Probabilistic reasoning in intelligent systems: networks of plausible inference
Probabilistic reasoning in intelligent systems: networks of plausible inference
The nature of statistical learning theory
The nature of statistical learning theory
Communications of the ACM
A maximum entropy approach to natural language processing
Computational Linguistics
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Machine Learning for the Detection of Oil Spills in Satellite Radar Images
Machine Learning - Special issue on applications of machine learning and the knowledge discovery process
An Algorithm that Learns What‘s in a Name
Machine Learning - Special issue on natural language learning
Relational learning of pattern-match rules for information extraction
AAAI '99/IAAI '99 Proceedings of the sixteenth national conference on Artificial intelligence and the eleventh Innovative applications of artificial intelligence conference innovative applications of artificial intelligence
The Frame-Based Module of the SUISEKI Information Extraction System
IEEE Intelligent Systems
Text Categorization with Suport Vector Machines: Learning with Many Relevant Features
ECML '98 Proceedings of the 10th European Conference on Machine Learning
Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
ICML '01 Proceedings of the Eighteenth International Conference on Machine Learning
Active Learning for Natural Language Parsing and Information Extraction
ICML '99 Proceedings of the Sixteenth International Conference on Machine Learning
Maximum Entropy Markov Models for Information Extraction and Segmentation
ICML '00 Proceedings of the Seventeenth International Conference on Machine Learning
A Theory-Refinement Approach to Information Extraction
ICML '01 Proceedings of the Eighteenth International Conference on Machine Learning
A Pragmatic Information Extraction Strategy for Gathering Data on Genetic Interactions
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Constructing Biological Knowledge Bases by Extracting Information from Text Sources
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on Innovative Applications of Artificial Intelligence
Building a large annotated corpus of English: the penn treebank
Computational Linguistics - Special issue on using large corpora: II
Extracting the names of genes and gene products with a hidden Markov model
COLING '00 Proceedings of the 18th conference on Computational linguistics - Volume 1
Ranking algorithms for named-entity extraction: boosting and the voted perceptron
ACL '02 Proceedings of the 40th Annual Meeting on Association for Computational Linguistics
Use of support vector learning for chunk identification
ConLL '00 Proceedings of the 2nd workshop on Learning language in logic and the 4th conference on Computational natural language learning - Volume 7
Representing sentence structure in hidden Markov models for information extraction
IJCAI'01 Proceedings of the 17th international joint conference on Artificial intelligence - Volume 2
Mining knowledge from text using information extraction
ACM SIGKDD Explorations Newsletter - Natural language processing and text mining
The relationship between Precision-Recall and ROC curves
ICML '06 Proceedings of the 23rd international conference on Machine learning
Collective information extraction with relational Markov networks
ACL '04 Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics
Multi-way relation classification: application to protein-protein interactions
HLT '05 Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing
Artificial Intelligence in Medicine
Relation extraction and the influence of automatic named-entity recognition
ACM Transactions on Speech and Language Processing (TSLP)
Kernel-based learning for biomedical relation extraction
Journal of the American Society for Information Science and Technology
Methodological Review: Extracting interactions between proteins from the literature
Journal of Biomedical Informatics
The role of syntactic features in protein interaction extraction
Proceedings of the 2nd international workshop on Data and text mining in bioinformatics
Foundations and Trends in Databases
Learning to Learn Biological Relations from a Small Training Set
CICLing '09 Proceedings of the 10th International Conference on Computational Linguistics and Intelligent Text Processing
Expert Systems with Applications: An International Journal
Analysis of link grammar on biomedical dependency corpus targeted at protein-protein interactions
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
A graph kernel for protein-protein interaction extraction
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Using automated feature optimisation to create an adaptable relation extraction system
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Static relations: a piece in the biomedical information extraction puzzle
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Identifying interaction sentences from biological literature using automatically extracted patterns
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Semi-supervised Prediction of Protein Interaction Sentences Exploiting Semantically Encoded Metrics
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
Classification of Protein Interaction Sentences via Gaussian Processes
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
Information Extraction as Link Prediction: Using Curated Citation Networks to Improve Gene Detection
WASA '09 Proceedings of the 4th International Conference on Wireless Algorithms, Systems, and Applications
SETQA-NLP '09 Proceedings of the Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing
ISMB '05 Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics
Two learning approaches for protein name extraction
Journal of Biomedical Informatics
A rich feature vector for protein-protein interaction extraction from multiple corpora
EMNLP '09 Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1 - Volume 1
Journal of Biomedical Informatics
Proceedings of the International Conference and Workshop on Emerging Trends in Technology
Measuring prediction capacity of individual verbs for the identification of protein interactions
Journal of Biomedical Informatics
Learning relations from biomedical corpora using dependency trees
KDECB'06 Proceedings of the 1st international conference on Knowledge discovery and emergent complexity in bioinformatics
DEEPER: a full parsing based approach to protein relation extraction
EvoBIO'08 Proceedings of the 6th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Advances in Artificial Intelligence - Special issue on artificial intelligence in neuroscience and systems biology: lessons learnt, open problems, and the road ahead
Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Joint entity and relation extraction using card-pyramid parsing
CoNLL '10 Proceedings of the Fourteenth Conference on Computational Natural Language Learning
Evaluating the impact of alternative dependency graph encodings on solving event extraction tasks
EMNLP '10 Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing
DTMBIO '10 Proceedings of the ACM fourth international workshop on Data and text mining in biomedical informatics
Simplicity is better: revisiting single kernel PPI extraction
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Entity-focused sentence simplification for relation extraction
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Using local alignments for relation recognition
Journal of Artificial Intelligence Research
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Protein interaction detection in sentences via Gaussian Processes: a preliminary evaluation
International Journal of Data Mining and Bioinformatics
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics: Posters
Multiple kernel learning in protein-protein interaction extraction from biomedical literature
Artificial Intelligence in Medicine
A study on dependency tree kernels for automatic extraction of protein-protein interaction
BioNLP '11 Proceedings of BioNLP 2011 Workshop
Neighborhood hash graph kernel for protein-protein interaction extraction
Journal of Biomedical Informatics
Extracting protein-protein interactions in biomedical literature using an existing syntactic parser
KDLL'06 Proceedings of the 2006 international conference on Knowledge Discovery in Life Science Literature
Datasets for generic relation extraction*
Natural Language Engineering
gProt: annotating protein interactions using google and gene ontology
KES'05 Proceedings of the 9th international conference on Knowledge-Based Intelligent Information and Engineering Systems - Volume Part III
Mixture of logistic models and an ensemble approach for protein-protein interaction extraction
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Semantic annotation of biomedical literature using google
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and Its Applications - Volume Part III
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Collaborative curation of data from bio-medical texts and abstracts and its integration
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Transactions on Computational Systems Biology II
GeneTUC, GENIA and google: natural language understanding in molecular biology literature
Transactions on Computational Systems Biology V
Extraction of genic interactions with the recursive logical theory of an ontology
CICLing'10 Proceedings of the 11th international conference on Computational Linguistics and Intelligent Text Processing
Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Tree kernel-based protein-protein interaction extraction from biomedical literature
Journal of Biomedical Informatics
Using a shallow linguistic kernel for drug-drug interaction extraction
Journal of Biomedical Informatics
Combining tree structures, flat features and patterns for biomedical relation extraction
EACL '12 Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics
Improving distantly supervised extraction of drug-drug and protein-protein interactions
ROBUS-UNSUP '12 Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP
Bootstrapping biomedical ontologies for scientific text using NELL
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
PubAnnotation: a persistent and sharable corpus and annotation repository
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
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Objective:: Automatically extracting information from biomedical text holds the promise of easily consolidating large amounts of biological knowledge in computer-accessible form. This strategy is particularly attractive for extracting data relevant to genes of the human genome from the 11 million abstracts in Medline. However, extraction efforts have been frustrated by the lack of conventions for describing human genes and proteins. We have developed and evaluated a variety of learned information extraction systems for identifying human protein names in Medline abstracts and subsequently extracting information on interactions between the proteins. Methods and Material:: We used a variety of machine learning methods to automatically develop information extraction systems for extracting information on gene/protein name, function and interactions from Medline abstracts. We present cross-validated results on identifying human proteins and their interactions by training and testing on a set of approximately 1000 manually-annotated Medline abstracts that discuss human genes/proteins. Results:: We demonstrate that machine learning approaches using support vector machines and maximum entropy are able to identify human proteins with higher accuracy than several previous approaches. We also demonstrate that various rule induction methods are able to identify protein interactions with higher precision than manually-developed rules. Conclusion:: Our results show that it is promising to use machine learning to automatically build systems for extracting information from biomedical text. The results also give a broad picture of the relative strengths of a wide variety of methods when tested on a reasonably large human-annotated corpus.