Semantic role labeling for protein transport predicates

<p>Abstract</p> <p>Background</p> <p>Automatic semantic role labeling (SRL) is a natural language processing (NLP) technique that maps sentences to semantic representations. This technique has been widely studied in the recent years, but mostly with data in newswire domains. Here, we report on a SRL model for identifying the semantic roles of biomedical predicates describing protein transport in GeneRIFs – manually curated sentences focusing on gene functions. To avoid the computational cost of syntactic parsing, and because the boundaries of our protein transport roles often did not match up with syntactic phrase boundaries, we approached this problem with a word-chunking paradigm and trained support vector machine classifiers to classify words as being at the beginning, inside or outside of a protein transport role.</p> <p>Results</p> <p>We collected a set of 837 GeneRIFs describing movements of proteins between cellular components, whose predicates were annotated for the semantic roles AGENT, PATIENT, ORIGIN and DESTINATION. We trained these models with the features of previous word-chunking models, features adapted from phrase-chunking models, and features derived from an analysis of our data. Our models were able to label protein transport semantic roles with 87.6% precision and 79.0% recall when using manually annotated protein boundaries, and 87.0% precision and 74.5% recall when using automatically identified ones.</p> <p>Conclusion</p> <p>We successfully adapted the word-chunking classification paradigm to semantic role labeling, applying it to a new domain with predicates completely absent from any previous studies. By combining the traditional word and phrasal role labeling features with biomedical features like protein boundaries and MEDPOST part of speech tags, we were able to address the challenges posed by the new domain data and subsequently build robust models that achieved F-measures as high as 83.1. This system for extracting protein transport information from GeneRIFs performs well even with proteins identified automatically, and is therefore more robust than the rule-based methods previously used to extract protein transport roles.</p

Investigations into semantic role labeling of propbank and nombank

Master'sMASTER OF SCIENC

The effect of syntactic representation on semantic role labeling

Almost all automatic semantic role labeling (SRL) systems rely on a preliminary parsing step that derives a syntactic structure from the sentence being analyzed. This makes the choice of syntactic representation an essential design decision. In this paper, we study the influence of syntactic representation on the performance of SRL systems. Specifically, we compare constituent-based and dependency-based representations for SRL of English in the FrameNet paradigm. Contrary to previous claims, our results demonstrate that the systems based on dependencies perform roughly as well as those based on constituents: For the argument classification task, dependency-based systems perform slightly higher on average, while the opposite holds for the argument identification task. This is remarkable because dependency parsers are still in their infancy while constituent parsing is more mature. Furthermore, the results show that dependency-based semantic role classifiers rely less on lexicalized features, which makes them more robust to domain changes and makes them learn more efficiently with respect to the amount of training data

Closing the gap in WSD: supervised results with unsupervised methods

Word-Sense Disambiguation (WSD), holds promise for many NLP applications requiring broad-coverage language understanding, such as summarization (Barzilay and Elhadad, 1997) and question answering (Ramakrishnan et al., 2003). Recent studies have also shown that WSD can benefit machine translation (Vickrey et al., 2005) and information retrieval (Stokoe, 2005). Much work has focused on the computational treatment of sense ambiguity, primarily using data-driven methods. The most accurate WSD systems to date are supervised and rely on the availability of sense-labeled training data. This restriction poses a significant barrier to widespread use of WSD in practice, since such data is extremely expensive to acquire for new languages and domains. Unsupervised WSD holds the key to enable such application, as it does not require sense-labeled data. However, unsupervised methods fall far behind supervised ones in terms of accuracy and ease of use. In this thesis we explore the reasons for this, and present solutions to remedy this situation. We hypothesize that one of the main problems with unsupervised WSD is its lack of a standard formulation and general purpose tools common to supervised methods. As a first step, we examine existing approaches to unsupervised WSD, with the aim of detecting independent principles that can be utilized in a general framework. We investigate ways of leveraging the diversity of existing methods, using ensembles, a common tool in the supervised learning framework. This approach allows us to achieve accuracy beyond that of the individual methods, without need for extensive modification of the underlying systems. Our examination of existing unsupervised approaches highlights the importance of using the predominant sense in case of uncertainty, and the effectiveness of statistical similarity methods as a tool for WSD. However, it also serves to emphasize the need for a way to merge and combine learning elements, and the potential of a supervised-style approach to the problem. Relying on existing methods does not take full advantage of the insights gained from the supervised framework. We therefore present an unsupervised WSD system which circumvents the question of actual disambiguation method, which is the main source of discrepancy in unsupervised WSD, and deals directly with the data. Our method uses statistical and semantic similarity measures to produce labeled training data in a completely unsupervised fashion. This allows the training and use of any standard supervised classifier for the actual disambiguation. Classifiers trained with our method significantly outperform those using other methods of data generation, and represent a big step in bridging the accuracy gap between supervised and unsupervised methods. Finally, we address a major drawback of classical unsupervised systems – their reliance on a fixed sense inventory and lexical resources. This dependence represents a substantial setback for unsupervised methods in cases where such resources are unavailable. Unfortunately, these are exactly the areas in which unsupervised methods are most needed. Unsupervised sense-discrimination, which does not share those restrictions, presents a promising solution to the problem. We therefore develop an unsupervised sense discrimination system. We base our system on a well-studied probabilistic generative model, Latent Dirichlet Allocation (Blei et al., 2003), which has many of the advantages of supervised frameworks. The model’s probabilistic nature lends itself to easy combination and extension, and its generative aspect is well suited to linguistic tasks. Our model achieves state-of-the-art performance on the unsupervised sense induction task, while remaining independent of any fixed sense inventory, and thus represents a fully unsupervised, general purpose, WSD tool

The Acquisition Of Lexical Knowledge From The Web For Aspects Of Semantic Interpretation

This work investigates the effective acquisition of lexical knowledge from the Web to perform semantic interpretation. The Web provides an unprecedented amount of natural language from which to gain knowledge useful for semantic interpretation. The knowledge acquired is described as common sense knowledge, information one uses in his or her daily life to understand language and perception. Novel approaches are presented for both the acquisition of this knowledge and use of the knowledge in semantic interpretation algorithms. The goal is to increase accuracy over other automatic semantic interpretation systems, and in turn enable stronger real world applications such as machine translation, advanced Web search, sentiment analysis, and question answering. The major contributions of this dissertation consist of two methods of acquiring lexical knowledge from the Web, namely a database of common sense knowledge and Web selectors. The first method is a framework for acquiring a database of concept relationships. To acquire this knowledge, relationships between nouns are found on the Web and analyzed over WordNet using information-theory, producing information about concepts rather than ambiguous words. For the second contribution, words called Web selectors are retrieved which take the place of an instance of a target word in its local context. The selectors serve for the system to learn the types of concepts that the sense of a target word should be similar. Web selectors are acquired dynamically as part of a semantic interpretation algorithm, while the relationships in the database are useful to iii stand-alone programs. A final contribution of this dissertation concerns a novel semantic similarity measure and an evaluation of similarity and relatedness measures on tasks of concept similarity. Such tasks are useful when applying acquired knowledge to semantic interpretation. Applications to word sense disambiguation, an aspect of semantic interpretation, are used to evaluate the contributions. Disambiguation systems which utilize semantically annotated training data are considered supervised. The algorithms of this dissertation are considered minimallysupervised; they do not require training data created by humans, though they may use humancreated data sources. In the case of evaluating a database of common sense knowledge, integrating the knowledge into an existing minimally-supervised disambiguation system significantly improved results – a 20.5% error reduction. Similarly, the Web selectors disambiguation system, which acquires knowledge directly as part of the algorithm, achieved results comparable with top minimally-supervised systems, an F-score of 80.2% on a standard noun disambiguation task. This work enables the study of many subsequent related tasks for improving semantic interpretation and its application to real-world technologies. Other aspects of semantic interpretation, such as semantic role labeling could utilize the same methods presented here for word sense disambiguation. As the Web continues to grow, the capabilities of the systems in this dissertation are expected to increase. Although the Web selectors system achieves great results, a study in this dissertation shows likely improvements from acquiring more data. Furthermore, the methods for acquiring a database of common sense knowledge could be applied in a more exhaustive fashion for other types of common sense knowledge. Finally, perhaps the greatest benefits from this work will come from the enabling of real world technologies that utilize semantic interpretation

A Survey on Semantic Processing Techniques

Semantic processing is a fundamental research domain in computational linguistics. In the era of powerful pre-trained language models and large language models, the advancement of research in this domain appears to be decelerating. However, the study of semantics is multi-dimensional in linguistics. The research depth and breadth of computational semantic processing can be largely improved with new technologies. In this survey, we analyzed five semantic processing tasks, e.g., word sense disambiguation, anaphora resolution, named entity recognition, concept extraction, and subjectivity detection. We study relevant theoretical research in these fields, advanced methods, and downstream applications. We connect the surveyed tasks with downstream applications because this may inspire future scholars to fuse these low-level semantic processing tasks with high-level natural language processing tasks. The review of theoretical research may also inspire new tasks and technologies in the semantic processing domain. Finally, we compare the different semantic processing techniques and summarize their technical trends, application trends, and future directions.Comment: Published at Information Fusion, Volume 101, 2024, 101988, ISSN 1566-2535. The equal contribution mark is missed in the published version due to the publication policies. Please contact Prof. Erik Cambria for detail

Domain adaptation and training data acquisition in wide-coverage word sense disambiguation and its application to information retrieval

Ph.DDOCTOR OF PHILOSOPH