iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching

Table 4 Overall results as in terms of end-to-end time/memory costs and F1 scores at different cutoffs. Note that gold and semi refer to the original GWAS results and semi-parallel GWAS results in plaintext, respectively. We expect teams will benefit from using our suggested semi-parallel algorithm to design their fully homomorphic encrypted counterpart, but we encouraged solutions to approximate the gold standard (plaintext original GWAS model) as much as possible to be useful in practice

Team	Submission	Schemes	End to End Performance		Evaluation result (F1- Score) at different cutoffs
			Running time (mins)	Peak Memory (M)	0.01		0.001		0.0001		0.00001
			Running time (mins)	Peak Memory (M)	Gold	Semi	Gold	Semi	Gold	Semi	Gold	Semi
A*FHE	A*FHE −1 +	HEAAN	922.48	3777	0.977	0.999	0.986	0.999	0.985	0.999	0.966	0.998
A*FHE	A*FHE −2	HEAAN	1632.97	4093	0.882	0.905	0.863	0.877	0.827	0.843	0.792	0.826
Chimera	Version 1 +	TFHE & HEAAN (Chimera)	201.73	10,375	0.979	0.993	0.987	0.991	0.988	0.989	0.982	0.974
Chimera	Version 2	TFHE & HEAAN (Chimera)	215.95	15,166	0.339	0.35	0.305	0.309	0.271	0.276	0.239	0.253
Delft Blue	Delft Blue	HEAAN	1844.82	10,814	0.965	0.969	0.956	0.944	0.951	0.935	0.884	0.849
UC San Diego	Logistic Regr +	HEAAN	1.66	14,901	0.983	0.993	0.993	0.987	0.991	0.989	0.995	0.967
UC San Diego	Linear Regr	HEAAN	0.42	3387	0.982	0.989	0.980	0.971	0.982	0.968	0.925	0.89
Duality Inc	Logistic Regr +	CKKS (Aka HEAAN), pkg.: PALISADE	3.8	10,230	0.982	0.993	0.991	0.993	0.993	0.991	0.990	0.973
Duality Inc	Chi2 test	CKKS (Aka HEAAN), pkg.: PALISADE	0.09	1512	0.968	0.983	0.981	0.985	0.980	0.985	0.939	0.962
Seoul National University	SNU-1	HEAAN	52.49	15,204	0.975	0.984	0.976	0.973	0.975	0.969	0.932	0.905
Seoul National University	SNU-2	HEAAN	52.37	15,177	0.976	0.988	0.979	0.975	0.974	0.969	0.939	0.909
IBM	IBM-Complex	CKKS (Aka HEAAN), pkg.: HElIb	23.35	8651	0.913	0.911	0.169	0.188	0.067	0.077	0.053	0.06
IBM	IBM- Real	CKKS (Aka HEAAN), pkg.: HElIb	52.65	15,613	0.542	0.526	0.279	0.28	0.241	0.255	0.218	0.229

ISSN: 1755-8794