id	sid	tid	token	lemma	pos
ht24wh26f73	1	1	biocomplexity	biocomplexity	NOUN
ht24wh26f73	1	2	is	be	AUX
ht24wh26f73	1	3	the	the	DET
ht24wh26f73	1	4	study	study	NOUN
ht24wh26f73	1	5	of	of	ADP
ht24wh26f73	1	6	the	the	DET
ht24wh26f73	1	7	complex	complex	ADJ
ht24wh26f73	1	8	relationships	relationship	NOUN
ht24wh26f73	1	9	among	among	ADP
ht24wh26f73	1	10	biological	biological	ADJ
ht24wh26f73	1	11	entities	entity	NOUN
ht24wh26f73	1	12	that	that	PRON
ht24wh26f73	1	13	are	be	AUX
ht24wh26f73	1	14	responsible	responsible	ADJ
ht24wh26f73	1	15	for	for	ADP
ht24wh26f73	1	16	life	life	NOUN
ht24wh26f73	1	17	.	.	PUNCT
ht24wh26f73	2	1	this	this	DET
ht24wh26f73	2	2	dissertation	dissertation	NOUN
ht24wh26f73	2	3	addresses	address	VERB
ht24wh26f73	2	4	two	two	NUM
ht24wh26f73	2	5	important	important	ADJ
ht24wh26f73	2	6	computational	computational	ADJ
ht24wh26f73	2	7	in	in	ADP
ht24wh26f73	2	8	biocomplexity	biocomplexity	NOUN
ht24wh26f73	2	9	:	:	PUNCT
ht24wh26f73	2	10	morphogenesis	morphogenesis	NOUN
ht24wh26f73	2	11	and	and	CCONJ
ht24wh26f73	2	12	protein	protein	NOUN
ht24wh26f73	2	13	-	-	PUNCT
ht24wh26f73	2	14	protein	protein	NOUN
ht24wh26f73	2	15	interaction	interaction	NOUN
ht24wh26f73	2	16	networks	network	NOUN
ht24wh26f73	2	17	.	.	PUNCT
ht24wh26f73	3	1	morphogenesis	morphogenesis	NOUN
ht24wh26f73	3	2	is	be	AUX
ht24wh26f73	3	3	the	the	DET
ht24wh26f73	3	4	development	development	NOUN
ht24wh26f73	3	5	of	of	ADP
ht24wh26f73	3	6	multicellular	multicellular	ADJ
ht24wh26f73	3	7	organisms	organism	NOUN
ht24wh26f73	3	8	.	.	PUNCT
ht24wh26f73	4	1	i	i	PRON
ht24wh26f73	4	2	develop	develop	VERB
ht24wh26f73	4	3	models	model	NOUN
ht24wh26f73	4	4	,	,	PUNCT
ht24wh26f73	4	5	algorithms	algorithm	NOUN
ht24wh26f73	4	6	,	,	PUNCT
ht24wh26f73	4	7	and	and	CCONJ
ht24wh26f73	4	8	software	software	NOUN
ht24wh26f73	4	9	that	that	PRON
ht24wh26f73	4	10	integrate	integrate	VERB
ht24wh26f73	4	11	the	the	DET
ht24wh26f73	4	12	genetic	genetic	ADJ
ht24wh26f73	4	13	regulatory	regulatory	ADJ
ht24wh26f73	4	14	network	network	NOUN
ht24wh26f73	4	15	and	and	CCONJ
ht24wh26f73	4	16	physical	physical	ADJ
ht24wh26f73	4	17	or	or	CCONJ
ht24wh26f73	4	18	generic	generic	ADJ
ht24wh26f73	4	19	cellular	cellular	ADJ
ht24wh26f73	4	20	mechanisms	mechanism	NOUN
ht24wh26f73	4	21	that	that	PRON
ht24wh26f73	4	22	explain	explain	VERB
ht24wh26f73	4	23	how	how	SCONJ
ht24wh26f73	4	24	cells	cell	NOUN
ht24wh26f73	4	25	interact	interact	VERB
ht24wh26f73	4	26	to	to	PART
ht24wh26f73	4	27	form	form	VERB
ht24wh26f73	4	28	tissues	tissue	NOUN
ht24wh26f73	4	29	.	.	PUNCT
ht24wh26f73	5	1	the	the	DET
ht24wh26f73	5	2	genetic	genetic	ADJ
ht24wh26f73	5	3	regulation	regulation	NOUN
ht24wh26f73	5	4	is	be	AUX
ht24wh26f73	5	5	modeled	model	VERB
ht24wh26f73	5	6	by	by	ADP
ht24wh26f73	5	7	a	a	DET
ht24wh26f73	5	8	combination	combination	NOUN
ht24wh26f73	5	9	of	of	ADP
ht24wh26f73	5	10	a	a	DET
ht24wh26f73	5	11	rule	rule	NOUN
ht24wh26f73	5	12	-	-	PUNCT
ht24wh26f73	5	13	based	base	VERB
ht24wh26f73	5	14	state	state	NOUN
ht24wh26f73	5	15	automaton	automaton	PROPN
ht24wh26f73	5	16	and	and	CCONJ
ht24wh26f73	5	17	a	a	DET
ht24wh26f73	5	18	set	set	NOUN
ht24wh26f73	5	19	of	of	ADP
ht24wh26f73	5	20	partial	partial	ADJ
ht24wh26f73	5	21	differential	differential	ADJ
ht24wh26f73	5	22	equations	equation	NOUN
ht24wh26f73	5	23	(	(	PUNCT
ht24wh26f73	5	24	pdes	pde	NOUN
ht24wh26f73	5	25	)	)	PUNCT
ht24wh26f73	5	26	;	;	PUNCT
ht24wh26f73	5	27	the	the	DET
ht24wh26f73	5	28	generic	generic	ADJ
ht24wh26f73	5	29	cellular	cellular	ADJ
ht24wh26f73	5	30	mechanisms	mechanism	NOUN
ht24wh26f73	5	31	include	include	VERB
ht24wh26f73	5	32	cell	cell	NOUN
ht24wh26f73	5	33	adhesion	adhesion	NOUN
ht24wh26f73	5	34	,	,	PUNCT
ht24wh26f73	5	35	cell	cell	NOUN
ht24wh26f73	5	36	differentiation	differentiation	NOUN
ht24wh26f73	5	37	,	,	PUNCT
ht24wh26f73	5	38	cell	cell	NOUN
ht24wh26f73	5	39	growth	growth	NOUN
ht24wh26f73	5	40	,	,	PUNCT
ht24wh26f73	5	41	mitosis	mitosis	NOUN
ht24wh26f73	5	42	,	,	PUNCT
ht24wh26f73	5	43	secretion	secretion	NOUN
ht24wh26f73	5	44	of	of	ADP
ht24wh26f73	5	45	morphogens	morphogen	NOUN
ht24wh26f73	5	46	,	,	PUNCT
ht24wh26f73	5	47	haptotaxis	haptotaxis	ADJ
ht24wh26f73	5	48	and	and	CCONJ
ht24wh26f73	5	49	chemotaxis.protein	chemotaxis.protein	NOUN
ht24wh26f73	5	50	networks	network	NOUN
ht24wh26f73	5	51	are	be	AUX
ht24wh26f73	5	52	part	part	NOUN
ht24wh26f73	5	53	of	of	ADP
ht24wh26f73	5	54	signaling	signaling	NOUN
ht24wh26f73	5	55	,	,	PUNCT
ht24wh26f73	5	56	metabolic	metabolic	NOUN
ht24wh26f73	5	57	,	,	PUNCT
ht24wh26f73	5	58	and	and	CCONJ
ht24wh26f73	5	59	other	other	ADJ
ht24wh26f73	5	60	biological	biological	ADJ
ht24wh26f73	5	61	pathways	pathway	NOUN
ht24wh26f73	5	62	important	important	ADJ
ht24wh26f73	5	63	to	to	ADP
ht24wh26f73	5	64	cells	cell	NOUN
ht24wh26f73	5	65	and	and	CCONJ
ht24wh26f73	5	66	organisms	organism	NOUN
ht24wh26f73	5	67	.	.	PUNCT
ht24wh26f73	6	1	we	we	PRON
ht24wh26f73	6	2	develop	develop	VERB
ht24wh26f73	6	3	a	a	DET
ht24wh26f73	6	4	new	new	ADJ
ht24wh26f73	6	5	algorithm	algorithm	NOUN
ht24wh26f73	6	6	called	call	VERB
ht24wh26f73	6	7	maximum	maximum	ADJ
ht24wh26f73	6	8	specificity	specificity	NOUN
ht24wh26f73	6	9	set	set	NOUN
ht24wh26f73	6	10	cover	cover	NOUN
ht24wh26f73	6	11	(	(	PUNCT
ht24wh26f73	6	12	mssc	mssc	PROPN
ht24wh26f73	6	13	)	)	PUNCT
ht24wh26f73	6	14	to	to	PART
ht24wh26f73	6	15	predict	predict	VERB
ht24wh26f73	6	16	protein	protein	NOUN
ht24wh26f73	6	17	-	-	PUNCT
ht24wh26f73	6	18	protein	protein	NOUN
ht24wh26f73	6	19	interactions	interaction	NOUN
ht24wh26f73	6	20	.	.	PUNCT
ht24wh26f73	7	1	the	the	DET
ht24wh26f73	7	2	predictions	prediction	NOUN
ht24wh26f73	7	3	by	by	ADP
ht24wh26f73	7	4	mssc	mssc	PROPN
ht24wh26f73	7	5	preserve	preserve	VERB
ht24wh26f73	7	6	not	not	PART
ht24wh26f73	7	7	only	only	ADV
ht24wh26f73	7	8	the	the	DET
ht24wh26f73	7	9	topological	topological	ADJ
ht24wh26f73	7	10	characteristics	characteristic	NOUN
ht24wh26f73	7	11	of	of	ADP
ht24wh26f73	7	12	protein	protein	NOUN
ht24wh26f73	7	13	interaction	interaction	NOUN
ht24wh26f73	7	14	networks	network	NOUN
ht24wh26f73	7	15	,	,	PUNCT
ht24wh26f73	7	16	but	but	CCONJ
ht24wh26f73	7	17	also	also	ADV
ht24wh26f73	7	18	the	the	DET
ht24wh26f73	7	19	protein	protein	NOUN
ht24wh26f73	7	20	co	co	NOUN
ht24wh26f73	7	21	-	-	NOUN
ht24wh26f73	7	22	expression	expression	NOUN
ht24wh26f73	7	23	.	.	PUNCT
ht24wh26f73	8	1	our	our	PRON
ht24wh26f73	8	2	method	method	NOUN
ht24wh26f73	8	3	outscores	outscore	VERB
ht24wh26f73	8	4	other	other	ADJ
ht24wh26f73	8	5	prediction	prediction	NOUN
ht24wh26f73	8	6	methods	method	NOUN
ht24wh26f73	8	7	in	in	ADP
ht24wh26f73	8	8	quality	quality	NOUN
ht24wh26f73	8	9	.	.	PUNCT