Datasets:

ClarusC64
/

ABX-RM-009_plasmid_transfer_coherence-v0.1

row_id string	series_id string	timepoint_h int64	organism string	donor_strain string	recipient_strain string	plasmid_id string	resistance_gene string	drug_name string	stress_index float64	transfer_rate_rel float64	plasmid_pos_frac float64	mic_drug_mg_L float64	resistant_mic_cutoff_mg_L float64	media string	assay_method string	source_type string	transfer_coherence_signal int64	earliest_transfer_coherence int64	notes string
ABXRM009-TR-0001	S1	0	Escherichia coli	EC-DON01	EC-REC01	IncF_pl1	blaCTX-M	ceftriaxone	0.1	1	0	0.25	2	LB	conjugation_assay	simulated	0	0	baseline low stress
ABXRM009-TR-0002	S1	6	Escherichia coli	EC-DON01	EC-REC01	IncF_pl1	blaCTX-M	ceftriaxone	0.8	2	0.05	0.25	2	LB	conjugation_assay	simulated	0	0	stress increases
ABXRM009-TR-0003	S1	12	Escherichia coli	EC-DON01	EC-REC01	IncF_pl1	blaCTX-M	ceftriaxone	0.85	3.4	0.14	0.25	2	LB	conjugation_assay	simulated	1	1	acceleration under stress
ABXRM009-TR-0004	S1	24	Escherichia coli	EC-DON01	EC-REC01	IncF_pl1	blaCTX-M	ceftriaxone	0.9	4	0.28	1	2	LB	conjugation_assay	simulated	1	0	MIC still below cutoff
ABXRM009-TR-0005	S1	48	Escherichia coli	EC-DON01	EC-REC01	IncF_pl1	blaCTX-M	ceftriaxone	0.9	4.2	0.7	8	2	LB	conjugation_assay	simulated	1	0	MIC crosses later
ABXRM009-TR-0006	S2	0	Klebsiella pneumoniae	KP-DON11	KP-REC11	IncN_pl2	blaKPC	meropenem	0.1	1	0	0.25	4	LB	conjugation_assay	simulated	0	0	baseline
ABXRM009-TR-0007	S2	12	Klebsiella pneumoniae	KP-DON11	KP-REC11	IncN_pl2	blaKPC	meropenem	0.2	1.1	0.01	0.25	4	LB	conjugation_assay	simulated	0	0	low stress no accel
ABXRM009-TR-0008	S2	24	Klebsiella pneumoniae	KP-DON11	KP-REC11	IncN_pl2	blaKPC	meropenem	0.25	1.1	0.02	0.25	4	LB	conjugation_assay	simulated	0	0	stable
ABXRM009-TR-0009	S3	0	Escherichia coli	EC-DON77	EC-REC77	IncF_pl9	blaTEM	ampicillin	0.1	1	0	1	8	LB	conjugation_assay	simulated	0	0	baseline
ABXRM009-TR-0010	S3	12	Escherichia coli	EC-DON77	EC-REC77	IncF_pl9	blaTEM	ampicillin	0.9	12	0.02	1	8	LB	conjugation_assay	simulated	0	0	rate spike not enough evidence

ABX-RM-009 Plasmid Transfer Coherence

Purpose

Detect accelerating horizontal transfer under stress before MIC crosses a resistant cutoff.

Core pattern

stress_index high
transfer_rate_rel rises across multiple timepoints
plasmid_pos_frac rises in the same window
MIC stays below resistant_mic_cutoff_mg_L during the acceleration
later MIC crosses resistant_mic_cutoff_mg_L

Files

data/train.csv
data/test.csv
scorer.py

Schema

Each row is one timepoint in a within donor recipient series.

Required columns

row_id
series_id
timepoint_h
organism
donor_strain
recipient_strain
plasmid_id
resistance_gene
drug_name
stress_index
transfer_rate_rel
plasmid_pos_frac
mic_drug_mg_L
resistant_mic_cutoff_mg_L
media
assay_method
source_type
transfer_coherence_signal
earliest_transfer_coherence

Labels

transfer_coherence_signal
- 1 for rows at or after the first confirmed coherence point
earliest_transfer_coherence
- 1 only for the first detected coherence row in that series

Scorer logic in v1

baseline is timepoint 0
candidate coherence point requires
- stress_index at least 0.80 at two consecutive steps
- transfer_rate_rel increases for two consecutive steps
- total transfer_rate_rel at least 3.0x baseline
- plasmid_pos_frac at least 0.12 and rising by 0.05 or more at that step
- MIC at that step below cutoff and at most 2x baseline
- exclude rate spike then snapback artifacts
confirmation
- later MIC crosses resistant cutoff

Evaluation

Run

python scorer.py --path data/test.csv

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