Add How Many Recognizition

qa4mre-alzheimer-task/.classpath

@@ -17,7 +17,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
@@ -27,5 +27,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="lib" path="/Users/Jerry/Downloads/lvg2013/lib/lvg2013api.jar"/>
+	<classpathentry kind="lib" path="/Users/Jerry/Downloads/lvg2013/lib/lvg2013dist.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

qa4mre-alzheimer-task/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,6 @@
+eclipse.preferences.version=1
+encoding//data/Biomedical_about_Alzheimer_Sample_GS_Docs=UTF-8
+encoding//data/medical_oov_updated2.txt=UTF-8
+encoding//data/oov_medical.txt=UTF-8
+encoding//src/main/java/edu/cmu/lti/deiis/hw5/candidate_sentence/QuestionCandSentAnswerMatcher.java=UTF-8
+encoding//src/main/java/edu/cmu/lti/deiis/hw5/candidate_sentence/QuestionCandSentAnswerMatcher21.java=UTF-8

qa4mre-alzheimer-task/.settings/org.eclipse.jdt.core.prefs

@@ -1,5 +1,8 @@
 eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
-org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.source=1.7

qa4mre-alzheimer-task/data/12-test-alzheimer/QA4MRE-2012_BIOMEDICAL_GS.xml

@@ -7,10 +7,10 @@ PLoS ONE: Genetics of Clusterin Isoform Expression and Alzheimer's Disease RiskO
 			</doc>
 				<q  q_id="1" >
 					<q_str>Which technique was used to determine the cellular locations of the CLU1 and CLU2 gene products?</q_str>
-					<answer a_id='1' >intracellular and secreted</answer>
+			 		<answer a_id='1' >intracellular and secreted</answer>
 					<answer a_id='2' >ER</answer>
 					<answer a_id='3' >intracellular localization</answer>
-					<answer a_id='4' >Golgi apparatus</answer>
+					<answer a_id='4' >Golgi apparatus</answer> 
 					<answer a_id='5'  correct="Yes">immunofluorescence experiments</answer>
 				</q>
 				<q  q_id="2" >

qa4mre-alzheimer-task/data/docindex/_1.fnm

@@ -0,0 +1 @@
+����id
sentid
text

qa4mre-alzheimer-task/data/docindex/_1.nrm

@@ -0,0 +1 @@
+NRM�||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||onqppppppqqpppomlloooopqppponnoppponnnooomnnqsuusponnnnpoooppommmnopopopnonnnppppooppppqrsqqoonppqrtqpoooooqrqppqqrssqppqpppuuuuuusppoopprpppqrqoonnnpppqppopnonpqqpnnoppqqqppppppoooppppppponppqpqponooppooppoopqqqrstqqpqpqpqpppqpqpqpqpqopprqrqqpqpqpqpqppprpqpppqpppqqqqpqpqopoppqprpppqpqpqpqppopqnmpppopqqpoppnnopoooopooooonnnpppnnpqppppoopqnonppppqqqqpoppqoppnnnqppoppqrqqpqppnnnnnoqqqqqppopqtrqpppppoopqqpppqsrqopqqppppprsqpopoppqqppqsqpppstrpooopqqppqrtqpppoonoprqooprrsstqpopqqqqponopppoooooooonoopopqtrqqqqqrsrqqprpqppoqprqrqrppopoppqopopopoppqpqpqprpqpqpqpqprppprpppqpqpqpqpqpqpqpqpqpqoppqpqpppqrnnppoooppqrqpppppqppooomnnpopoooqqqpooppqqpppppppppoononoppponoopppppqpppppoommnooommmopqppprpqppoooopppoppqpppoooopqqqnnnpppqpqoopqppoppqqppoppppponooooponnonoopqppppqqqpqqpppponopqppppqppqpppqqrrrrrtsqqprrqqqqqqqqqqqqqqqqqqqqqqqqrrrqqqrrrrrrqqqrrrpppqqqrrrqqqqqqqqqpppppprrrrrrqqpqqqpprqqpqqrrrqqqrrrrrrqqqqqqqqqrrrrrrqqqqqqqqqrrrqqqqqqqqqrrrppprrrtrrrrqqsssrrqqqqqqqqqqqqqqqqqqrrrrrrqqqssssssrqqqqqrrrqqqpppqqqqqqqqqrrrqqqqqqqqqqqqrrrqqpqqqqqlmmnoopppopqqpoonnnnooonnnooooopppoonooqnnnopmnnppppppppnppponpnooqqrtpooonnopponnnopnmnppooprtrpppppqqrpppqppoppppsttqponooooppoooonnnnnnopoonpqsqqppppooptuutqpopprsurpnnnpppppppnnnooooppppppppnnnoonoppooppppoopqppppopppoonnnommnqmmmpponnonnnnomnmnmnnpppppqppqrnnnppoopponpopopnnmnonnnqppqppnpprppppppppopqqonnprsppprstttppoqprpqpqpqpqppprpqoqpqpqpqppoqpqopoqopopopoqpqpqpqpqppoqopopopoqpqoppqppoqopoqpqpqopopp

qa4mre-alzheimer-task/data/oov_medical.txt

@@ -0,0 +1,168 @@
+AD : alzheimer's disease, disease, Alzheimer (DISEASE)
+AICD : amyloid precursor protein intracellular domain,peptide fragment (FRAGMENT) (PEPTIDE) (PROTEIN)
+AIDS : acquired immunodeficiency syndrome, disease (DISEASE)
+APH1 : anterior pharynx-defective protein 1, protein gene, notch signaling pathway (PROTEIN) (GENE)
+APP : amyloid precursor protein, protein (PROTEIN)
+APP-CTF : amyloid precursor protein C-terminal fragments (FRAGMENT)
+APP23:	amyloid precursor protein23 (PROTEIN)
+ARV : anti-retroviral, antiretroviral (DRUG)
+ApoE : apoE, apo-E, apolipoprotein E, chylomicron,  intermediate-density lipoprotein, gene, protein (GENE) (PROTEIN)
+A��� : amyloidbeta, amyloid beta, amyloid-beta, ���amyloid (PEPTIDE)
+BACE1 :	beta-secretase1, ���-secretase (GENE) (ENZYME)
+BOEM : united states bureau of ocean energy, agency (AGENCY)
+BP :british petroleum, company, agency (ORGANIZATION)
+BV-2:bacterial vaginosis-2, disease (DISEASE)
+C100-His: plasmids, polypeptide (PROTEIN) (PEPTIDE) 
+CAFTA : central america free trade agreement, document, treaty (AGREEMENT)
+CALLA : common acute lymphoblastic leukemia antigen,neprilysin, membrane metallo-endopeptidase,neutral endopeptidase, CD10,  zinc-dependent metalloprotease enzyme (ENZYME)
+CD44 : gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+CDC : Centers for Disease Control (ORGANIZATION)
+CEO : chief executive officer, leader, president (PERSON)
+CFC : chlorofluorocarbons (CHEMICAL)
+CJD : creutzfeldt-jakob disease, brain disorder, disease, neurodegeneration (DISEASE)
+CLU	: clusterin (GENE) (PROTEIN-CODING)
+CNS :central nervous system (NERVOUS)
+CO2 : carbon dioxide, gas (CHEMICAL)
+CPE : carboxypeptidase E, protein coding gene (GENE) (PROTEIN-CODING)
+CR1 :(GENE) (PROTEIN-CODING)
+CSF : cerebrospinal fluid (CHEMICAL) (HORMONE)
+D257A : mutation of Presenilin-1 (MUTATION) (GENE)
+D257A : mutation of Presenilin-1 (MUTATION) (GENE) 
+D385A : mutation of Presenilin-1 (MUTATION) (GENE) 
+DCC : gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+DDAA:  mutation of Presenilin-1 (MUTATION) (GENE) 
+DoE: department of energy (ORGANIZATION)
+E-cadherin : gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+EC : european commission (ORGANIZATION)
+EDM :electronic dance music (whatever)
+EERD: extraesophageal reflux disease, silent reflux, disease (DISEASE)
+ELISA : enzyme linked immunosorbent assay (TEST)
+EPA :environmental protection agency (ORGANIZATION)
+ER: endoplasmic reticulum (CELL) (NERVOUS)
+EphA :gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+ErbB4 : ERBB4, gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+FAD: familial alzheimer's disease,  hereditary alzheimer's disease, ancestral alzheimer's disease (DISEASE)
+FDA	:food and drug administration (ORGANIZATION)
+FTLD : frontotemporal lobar degeneration,disease, neurodegeneration,brain disorder(DISEASE)
+G77 : group of 77 (ORGANIZATION)
+G8 : group of eight (ORGANIZATION)
+GAP :global access project (ORGANIZATION)
+GDP : gross Domestic Product (METRIC)
+GFATM: global fund to fight AIDS, tuberculosis and malaria (ORGANIZATION)
+GHG :greenhouse gases, chlorofluorocarbons (CHEMICAL)
+GOP :grand old party (ORGANIZATION)
+HCFC : hydrochlorofluorocarbons, ozone depleting substances (CHEMICAL)
+HFC : hydrofluorocarbons,ozone depleting substances (CHEMICAL)
+HIV :human immunodeficiency virus (VIRUS) (DISEASE)
+I-CLiPs: Intramembrane-Cleaving Proteases, enzyme (ENZYME)
+IDE : insulin degrading enzyme (ENZYME)
+IDL : intermediate-density lipoprotein (LIPOPROTEIN) (PROTEIN) (FATTY ACIDS)
+IPCC : intergovernmental panel on climate change (ORGANIZATION)
+IgG : immunoglobulin g (ANTIBODY) (PROTEIN)
+L13A : 	ribosomal protein (PROTEIN)	
+L166P : point mutation, mutations is PSEN1 (MUTATION) 
+LCF : lymphocyte chemoattractant factor,tetrameric glycoprotein,interleukin-16, chemoattractant factor (PROTEIN)
+LDL : low density lipoprotein, receptor (PROTEIN)
+LPR2 : laryngopharyngeal reflux2, extraesophageal reflux disease, silent reflux, disease (DISEASE)
+LRP1 : lipoprotein receptor (PROTEIN)
+MB : methyl bromide (CHEMICAL)
+NCT: nicastrin, PROTEIN (PROTEIN)
+NEP : neprilysin, membrane metallo-endopeptidase,neutral endopeptidase, CD10, common acute lymphoblastic leukemia antigen, zinc-dependent metalloprotease enzyme (ENZYME)
+NEUREXIN-3���: substrate, presynaptic protein, (SUBSTRATE) (PROTEIN)
+NICD : notch intracellular domain,peptide fragment (FRAGMENT) (PEPTIDE) (PROTEIN)
+NO: nitric oxide (CHEMICAL)
+NRDC : national resource defense council, organization (ORGANIZATION)
+Notch : gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+P436Q: mutations of PSEN1, PS1 (GENE) (MUTATION)
+PCR : polymerase chain reaction (TECHNIQUE) (REACTION)
+PEN2: presenilin enhancer two, protein (PROTEIN)
+PEPFAR : resident's emergency plan for AIDS relief (PLAN) 
+PFC : perfluorocarbons, ozone depleting substances (CHEMICAL)
+PICALM :phosphatidylinositol binding clathrin assembly protein (GENE) (PROTEIN-CODING)
+PNGase : peptide-N-glycosidase,enzymatic method (TECHNIQUE)
+PS1 : presenilin-one,polytopic proteins (PROTEIN) (GENE)
+PS2 : presenilin-one,polytopic proteins (PROTEIN) (GENE)
+PSEN1 : presenilin gene, gene (GENE)
+REDD : reduce emissions from deforestation and forest degradation (ORGANIZATION)
+RNA polymerase : substance that synthesizes RNA (ENZYME)
+RT-PCR : real time polymerase chain reaction (TECHNIQUE) (REACTION)
+SIV : simian immunodeficiency virus, disease (DISEASE)
+SNAP : significant new alternatives policy (PLAN)
+SNP : single nucleotide polynorphism (whatever)
+SSTR-2 : somatostatin receptors-2 (PROTEIN) (GENE)
+TB :tuberculosis, disease (DISEASE)
+TGN: trans-golgi network, secretory pathway sorting station (NERVOUS)
+TGN: trans-golgi network, secretory pathway sorting station (NERVOUS)
+UK : united kingdom (COUNTRY)
+UNAIDS: joint united nations programme on HIV/AIDS (PLAN)
+UNDP :united nations development programme (ORGANIZATION)
+UNFCCC :united nations framework convention on climate change (ORGANIZATION)
+US : united states (COUNTRY)
+USAID: united states agency for international development (ORGANIZATION)
+WB : western blot, protein immunoblot, analytical technique used to detect specific proteins (TECHNIQUE)
+WTO : world trade organisation (ORGANIZATION)
+alzheimer: alzheimer's disease, disease, neurodegeneration,brain disorder (DISEASE)
+amphetamine : central nervous system stimulant, drug (DRUG) (TREATMENT)
+amyloidbeta: amyloidbeta, amyloid, beta, A���, peptide amino acid, amino acid (PROTEIN)
+amyloids : fibrous protein aggregates (PROTEIN)
+antiretroviral : antiretroviral (DRUG)
+antiviral : (DRUG) (TREATMENT)
+arthritis :affects the musculoskeletal system, specifically the joints(DISEASE)
+bacteria :prokaryotic microorganisms (DISEASE)
+beta-amyloid : peptide, amyloid precursor protein (PROTEIN) (PEPTIDE)
+bexarotene : oral antineoplastic agent ,targretin, prescription drug (DRUG) (TREATMENT)
+c193555 :antibody (DRUG) (TREATMENT)
+cDNA: complementary DNA (DNA)
+cancer : disease (DISEASE)
+cataract : eye vison loss, disease (DISEASE)
+cell : (CELL) (NERVOUS)
+cerebral : cerebrum, nervous (NERVOUS) 
+chemotherapy : cancer treatment (TREATMENT)
+cortex : cerebrum (NERVOUS)
+dopamine : neurotransmitter,endogenous chemical (HORMONE) (CHEMICAL)
+enhancer: short region of DNA, helps with transcription (DNA) (NERVOUS)
+enzyme : large biological molecules (MOLECULE) (ENZYME)
+ephrinB2 : gamma secretease proteins, substrate (SUBSTRATE) (PROTEIN)
+fluorocarbon :ozone depleting substances (CHEMICAL)
+gamma secretase : multi-subunit protease complex, membrane protein (PROTEIN)
+hAPH1aL-HA : human APH1aL-HA, lentiviral vectors, virus (VIRUS) (DISEASE) 
+hNCT-V5 : human NCT-V5,lentiviral vectors, virus (VIRUS) (DISEASE) 
+hippocampus : brain, nervous (NERVOUS)
+hydrocarbon : (CHEMICAL)
+immune : resistant to a particular infection (TREATMENT) 
+immunodeficiency: sick, disease (DISEASE)
+infection: disease (DISEASE)
+inflammation : infection, disease (DISEASE)
+mRNA : messenger RNA (MOLECULE)
+maladies :disease (DISEASE)
+malaria : disease (DISEASE)
+metereddose : inhaler, device (DEVICE)
+mtDMA: dimethyl adipate,  cerebrospinal fluid (ENZYME) (HORMONE) (CHEMICAL)
+murine : relating to mice, mice, mouse (ANIMAL)
+neurodegenerative : parkinson������, alzheimer������, huntington������, disease, brain disorder (DISEASE) 
+neurodegneration : parkinson������, alzheimer������, huntington������, disease, brain disorder (DISEASE) 
+neuron : cell, nervous system (NERVOUS) (CELL)
+neurotransmitter :  endogenous chemicals, norepinephrine, dopamine (HORMONE) (CHEMICAL)
+norepinephrine: neurotransmitter, endogenous chemicals (HORMONE) (CHEMICAL)
+pB1P-A : mutated fragments, BACE1 (MUTATION) (FRAGMENT) (GENE)
+pB1P-A : mutated fragments, BACE1 (MUTATION) (FRAGMENT) (GENE)
+pandemic : epidemic of infectious disease, epidemic, disease (DISEASE)
+parkinsons :disease, neurodegeneration,brain disorder (DISEASE)
+perfluorocarbons :ozone depleting substances (CHEMICAL)
+permeates : spread throughout, pervade (whatever)
+phagocytosis : immune (TREATMENT) (TECHNIQUE)
+pharmaceutical : drugs, treatment, medicine (DRUG) (TREATMENT)
+physiological : scientific study of function in living systems (NERVOUS)
+promoter: initiates transcription of a particular gene,region of DNA (DNA)
+prostate :gland (GLAND) (ORGAN)
+protein :chains of amino acid residues,large biological molecules (PROTEIN)
+pulmonary tuberculosis : tuberculosis, disease (DISEASE)
+siRNA: small interfering RNA (MOLECULE)
+targretin :oral antineoplastic agent ,targretin, prescription drug (DRUG) (TRATEMENT)
+therapeutics : drugs, treatment,care (DRUG) (TREATMENT)
+treatment : care, therapeutics (TREATMENT)
+vaccine : drug, treatment (DRUG)
+vertigo : dizziness, whirling, spinning, disease (DISEASE)
+vinyl : chemical (CHEMICAL)
+viral : disease, relating to virus (DISEASE)
+virus : disease, infection (DISEASE)

qa4mre-alzheimer-task/data/stopwords.txt

@@ -0,0 +1,174 @@
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