179 research outputs found
Combining active learning and semi-supervised learning techniques to extract protein interaction sentences
Background: Protein-protein interaction (PPI) extraction has been a focal point of many biomedical research and database curation tools. Both Active Learning and Semi-supervised SVMs have recently been applied to extract PPI automatically. In this paper, we explore combining the AL with the SSL to improve the performance of the PPI task. Methods: We propose a novel PPI extraction technique called PPISpotter by combining Deterministic Annealing-based SSL and an AL technique to extract protein-protein interaction. In addition, we extract a comprehensive set of features from MEDLINE records by Natural Language Processing (NLP) techniques, which further improve the SVM classifiers. In our feature selection technique, syntactic, semantic, and lexical properties of text are incorporated into feature selection that boosts the system performance significantly. Results: By conducting experiments with three different PPI corpuses, we show that PPISpotter is superior to the other techniques incorporated into semi-supervised SVMs such as Random Sampling, Clustering, and Transductive SVMs by precision, recall, and F-measure. Conclusions: Our system is a novel, state-of-the-art technique for efficiently extracting protein-protein interaction pairs.X116sciescopu
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HOLMES: A Hybrid Ontology-Learning Materials Engineering System
Designing and discovering novel materials is challenging problem in many domains such as fuel additives, composites, pharmaceuticals, and so on. At the core of all this are models that capture how the different domain-specific data, information, and knowledge regarding the structures and properties of the materials are related to one another. This dissertation explores the difficult task of developing an artificial intelligence-based knowledge modeling environment, called Hybrid Ontology-Learning Materials Engineering System (HOLMES) that can assist humans in populating a materials science and engineering ontology through automatic information extraction from journal article abstracts. While what we propose may be adapted for a generic materials engineering application, our focus in this thesis is on the needs of the pharmaceutical industry. We develop the Columbia Ontology for Pharmaceutical Engineering (COPE), which is a modification of the Purdue Ontology for Pharmaceutical Engineering. COPE serves as the basis for HOLMES.
The HOLMES framework starts with journal articles that are in the Portable Document Format (PDF) and ends with the assignment of the entries in the journal articles into ontologies. While this might seem to be a simple task of information extraction, to fully extract the information such that the ontology is filled as completely and correctly as possible is not easy when considering a fully developed ontology.
In the development of the information extraction tasks, we note that there are new problems that have not arisen in previous information extraction work in the literature. The first is the necessity to extract auxiliary information in the form of concepts such as actions, ideas, problem specifications, properties, etc. The second problem is in the existence of multiple labels for a single token due to the existence of the aforementioned concepts. These two problems are the focus of this dissertation.
In this work, the HOLMES framework is presented as a whole, describing our successful progress as well as unsolved problems, which might help future research on this topic. The ontology is then presented to help in the identification of the relevant information that needs to be retrieved. The annotations are next developed to create the data sets necessary for the machine learning algorithms to perform. Then, the current level of information extraction for these concepts is explored and expanded. This is done through the introduction of entity feature sets that are based on previously extracted entities from the entity recognition task. And finally, the new task of handling multiple labels for tagging a single entity is also explored by the use of multiple-label algorithms used primarily in image processing
PersoNER: Persian named-entity recognition
© 1963-2018 ACL. Named-Entity Recognition (NER) is still a challenging task for languages with low digital resources. The main difficulties arise from the scarcity of annotated corpora and the consequent problematic training of an effective NER pipeline. To abridge this gap, in this paper we target the Persian language that is spoken by a population of over a hundred million people world-wide. We first present and provide ArmanPerosNERCorpus, the first manually-annotated Persian NER corpus. Then, we introduce PersoNER, an NER pipeline for Persian that leverages a word embedding and a sequential max-margin classifier. The experimental results show that the proposed approach is capable of achieving interesting MUC7 and CoNNL scores while outperforming two alternatives based on a CRF and a recurrent neural network
Multi-criteria-based active learning for named entity recognition
Master'sMASTER OF SCIENC
Symbol Emergence in Robotics: A Survey
Humans can learn the use of language through physical interaction with their
environment and semiotic communication with other people. It is very important
to obtain a computational understanding of how humans can form a symbol system
and obtain semiotic skills through their autonomous mental development.
Recently, many studies have been conducted on the construction of robotic
systems and machine-learning methods that can learn the use of language through
embodied multimodal interaction with their environment and other systems.
Understanding human social interactions and developing a robot that can
smoothly communicate with human users in the long term, requires an
understanding of the dynamics of symbol systems and is crucially important. The
embodied cognition and social interaction of participants gradually change a
symbol system in a constructive manner. In this paper, we introduce a field of
research called symbol emergence in robotics (SER). SER is a constructive
approach towards an emergent symbol system. The emergent symbol system is
socially self-organized through both semiotic communications and physical
interactions with autonomous cognitive developmental agents, i.e., humans and
developmental robots. Specifically, we describe some state-of-art research
topics concerning SER, e.g., multimodal categorization, word discovery, and a
double articulation analysis, that enable a robot to obtain words and their
embodied meanings from raw sensory--motor information, including visual
information, haptic information, auditory information, and acoustic speech
signals, in a totally unsupervised manner. Finally, we suggest future
directions of research in SER.Comment: submitted to Advanced Robotic
Text Mining for Chemical Compounds
Exploring the chemical and biological space covered by patent and journal publications is crucial in early- stage medicinal chemistry activities. The analysis provides understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration.
Extracting chemical and biological entities from patents and journals through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process.
In this book, we addressed the lack of quality measurements for assessing the correctness of structural representation within and across chemical databases; lack of resources to build text-mining systems; lack of high performance systems to extract chemical compounds from journals and patents; and lack of automated systems to identify relevant compounds in patents. The consistency and ambiguity of chemical identifiers was analyzed within and between small- molecule databases in Chapter 2 and Chapter 3. In Chapter 4 and Chapter 7 we developed resources to enable the construction of chemical text-mining systems. In Chapter 5 and Chapter 6, we used community challenges (BioCreative V and BioCreative VI) and their corresponding resources to identify mentions of chemical compounds in journal abstracts and patents. In Chapter 7 we used our findings in previous chapters to extract chemical named entities from patent full text and to classify the relevancy of chemical compounds
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