Minlie Huang

Discovering patterns to extract protein--protein interactions from full texts

MOTIVATION Although there are several databases storing protein-protein interactions, most such data still exist only in the scientific literature. They are scattered in scientific literature written in natural languages, defying data mining efforts. Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a robust and powerful methodology to mine protein-protein interactions from biomedical texts. RESULTS We present a novel and robust approach for extracting protein-protein interactions from literature. Our method uses a dynamic programming algorithm to compute distinguishing patterns by aligning relevant sentences and key verbs that describe protein interactions. A matching algorithm is designed to extract the interactions between proteins. Equipped only with a dictionary of protein names, our system achieves a recall rate of 80.0% and precision rate of 80.5%. AVAILABILITY The program is available on request from the authors.

The gene normalization task in BioCreative III

BackgroundWe report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k).ResultsWe received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively.ConclusionsBy using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance.

Discovering patterns to extract protein–protein interactions from the literature: Part II

MOTIVATION An enormous number of protein-protein interaction relationships are buried in millions of research articles published over the years, and the number is growing. Rediscovering them automatically is a challenging bioinformatics task. Solutions to this problem also reach far beyond bioinformatics. RESULTS We study a new approach that involves automatically discovering English expression patterns, optimizing them and using them to extract protein-protein interactions. In a sister paper, we described how to generate English expression patterns related to protein-protein interactions, and this approach alone has already achieved precision and recall rates significantly higher than those of other automatic systems. This paper continues to present our theory, focusing on how to improve the patterns. A minimum description length (MDL)-based pattern-optimization algorithm is designed to reduce and merge patterns. This has significantly increased generalization power, and hence the recall and precision rates, as confirmed by our experiments. AVAILABILITY http://spies.cs.tsinghua.edu.cn.

Recommending MeSH terms for annotating biomedical articles

Background Due to the high cost of manual curation of key aspects from the scientific literature, automated methods for assisting this process are greatly desired. Here, we report a novel approach to facilitate MeSH indexing, a challenging task of assigning MeSH terms to MEDLINE citations for their archiving and retrieval. Methods Unlike previous methods for automatic MeSH term assignment, we reformulate the indexing task as a ranking problem such that relevant MeSH headings are ranked higher than those irrelevant ones. Specifically, for each document we retrieve 20 neighbor documents, obtain a list of MeSH main headings from neighbors, and rank the MeSH main headings using ListNet–a learning-to-rank algorithm. We trained our algorithm on 200 documents and tested on a previously used benchmark set of 200 documents and a larger dataset of 1000 documents. Results Tested on the benchmark dataset, our method achieved a precision of 0.390, recall of 0.712, and mean average precision (MAP) of 0.626. In comparison to the state of the art, we observe statistically significant improvements as large as 39% in MAP (p-value <0.001). Similar significant improvements were also obtained on the larger document set. Conclusion Experimental results show that our approach makes the most accurate MeSH predictions to date, which suggests its great potential in making a practical impact on MeSH indexing. Furthermore, as discussed the proposed learning framework is robust and can be adapted to many other similar tasks beyond MeSH indexing in the biomedical domain. All data sets are available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/indexing.

PatentMiner: topic-driven patent analysis and mining

Patenting is one of the most important ways to protect companys core business concepts and proprietary technologies. Analyzing large volume of patent data can uncover the potential competitive or collaborative relations among companies in certain areas, which can provide valuable information to develop strategies for intellectual property (IP), R&D, and marketing. In this paper, we present a novel topic-driven patent analysis and mining system. Instead of merely searching over patent content, we focus on studying the heterogeneous patent network derived from the patent database, which is represented by several types of objects (companies, inventors, and technical content) jointly evolving over time. We design and implement a general topic-driven framework for analyzing and mining the heterogeneous patent network. Specifically, we propose a dynamic probabilistic model to characterize the topical evolution of these objects within the patent network. Based on this modeling framework, we derive several patent analytics tools that can be directly used for IP and R&D strategy planning, including a heterogeneous network co-ranking method, a topic-level competitor evolution analysis algorithm, and a method to summarize the search results. We evaluate the proposed methods on a real-world patent database. The experimental results show that the proposed techniques clearly outperform the corresponding baseline methods.

GeneTUKit: a software for document-level gene normalization.

Motivation: Linking gene mentions in an article to entries of biological databases can facilitate indexing and querying biological literature greatly. Due to the high ambiguity of gene names, this task is particularly challenging. Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value. Results: We developed GeneTUKit, a document-level gene normalization software for full-text articles. This software employs both local context surrounding gene mentions and global context from the whole full-text document. It can normalize genes of different species simultaneously. When participating in BioCreAtIvE III, the system obtained good results among 37 runs: the system was ranked first, fourth and seventh in terms of TAP-20, TAP-10 and TAP-5, respectively on the 507 full-text test articles. Availability and implementation: The software is available at http://www.qanswers.net/GeneTUKit/. Contact: aihuang@tsinghua.edu.cn

Attention-based LSTM for Aspect-level Sentiment Classification.

Aspect-level sentiment classification is a fine-grained task in sentiment analysis. Since it provides more complete and in-depth results, aspect-level sentiment analysis has received much attention these years. In this paper, we reveal that the sentiment polarity of a sentence is not only determined by the content but is also highly related to the concerned aspect. For instance, “The appetizers are ok, but the service is slow.”, for aspect taste, the polarity is positive while for service, the polarity is negative. Therefore, it is worthwhile to explore the connection between an aspect and the content of a sentence. To this end, we propose an Attention-based Long Short-Term Memory Network for aspect-level sentiment classification. The attention mechanism can concentrate on different parts of a sentence when different aspects are taken as input. We experiment on the SemEval 2014 dataset and results show that our model achieves state-ofthe-art performance on aspect-level sentiment classification.

A Generative Probabilistic Model for Multi-label Classification

Traditional discriminative classification method makes little attempt to reveal the probabilistic structure and the correlation within both input and output spaces. In the scenario of multi-label classification, most of the classifiers simply assume the predefined classes are independently distributed, which would definitely hinder the classification performance when there are intrinsic correlations between the classes. In this article, we propose a generative probabilistic model, the Correlated Labeling Model (CoL Model), to formulate the correlation between different classes. The CoL model is presented to capture the correlation between classes and the underlying structures via the latent random variables in a supervised manner. We develop a variational procedure to approximate the posterior distribution and employ the EM algorithm for the empirical Bayes parameter estimation. In our evaluations, the proposed model achieved promising results on various data sets.

Mining physical protein-protein interactions from the literature

Background:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual curation is intensive in terms of time and cost, there is an urgent need for text-mining tools to facilitate the extraction of such information. The BioCreative (Critical Assessment of Information Extraction systems in Biology) challenge evaluation provided common standards and shared evaluation criteria to enable comparisons among different approaches.Results:During the benchmark evaluation of BioCreative 2006, all of our results ranked in the top three places. In the task of filtering articles irrelevant to physical protein interactions, our method contributes a precision of 75.07%, a recall of 81.07%, and an AUC (area under the receiver operating characteristic curve) of 0.847. In the task of identifying protein mentions and normalizing mentions to molecule identifiers, our method is competitive among runs submitted, with a precision of 34.83%, a recall of 24.10%, and an F1 score of28.5%. In extracting protein interaction pairs, our profile-based method was competitive on the SwissProt-only subset (precision = 36.95%, recall = 32.68%, and F1 score = 30.40%) and on the entire dataset (30.96%, 29.35%, and26.20%, respectively). From the biologists point of view, however, these findings are far from satisfactory. The error analysis presented in this report provides insight into how performance could be improved: three-quarters of false negatives were due to protein normalization problems (532/698), and about one-quarter were due to problems with correctly extracting interactions for this system.Conclusion:We present a text-mining framework to extract physical protein-protein interactions from the literature. Three key issues are addressed, namely filtering irrelevant articles, identifying protein names and normalizing them to molecule identifiers, and extracting protein-protein interactions. Our system is among the top three performers in the benchmark evaluation of BioCreative 2006. The tool will be helpful for manual interaction curation and can greatly facilitate the process of extracting protein-protein interactions.

TransG : A Generative Model for Knowledge Graph Embedding.

Recently, knowledge graph embedding, which projects symbolic entities and relations into continuous vector space, has become a new, hot topic in artificial intelligence. This paper proposes a novel generative model (TransG) to address the issue of multiple relation semantics that a relation may have multiple meanings revealed by the entity pairs associated with the corresponding triples. The new model can discover latent semantics for a relation and leverage a mixture of relationspecific component vectors to embed a fact triple. To the best of our knowledge, this is the first generative model for knowledge graph embedding, and at the first time, the issue of multiple relation semantics is formally discussed. Extensive experiments show that the proposed model achieves substantial improvements against the state-of-the-art baselines.