Improving Term Frequency Normalization for Multi-topical Documents, and Application to Language Modeling Approaches

Term frequency normalization is a serious issue since lengths of documents are various. Generally, documents become long due to two different reasons - verbosity and multi-topicality. First, verbosity means that the same topic is repeatedly mentioned by terms related to the topic, so that term frequency is more increased than the well-summarized one. Second, multi-topicality indicates that a document has a broad discussion of multi-topics, rather than single topic. Although these document characteristics should be differently handled, all previous methods of term frequency normalization have ignored these differences and have used a simplified length-driven approach which decreases the term frequency by only the length of a document, causing an unreasonable penalization. To attack this problem, we propose a novel TF normalization method which is a type of partially-axiomatic approach. We first formulate two formal constraints that the retrieval model should satisfy for documents having verbose and multi-topicality characteristic, respectively. Then, we modify language modeling approaches to better satisfy these two constraints, and derive novel smoothing methods. Experimental results show that the proposed method increases significantly the precision for keyword queries, and substantially improves MAP (Mean Average Precision) for verbose queries.Comment: 8 pages, conference paper, published in ECIR '0

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Many Task Learning with Task Routing

Typical multi-task learning (MTL) methods rely on architectural adjustments and a large trainable parameter set to jointly optimize over several tasks. However, when the number of tasks increases so do the complexity of the architectural adjustments and resource requirements. In this paper, we introduce a method which applies a conditional feature-wise transformation over the convolutional activations that enables a model to successfully perform a large number of tasks. To distinguish from regular MTL, we introduce Many Task Learning (MaTL) as a special case of MTL where more than 20 tasks are performed by a single model. Our method dubbed Task Routing (TR) is encapsulated in a layer we call the Task Routing Layer (TRL), which applied in an MaTL scenario successfully fits hundreds of classification tasks in one model. We evaluate our method on 5 datasets against strong baselines and state-of-the-art approaches.Comment: 8 Pages, 5 Figures, 2 Table