Datasets:

gene-ctx-2412
/

GeneContext-Dataset

protein_id stringlengths 10 14	genome_name stringclasses 51 values	contig stringclasses 51 values	start int64 131k 6.39M	end int64 132k 6.39M	strand stringclasses 2 values	label stringclasses 2 values	split stringclasses 3 values	gene_length int64 72 18.3k	max_context_per_side_bp int64 131k 3.62M	cog_category stringclasses 108 values	ec_classes stringlengths 7 75 ⌀	og_id stringlengths 5 7
WP_005790584.1	NC_016776	NC_016776_0	4,152,588	4,153,206	-	Yes	train	618	1,219,915	S	null	2Z7I5
WP_008761105.1	NC_004663	NC_004663_0	2,522,697	2,523,312	-	No	test	615	2,522,697	S	null	2Z7I5
WP_005874327.1	NC_010729	NC_010729_0	1,283,036	1,283,639	-	No	train	603	1,071,247	S	null	2Z7I5
WP_003016600.1	AJ749949	AJ749949_0	766,570	767,387	+	Yes	train	817	766,570	S	null	2Z7J9
NP_251774.1	AE004091	AE004091_0	3,463,055	3,463,856	-	No	train	801	2,800,548	S	null	2Z7J9
WP_011071859.1	NC_004347	NC_004347_0	1,805,471	1,806,296	-	No	train	825	1,805,471	S	null	2Z7J9
CAG69105.1	NC_005966	NC_005966_0	2,285,708	2,286,582	+	No	train	874	1,312,039	S	null	2Z7J9
ABJ12317.1	NC_008463	NC_008463_0	2,104,432	2,105,234	+	No	train	802	2,104,432	S	null	2Z7J9
ABK89608.1	NC_008601	NC_008601_0	771,323	772,140	+	No	validation	817	771,323	S	null	2Z7J9
ABO12101.2	NC_009085	NC_009085_0	1,950,016	1,950,887	-	No	train	871	1,950,016	S	null	2Z7J9
CAG69250.1	NC_005966	NC_005966_0	2,445,375	2,446,438	+	Yes	train	1,063	1,152,183	S	null	2Z7PG
ABJ11604.1	NC_008463	NC_008463_0	2,928,082	2,929,112	-	No	train	1,030	2,928,082	S	null	2Z7PG
WP_004521465.1	NC_006350	NC_006350_0	1,935,437	1,936,314	+	Yes	train	877	1,935,437	S	null	2Z7Q6
WP_011003482.1	NC_003295	NC_003295_0	208,483	209,399	-	No	train	916	208,483	S	null	2Z7Q6
WP_008761733.1	NC_004663	NC_004663_0	3,873,166	3,873,871	+	Yes	test	705	2,386,490	C	null	2Z7RU
WP_231621359.1	NC_007595	NC_007595_0	312,402	313,020	-	No	validation	618	312,402	C	null	2Z7RU
WP_012457555.1	NC_010729	NC_010729_0	542,850	543,543	+	No	train	693	542,850	S	null	2Z7RU
WP_001301703.1	NZ_CP008957	NZ_CP008957_0	737,689	738,250	+	Yes	train	561	737,689	M	2.3.1.251	2Z7SY
AAC73723.1	NC_000913	NC_000913_0	656,555	657,117	+	No	test	562	656,555	M	2.3.1.251	2Z7SY
AAL19579.1	NC_003197	NC_003197_0	692,156	692,730	+	No	test	574	692,156	M	2.3.1.251	2Z7SY
AAO69841.1	NC_004631	NC_004631_0	2,303,578	2,304,152	-	No	train	574	2,303,578	M	2.3.1.251	2Z7SY
WP_000289054.1	NC_016810	NC_016810_0	691,641	692,215	+	No	train	574	691,641	M	2.3.1.251	2Z7SY
WP_014656133.1	NZ_CP017054	NZ_CP017054_0	920,864	921,441	+	No	train	577	920,864	M	2.3.1.251	2Z7SY
CCP42954.1	NC_000962	NC_000962_0	269,832	271,564	-	Yes	train	1,732	269,832	null	null	2Z7TU
WP_033711070.1	CP029332	CP029332_0	363,734	365,432	-	No	validation	1,698	363,734	null	null	2Z7TU
AAC71403.1	NC_000908	NC_000908_0	210,389	211,344	+	Yes	train	955	210,389	J	2.1.1.72	2Z7VI
WP_010874555.1	NC_000912	NC_000912_0	238,363	239,323	+	Yes	test	960	238,363	J	2.1.1.72	2Z7VI
WP_012458261.1	NC_010729	NC_010729_0	1,588,290	1,589,259	+	No	train	969	765,627	H	null	2Z7VI
WP_011108379.1	NC_004663	NC_004663_0	3,236,801	3,238,100	-	Yes	test	1,299	3,022,261	S	null	2Z7X2
WP_014298160.1	NC_016776	NC_016776_0	260,588	261,953	+	No	train	1,365	260,588	S	null	2Z7X2
WP_001301910.1	NZ_CP008957	NZ_CP008957_0	387,421	388,285	+	Yes	train	864	387,421	S	null	2Z84Q
AAC73422.1	NC_000913	NC_000913_0	335,923	336,788	+	No	test	865	335,923	S	null	2Z84Q
WP_040132655.1	NZ_CP017054	NZ_CP017054_0	2,797,816	2,798,747	+	No	train	931	1,808,746	S	null	2Z84Q
WP_011108420.1	NC_004663	NC_004663_0	3,293,836	3,295,642	+	No	test	1,806	2,964,719	S	null	2Z86V
WP_012457617.1	NC_010729	NC_010729_0	635,150	636,635	+	No	train	1,485	635,150	S	null	2Z86V
WP_014298130.1	NC_016776	NC_016776_0	227,995	229,390	-	Yes	train	1,395	227,995	S	null	2Z86V
WP_004551511.1	NC_006350	NC_006350_0	1,010,505	1,012,153	-	Yes	train	1,648	1,010,505	S	null	2Z889
WP_012493022.1	AM747720	AM747720_0	188,049	189,679	-	No	validation	1,630	188,049	S	null	2Z889
CAG68516.1	NC_005966	NC_005966_0	1,675,468	1,677,020	+	No	train	1,552	1,675,468	S	null	2Z889
WP_025404196.1	NC_007650	NC_007650_0	1,933,755	1,935,397	+	No	train	1,642	1,933,755	S	null	2Z889
ABO12089.2	NC_009085	NC_009085_0	1,933,710	1,935,280	+	No	train	1,570	1,933,710	S	null	2Z889
AAC74682.1	NC_000913	NC_000913_0	1,684,257	1,685,188	+	Yes	test	931	1,684,257	J	null	2Z895
AAL20390.1	NC_003197	NC_003197_0	1,545,390	1,546,321	-	No	test	931	1,545,390	J	null	2Z895
AAO68986.1	NC_004631	NC_004631_0	1,399,390	1,400,321	-	No	train	931	1,399,390	J	null	2Z895
WP_000092490.1	NC_016810	NC_016810_0	1,502,251	1,503,182	-	No	train	931	1,502,251	J	null	2Z895
WP_001322334.1	NZ_CP008957	NZ_CP008957_0	2,378,520	2,379,450	+	No	train	930	2,378,520	J	null	2Z895
WP_001097010.1	NZ_CP017054	NZ_CP017054_0	161,230	162,107	-	No	train	877	161,230	L	null	2Z895
WP_004531333.1	NC_006350	NC_006350_0	1,906,031	1,906,620	+	Yes	train	589	1,906,031	S	null	2Z897
WP_012493052.1	AM747720	AM747720_0	319,950	320,497	+	No	validation	547	319,950	S	null	2Z897
CAG69311.1	NC_005966	NC_005966_0	2,506,055	2,506,659	-	No	train	604	1,091,962	S	null	2Z897
AAF94645.1	NC_002505	NC_002505_0	1,595,798	1,596,342	-	Yes	validation	544	1,595,798	D	null	2Z8AH
AAC74032.2	NC_000913	NC_000913_0	1,005,950	1,006,494	+	No	test	544	1,005,950	D	null	2Z8AH
AAL19992.1	NC_003197	NC_003197_0	1,148,123	1,148,667	+	No	test	544	1,148,123	D	null	2Z8AH
WP_011072541.1	NC_004347	NC_004347_0	2,719,059	2,719,593	-	No	train	534	2,250,218	D	null	2Z8AH
AAO69479.1	NC_004631	NC_004631_0	1,923,092	1,923,639	-	No	train	547	1,923,092	D	null	2Z8AH
WP_001220671.1	NC_016810	NC_016810_0	1,104,457	1,105,001	+	No	train	544	1,104,457	D	null	2Z8AH
WP_001301917.1	NZ_CP008957	NZ_CP008957_0	1,222,754	1,223,297	+	No	train	543	1,222,754	D	null	2Z8AH
WP_004918182.1	NZ_CP017054	NZ_CP017054_0	4,269,864	4,270,411	+	No	train	547	337,082	D	null	2Z8AH
CCP42978.1	NC_000962	NC_000962_0	300,832	301,655	-	Yes	train	823	300,832	S	null	2Z8CG
WP_033710767.1	CP029332	CP029332_0	407,520	408,348	-	No	validation	828	407,520	S	null	2Z8CG
WP_000960581.1	NZ_CP008957	NZ_CP008957_0	5,412,767	5,416,127	+	Yes	train	3,360	131,196	null	null	2Z8ER
ABJ15224.1	NC_008463	NC_008463_0	309,747	311,728	+	No	train	1,981	309,747	null	null	2Z8ER
WP_001008054.1	NZ_CP008957	NZ_CP008957_0	5,276,671	5,277,541	-	Yes	train	870	269,782	S	null	2Z8ET
AAC77105.1	NC_000913	NC_000913_0	4,373,363	4,374,234	-	No	test	871	267,418	S	null	2Z8ET
AAL23155.1	NC_003197	NC_003197_0	4,577,416	4,578,275	-	No	test	859	373,108	S	null	2Z8ET
AAO71835.1	NC_004631	NC_004631_0	4,536,796	4,537,655	-	No	train	859	254,306	S	null	2Z8ET
WP_001229227.1	NC_016810	NC_016810_0	4,597,981	4,598,840	-	No	train	859	468,610	S	null	2Z8ET
WP_012457633.1	NC_010729	NC_010729_0	652,958	653,945	-	No	train	987	652,958	S	null	2Z8G6
WP_005776801.1	NC_016776	NC_016776_0	2,459,204	2,460,212	+	No	train	1,008	2,459,204	S	null	2Z8G6
WP_011108207.1	NC_004663	NC_004663_0	2,868,610	2,869,618	-	Yes	test	1,008	2,868,610	S	null	2Z8G6
AAC74513.1	NC_000913	NC_000913_0	1,502,455	1,503,125	+	Yes	test	670	1,502,455	M	null	2Z8IX
WP_001261013.1	NZ_CP008957	NZ_CP008957_0	2,075,148	2,075,817	-	Yes	train	669	2,075,148	M	null	2Z8IX
AAL20525.1	NC_003197	NC_003197_0	1,697,530	1,698,200	-	No	test	670	1,697,530	M	null	2Z8IX
AAO69151.1	NC_004631	NC_004631_0	1,573,024	1,573,694	-	No	train	670	1,573,024	M	null	2Z8IX
ABJ12613.1	NC_008463	NC_008463_0	1,773,137	1,773,813	+	No	train	676	1,773,137	S	null	2Z8IX
WP_001259025.1	NC_016810	NC_016810_0	1,654,389	1,655,059	-	No	train	670	1,654,389	M	null	2Z8IX
AAC76423.1	NC_000913	NC_000913_0	3,526,467	3,528,604	+	Yes	test	2,137	1,113,048	S	null	2Z8KK
WP_000104518.1	NZ_CP008957	NZ_CP008957_0	4,326,289	4,328,425	+	Yes	train	2,136	1,218,898	S	null	2Z8KK
AAL22357.1	NC_003197	NC_003197_0	3,650,193	3,652,327	+	No	test	2,134	1,299,056	S	null	2Z8KK
AAO71481.1	NC_004631	NC_004631_0	4,162,921	4,165,055	-	No	train	2,134	626,906	S	null	2Z8KK
WP_000104094.1	NC_016810	NC_016810_0	3,671,704	3,673,838	+	No	train	2,134	1,393,612	S	null	2Z8KK
WP_004916096.1	NZ_CP017054	NZ_CP017054_0	2,872,454	2,874,549	-	No	train	2,095	1,732,944	S	null	2Z8KK
WP_004540305.1	NC_006350	NC_006350_0	2,485,159	2,486,636	-	Yes	train	1,477	2,485,159	null	null	2Z8P8
WP_006482820.1	AM747720	AM747720_0	951,502	952,970	+	No	validation	1,468	951,502	null	null	2Z8P8
WP_009895619.1	NC_007650	NC_007650_0	654,012	655,489	+	No	train	1,477	654,012	null	null	2Z8P8
WP_000950813.1	NZ_CP008957	NZ_CP008957_0	924,391	925,372	+	Yes	train	981	924,391	null	null	2Z8RE
AAL21040.1	NC_003197	NC_003197_0	2,231,492	2,232,540	+	No	test	1,048	2,231,492	null	null	2Z8RE
WP_000400600.1	NC_016810	NC_016810_0	4,396,661	4,397,691	+	No	train	1,030	669,759	null	null	2Z8RE
WP_001024949.1	NZ_CP008957	NZ_CP008957_0	2,642,642	2,643,245	+	Yes	train	603	2,642,642	S	null	2Z8S1
WP_006486296.1	AM747720	AM747720_0	423,109	423,788	+	No	validation	679	423,109	S	null	2Z8S1
AAC74932.2	NC_000913	NC_000913_0	1,946,249	1,946,853	+	No	test	604	1,946,249	S	null	2Z8S1
AAL20813.1	NC_003197	NC_003197_0	1,992,622	1,993,223	+	No	test	601	1,992,622	S	null	2Z8S1
AAO68652.1	NC_004631	NC_004631_0	1,068,294	1,068,895	-	No	train	601	1,068,294	S	null	2Z8S1
WP_000716748.1	NC_016810	NC_016810_0	1,950,192	1,950,793	+	No	train	601	1,950,192	S	null	2Z8S1
WP_004919702.1	NZ_CP017054	NZ_CP017054_0	572,241	572,824	-	No	train	583	572,241	S	null	2Z8S1
AAL21410.1	NC_003197	NC_003197_0	2,647,590	2,648,551	-	Yes	test	961	2,302,832	null	null	2Z8V8
WP_001149066.1	NC_016810	NC_016810_0	2,645,306	2,646,267	-	Yes	train	961	2,421,183	null	null	2Z8V8
AAO68062.1	NC_004631	NC_004631_0	392,046	393,013	+	No	train	967	392,046	null	null	2Z8V8
WP_000713407.1	NC_014171	NC_014171_0	1,465,985	1,466,697	+	Yes	train	712	1,465,985	null	null	2Z8XG
CAB14197.1	NC_000964	NC_000964_0	2,387,852	2,388,588	-	No	test	736	1,827,018	null	null	2Z8XG

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GeneContext Dataset

The GeneContext dataset is a subsample of the BacBench Essential Genes Dataset designed to evaluate the ability of Genome Language Models (gLMs) to interpret genomic context using an essentiality-based benchmark. The primary dataset contains genes from "mixed essentiality" orthologous groups (i.e. groups containing at least one essential and one non-essential gene) with essentiality labels as predictive targets for a linear probe.

Dataset Structure

The repository contains four datasets to ensure full reproducibility of the paper's experiments:

main: The primary subsample of BacBench mixed-essentiality groups used for probing experiments.
bacbench_full: The full BacBench dataset before any filtering was applied, augmented with additional annotations
f4_og_pairs: Pairwise identifiers used to for context swapping experiments.
og_metadata: Comprehensive mapping of genes to eggNOG orthologous groups.

Dataset Creation & Provenance

Source Data: Subsampled from the BacBench Essential Genes Dataset.
Annotation: Orthology labels assigned using eggNOG-mapper v2.
Curation: Specifically filtered for orthologous groups containing at least one essential and one non-essential representative to isolate context-dependent signals.

This dataset is part of a submission to NeurIPS 2026.

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