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Fix two issues with canonical Illumina evals #4

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Fix two issues with canonical Illumina evals #4

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e53fc3a
Fix Illumina ground truth for batch key selection.
ozan Feb 10, 2026
e136923
Fix threshold for Illumina QC to match GT
ozan Feb 10, 2026
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2 changes: 1 addition & 1 deletion evals_canonical/illumina/illumina_dimred_choose_batch_key.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"grader": {
"type": "multiple_choice",
"config": {
"correct_answer": "B",
"correct_answer": "A",
"options": {
"A": "sample",
"B": "age_group"
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2 changes: 1 addition & 1 deletion evals_canonical/illumina/illumina_qc_report_initial_nuclei.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"id": "snrna_qc_01_report_initial_nuclei_after_gene_threshold",
"task": "Attached is a DRG snRNA-seq dataset with obs column age_group in {Adult, Aged}.\n\nGoal: deterministically compute how many nuclei pass an initial gene-detection threshold.\n\nInstructions:\n1) Use the raw UMI count matrix (integer counts).\n2) For each nucleus compute n_genes = number of genes with count > 0.\n3) Keep nuclei with n_genes > 1000.\n4) Report counts for total, Adult, Aged after this filter.\n\nReturn EXACTLY:\n<EVAL_ANSWER>\n{\"total\": <int>, \"Adult\": <int>, \"Aged\": <int>}\n</EVAL_ANSWER>\n",
"task": "Attached is a DRG snRNA-seq dataset with obs column age_group in {Adult, Aged}.\n\nGoal: deterministically compute how many nuclei pass an initial gene-detection threshold.\n\nInstructions:\n1) Use the raw UMI count matrix (integer counts).\n2) For each nucleus compute n_genes = number of genes with count > 0.\n3) Keep nuclei with n_genes >= 1000.\n4) Report counts for total, Adult, Aged after this filter.\n\nReturn EXACTLY:\n<EVAL_ANSWER>\n{\"total\": <int>, \"Adult\": <int>, \"Aged\": <int>}\n</EVAL_ANSWER>\n",
"data_node": "latch://158807664.node",
"grader": {
"type": "numeric_tolerance",
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