Archive 3 checkpoints (1-3)

paper-releases/pbisc-diffusion/updates/20261006T125143Z-supp-fig-s1-corpus/diffusion/metadata/NOTE.md

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+# PBISC-diffusion update 20261006T125143Z-supp-fig-s1-corpus
+
+Detailed pretraining-corpus figure placed in the Supplementary as Fig. S1 with a new Supplementary Methods subsection S1.1 (Pretraining corpus: platforms, condition families, CMV-seropositive and in vitro shares, GEO-completed metadata, cell-type shares; labels never model inputs); later supplementary figures renumber by one (all \ref-based). Methods Training data now gives 3,199 donors and 6,507 samples and points to Note S1 / Fig. S1. Disease family renamed Hematologic (American spelling) in tables and both corpus figures. main.pdf and supplementary.pdf rebuilt with tectonic.
+
+Payload states are recorded as supplied. Inference locations are pointers, not archived generated outputs.

paper-releases/pbisc-diffusion/updates/20261006T125143Z-supp-fig-s1-corpus/diffusion/metadata/inference_locations.json

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+{
+  "locations": [],
+  "project_id": "pbisc-diffusion",
+  "update_id": "20261006T125143Z-supp-fig-s1-corpus"
+}

paper-releases/pbisc-diffusion/updates/20261006T125143Z-supp-fig-s1-corpus/diffusion/metadata/request.json

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+{
+  "assets": [
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.pdf",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.png",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "config",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.provenance.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.svg",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.pdf",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.png",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "config",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.provenance.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.svg",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/main.pdf",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_corpus_tables.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_figure1_corpus.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods.tex",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/overview_figure.tex",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/supplementary_methods.tex",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/README.md",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_assay_condition.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_cellgroups.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_celltypes.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_datasets.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_samples.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "config",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_summary.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/dataset_info.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/supplementary.pdf",
+      "state": "completed"
+    }
+  ],
+  "inference_locations": [],
+  "project_id": "pbisc-diffusion",
+  "summary": "Detailed pretraining-corpus figure placed in the Supplementary as Fig. S1 with a new Supplementary Methods subsection S1.1 (Pretraining corpus: platforms, condition families, CMV-seropositive and in vitro shares, GEO-completed metadata, cell-type shares; labels never model inputs); later supplementary figures renumber by one (all \\ref-based). Methods Training data now gives 3,199 donors and 6,507 samples and points to Note S1 / Fig. S1. Disease family renamed Hematologic (American spelling) in tables and both corpus figures. main.pdf and supplementary.pdf rebuilt with tectonic."
+}