Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

BACKGROUND: Extensive protein interaction maps are being constructed for yeast, worm, and fly to ask how the proteins organize into pathways and systems, but no such genome-wide interaction map yet exists for the set of human proteins. To prepare for studies in humans, we wished to establish tests for the accuracy of future interaction assays and to consolidate the known interactions among human proteins. RESULTS: We established two tests of the accuracy of human protein interaction datasets and measured the relative accuracy of the available data. We then developed and applied natural language processing and literature-mining algorithms to recover from Medline abstracts 6,580 interactions among 3,737 human proteins. A three-part algorithm was used: first, human protein names were identified in Medline abstracts using a discriminator based on conditional random fields, then interactions were identified by the co-occurrence of protein names across the set of Medline abstracts, filtering the interactions with a Bayesian classifier to enrich for legitimate physical interactions. These mined interactions were combined with existing interaction data to obtain a network of 31,609 interactions among 7,748 human proteins, accurate to the same degree as the existing datasets. CONCLUSION: These interactions and the accuracy benchmarks will aid interpretation of current functional genomics data and provide a basis for determining the quality of future large-scale human protein interaction assays. Projecting from the approximately 15 interactions per protein in the best-sampled interaction set to the estimated 25,000 human genes implies more than 375,000 interactions in the complete human protein interaction network. This set therefore represents no more than 10% of the complete network

Learning to extract relations from the web using minimal supervision

We present a new approach to relation extraction that requires only a handful of training examples. Given a few pairs of named entities known to exhibit or not exhibit a particular relation, bags of sentences containing the pairs are extracted from the web. We extend an existing relation extraction method to handle this weaker form of supervision, and present experimental results demonstrating that our approach can reliably extract relations from web documents.

Learning for collective information extraction

An Information Extraction (IE) system analyses a set of documents with the aim of identifying certain types of entities and relations between them. Most IE systems treat separate potential extractions as independent. However, in many cases, considering influences between different candidate extractions could improve overall accuracy. For example, phrase repetitions inside a document are usually associated with the same entity type, the same being true for acronyms and their corresponding long form. One of our goals in this thesis is to show how these and potentially other types of correlations can be captured by a particular type of undirected probabilistic graphical model. Inference and learning using this graphical model allows for “collective information extraction ” in a way that exploits the mutual influence between possible extractions. Preliminary experiments on learning to extract named entities from biomedical and newspaper text demonstrate the advantages of our approach. The benefit of doing collective classification comes however at a cost: in the general case, exact inference in the resulting graphical model has an exponential time complexity. The standard solution, which is also the one that we used in our initial work, is to resort to approximate inference. In this proposal we show that by considering only a selected subset of mutual influences between candidate extractions

Relational Markov Networks for Collective Information Extraction”, Relational Learning and Its Connection to Other Fields (SRL- 2004

Most information extraction (IE) systems treat separate potential extractions as independent. However, in many cases, considering influences between different potential extractions could improve overall accuracy. Statistical methods based on undirected graphical models, such as conditional random fields (CRFs), have been shown to be an effective approach to learning accurate IE systems. We present a new IE method that employs Relational Markov Networks, which can represent arbitrary dependencies between extractions. This allows for “collective information extraction ” that exploits the mutual influence between possible extractions. Experiments on learning to extract protein names from biomedical text demonstrate the advantages of this approach. 1