Task Objective¶
This task focuses on predicting Bacillus Calmette-Guérin(BCG) response subtypes (BRS1, BRS2, BRS3) from H&E-stained histopathology slides of high-risk non-muscle-invasive bladder cancer (HR-NMIBC) patients. These subtypes are defined using a validated biomarker signature [1] and are associated with response to BCG therapy. Final evaluation will focus on binary classification:
BRS3 vs. BRS1/2, as this is clinically relevant for treatment decision-making.
Here is a schematic illustrates a multi-modal deep learning pipeline.
Data Details - Training Data¶
• 🧠 Histopathology: A single H&E-stained whole slide image (WSI) per patient, with 0.25 µm/pixel resolution at its highest resolution. Note that this WSI is either of an adjacent section of the H&E slide used for bulk RNA-seq ("adjacent"), the same H&E slide with a punched cavity on the tissue section ("used in RNA-seq"), or an H&E slide of another tumor of the same patient ("another tumor").
• 🧠 Histopathology: Binary tissue mask outlining the tissue section
• (Upcoming) A list detailing the type of tissue present in the H&E WSI (i.e. adjacent section, used in RNA-seq, another tumor)
• 📋 Clinical Data: Containing clinical history, tumor characteristics, treatment details and BRS subtype labels derived from bulk RNA-sequencing using a validated gene expression signature [1]
| Feature | Type / Values | Description |
|---|---|---|
| age | Integer (years) | Age of the patient in years |
| sex | m = male, f = female |
Biological sex of the patient |
| smoking | Yes / No / Missing | Smoking history |
| tumor | Primary / Recurrence | Indicates whether the tumor is primary or recurrent |
| stage | TaHG / T1HG / T2HG | Tumor stage: Ta (inner lining), T1 (connective tissue), T2 (muscle invasion); all high-grade |
| substage | T1m / T1e | T1m: ≤ 0.5mm invasion; T1e: > 0.5mm invasion |
| grade | G2 / G3 | G2: moderately differentiated; G3: poorly differentiated |
| reTUR | Yes / No | Re-transurethral resection (TUR) performed before BCG induction |
| LVI | Yes / No | Lymphovascular invasion observed on H&E slide |
| variant | UCC / UCC + Variant | Urothelial carcinoma alone or with variant histology |
| EORTC | High risk / Highest risk | European Organization for Research and Treatment of Cancer (EORTC) risk classification |
| no_instillations | Integer | Total number of BCG instillations. "-1" indicates missing data. |
| Reference Standard | ||
| BRS | BRS1 / BRS2 / BRS3 | Biomarker-derived BCG response subtype from RNA-seq |
| Additional information (not available in evaluation/test) | ||
| progression | 0 / 1 | Progression to advanced disease (1-true/0-false) |
| HG_recur_BCG_failure | 0 / 1 | BCG failure (1-true/0-false) |
| time_to_prog_or_FUend | Float (months) | Time to progression or end of follow-up in months |
| time_to_HG_recur_or_FUend | Float (months) | Time to high-grade recurrence or end of follow-up in months |
| time_to_FUend | Float (months) | Time to end of follow-up in months |
Evaluation Metric¶
The F1 score will be used to evaluate the model's classification accuracy at the image level based on molecular analysis, combining precision and recall into a single metric. Additionally, the AUROC is used to assess the global discrimination power of the model across various thresholds. Together, these metrics provide a robust evaluation framework for classification tasks involving biomarker response subtypes (BRS). The pipeline will be openly available.
Download Training Data¶
- Install AWS CLI https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html
- Bucket name:
s3://chimera-challenge/task2/ - Command line:
aws s3 sync --no-sign-request s3://chimera-challenge/task2/ <destination_path>