ContextTAD

ContextTAD is a deep-learning TAD caller that learns boundary evidence from broader local Hi-C windows that capture TAD-scale structural context. Instead of treating boundary prediction as an isolated per-bin classification problem, ContextTAD uses a context-aware representation to produce left- and right-boundary tracks that are explicitly optimized for downstream TAD assembly.

Our github repo: https://github.com/ai4nucleome/ContextTAD

Environment setup

Create a conda environment named contexttad.

conda create -n contexttad python=3.12 -y
conda activate contexttad
pip install -r requirements.txt

Additional external tools required by some evaluation/plotting scripts:

• Rscript (for structural protein enrichment)
• coolpup.py (for coolpup pileups)
• pyGenomeTracks (for genome track visualizations)

Data preparation

The full processed dataset is too large to keep in the Git repository. The expected layout, array format, and preprocessing inputs are documented in 0-data/README.md.

Note: Most processed resources are available from Zenodo. Raw .mcool files should be downloaded from the 4DN Data Portal.

The two required data roots are:

0-data/1_dp_train_infer_data/
0-data/2_eval_tads_data/

You may place them elsewhere and set:

export TAD_DATA_DIR=/path/to/1_dp_train_infer_data
export EVAL_DATA_ROOT=/path/to/2_eval_tads_data

Main data sources

Category	Cell line	Identifier or file	Source
Hi-C	GM12878	4DNFIXP4QG5B and downsampled fractions	4DN Data Portal
Hi-C	K562	4DNFI4DGNY7J	4DN Data Portal
Hi-C	IMR90	4DNFIJTOIGOI	4DN Data Portal
CTCF ChIP-seq	GM12878	ENCFF796WRU	ENCODE
CTCF signal bigWig	GM12878	ENCFF232FCT	ENCODE
CTCF ChIP-seq	K562	ENCFF901CBP	ENCODE
CTCF ChIP-seq	IMR90	ENCFF203SRF	ENCODE
CTCF ChIA-PET	GM12878	GSE72816	GEO
CTCF ChIA-PET	K562	ENCFF001THV	ENCODE
CTCF ChIA-PET	IMR90	ENCFF682YFU	ENCODE
H3K27me3 ChIP-seq	GM12878	ENCFF039JOT	ENCODE
H3K36me3 ChIP-seq	GM12878	ENCFF171MDW	ENCODE

The data sourcing follows the resources described by RefHiC.

How to run (step by step)

The workflow is deliberately separated into data preparation, training, inference/TAD construction, and evaluation. Run commands from the repository root unless stated otherwise.

Step 1: prepare training and inference arrays

Build the GM12878 windows after configuring the raw Hi-C and genomic-track paths required by the preprocessing scripts:

python 1-prepare_data/step2_prepare_labels/scripts/prepare_data.py

The command will create the seven coverage directories, shared DP-refined labels, and window_list.json under TAD_DATA_DIR. To process only a subset of the coverage levels, use one of the following mutually exclusive options:

# Build only the 4000M arrays.
python 1-prepare_data/step2_prepare_labels/scripts/prepare_data.py --only-4000M

# Build all downsampled arrays while reusing an existing 4000M directory.
python 1-prepare_data/step2_prepare_labels/scripts/prepare_data.py --skip-4000M

Build K562 or IMR90 arrays for cross-cell inference with:

python 1-prepare_data/step1_process_data/scripts/prepare_othercell_inference_data.py \
  --mcool /path/to/cell_line.mcool::/resolutions/5000 \
  --out_data_dir "$TAD_DATA_DIR/other_celltypes/K562" \
  --coverage_tag K562

Here, --mcool selects the 5-kb matrix, --out_data_dir is the destination for the processed windows, and --coverage_tag is the identifier written into the generated metadata. Replace K562 with IMR90 for the second cell line.

Step 2: train the base model

The base experiment uses O/E inputs, a diagonal radius of 50 bins, and random coverage sampling for both training and validation.

bash 2-training/step1_train/scripts/run_train_base.sh \
  --gpu-ids 0 \
  --run-id train_base_$(date +%Y%m%d_%H%M%S) \
  --epochs 50 \
  --batch-size 16

--gpu-ids selects the devices exposed to Accelerate; use --gpu-ids 0,1, ... for multi-GPU distributed training.

Outputs are written under:

2-training/step1_train/outputs/<run_id>/
├── logs/
├── run_command.sh
└── train_outputs/
    ├── args.json
    ├── best_model.pt
    ├── final_model.pt
    ├── history.json
    └── checkpoints/

Inspect the training curves with:

tensorboard --logdir 2-training/step1_train/outputs

Step 3: infer GM12878 TADs

Run the best checkpoint on all seven GM12878 coverage levels for held-out chromosomes 15, 16, and 17:

bash 2-training/step2_infer_decode/scripts/run_infer_decode_gm12878.sh \
  --checkpoint /path/to/best_model.pt \
  --gpu-id 0 \
  --run-id infer_gm12878_$(date +%Y%m%d_%H%M%S)

--checkpoint accepts a checkpoint produced in Step 2 or downloaded from Hugging Face. --gpu-id selects the inference device, and --run-id names the output directory.

This stage writes chromosome-level boundary tracks, FDR-selected pair candidates, postprocessing statistics, and final BED files under 2-training/step2_infer_decode/outputs/<run_id>/.

Step 4: infer K562 and IMR90 TADs (optional)

Cross-cell inference uses the same checkpoint and decoder:

bash 2-training/step2_infer_decode/scripts/run_infer_decode_othercell.sh \
  --checkpoint /path/to/best_model.pt \
  --gpu-id 0 \
  --run-id infer_othercell_$(date +%Y%m%d_%H%M%S) \
  --data-root "$OTHERCELL_DATA_ROOT"

--data-root must contain the processed K562/ and IMR90/ array directories. If omitted, the script uses the default location documented in 0-data/README.md.

Step 5: evaluate the predictions

Evaluate the main GM12878 and cross-cell results against the reference callers:

bash 3-evaluation/step1_main_results_vs_tools/scripts/run_main_results.sh \
  --gm12878-beds /path/to/gm12878_beds \
  --othercell-beds /path/to/othercell_beds \
  --run-id main_results_$(date +%Y%m%d_%H%M%S) \
  --run-coolpup \
  --run-histone

--gm12878-beds refers to the seven-coverage output from Step 3, while --othercell-beds refers to the K562/IMR90 output from Step 4. --run-histone enables the histone permutation test, and --run-coolpup enables aggregate pileup analysis. Omit either flag to skip that optional experiment. TAD-size statistics are always computed because they only require the 250M BED files.

Evaluate one ContextTAD variant on the core GM12878 experiments with:

bash 3-evaluation/step2_model_ablation_ours_only/scripts/run_model_ablation_eval.sh \
  --gm12878-beds /path/to/gm12878_beds \
  --run-id ablation_eval_$(date +%Y%m%d_%H%M%S)

This lightweight route runs exp1, exp3, exp4, and exp6 without requiring other-cell data, histone tracks, or .mcool files.

Evaluation experiment catalog

Experiment	Analysis	Main manuscript use
exp1_tadnum_ctcf_chiapet	250M CTCF ChIA-PET-supported L0/L1+ TAD counts	Figure 2b
exp2_struct_protein	CTCF, RAD21, and SMC3 boundary enrichment	Figure 2c
exp3_tadb_left_ctcf_chipseq	Left-boundary CTCF ChIP-seq support	Figure 2d
exp4_tadb_right_ctcf_chipseq	Right-boundary CTCF ChIP-seq support	Figure 2e
exp5_coolpup	Aggregate TAD pileups	Figure 5
exp6_tadnum_ctcf_chiapet_downsample	Seven-coverage TAD counts and CTCF support	Figure 3
exp7_othercell_tadnum_ctcf_chiapet	K562/IMR90 CTCF ChIA-PET support	Figure 4
exp8_othercell_both_ctcf_chipseq	K562/IMR90 directional boundary support	Figure 4
exp9_tad_size	250M TAD-size distribution and median ranking	Figure 2a
exp10_histone_modification	H3K27me3/H3K36me3 contrast permutation test	Figure 2f
exp11_pairscore_structure	Pair-score quartile pileups, boundary insulation, and representative regions	Figure 6

Each directory under 3-evaluation/common/ contains its executable entry point and a DATA_REQUIREMENTS.md file describing the required inputs and metric.

Run the two additional Figure 2 analyses independently with:

# TAD-size statistics (Figure 2a).
EVAL_DATA_ROOT=/path/to/2_eval_tads_data \
bash 3-evaluation/common/exp9_tad_size/run_exp9.sh

# Histone-modification contrast (Figure 2f).
EVAL_DATA_ROOT=/path/to/2_eval_tads_data \
RSCRIPT_BIN=/path/to/Rscript \
BEDTOOLS_BIN=/path/to/bedtools \
bash 3-evaluation/common/exp10_histone_modification/run_exp10.sh

EVAL_DATA_ROOT supplies the reference callers and benchmark tracks. RSCRIPT_BIN and BEDTOOLS_BIN may be omitted when both commands are already available on PATH.

Run the Figure 6 structural characterization independently because it requires both final calls and the scored raw candidates from the same 4000M inference run:

bash 3-evaluation/common/exp11_pairscore_structure/run_exp11.sh \
  --final-bed /path/to/GM12878_4000M_contexttad.bed \
  --raw-bed /path/to/ContextTAD_structure_4000M.bed \
  --mcool /path/to/GM12878_4000M.mcool \
  --chiapet /path/to/gm12878_ctcf_chiapet.bedpe \
  --ctcf /path/to/ENCFF232FCT_CTCF.bigWig \
  --h3k27 /path/to/ENCFF039JOT_H3K27me3.bigWig \
  --h3k36 /path/to/ENCFF171MDW_H3K36me3.bigWig \
  --output-dir /path/to/figure6_results \
  --cache-dir /path/to/figure6_cache

This produces the pair-score quartile pileups, left/right insulation profiles, three representative genomic regions, and fig6_final.{png,pdf}. See exp11_pairscore_structure/DATA_REQUIREMENTS.md for exact formats.

Step 6: run the complete pipeline with one command

The shortest command trains on GPU 0, infers on GPU 0, and runs the core GM12878 evaluation suite:

bash 4-fullpipeline/run_full_pipeline.sh \
  --train-gpus 0 \
  --infer-gpu 0

The omitted options use an automatically generated run ID, batch size 16, the default Accelerate port, and the default 50-epoch schedule.

Run the complete suite, including K562/IMR90 inference, coolpup, TAD-size, and histone-modification analyses, with:

bash 4-fullpipeline/run_full_pipeline.sh \
  --train-gpus 0 \
  --infer-gpu 0 \
  --run-id full_$(date +%Y%m%d_%H%M%S) \
  --train-epochs 50 \
  --batch-size 16 \
  --master-port 29600 \
  --all-exps

--train-gpus accepts one or more comma-separated devices, whereas --infer-gpu selects one inference device. --all-exps enables other-cell inference and the ten standard benchmark workflows. Figure 6 remains a standalone analysis because it additionally consumes scored raw candidates and genome-track files. The full-pipeline output contains symlinks to stage-specific products; model weights remain only under 2-training/step1_train/outputs/.

Step 7: run ablation experiments

All ablations retain the base architecture and optimization settings unless explicitly changed. Each wrapper accepts the same arguments as run_train_base.sh:

# Observed contact matrix instead of O/E.
bash 2-training/step1_train/scripts/run_train_obs_input.sh \
  --gpu-ids 0 --run-id obs_input_run --epochs 50 --batch-size 16

# Pair objective removed.
bash 2-training/step1_train/scripts/run_train_no_pairloss.sh \
  --gpu-ids 0 --run-id no_pair_run --epochs 50 --batch-size 16

# Count objective removed.
bash 2-training/step1_train/scripts/run_train_no_count.sh \
  --gpu-ids 0 --run-id no_count_run --epochs 50 --batch-size 16

# Boundary BCE plus count objective, without pair loss.
bash 2-training/step1_train/scripts/run_train_boundary_count.sh \
  --gpu-ids 0 --run-id boundary_count_run --epochs 50 --batch-size 16