Workshop	
  Notes	
  
                                                      	
  




                                                                                                                               	
  
                                                                	
  
                                                                	
  
                                                                	
  
                                   Second	
  international	
  workshop	
  on	
  
                                                      	
  
       Advances	
  in	
  Bioinformatics	
  and	
  Artificial	
  Intelligence:	
  
                            Bridging	
  the	
  Gap	
  (BAI)	
  
                                          	
  
	
  
                                                           	
  
                                   New-­‐York	
  city,	
  USA,	
  July	
  11,	
  2016	
  
                                                           	
  
                                http://bioinfo.uqam.ca/IJCAI_BAI2016/	
  
	
  
	
  
	
  
Editors	
  :	
  
Names	
                                  Affiliations	
  
Abdoulaye	
  Baniré	
  Diallo	
          University	
  of	
  Quebec	
  at	
  Montreal	
  (Canada)	
  
                                         Diallo.abdoulaye@uqam.ca	
  	
  
                                         http://labo.bioinfo.uqam.ca	
  	
  
Engelbert	
  Mephu	
  Nguifo	
           LIMOS,	
  Blaise	
  Pascal	
  University	
  (France)	
  
                                         mephu@isima.fr	
  
                                         http://www.isima.fr/mephu	
  	
  
Mohammed	
  Zaki	
                       Rensselaer	
  Polytechnic	
  Institute,	
  NY	
  (USA)	
  
                                         zaki@cs.rpi.edu	
  	
  
                                         http://www.cs.rpi.edu/~zaki/	
  	
  
                                                                	
  
Proceedings	
  managers	
  :	
  
	
                                       	
  
Wajdi	
  Dhifli	
   	
                   ISSB,	
  University	
  of	
  Evry-­‐Val-­‐d'Essonne,	
  Evry,	
  (France)	
  
Jerry	
  Lonlac	
  Konlac	
              LIMOS,	
  Blaise	
  Pascal	
  University,	
  Clermont-­‐Ferrand	
  (France)	
  	
  
                                                           Preface	
  
	
  
The	
  goal	
  of	
  this	
  workshop	
  called	
  Bioinformatics	
  and	
  Artificial	
  Intelligence	
  (BAI)	
  is	
  to	
  
bring	
   together	
   active	
   scholars	
   and	
   practitioners	
   at	
   the	
   frontiers	
   of	
   Artificial	
  
Intelligence	
  (AI)	
  and	
  Bioinformatics.	
  AI	
  holds	
  a	
  tremendous	
  repertoire	
  of	
  algorithms	
  
and	
   methods	
   that	
   constitute	
   the	
   core	
   of	
   different	
   topics	
   of	
   bioinformatics	
   and	
  
computational	
  biology	
  research.	
  BAI	
  goals	
  are	
  twofolds	
  :	
  	
  
       -­‐ How	
  can	
  AI	
  techniques	
  contribute	
  to	
  bioinformatics	
  research	
  ?,	
  and	
  	
  
       -­‐ How	
  can	
  bioinformatics	
  research	
  raise	
  new	
  fundamental	
  questions	
  in	
  AI	
  ?	
  
Contributions	
   clearly	
   points	
   out	
   answers	
   to	
   one	
   of	
   these	
   goals	
   focusing	
   on	
   AI	
  
techniques	
  as	
  well	
  as	
  focusing	
  on	
  biological	
  problems.	
  	
  
	
  
Aims	
  and	
  Scope	
  :	
  
AI	
  has	
  played	
  an	
  increasingly	
  important	
  role	
  in	
  the	
  analysis	
  of	
  sequence,	
  structure	
  
and	
  functional	
  patterns	
  or	
  models	
  from	
  sequence	
  databases.	
  Bioinformatics	
  aims	
  to	
  
store,	
   organize,	
   explore,	
   extract,	
   analyze,	
   interpret,	
   and	
   utilize	
   information	
   from	
  
biological	
   data.	
   The	
   main	
   outcome	
   of	
   this	
   workshop	
   is	
   to	
   present	
   latest	
   results	
   in	
  
this	
  exciting	
  area	
  at	
  the	
  intersection	
  of	
  biology	
  and	
  AI.	
  	
  
	
  
AI	
   approaches	
   can	
   revolutionize	
   new	
   age	
   of	
   bioinformatics	
   and	
   computational	
  
biology	
  with	
  discoveries	
  in	
  basic	
  biology,	
  evolution,	
  metagenomics,	
  system	
  biology,	
  
regulatory	
   genomics,	
   population	
   genomics	
   and	
   diseases,	
   structural	
   bioinformatics,	
  
protein	
   docking,	
   next-­‐generation	
   sequencing	
   (NGS)	
   data	
   processing,	
  
chemoinformatics,	
  	
  etc.	
  	
  
	
  
Bioinformatics	
  provides	
  opportunities	
  for	
  developing	
  novel	
  AI	
  methods.	
  Some	
  of	
  the	
  
grand	
   challenges	
   in	
   bioinformatics	
   include	
   protein	
   structure	
   prediction,	
   homology	
  
search,	
   epigenetics,	
   multiple	
   alignment	
   and	
   phylogeny	
   construction,	
   genomic	
  
sequence	
   analysis,	
   gene	
   finding	
   and	
   gene	
   mapping,	
   as	
   well	
   as	
   applications	
   in	
   gene	
  
expression	
  data	
  analysis,	
  drug	
  discovery	
  in	
  pharmaceutical	
  industry,	
  etc.	
  	
  
	
  
Two	
  questions	
  were	
  at	
  the	
  heart	
  of	
  this	
  workshop	
  :	
  
       -­‐ How	
   can	
   AI	
   techniques	
   contribute	
   to	
   Bioinformatics	
   research,	
   and	
   in	
  
             particular	
  dealing	
  with	
  biological	
  problems	
  ?	
  
       -­‐ How	
   can	
   Bioinformatics	
   raise	
   new	
   fundamental	
   research	
   problem	
   for	
   AI	
  
             research	
  ?	
  
	
  
This	
  one-­‐day	
  workshop	
  aims	
  at	
  bringing	
  together	
  scholars	
  and	
  practitioners	
  active	
  
in	
  Artificial	
  Intelligence	
  driven	
  Bioinformatics,	
  to	
  present	
  and	
  discuss	
  their	
  research,	
  
share	
  their	
  knowledge	
  and	
  experiences,	
  and	
  discuss	
  the	
  current	
  state	
  of	
  the	
  art	
  and	
  
the	
   future	
   improvements	
   to	
   advance	
   the	
   intelligent	
   practice	
   of	
   computational	
  
biology.	
  
	
  
	
  
  Workshop	
  topics	
  :	
  
  Topics	
  of	
  interest	
  lie	
  at	
  the	
  intersection	
  of	
  AI	
  and	
  Bioinformatics.	
  They	
  include,	
  but	
  
  are	
  not	
  limited	
  to,	
  the	
  following	
  inter-­‐linked	
  topics:	
  	
  

  Artificial	
  Intelligence	
  :	
  
       -­‐   Constraints,	
  satisfiability	
  and	
  search	
  
       -­‐   Knowledge	
  representation,	
  reasoning	
  and	
  logic	
  
       -­‐   Machine	
  learning	
  and	
  data	
  mining	
  
       -­‐   Planning	
  and	
  scheduling	
  
       -­‐   Agent-­‐based	
  and	
  multi-­‐agent	
  systems	
  
       -­‐   Web	
  and	
  knowledge-­‐based	
  information	
  systems	
  
       -­‐   Natural	
  language	
  processing	
  
       -­‐   Uncertainty	
  
  	
  
  Bioinformatics	
  :	
  
       -­‐ Comparative	
  genomics	
  
       -­‐ Evolution	
  and	
  phylogenetics	
  
       -­‐ Epigenetics	
  
       -­‐ Functional	
  genomics	
  
       -­‐ Genome	
  organization	
  and	
  annotation	
  
       -­‐ Genetic	
  variation	
  analysis	
  
       -­‐ Metagenomics	
  
       -­‐ Pathogen	
  informatics	
  
       -­‐ Population	
  genetics,	
  variation	
  and	
  evolution	
  
       -­‐ Protein	
  structure	
  and	
  function	
  prediction	
  and	
  analysis	
  
       -­‐ Proteomics	
  
       -­‐ Sequence	
  analysis	
  
       -­‐ Systems	
  biology	
  and	
  networks	
  
	
  
  Workshop	
  contributions	
  :	
  
  This	
  year,	
  the	
  papers	
  submitted	
  to	
  the	
  workshop	
  were	
  carefully	
  peer-­‐reviewed	
  by	
  at	
  
  least	
  three	
  members	
  of	
  the	
  program	
  committee	
  and	
  among	
  the	
  	
  12	
  submissions,	
  7	
  
  papers	
   with	
   the	
   highest	
   scores	
   were	
   selected.	
   We	
   would	
   like	
   to	
   thank	
   all	
   the	
   PC	
  
  members	
   and	
   the	
   reviewers	
   for	
   their	
   reviews,	
   as	
   well	
   as	
   all	
   the	
   authors	
   for	
   their	
  
  contributions.	
  
  The	
   workshop	
   was	
   a	
   one	
   day	
   format	
   with	
   one	
   keynote	
   speakers,	
   two	
   invited	
  
  speaker,	
  and	
  seven	
  oral	
  presentations.	
  
  	
  
                                                     Keynote	
  Speaker	
  :	
  
  The	
  keynote	
  speaker	
  was	
  Dr.	
  Dmitri	
  Chklovskii,	
  leader	
  of	
  the	
  neuroscience	
  group	
  
  at	
   Simons	
   Foundation,	
   New-­‐York	
   (USA).	
   	
   His	
   talk	
   was	
   entitled	
  :	
   «	
  Biologically	
  
  inspired	
   machine	
   learning	
   ».	
   Inspired	
   by	
   experimental	
   neuroscience	
   results	
   they	
  
  developed	
   a	
   family	
   of	
   online	
   algorithms	
   that	
   reduce	
   dimensionality,	
   cluster	
   and	
  
  discover	
  features	
  in	
  streaming	
  data.	
  The	
  novelty	
  of	
  their	
  approach	
  is	
  in	
  starting	
  with	
  
similarity	
   matching	
   objective	
   functions	
   used	
   offline	
   in	
   Multidimensional	
   Scaling	
   and	
  
Symmetric	
   Nonnegative	
   Matrix	
   Factorization.	
   They	
   derived	
   online	
   distributed	
  
algorithms	
  that	
  can	
  be	
  implemented	
  by	
  biological	
  neural	
  networks	
  resembling	
  brain	
  
circuits.	
  Such	
  algorithms	
  may	
  also	
  be	
  used	
  for	
  Big	
  Data	
  applications.	
  
	
  
                                                             Invited	
  Speakers	
  :	
  
The	
   first	
   invited	
   speaker	
   was	
   Dr.	
   Laxmi	
   Parida,	
   Distinguished	
   Research	
   Staff	
  
Member	
   and	
   Manager	
   of	
   the	
   Computational	
   Genomics	
   Group	
   at	
   IBM,	
   New-­‐York	
  
(USA).	
   Her	
   talk	
   was	
   entitled	
  :	
   «	
  Watson	
   for	
   Genomics:	
   a	
   cognitive	
   approach	
   to	
  
clinical	
   oncology	
   »	
   .	
   	
   The	
   confluence	
   of	
   genomic	
   technologies,	
   algorithmics	
   and	
  
cognitive	
   computing	
   has	
   brought	
   us	
   to	
   the	
   doorstep	
   of	
   widespread	
   usage	
   of	
  
personalized	
   medicine.	
   She	
   talked	
   about	
   Watson	
   for	
   Genomics	
   that	
   attempts	
   to	
  
integrate	
   the	
   current	
   state	
   of	
   knowledge	
   of	
   molecular	
   oncology	
   and	
  
pharmacogenomics	
  with	
  the	
  ever-­‐expanding	
  body	
  of	
  literature	
  to	
  assist	
  physicians	
  
in	
  analyzing	
  and	
  acting	
  on	
  patient	
  genomic	
  profiles.	
  
	
  
The	
   second	
   invited	
   speaker	
   was	
   Achille	
   Fokoué,	
   research	
   staff	
   member	
   at	
   IBM	
  
New-­‐York	
   (USA),	
   who	
   gives	
   a	
   talk	
   on	
   Tiresias,	
   a	
   system	
   for	
   predicting	
   Drug-­‐Drug	
  
Interactions	
   Through	
   Similarity-­‐Based	
   Link	
   Prediction.	
   Drug-­‐Drug	
   Interactions	
  
(DDIs)	
   are	
   a	
   major	
   cause	
   of	
   preventable	
   adverse	
   drug	
   reactions	
   (ADRs),	
   causing	
   a	
  
significant	
   burden	
   on	
   the	
   patients'	
   health	
   and	
   the	
   healthcare	
   system.	
   It	
   is	
   widely	
  
known	
  that	
  clinical	
  studies	
  cannot	
  sufficiently	
  and	
  accurately	
  identify	
  DDIs	
  for	
  new	
  
drugs	
   before	
   they	
   are	
   made	
   available	
   on	
   the	
   market.	
   In	
   addition,	
   existing	
   public	
   and	
  
proprietary	
   sources	
   of	
   DDI	
   information	
   are	
   known	
   to	
   be	
   incomplete	
   and/or	
  
inaccurate	
  and	
  so	
  not	
  reliable.	
  As	
  a	
  result,	
  there	
  is	
  an	
  emerging	
  body	
  of	
  research	
  on	
  
in-­‐silico	
   prediction	
   of	
   drug-­‐drug	
   interactions.	
   He	
   presents	
   Tiresias,	
   a	
   framework	
  
that	
   takes	
   in	
   various	
   sources	
   of	
   drug-­‐related	
   data	
   and	
   knowledge	
   as	
   inputs,	
   and	
  
provides	
  DDI	
  predictions	
  as	
  outputs.	
  The	
  process	
  starts	
  with	
  semantic	
  integration	
  of	
  
the	
   input	
   data	
   that	
   results	
   in	
   a	
   knowledge	
   graph	
   describing	
   drug	
   attributes	
   and	
  
relationships	
   with	
   various	
   related	
   entities	
   such	
   as	
   enzymes,	
   chemical	
   structures,	
  
and	
   pathways.	
   The	
   knowledge	
   graph	
   is	
   then	
   used	
   to	
   compute	
   several	
   similarity	
  
measures	
   between	
   all	
   the	
   drugs	
   in	
   a	
   scalable	
   and	
   distributed	
   framework.	
   The	
  
resulting	
   similarity	
   metrics	
   are	
   used	
   to	
   build	
   features	
   for	
   a	
   large-­‐scale	
   logistic	
  
regression	
   model	
   to	
   predict	
   potential	
   DDIs.	
   We	
   highlight	
   the	
   novelty	
   of	
   our	
  
proposed	
   approach	
   and	
   perform	
   thorough	
   evaluation	
   of	
   the	
   quality	
   of	
   the	
  
predictions.	
   The	
   results	
   show	
   the	
   effectiveness	
   of	
   Tiresias	
   in	
   both	
   predicting	
   new	
  
interactions	
  among	
  existing	
  drugs	
  and	
  among	
  newly	
  developed	
  and	
  existing	
  drugs.	
  
	
  
                                                        Oral	
  presentations	
  :	
  
The	
   seven	
   accepted	
   papers	
   were	
   then	
   presented,	
   among	
   which	
   six	
   new	
  
contributions	
   (in	
   this	
   proceedings)	
   and	
   one	
   highlight	
   (from	
   the	
   journal	
   of	
  
computational	
   biology)	
   devoted	
   on	
   prediction	
   of	
   ionizing	
   radiation	
   resistance	
   in	
  
Bacteria	
  using	
  a	
  multiple	
  instance	
  learning	
  model.	
  
	
  
	
                                                 	
  
Workshop	
  Program	
  :	
  
	
  
     Time	
                                                      Event	
  
08:00-­‐08:45	
   Registration	
  
08:45-­‐09:00	
   Opening	
  ceremony	
  
09:00-­‐10:00	
   Keynote	
  speaker:	
  Dmitri	
  Chklovskii	
  
                  Biologically	
  inspired	
  machine	
  learning.	
  
10:00-­‐10:30	
   César	
  Aguilar	
  and	
  Olga	
  Acosta.	
  	
  
                  Design	
   of	
   a	
   Extraction	
   System	
   for	
   Definitional	
   Contexts	
   from	
  
                  Biomedical	
  Corpora	
  
10:30-­‐11:00	
   Coffee	
  Break	
  
11:00-­‐11:30	
   Sylvester	
   Olubolu	
   Orimaye,	
   Jojo	
   Sze-­‐Meng	
   Wong	
   and	
   Judyanne	
  
                  Sharmini	
  Gilbert	
  Fernandez.	
  	
  
                  Deep-­‐Deep	
   Neural	
   Network	
   Language	
   Models	
   for	
   Predicting	
   Mild	
  
                  Cognitive	
  Impairment	
  
11:30-­‐12:00	
   Ricardo	
   Souza	
   Jacomini,	
   David	
   Correa	
   Martins-­‐Jr,	
   Felipe	
   Leno	
   Da	
  
                  Silva	
  and	
  Anna	
  Helena	
  Reali	
  Costa.	
  	
  
                  A	
   Framework	
   for	
   Scalable	
   Inference	
   of	
   Temporal	
   Gene	
   Regulatory	
  
                  Networks	
  based	
  on	
  Clustering	
  and	
  Multivariate	
  Analysis	
  
12:00-­‐12:30	
   Highlight	
   presentation	
  :	
   Sabeur	
   Aridhi,	
   Haitham	
   Sghaier,	
   Manel	
  
                  Zoghlami,	
  Mondher	
  Maddouri	
  and	
  Engelbert	
  Mephu	
  Nguifo.	
  	
  
                  Prediction	
  of	
  ionizing	
  radiation	
  resistance	
  in	
  bacteria	
  using	
  a	
  multiple	
  
                  instance	
  learning	
  model	
  
12:30-­‐14:00	
   Lunch	
  
14:00-­‐14:40	
   Invited	
  speaker:	
  Laxmi	
  Parida	
  
                  Watson	
  for	
  Genomics:	
  a	
  cognitive	
  approach	
  to	
  clinical	
  oncology.	
  
14:40-­‐15:10	
   Sidak	
   Pal	
   Singh,	
   Sopan	
   Khosla,	
   Sajal	
   Rustagi,	
   Manisha	
   Patel	
   and	
  
                  Dhaval	
  Patel.	
  	
  
                  SL-­‐FII:	
   Syntactic	
   and	
   Lexical	
   Constraints	
   with	
   Frequency	
   based	
  
                  Iterative	
   Improvement	
   for	
   Disease	
   Mention	
   Recognition	
   in	
   News	
  
                  Headlines	
  
15:10-­‐15:40	
   Michael	
  Benedikt,	
  Rodrigo	
  Lopez-­‐Serrano	
  and	
  Efthymia	
  Tsamoura.	
  	
  
                  Biological	
  Web	
  Services:	
  Integration,	
  Optimization,	
  and	
  Reasoning	
  
15:40-­‐16:00	
   Coffee	
  Break	
  
16:00-­‐16:30	
   Samuel	
   Sloate,	
   Vincent	
   Hsiao,	
   Nina	
   Charness,	
   Ethan	
   Lowman,	
  
                  Christopher	
   J.	
   Maxey,	
   Sam	
   Guannan	
   Ren,	
   Nathan	
   Fields	
   and	
   Leora	
  
                  Morgenstern.	
  	
  
                  Extracting	
  Protein-­‐Reaction	
  Information	
  from	
  Tables	
  of	
  Unpredictable	
  
                  Format	
  and	
  Content	
  in	
  the	
  Molecular	
  Biology	
  Literature	
  
16:30-­‐17:10	
   Invited	
  speaker:	
  Achille	
  Fokoue.	
  
                  Tiresias:	
   A	
   system	
   for	
   predicting	
   Drug-­‐Drug	
   Interactions	
   Through	
  
                  Similarity-­‐Based	
  Link	
  Prediction.	
  
17:10-­‐17:30	
   Discussion	
  and	
  Closing	
  session	
  
	
  
	
                                     	
  
Program	
  committee	
  :	
  
	
  
     Firstname	
                 Name	
                                               Affiliation	
  
Sabeur	
                Aridhi	
                     Aalto	
  University,	
  School	
  of	
  Science,	
  Finland.	
  
Abdoulaye	
             Baniré	
  Diallo	
   University	
  of	
  Quebec	
  at	
  Montreal	
  (UQAM),	
  Canada	
  
Simon	
                 De	
  Givry	
                INRA	
  –	
  UBIA,	
  France	
  
Marcilio	
              De	
  Souto	
                LIFO/University	
  of	
  Orleans,	
  France	
  
Wajdi	
                 Dhifli	
                     University	
  of	
  Quebec	
  At	
  Montreal,	
  Canada	
  
Jason	
                 Ernst	
                      UCLA,	
  USA	
  
Anna	
                  Gambin	
                     Institute	
  of	
  Informatics,	
  Warsaw	
  University,	
  Poland	
  
Tu	
  Bao	
             Ho	
                         Japan	
  Advanced	
  Institute	
  of	
  Science	
  and	
  Technology	
  
Frédérique	
   Lisacek	
                             Swiss	
  Institute	
  of	
  Bioinformatics,	
  Swizerland	
  
Mondher	
               Maddouri	
                   URPAH,	
  Faculty	
  of	
  sciences	
  El	
  Manar,	
  Tunis,	
  Tunisia	
  
Osamu	
                 Maruyama	
                   Kyushu	
  University,	
  Japan	
  
Engelbert	
             Mephu	
  Nguifo	
   LIMOS	
  -­‐	
  Blaise	
  Pascal	
  University	
  –	
  CNRS,	
  France	
  
Claire	
                Nédellec	
                   INRA,	
  France	
  	
  
Gaurav	
                Pandey	
                     Mount	
  Sinai	
  School	
  of	
  Medicine	
  
David	
                 Ritchie	
                    INRIA,	
  France	
  
Sushmita	
              Roy	
                        University	
  of	
  Wisconsin,	
  Madison,	
  USA	
  
Dechang	
               Xu	
                         Harbin	
  Institute	
  of	
  Technology,	
  China	
  
Mohammed	
   Zaki	
                                  RPI,	
  NY,	
  USA	
  
	
  
	
  
Additional	
  reviewers	
  :	
  
Thanks	
   to	
   the	
   following	
   additional	
   reviewers	
   for	
   their	
   help	
   during	
   the	
   reviewing	
  
process	
  :	
   Eselle	
   Chaix,	
   Wojciech	
   Jaworski,	
   Om	
   Prakash	
   Pandey,	
   Jacek	
   Sroka,	
   Ana	
  
Stanescu.	
  
	
  
Acknowledgements	
  :	
  
We	
   would	
   like	
   to	
   thank	
   the	
   following	
   people	
   for	
   their	
   involvement	
   on	
   workshop	
  
duties	
  :	
   Wajdi	
   Dhifli	
   and	
   Jerry	
   Lonlac	
   Konlac.	
   Special	
   thanks	
   to	
   Wajdi	
   Dhifli	
  
especially	
   for	
   the	
   workshop	
   website	
   management.	
   We	
   would	
   also	
   like	
   to	
   thank	
   all	
  
authors	
   for	
   contributing	
   to	
   our	
   workshop	
   and	
   for	
   their	
   great	
   presentation	
   at	
   the	
  
workshop.	
  Furthermore,	
  we	
  thank	
  all	
  reviewers	
  and	
  subreviewers	
  for	
  their	
  time	
  and	
  
efforts	
  in	
  helping	
  us	
  build	
  an	
  interesting	
  program.	
  
	
  
	
  
	
  
	
  
                                                                                                 Abdoulaye	
  Baniré	
  Diallo	
  
                                                                                                 Engelbert	
  Mephu	
  Nguifo	
  
                                                                                                          Mohammed	
  Zaki	
  
                                                                                                                        (Eds.)