README.md

metadata

library_name: pytorch
tags:
  - bulk-rna-seq
  - single-cell-rna-seq
  - cvae
  - set-transformer
  - bioinformatics

PBISC

Private research snapshot for PBISC bulk RNA-seq to pseudo-single-cell generation.

This repository contains the active training code and the core checkpoint lineage. Raw single-cell source matrices, recipe blocks, patient-level inputs, generated cell matrices, and large analysis outputs are intentionally excluded.

Checkpoint lineage

Folder	Role	State
checkpoints/B048_L1_10x	Hard-routed expert CVAE baseline and warm-start anchor	Complete
checkpoints/Model2_A2_SetLoss	B048 warm-start with set-level MMD, pseudobulk, and variance losses	Complete
checkpoints/M001_R4_ISAB	B048-based bulk-gated ISAB communication refiner with joint fine-tuning	Complete, 6,144 steps
checkpoints/M2A2_R4_Joint	Model2-A2 base plus the R4 communication refiner	Interrupted at 2,158/3,072 steps

Use checkpoint_best.pt for evaluation or inference. Use checkpoints/M2A2_R4_Joint/checkpoint_latest.pt to resume the interrupted M2A2-R4 run. That resume checkpoint includes model, refiner, optimizer, scheduler, and run state.

The exact Model2-A2 initialization expected by M2A2-R4 is checkpoints/Model2_A2_SetLoss/checkpoint_latest.pt.

Code layout

• code/model/vae_bulk2sc: base CVAE, M001 communication architecture, trainers, tests, and reproduction notes.
• code/model_2_setloss_cvae: set-loss experiments and disease-signal evaluation code.
• code/model_3_set_transformer: decoder-side set-transformer experiment. This branch was concluded negative and is retained as research evidence.
• code/model_4_population_refiner: population-refiner planning and implementation records.
• code/inference: retained PBISC inference utilities.
• code/project_docs: reassembly, missing-asset, and project manifest documents.

Data required for retraining

The upload does not contain the approximately 107 GB training data. Local retraining uses:

• single-cell-data-block-blood source block.
• blood-kmatrix-recipes-v1.
• Repaired blood-kmatrix-recipes-v1-10x overlay.
• The 20,097-gene metadata/var.parquet panel.

The original environment used Python 3.12.13 and PyTorch 2.12.0.dev20260306+cu128. A historical environment freeze is retained under code/model/vae_bulk2sc/_REPRODUCE/env.

Relocation warning

Historical run metadata contains absolute paths under /home/sj_server_1/PBISC. M2A2-R4 resume validation compares recipe_root, source_root, and gene_panel_path against the values embedded in checkpoint_latest.pt. Preserve a compatibility symlink for the old project root, or migrate those three saved path values before resuming.

Integrity and trust

SHA-256 values are recorded in manifests/CHECKPOINTS.sha256. These PyTorch checkpoints come from the private PBISC training environment and may require torch.load(..., weights_only=False). Do not load modified copies from untrusted sources.