Linguistic Pattern-Aware Dependency Tree Kernel (LPTK) Patterns: This supplementary contains linguistic patterns obtained via separate experiments on abstracts from CDR, CHEMPROT and PPI corpus. Since the relational entities are different for each corpus, we have showcased patterns from each dataset in separate sections structured as: - Chemical Induced Disease (CID) Patterns - Chemical Protein Relation (CPR) Patterns - Protein Protein Interaction (PPI) Patterns Respective section for each relation type contain top 10 pattern hits for each interaction type (+ve and -ve) from each task. Original pattern dump contain sizeable number of interaction patterns (upto 800 for each corpus). Therefore, to furnish task specificity and convey the readability of the generated patterns, we enlisted a sufficient number for representation purpose. Representation format for patterns is universal across all datasets with the exception of normalized Entity name. Each pattern is defined in a group of 3 contexts as mentioned below: pattern(interaction-type/interaction-class):[pattern-id] RELATION |POS-TAG pattern for RELATION ENTITY1 |POS-TAG pattern for ENTITY1 ENTITY2 |POS-TAG pattern for ENTITY2 where RELATION - normalized proximal-verb term ENTITY1 - replaced by CHEMICAL or PROTEINAGENT : normalized-term in CID,CPR and PPI respectively ENTITY2 - replaced by DISEASE or GENEPRO or PROTEINTARGET : normalized-term in CID,CPR and PPI respectively interaction-type/class - represent +ve/-ve or sub-class type for interaction e.g. In CPR interactions are represented by class:9,6,5,4,3 and non-interacting class:-1. In CID and PPI, interaction and non-interaction is represented by 1 and -1 respectively. All the 3/2 contexts in each pattern are used in optimizing feature representation via pruning GRCT (depending upon interaction type i.e. +ve/-ve). ************************************************************************************* Chemical Induced Disease (CID) Patterns pattern1:1 RELATION |VBN TO CHEMICALPRI VBD RELATION CHEMICAL |IN DISEASE VBN TO CHEMICALPRI DISEASE |NN NNS VBD JJ DISEASEPRI pattern1:2 RELATION |RELATION CHEMICAL |NN IN CHEMICAL CC CHEMICALPRI DISEASE |RELATION NN IN DISEASEPRI pattern1:3 RELATION |RELATION CHEMICAL |RELATION CHEMICALPRI DISEASE |RELATION CHEMICALPRI RB RB DISEASEPRI pattern1:4 RELATION |IN CHEMICAL IN CHEMICALPRI RELATION CHEMICAL |NN IN CHEMICAL IN CHEMICALPRI DISEASE |CHEMICAL IN CHEMICALPRI RELATION DISEASEPRI pattern1:5 RELATION |. CD NNS CD RELATION CHEMICAL |NN VBD VBN IN CHEMICALPRI DISEASE |CD VBD NNP CD DISEASEPRI pattern1:6 RELATION |NN NN CHEMICALPRI NNS RELATION CHEMICAL |VBN IN NN NN CHEMICALPRI DISEASE |CD CC CD IN DISEASEPRI pattern1:7 RELATION |RBR JJ JJ NNS RELATION CHEMICAL |CC DISEASE . CHEMICAL CHEMICALPRI DISEASE |JJ JJ NNS RELATION DISEASEPRI pattern1:8 RELATION |IN CHEMICAL IN CHEMICALPRI RELATION CHEMICAL |NNS IN CHEMICAL IN CHEMICALPRI DISEASE |CHEMICAL IN CHEMICALPRI RELATION DISEASEPRI pattern1:9 RELATION |IN DISEASE . PRP RELATION CHEMICAL |NN VBD VBN IN CHEMICALPRI DISEASE |. PRP RELATION DISEASE DISEASEPRI pattern1:10 RELATION |DT RBS RB RELATION CHEMICAL |RELATION JJ NNS IN CHEMICALPRI DISEASE |DISEASE DISEASE DISEASE CC DISEASEPRI pattern-1:1 CHEMICAL |CHEMICALPRI DISEASE |IN JJ DISEASE IN DISEASEPRI pattern-1:2 CHEMICAL |CHEMICALPRI DISEASE |DT JJ NN TO DISEASEPRI pattern-1:3 CHEMICAL |CHEMICALPRI DISEASE |CHEMICALPRI VBZ DISEASEPRI pattern-1:4 CHEMICAL |CHEMICALPRI DISEASE |CHEMICALPRI DISEASEPRI pattern-1:5 CHEMICAL |DT JJ NN IN CHEMICALPRI DISEASE |NN IN CHEMICAL VBD DISEASEPRI pattern-1:6 CHEMICAL |NN IN CHEMICAL CC CHEMICALPRI DISEASE |NN IN CHEMICAL VBD DISEASEPRI pattern-1:7 CHEMICAL |NN IN CHEMICAL CC CHEMICALPRI DISEASE |IN DT NN IN DISEASEPRI pattern-1:8 CHEMICAL |DT JJ NN IN CHEMICALPRI DISEASE |DT NN IN JJ DISEASEPRI pattern-1:9 CHEMICAL |NN IN CHEMICAL CC CHEMICALPRI DISEASE |DT NN IN JJ DISEASEPRI pattern-1:10 CHEMICAL |DT JJ NN IN CHEMICALPRI DISEASE |NNS IN CHEMICAL VBD DISEASEPRI ************************************************************************************* Chemical Protein Relation (CPR) Patterns pattern9:1 RELATION |RELATION GENEPROPRI VBN CHEMICAL |CHEMICALPRI RELATION GENEPROPRI GENEPRO |GENEPROPRI VBN CHEMICALPRI pattern9:2 RELATION |RELATION GENEPROPRI VBG CHEMICAL |CHEMICALPRI CD CC GENEPRO |GENEPROPRI VBG NNS pattern9:3 RELATION |RELATION RB GENEPROPRI CHEMICAL |CHEMICALPRI CC JJS GENEPRO |GENEPROPRI VBG NN pattern9:4 RELATION |RELATION IN CD CHEMICAL |CHEMICALPRI NN CD GENEPRO |GENEPROPRI NN CD pattern9:5 RELATION |RELATION . . CHEMICAL |CHEMICALPRI . . GENEPRO |GENEPROPRI . NN pattern9:6 RELATION |RELATION NN VBZ CHEMICAL |CHEMICALPRI RELATION NN GENEPRO |GENEPROPRI DT CHEMICALPRI pattern9:7 RELATION |RELATION RB TO CHEMICAL |CHEMICALPRI WDT VBZ GENEPRO |GENEPROPRI TO CHEMICALPRI pattern9:8 RELATION |RELATION NNS NN CHEMICAL |CHEMICALPRI FW FW GENEPRO |GENEPROPRI JJ NN pattern9:9 RELATION |RELATION CHEMICALPRI GENEPROPRI CHEMICAL |CHEMICALPRI GENEPROPRI VBZ GENEPRO |GENEPROPRI GENEPRO VBG pattern9:10 RELATION |RELATION . . CHEMICAL |CHEMICALPRI . . GENEPRO |GENEPROPRI . . pattern6:1 RELATION |NN RELATION GENEPROPRI CHEMICAL |CHEMICALPRI VBZ GENEPRO |RELATION GENEPROPRI NN pattern6:2 RELATION |RELATION CC PRP$ CHEMICAL |CHEMICALPRI VBG NNS GENEPRO |GENEPROPRI NNS VBD pattern6:3 RELATION |RELATION . . CHEMICAL |CHEMICALPRI . . GENEPRO |GENEPROPRI . . pattern6:4 RELATION |RELATION IN IN CHEMICAL |CHEMICALPRI IN GENEPROPRI GENEPRO |GENEPROPRI RELATION IN pattern6:5 RELATION |RELATION TO DT CHEMICAL |CHEMICALPRI JJ NN GENEPRO |GENEPROPRI NEGVBD NEGRB pattern6:6 RELATION |RELATION . CHEMICAL CHEMICAL |CHEMICALPRI . . GENEPRO |GENEPROPRI . . pattern6:7 RELATION |RELATION RP CHEMICAL |CHEMICALPRI VBP JJ GENEPRO |GENEPROPRI IN NN pattern6:8 RELATION |RELATION JJ NNS CHEMICAL |CHEMICALPRI RELATION JJ GENEPRO |GENEPROPRI DT NNS pattern6:9 RELATION |RELATION JJ NNS CHEMICAL |CHEMICALPRI IN NN GENEPRO |GENEPROPRI . . pattern6:10 RELATION |RELATION IN JJ CHEMICAL |CHEMICALPRI VBD JJ GENEPRO |GENEPROPRI NNS NN pattern5:1 RELATION |RELATION NNS IN CHEMICAL |CHEMICALPRI CC IN GENEPRO |GENEPROPRI NNS GENEPRO pattern5:2 RELATION |RELATION VBZ DT CHEMICAL |CHEMICALPRI RB RELATION GENEPRO |GENEPROPRI DT CHEMICAL pattern5:3 RELATION |RELATION CHEMICALPRI VBN CHEMICAL |CHEMICALPRI VBN NN GENEPRO |GENEPROPRI NNS CHEMICAL pattern5:4 RELATION |RELATION IN NNS CHEMICAL |CHEMICALPRI WDT VBP GENEPRO |GENEPROPRI VBZ RELATION pattern5:5 RELATION |RELATION CHEMICALPRI JJ CHEMICAL |CHEMICALPRI JJ NN GENEPRO |GENEPROPRI . . pattern5:6 RELATION |RELATION DT RB CHEMICAL |CHEMICALPRI CHEMICAL NNP GENEPRO |GENEPROPRI GENEPRO NN pattern5:7 RELATION |RELATION IN CC CHEMICAL |CHEMICALPRI NN CC GENEPRO |GENEPROPRI CC NN pattern5:8 RELATION |RELATION IN GENEPROPRI CHEMICAL |CHEMICALPRI VBD TO GENEPRO |GENEPROPRI VBN NN pattern5:9 RELATION |RELATION RB RB CHEMICAL |CHEMICALPRI GENEPRO CC GENEPRO |GENEPROPRI VBZ VBN pattern5:10 RELATION |RELATION TO VB CHEMICAL |CHEMICALPRI VBD RELATION GENEPRO |GENEPROPRI IN NNS pattern4:1 RELATION |RELATION JJS TO CHEMICAL |CHEMICALPRI GENEPROPRI VBZ GENEPRO |GENEPROPRI RELATION JJS pattern4:2 RELATION |IN RELATION GENEPROPRI CHEMICAL |GENEPROPRI CHEMICALPRI CHEMICAL GENEPRO |RELATION GENEPROPRI CHEMICALPRI pattern4:3 RELATION |RELATION . . CHEMICAL |CHEMICALPRI . . GENEPRO |GENEPROPRI JJ NNS pattern4:4 RELATION |RELATION CD JJR CHEMICAL |CHEMICALPRI RELATION CD GENEPRO |GENEPROPRI CD RBR pattern4:5 RELATION |GENEPROPRI RELATION CHEMICALPRI CHEMICAL |RELATION CHEMICALPRI NNS GENEPRO |IN GENEPROPRI RELATION pattern4:6 RELATION |RELATION VBN RB CHEMICAL |CHEMICALPRI PRP RELATION GENEPRO |GENEPROPRI VBZ DT pattern4:7 RELATION |RELATION CHEMICALPRI CHEMICAL |RELATION CHEMICALPRI IN GENEPRO |NN GENEPROPRI GENEPRO pattern4:8 RELATION |RELATION NN CHEMICAL CHEMICAL |CHEMICALPRI NN DT GENEPRO |GENEPROPRI CHEMICAL CC pattern4:9 RELATION |RELATION RB GENEPROPRI CHEMICAL |CHEMICALPRI RB RB GENEPRO |GENEPROPRI VBN NNS pattern4:10 RELATION |RELATION . . CHEMICAL |CHEMICALPRI . . GENEPRO |GENEPROPRI . . pattern3:1 RELATION |RELATION CD SYM CHEMICAL |CHEMICALPRI VBD RELATION GENEPRO |GENEPROPRI NN TO pattern3:2 RELATION |RELATION CD JJR CHEMICAL |CHEMICALPRI RELATION CD GENEPRO |GENEPROPRI . . pattern3:3 RELATION |RELATION GENEPROPRI VBG CHEMICAL |CHEMICALPRI CHEMICAL NN GENEPRO |GENEPROPRI VBG TO pattern3:4 RELATION |RELATION GENEPROPRI GENEPRO CHEMICAL |CHEMICALPRI NEGVBD NEGDT GENEPRO |GENEPROPRI GENEPRO RB pattern3:5 RELATION |RELATION IN GENEPRO CHEMICAL |CHEMICALPRI NNS VBD GENEPRO |GENEPROPRI NNS VBD pattern3:6 RELATION |GENEPROPRI RELATION NN CHEMICAL |NN CHEMICALPRI CC GENEPRO |CHEMICAL GENEPROPRI RELATION pattern3:7 RELATION |RELATION TO CHEMICAL CHEMICAL |CHEMICALPRI CC VBD GENEPRO |GENEPROPRI TO DT pattern3:8 RELATION |RELATION JJ TO CHEMICAL |CHEMICALPRI JJ TO GENEPRO |GENEPROPRI VBN IN pattern3:9 RELATION |RELATION GENEPROPRI JJ CHEMICAL |CHEMICALPRI NNS DT GENEPRO |GENEPROPRI JJ TO pattern3:10 RELATION |RELATION TO VB CHEMICAL |CHEMICALPRI VBD RB GENEPRO |GENEPROPRI CC VB pattern-1:1 CHEMICAL |CHEMICALPRI GENEPROPRI GENEPRO |CHEMICALPRI GENEPROPRI VBD pattern-1:2 CHEMICAL |DT CHEMICALPRI GENEPROPRI GENEPRO |CHEMICALPRI GENEPROPRI CHEMICAL pattern-1:3 CHEMICAL |CHEMICALPRI CC NEGRB GENEPRO |GENEPROPRI NN NEGVBD pattern-1:4 CHEMICAL |GENEPRO CHEMICALPRI GENEPROPRI GENEPRO |CHEMICALPRI GENEPROPRI GENEPRO pattern-1:5 CHEMICAL |GENEPROPRI CHEMICALPRI CD GENEPRO |NN GENEPROPRI CHEMICALPRI pattern-1:6 CHEMICAL |DT CHEMICALPRI GENEPRO GENEPRO |GENEPROPRI NNS pattern-1:7 CHEMICAL |CHEMICALPRI NEGNEGVBZ GENEPRO |IN GENEPROPRI JJ pattern-1:8 CHEMICAL |CHEMICALPRI . NEGRB GENEPRO |GENEPROPRI CC . pattern-1:9 CHEMICAL |GENEPROPRI CHEMICALPRI JJ GENEPRO |JJ GENEPROPRI CHEMICALPRI pattern-1:10 CHEMICAL |CHEMICALPRI WDT GENEPRO |DT GENEPROPRI VBD ************************************************************************************* Protein Protein Interaction (PPI) Patterns pattern1:1 RELATION |IN RELATION PROTEINAGENTPRI PROTEINAGENT |RELATION PROTEINAGENTPRI PROTEINTARGETPRI PROTEINTARGET |PROTEINAGENTPRI PROTEINTARGETPRI JJ pattern1:2 RELATION |PROTEIN RELATION PROTEINTARGETPRI PROTEINAGENT |PROTEINAGENTPRI PROTEIN PROTEINTARGET |RELATION PROTEINTARGETPRI DT pattern1:3 RELATION |PROTEINAGENTPRI RELATION PROTEINTARGETPRI PROTEINAGENT |PROTEINAGENTPRI RELATION PROTEINTARGET |RELATION PROTEINTARGETPRI JJ pattern1:4 RELATION |RELATION JJR PROTEIN PROTEINAGENT |PROTEINAGENTPRI RELATION JJR PROTEINTARGET |PROTEINTARGETPRI IN VBZ pattern1:5 RELATION |RELATION JJR NN PROTEINAGENT |PROTEINAGENTPRI RELATION JJR PROTEINTARGET |PROTEINTARGETPRI IN VBD pattern1:6 RELATION |PROTEINTARGETPRI RELATION NN PROTEINAGENT |PROTEINAGENTPRI PROTEIN PROTEINTARGET |DT PROTEINTARGETPRI RELATION pattern1:7 RELATION |PROTEINAGENTPRI RELATION PROTEINTARGETPRI PROTEINAGENT |PROTEINAGENTPRI RELATION PROTEINTARGET |RELATION PROTEINTARGETPRI TO pattern1:8 RELATION |RELATION NN MD PROTEINAGENT |PROTEINAGENTPRI WDT IN PROTEINTARGET |PROTEINTARGETPRI NNS TO pattern1:9 RELATION |NN RELATION PROTEINTARGETPRI PROTEINAGENT |PROTEINAGENTPRI CD PROTEINTARGET |RELATION PROTEINTARGETPRI CC pattern1:10 RELATION |RELATION PRP TO PROTEINAGENT |PROTEINAGENTPRI TO JJ PROTEINTARGET |PROTEINTARGETPRI RELATION PRP pattern-1:1 PROTEINAGENT |PROTEINAGENTPRI CD SYM PROTEINTARGET |PROTEINTARGETPRI CD SYM pattern-1:2 PROTEINAGENT |PROTEINAGENTPRI VBD PROTEINTARGET |VBD PROTEINTARGETPRI VBN pattern-1:3 PROTEINAGENT |PROTEINAGENTPRI VBD JJR PROTEINTARGET |PROTEINTARGETPRI IN VBD pattern-1:4 PROTEINAGENT |PROTEINAGENTPRI VBD PROTEINTARGET |IN PROTEINTARGETPRI CD pattern-1:5 PROTEINAGENT |PROTEINAGENTPRI PROTEINTARGETPRI . PROTEINTARGET |PROTEINTARGETPRI . . pattern-1:6 PROTEINAGENT |PROTEINAGENTPRI WP$ NN PROTEINTARGET |PROTEINTARGETPRI RB NN pattern-1:7 PROTEINAGENT |PROTEINAGENTPRI VBD RBS PROTEINTARGET |PROTEINTARGETPRI JJ JJ pattern-1:8 PROTEINAGENT |PROTEINAGENTPRI NN PROTEINTARGET |DT PROTEINTARGETPRI WDT pattern-1:9 PROTEINAGENT |PROTEINAGENTPRI WDT PROTEINTARGET |NN PROTEINTARGETPRI CC pattern-1:10 PROTEINAGENT |PROTEINAGENTPRI VBD PROTEINTARGET |CD PROTEINTARGETPRI IN