioconductor-dada2", "mcp_bioconductor-data-packages", "mcp_bioconductor-decipher", "mcp_bioconductor-decontam", "mcp_bioconductor-decontx", "mcp_bioconductor-deconvobuddies", "mcp_bioconductor-delayedmatrixstats", "mcp_bioconductor-despace", "mcp_bioconductor-diffbind", "mcp_bioconductor-dino", "mcp_bioconductor-dirichletmultinomial", "mcp_bioconductor-dnacopy", "mcp_bioconductor-dose", "mcp_bioconductor-ensembldb", "mcp_bioconductor-erma", "mcp_bioconductor-escher", "mcp_bioconductor-experimentsubset", "mcp_bioconductor-fgsea", "mcp_bioconductor-genefilter", "mcp_bioconductor-geneplotter", "mcp_bioconductor-genomeinfodb", "mcp_bioconductor-genomeinfodbdata", "mcp_bioconductor-genomicalignments", "mcp_bioconductor-genomicfeatures", "mcp_bioconductor-genomicranges", "mcp_bioconductor-geomxtools", "mcp_bioconductor-ggsc", "mcp_bioconductor-ggspavis", "mcp_bioconductor-ggtree", "mcp_bioconductor-glmgampoi", "mcp_bioconductor-go.db", "mcp_bioconductor-gosemsim", "mcp_bioconductor-graph", "mcp_bioconductor-gsva", "mcp_bioconductor-hcatonsildata", "mcp_bioconductor-hdf5array", "mcp_bioconductor-hoodscanr", "mcp_bioconductor-humanhippocampus2024", "mcp_bioconductor-imcdatasets", "mcp_bioconductor-imcrtools", "mcp_bioconductor-impute", "mcp_bioconductor-infercnv", "mcp_bioconductor-interactivedisplaybase", "mcp_bioconductor-iranges", "mcp_bioconductor-irisfgm", "mcp_bioconductor-jazzpanda", "mcp_bioconductor-keggrest", "mcp_bioconductor-lisaclust", "mcp_bioconductor-mastr", "mcp_bioconductor-matrixgenerics", "mcp_bioconductor-merfishdata", "mcp_bioconductor-metabolomicsworkbenchr", "mcp_bioconductor-metapod", "mcp_bioconductor-mia", "mcp_bioconductor-moleculeexperiment", "mcp_bioconductor-mosim", "mcp_bioconductor-mousegastrulationdata", "mcp_bioconductor-mspurity", "mcp_bioconductor-multiassayexperiment", "mcp_bioconductor-multtest", "mcp_bioconductor-nebulosa", "mcp_bioconductor-nnsvg", "mcp_bioconductor-noiseq", "mcp_bioconductor-orfhunter", "mcp_bioconductor-org.ce.eg.db", "mcp_bioconductor-org.hs.eg.db", "mcp_bioconductor-org.mm.eg.db", "mcp_bioconductor-partcnv", "mcp_bioconductor-phemd", "mcp_bioconductor-phyloseq", "mcp_bioconductor-pipecomp", "mcp_bioconductor-poem", "mcp_bioconductor-preprocesscore", "mcp_bioconductor-proteomicsannotationhubdata", "mcp_bioconductor-protgenerics", "mcp_bioconductor-qvalue", "mcp_bioconductor-rbgl", "mcp_bioconductor-reactomegsa.data", "mcp_bioconductor-regionalst", "mcp_bioconductor-rforproteomics", "mcp_bioconductor-rgraphviz", "mcp_bioconductor-rhdf5", "mcp_bioconductor-rhdf5filters", "mcp_bioconductor-rhdf5lib", "mcp_bioconductor-rhtslib", "mcp_bioconductor-rsamtools", "mcp_bioconductor-rsubread", "mcp_bioconductor-scaledmatrix", "mcp_bioconductor-scalign", "mcp_bioconductor-scarray.sat", "mcp_bioconductor-scbfa", "mcp_bioconductor-scbubbletree", "mcp_bioconductor-sccb2", "mcp_bioconductor-scclassifr", "mcp_bioconductor-scdataviz", "mcp_bioconductor-scdotplot", "mcp_bioconductor-scfeatures", "mcp_bioconductor-scider", "mcp_bioconductor-scmageck", "mcp_bioconductor-scqtltools", "mcp_bioconductor-scran", "mcp_bioconductor-screpertoire", "mcp_bioconductor-scrnaseq", "mcp_bioconductor-sctreeviz", "mcp_bioconductor-scuttle", "mcp_bioconductor-scvir", "mcp_bioconductor-seraster", "mcp_bioconductor-shortread", "mcp_bioconductor-signifinder", "mcp_bioconductor-singlecellmultimodal", "mcp_bioconductor-smoothclust", "mcp_bioconductor-smoppix", "mcp_bioconductor-sosta", "mcp_bioconductor-spacetrooper", "mcp_bioconductor-spaniel", "mcp_bioconductor-spari", "mcp_bioconductor-sparsematrixstats", "mcp_bioconductor-spatialcpie", "mcp_bioconductor-spatialdatasets", "mcp_bioconductor-spatialdecon", "mcp_bioconductor-spatialdmelxsim", "mcp_bioconductor-spatialexperiment", "mcp_bioconductor-spatialexperimentio", "mcp_bioconductor-spatialfda", "mcp_bioconductor-spatialfeatureexperiment", "mcp_bioconductor-spatialheatmap", "mcp_bioconductor-speckle", "mcp_bioconductor-spoon", "mcp_bioconductor-spotclean", "mcp_bioconductor-spotsweeper", "mcp_bioconductor-standr", "mcp_bioconductor-statial", "mcp_bioconductor-stjoincount", "mcp_bioconductor-summarizedexperiment", "mcp_bioconductor-svp", "mcp_bioconductor-tenxxeniumdata", "mcp_bioconductor-tidyomics", "mcp_bioconductor-tidyspatialexperiment", "mcp_bioconductor-treesummarizedexperiment", "mcp_bioconductor-tximport", "mcp_bioconductor-variantannotation", "mcp_bioconductor-vectrapolarisdata", "mcp_bioconductor-visiumio", "mcp_bioconductor-weberdivechalcdata", "mcp_bioconductor-xcms", "mcp_bioconductor-xenlite", "mcp_bioconductor-xvector", "mcp_bioconductor-zlibbioc", "mcp_biopython", "mcp_bowtie", "mcp_bowtie2", "mcp_bpipe", "mcp_brooklyn_plot", "mcp_busco", "mcp_bx-python", "mcp_c-ares", "mcp_cascade-reg", "mcp_cd-hit", "mcp_cdbtools", "mcp_cell2cell", "mcp_cellitac", "mcp_cellqc", "mcp_cellrank", "mcp_cellsnake", "mcp_celltypist", "mcp_celltypist-so", "mcp_checkatlas", "mcp_checkm-genome" ] } } }, "aggregate": { "run_count": 2, "mean_retrieval_recall@1": 0.25, "mean_retrieval_recall@3": 0.5, "mean_retrieval_recall@5": 1.0, "mean_retrieval_recall@10": 1.0, "mean_retrieval_recall@20": 1.0, "mean_retrieval_recall@50": 1.0, "tool_selection_accuracy": 1.0, "workflow_validity": 1.0, "execution_success_rate": 1.0, "mean_context_tokens_rough": 900.0, "mean_planning_latency_seconds": null }, "results": [ { "task_id": "transcript-quant", "run_dir": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/transcript-quant_20260513_065059", "retrieval_recall_at_k": { "1": 0.0, "3": 0.5, "5": 1.0, "10": 1.0, "20": 1.0, "50": 1.0 }, "tool_selection_accuracy": true, "workflow_validity": { "valid": true, "steps_matched": 4, "steps_total": 4, "matched_step_names": [ "build_transcriptome_index", "quantify_paired_reads", "extract_counts", "write_tsv" ] }, "execution_success": true, "context_tokens_rough": 886, "planning_latency_seconds": null, "retrieved_candidate_count": 612, "execution_evidence_count": 2510 }, { "task_id": "transcript-quant", "run_dir": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/transcript-quant_20260513_105632", "retrieval_recall_at_k": { "1": 0.5, "3": 0.5, "5": 1.0, "10": 1.0, "20": 1.0, "50": 1.0 }, "tool_selection_accuracy": true, "workflow_validity": { "valid": true, "steps_matched": 4, "steps_total": 4, "matched_step_names": [ "build_transcriptome_index", "quantify_paired_reads", "extract_counts", "write_tsv" ] }, "execution_success": true, "context_tokens_rough": 914, "planning_latency_seconds": null, "retrieved_candidate_count": 619, "execution_evidence_count": 2801 } ] }