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Automated quality control for genomic machine learning datasets: scores the biases, duplicates and data leakage a classifier could exploit before you train on it.
Searching test set enhancer_promoter_interaction_HeLa_S3_val.csv.gz against train set enhancer_promoter_interaction_HeLa_S3_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:34

Basic Descriptive Statistics

Filename enhancer_promoter_interaction_HeLa_S3_val.csv.gz enhancer_promoter_interaction_HeLa_S3_train.csv.gz
Number of sequences 2000 10000
Minimum length 5000 5000
Mean length 5000.00 5000.00
Maximum length 5000 5000

Every test sequence searched against the train set with MMseqs2, and scored on its best hit. Similarity is min(query coverage, target coverage) × percent identity: how much of the shorter sequence the alignment spans, times how much of that matches. The histogram is the distribution of those best hits.

The flag is the percentage of test sequences at or above the threshold: Pass at 0%, Warning below 2%, Fail at 2% or more. A test sequence that near-duplicates a training one is one the model has already seen, so the accuracy it earns there is not evidence. What to do about it →

The panel under the histogram lists those alignments, up to the first 100; every one of them, listed or not, is exported to mmseqs/mmseqs2_search_result.tsv beside this report. Its columns are:

Query (Q)
Identifier of the test sequence: seq_<i>_test, where i is its 0-based position in the input test file.
Target (T)
Identifier of the train sequence: seq_<i>_train, where i is its 0-based position in the input train file.
Q Cov.
Fraction of the query sequence covered by the alignment (0–1).
T Cov.
Fraction of the target sequence covered by the alignment (0–1).
% Identity
Percent identical aligned positions in the aligned region.
% Similarity
Similarity score used for leakage detection, calculated as min(Q Cov., T Cov.) × % Identity.
E-value
MMseqs2 E-value (lower is more "significant").
Alignment
Click “Show” to expand the alignment visualisation for a row.
Filename enhancer_promoter_interaction_HeLa_S3_val.csv.gz enhancer_promoter_interaction_HeLa_S3_train.csv.gz
Data Leakage (percentage) 1.80% 0.36%
Data Leakage (count) 36 36
Similarity Histogram
36 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_1918_test seq_4276_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1949_test seq_2936_train 0.99 0.99 99.5 98.50 0.00e+00
seq_505_test seq_8226_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1115_test seq_444_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1211_test seq_5890_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1446_test seq_2074_train 0.99 0.99 99.4 98.41 0.00e+00
seq_655_test seq_1880_train 0.99 0.99 99.4 98.41 0.00e+00
seq_891_test seq_4642_train 0.99 0.99 99.4 98.41 0.00e+00
seq_767_test seq_8088_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1613_test seq_9400_train 0.99 0.99 99.4 98.41 0.00e+00
seq_367_test seq_4514_train 0.99 0.99 99.4 98.41 0.00e+00
seq_454_test seq_9061_train 0.99 0.99 99.4 98.41 0.00e+00
seq_458_test seq_8132_train 0.99 0.99 99.4 98.41 0.00e+00
seq_522_test seq_8355_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1555_test seq_3904_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1838_test seq_8357_train 0.99 0.99 99.4 98.41 0.00e+00
seq_451_test seq_6267_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1792_test seq_8819_train 0.99 0.99 99.4 98.41 0.00e+00
seq_414_test seq_2658_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1869_test seq_5099_train 0.99 0.99 99.4 98.41 0.00e+00
seq_275_test seq_7432_train 0.99 0.99 99.4 98.41 0.00e+00
seq_42_test seq_547_train 0.99 0.99 99.4 98.41 0.00e+00
seq_690_test seq_4475_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1217_test seq_5008_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1908_test seq_6739_train 0.99 0.99 99.4 98.41 0.00e+00
seq_186_test seq_772_train 0.99 0.99 99.3 98.31 0.00e+00
seq_650_test seq_2994_train 0.99 0.99 99.3 98.31 0.00e+00
seq_938_test seq_6238_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1399_test seq_212_train 0.99 0.99 99.3 98.31 0.00e+00
seq_530_test seq_5191_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1372_test seq_6425_train 0.99 0.99 99.2 98.21 0.00e+00
seq_1561_test seq_7817_train 0.99 0.99 99.2 98.21 0.00e+00
seq_1516_test seq_1965_train 0.99 1.00 99.0 98.11 0.00e+00
seq_71_test seq_3727_train 0.99 0.99 99.1 98.11 0.00e+00
seq_533_test seq_3508_train 1.00 0.99 99.0 98.01 0.00e+00
seq_408_test seq_7709_train 0.98 0.98 99.3 97.31 0.00e+00