Summary Statistics

48,779 pathway diagram images → 1.4M edges, 1.4M nodes, 3 KEGG assignment signals

Dataset Size

48,779

Images

1.38M

Edges

1.36M

Nodes

249

KEGG Pathways Hit

Data Samples

metadata.csv (20 columns)

One row per image. KEGG assignments from three independent signals plus Gemini's own label and related pathways.

pmc_id	filename	figure_number	gemini_label	gemini_related_pathways	n_genes	jaccard_kegg_id	jaccard_kegg_name	jaccard_score	caption_kegg_id	caption_kegg_name	caption_confidence	caption_reasoning	caption_jaccard	metadata_kegg_id	metadata_kegg_name	metadata_confidence	metadata_reasoning	metadata_jaccard	year
PMC5403593	PMC5403593__F2.jpg	F2	Cell cycle	MAPK/ERK signaling\|Hippo signaling\|PI3K-AKT signaling	2	hsa04392	Hippo signaling pathway - multiple species	0.03333						hsa04014	Ras signaling pathway	0.6	The paper's keywords explicitly list KRAS, RAS…	0.00000	2017
PMC5795421	PMC5795421__F2.jpg	F2	MicroRNA biogenesis	RNA interference\|Gene silencing\|Post-transcriptional regulation	5	hsa03013	Nucleocytoplasmic transport	0.00893						hsa03250	Viral life cycle - HIV-1	0.6	The paper discusses therapies to achieve an HI…	0.00000	2017
PMC6599049	PMC6599049__F6.jpg	F6	cGAS-STING signaling	Antiviral innate immunity\|Mitochondrial signaling	4	hsa04623	Cytosolic DNA-sensing pathway	0.04819	hsa04623	Cytosolic DNA-sensing pathway	0.9	The caption explicitly describes the mechanism…	0.04819	hsa04623	Cytosolic DNA-sensing pathway	0.9	The paper title and abstract explicitly attrib…	0.04819	2019
PMC4509066	PMC4509066__F2.jpg	F2	Apoptosis	Calcium signaling\|MAPK signaling\|G protein signaling	11	hsa04215	Apoptosis - multiple species	0.20000						hsa04210	Apoptosis	0.8	The abstract explicitly states that the 'most…	0.05755	2015
PMC3309942	PMC3309942__F1.jpg	F1	RANK signaling	NF-kB signaling\|Autophagy\|MAPK signaling	6	hsa04064	NF-kappa B signaling pathway	0.02778	hsa04064	NF-kappa B signaling pathway	1.0	The caption explicitly describes the role of p…	0.02778	hsa04064	NF-kappa B signaling pathway	0.8	The abstract details the role of p62 as a scaf…	0.02778	2012

edges.csv (7 columns)

One row per directed interaction extracted from a figure.

pmc_id	filename	figure_number	source	target	interaction	uncertain
PMC8096095	PMC8096095__F5.jpg	F5	CASP3	PARP1	inhibition	False
PMC8096095	PMC8096095__F5.jpg	F5	CASP3	Apoptosis	activation	False
PMC8096095	PMC8096095__F5.jpg	F5	DNA Damage	ATM	activation	False
PMC8096095	PMC8096095__F5.jpg	F5	ATM	TP53	activation	False
PMC8096095	PMC8096095__F5.jpg	F5	TP53	Apoptosis	activation	True

nodes.csv (8 columns)

One row per node extracted from a figure. Genes mapped to Entrez IDs where possible.

pmc_id	filename	figure_number	label	node_type	entrez_id	is_family_representative	notes
PMC5403593	PMC5403593__F2.jpg	F2	YAP1	gene	10413	False
PMC5403593	PMC5403593__F2.jpg	F2	ERK	gene		True	MAPK family
PMC5403593	PMC5403593__F2.jpg	F2	PI3K	complex		True
PMC5403593	PMC5403593__F2.jpg	F2	beta-catenin	gene	1499	False	CTNNB1
PMC5403593	PMC5403593__F2.jpg	F2	G0	phenotype		False	Quiescence

Per-Image Stats

	Nodes/Image	Edges/Image
mean	27.9	28.3
std	16.1	16.0
min	0	0
25%	16	16
50%	24	25
75%	35	37
max	135	194

Images by year, average nodes and edges per image over time

Left: image volume by publication year. Center/right: average graph complexity over time.

Signal Coverage

Three independent KEGG pathway assignment signals:

Jaccard (best-match) — gene-set overlap between image nodes and every KEGG pathway

Caption KEGG — LLM assignment from figure caption

Metadata KEGG — LLM assignment from paper title/abstract/MeSH

Signal	Images	Coverage
Jaccard (best-match)	47,526	97.4%
Caption KEGG	32,299	66.2%
Caption Jaccard	29,662	60.8%
Metadata KEGG	46,577	95.5%
Metadata Jaccard	44,200	90.6%
Caption OR Metadata	47,719	97.8%
Any signal	48,747	99.9%

Signal Agreement

Pairwise agreement on KEGG pathway assignment (n = 31,157 images with both caption and metadata):

Pair	Agree	Rate
Caption = Metadata	17,666	56.7%
Caption = Best Jaccard	9,799	31.5%
Metadata = Best Jaccard	7,584	24.3%
All 3 agree	6,687	21.5%

Agreement by Confidence Tier

Caption–Metadata agreement stratified by confidence. At 1.0/1.0, agreement reaches 88.9%.

Caption Conf	Metadata Conf	n	Agree	Rate
1.0	1.0	5,390	4,794	88.9%
1.0	0.8	6,415	4,540	70.8%
1.0	0.6	2,459	815	33.1%
0.8	1.0	822	414	50.4%
0.8	0.8	4,001	2,390	59.7%
0.8	0.6	2,826	1,052	37.2%
0.6	1.0	158	55	34.8%
0.6	0.8	592	241	40.7%
0.6	0.6	825	351	42.5%

Jaccard Score Distributions

	Best-match	Caption	Metadata
count	47,684	29,662	44,200
mean	0.093	0.070	0.053
std	0.084	0.088	0.071
25%	0.042	0.019	0.011
50%	0.068	0.043	0.031
75%	0.114	0.084	0.067
max	0.957	0.957	0.938

Best-match is highest by construction. Caption-assigned pathways have higher Jaccard than metadata-assigned, suggesting captions are more figure-specific.

Jaccard score histograms for best-match, caption-assigned, and metadata-assigned pathways.

Top 25 Genes

PI3K/AKT/mTOR axis dominates. AKT and Akt counted separately (case-sensitive Gemini labels).

#	Gene	Appearances	#	Gene	Appearances
1	PI3K	6,797	14	NF-kB	2,771
2	AKT	5,980	15	ERK1	2,663
3	mTOR	4,991	16	ERK2	2,655
4	Akt	4,290	17	TLR4	2,636
5	ERK	4,277	18	TRAF6	2,360
6	PTEN	3,627	19	MAPK	2,310
7	JNK	3,601	20	PKC	2,289
8	IL-6	3,277	21	MyD88	2,282
9	STAT3	3,134	22	PDK1	2,199
10	p53	3,115	23	beta-catenin	2,164
11	Ras	3,056	24	Wnt	2,059
12	EGFR	2,939	25	APC	2,000
13	MEK	2,842

Top 10 most frequently extracted genes by publication year.

Top 40 Pathways by Signal

Sorted by total count across all three signals. Jaccard favors smaller, specific pathways (ErbB, Prolactin) where gene overlap is high; LLM signals favor broader well-known pathways (PI3K-Akt, MAPK, JAK-STAT).

Pathway	Caption	Metadata	Jaccard
Toll-like receptor signaling	1,497	1,807	2,182
Wnt signaling	1,884	2,303	1,074
PI3K-Akt signaling	1,777	2,224	44
TGF-beta signaling	1,270	1,699	1,019
NF-kappa B signaling	1,035	1,437	1,041
ErbB signaling	453	699	2,160
MAPK signaling	1,233	1,668	97
Apoptosis	960	1,548	254
p53 signaling	473	669	1,474
JAK-STAT signaling	1,064	1,243	300
Apoptosis - multiple species	4	2	2,475
mTOR signaling	762	1,162	546
Hedgehog signaling	426	620	927
Cell cycle	620	920	391
VEGF signaling	214	383	1,289
Cytosolic DNA-sensing	380	409	1,001
RIG-I-like receptor signaling	414	469	842
HIF-1 signaling	390	533	800
Protein processing in ER	569	735	380
Adipocytokine signaling	232	406	1,001
Complement & coagulation cascades	359	611	608
Autophagy - animal	548	901	65
Hippo signaling	588	707	219
Insulin signaling	468	758	284
NOD-like receptor signaling	592	684	68
AMPK signaling	372	417	549
Prolactin signaling	28	41	1,241
Notch signaling	361	449	487
IL-17 signaling	110	188	987
Ferroptosis	338	384	547
Th17 cell differentiation	91	156	980
T cell receptor signaling	359	582	253
Pluripotency signaling	269	578	339
Glycolysis / Gluconeogenesis	354	559	211
Autophagy - other	7	7	1,095
TNF signaling	258	319	426
Adherens junction	65	93	838
PPAR signaling	262	460	223
Fc epsilon RI signaling	40	67	794
Regulation of actin cytoskeleton	306	513	45

Top 10 pathways (by metadata signal) over publication year.

Full Distribution — All 249 Pathways

249 KEGG pathways have at least one figure assigned by any signal:

Signal	Pathways with ≥1 figure
Caption	229
Metadata	240
Jaccard	237

All 249 KEGG pathways with figure counts from each assignment signal.