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Published at October 21

LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs -- Evaluation through Synthetic Data Generation

cs.CL

cs.AI

cs.SD

eess.AS

Released Date: October 21, 2024

Authors: Tejumade Afonja¹, Ivaxi Sheth¹, Ruta Binkyte¹, Waqar Hanif², Thomas Ulas², Matthias Becker³, Mario Fritz¹

Aff.: ¹CISPA Helmholtz Center for Information Security; ²Das Life & Medical Sciences-Institut (LIMES), University of Bonn; ³German Center for Neurodegenerative Diseases (DZNE)

Arxiv: https://arxiv.org/abs/2410.15828v1

	Setting 1 $\text{KB}^{\text{H}}$
		Cosine distance $\downarrow$	Euclidean distance $\downarrow$	MMD $\downarrow$	RF AUROC $\downarrow$
PBMC-ALL	Baseline
	Control	0.00029 $\pm$ 0.00008	100 $\pm$ 16	0.0051 $\pm$ 0.001	0.49 $\pm$ 0.017
	Stage 1	0.00036 $\pm$ 0.00009	107 $\pm$ 15	0.0057 $\pm$ 0.005	0.55 $\pm$ 0.021
	$\text{KB}^{\text{Random}}$	0.00132 $\pm$ 0.00101	187 $\pm$ 79	0.0214 $\pm$ 0.009	0.86 $\pm$ 0.080
	GPT-4	0.00024 $\pm$ 0.00004	89 $\pm$ 7	0.0072 $\pm$ 0.001	0.63 $\pm$ 0.043
	GRNBoost2	0.00047 $\pm$ 0.00021	121 $\pm$ 25	0.0139 $\pm$ 0.006	0.73 $\pm$ 0.050
	Random	0.00045 $\pm$ 0.00013	121 $\pm$ 22	0.0166 $\pm$ 0.003	0.85 $\pm$ 0.019
	Setting 2 $\text{KB}^{\text{GPT4}}$
	GPT-4	0.00026 $\pm$ 0.00009	90 $\pm$ 13	0.0206 $\pm$ 0.001	0.86 $\pm$ 0.018
	GRNBoost2	0.00023 $\pm$ 0.00008	83 $\pm$ 17	0.0069 $\pm$ 0.001	0.59 $\pm$ 0.028
	Random	0.00026 $\pm$ 0.00011	92 $\pm$ 14	0.0226 $\pm$ 0.002	0.87 $\pm$ 0.018
PBMC-CTL	Baseline
	Control	0.00020 $\pm$ 0.00005	57 $\pm$ 7	0.0045 $\pm$ 0.000	0.54 $\pm$ 0.007
	Stage 1	0.00023 $\pm$ 0.00003	63 $\pm$ 4	0.0049 $\pm$ 0.000	0.57 $\pm$ 0.030
	$\text{KB}^{\text{Random}}$	0.00016 $\pm$ 0.00002	51 $\pm$ 3	0.0071 $\pm$ 0.000	0.73 $\pm$ 0.022
	Setting 1 $\text{KB}^{\text{H}}$
	GPT-4	0.00265 $\pm$ 0.00253	176 $\pm$ 115	0.0238 $\pm$ 0.020	0.79 $\pm$ 0.206
	GRNBoost2	0.00025 $\pm$ 0.00004	65 $\pm$ 6	0.0053 $\pm$ 0.000	0.59 $\pm$ 0.028
	Random	0.00027 $\pm$ 0.0001	66 $\pm$ 7	0.0085 $\pm$ 0.001	0.75 $\pm$ 0.021
	Setting 2 $\text{KB}^{\text{GPT4}}$
	GPT-4	0.00028 $\pm$ 0.00009	67 $\pm$ 11	0.0067 $\pm$ 0.001	0.70 $\pm$ 0.025
	GRNBoost2	0.00020 $\pm$ 0.00004	57 $\pm$ 6	0.0049 $\pm$ 0.000	0.59 $\pm$ 0.019
	Random	0.00022 $\pm$ 0.00005	59 $\pm$ 7	0.0080 $\pm$ 0.000	0.76 $\pm$ 0.023
Bone Marrow	Baseline
	Control	0.00205 $\pm$ 0.00018	80 $\pm$ 4	0.0109 $\pm$ 0.001	0.60 $\pm$ 0.037
	Stage 1	0.00320 $\pm$ 0.00115	101 $\pm$ 16	0.0197 $\pm$ 0.007	0.66 $\pm$ 0.037
	$\text{KB}^{\text{Random}}$	0.00206 $\pm$ 0.00034	80 $\pm$ 7	0.0156 $\pm$ 0.002	0.75 $\pm$ 0.048
	Setting 1 $\text{KB}^{\text{H}}$
	GPT-4	0.00238 $\pm$ 0.00052	86 $\pm$ 9	0.0124 $\pm$ 0.001	0.70 $\pm$ 0.080
	GRNBoost2	0.00190 $\pm$ 0.00023	77 $\pm$ 5	0.0118 $\pm$ 0.001	0.64 $\pm$ 0.023
	Random	0.00219 $\pm$ 0.00030	82 $\pm$ 6	0.0150 $\pm$ 0.003	0.75 $\pm$ 0.041
	Setting 2 $\text{KB}^{\text{GPT4}}$
	GPT-4	0.00217 $\pm$ 0.00050	82 $\pm$ 10	0.0137 $\pm$ 0.003	0.72 $\pm$ 0.044
	GRNBoost2	0.00193 $\pm$ 0.00023	78 $\pm$ 4	0.0119 $\pm$ 0.001	0.64 $\pm$ 0.033
	Random	0.00297 $\pm$ 0.00080	96 $\pm$ 13	0.0172 $\pm$ 0.004	0.79 $\pm$ 0.046