Data Mining: Information Extraction
Methods and challenges in information extraction for data mining
by Niket Bhargava*,
- Published in Journal of Advances in Science and Technology, E-ISSN: 2230-9659
Volume 3, Issue No. 4, Feb 2012, Pages 0 - 0 (0)
Published by: Ignited Minds Journals
ABSTRACT
Animportant approach to text mining involves the use of natural-languageinformation extraction. Information extraction (IE) distills structured data orknowledge from un-structured text by identifying references to named entitiesas well as stated relationships between such entities. IE systems can be usedto directly extricate abstract knowledge from a text corpus, or to extract concretedata from a set of documents which can then be further analyzed withtraditional data-mining techniques to discover more general patterns. Wediscuss methods and implemented systems for both of these approaches andsummarize results on mining real text corpora of biomedical abstracts, jobannouncements, and product descriptions. We also discuss challenges that arisewhen employing current information extraction technology to discover knowledgein text
KEYWORD
data mining, information extraction, natural-language, named entities, relationships, text corpus, documents, data-mining techniques, patterns, biomedical abstracts
Introduction
Most data-mining research assumes that the information to be “mined” is already in the form of a relational database. Unfortunately, for many applications, available electronic information is in the form of unstructured natural-language documents rather than structured databases. Consequently, the problem of text mining, i.e. discovering useful knowledge from unstructured text, is becoming an increasingly important aspect of KDD. Much of the work in text mining does not exploit any form of natural-language processing (NLP), treating documents as an unordered “bag of words” as is typical in information retrieval. The standard a vector space model of text represents a document as a sparse vector that specifies a weighted frequency for each of the large number of distinct words or tokens that appear in a corpus [2]. Such a simplified representation of text has been shown to be quite effective for a number of standard tasks such as document retrieval, classification, and clustering [2; 16; 66;
60].
However, most of the knowledge that might be mined from text cannot be discovered using a simple bag-of-words representation. The entities referenced in a document and the properties and relationships asserted about and between these entities cannot be determined using a standard vector-space representation. Although full natural-language understanding is still far from the capabilities of current technology, existing methods in information extraction (IE) are, with Figure 1: Medline abstract with proteins underlined. reasonable accuracy, able to recognize several types of entities in text and identify some relationships that are asserted between them [14; 25; 53]. Therefore, IE can serve an important technology for text mining. If the knowledge to be discovered is expressed directly in the documents to be mined, then IE alone can serve as an effective approach to text mining. However, if the documents contain concrete data in unstructured form rather than abstract knowledge, it may be useful to first use IE to transform the unstructured data in the document
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corpus into a structured database, and then use traditional data- mining tools to identify abstract patterns in this extracted data. In this article, we review these two approaches to text mining with information extraction, using one of our own research projects to illustrate each approach. First, we introduce the basics of information extraction. Next, we discuss using IE to directly extract knowledge from text. Finally, we discuss discovering knowledge by mining data that is first extracted from unstructured or semi-structured text.
2. INFORMATION EXTRACTION
IE Problems - Information Extraction (IE) concerns locating specific pieces of data in natural-language documents, thereby extracting structured information from unstructured text. One type of IE, named entity recognition, involves identifying references to particular kinds of objects such as names of people, companies, and locations [4]. In this paper, we consider the task of identifying names of human proteins in abstracts of biomedical journal articles [10]. Figure 1 shows part of a sample abstract in which the protein names are underlined. In addition to recognizing entities, an important problem is extracting specific types of relations between entities. For example, in newspaper text, one can identify that an organization is located in a particular city or that a person is Sample Job Posting: Job Title : Senior DBMS Consultant Location : Dallas,TX Responsibilities : DBMS Applications consultant works with project teams to define DBMS based solutions that support the enterprise deployment of Electronic Commerce, Sales Force Automation, and Customer Service applications. Desired Requirements - 3-5 years exp. developing Oracle or SQL Server apps using Visual Basic, C/C++, Powerbuilder, Progress, or similar. Recent experience related to installing and configuring Oracle or SQL Server in both dev. and deployment environments. Desired Skills - Understanding of UNIX or NT, scripting language. Know principles of structured software engineering and project management Filled Job Template: Title : Senior DBMS Consultant State : TX City : Dallas Country : US Language : Powerbuilder, Progress, C, C++, Visual Basic Platform : UNIX, NT Application : SQL Server, Oracle Area : Electronic Commerce, Customer Service required years of experience: 3 desired years of experience: 5 Figure 2 : Sample Job Posting and Filled Template affiliated with a specific organization [73; 24]. In biomedical text, one can identify that a protein interacts with another protein or that a protein is located in a particular part of the cell [10; 23]. For example, identifying protein interactions in the abstract excerpt in Figure 1 would require extracting the relation: interacts(NOSIP, eNOS). IE can also be used to extract fillers for a predetermined set of slots (roles) in a particular template (frame) relevant to the domain. In this paper, we consider the task of extracting a database from postings to the USENET newsgroup, Austin jobs [12]. Figure 2 shows a sample message from the newsgroup and the filled computer- science job template where several slots may have multiple fillers. For example, slots such as languages, platforms, applications, and areas usually have more than one filler, while slots related to the job’s title or location usually have only one filler. Similar applications include extracting relevant sets of pre defined slots from university colloquium announcements [29] or apartment rental ads [67]. Another application of IE is extracting structured data from unstructured or semi-structured web pages. When applied to semi-structured HTML, typically generated from an
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underlying database by a program on a web server, an IE system is typically called a wrapper [37], and the process is sometimes referred to as screen scraping. A typical application is extracting data on commercial items from web stores for a comparison shopping agent (shopbot) [27] such as My Simon (www.mysimon.com) or Froogle (froogle.google.com). For example, a wrapper may extract the title, author, ISBN number, publisher, and price of book from an Amazon web page. IE systems can also be used to extract data or knowledge from less-structured web sites by using both the HTML text in their pages as well as the structure of the hyperlinks between their pages. For example, the WebKB project at Carnegie Mellon University has explored extracting structured information from university computer- science departments [22]. The overall WebKB system attempted to identify all faculty, students, courses, and research projects in a department as well as relations between these entities such as: instructor(prof, course), advisor(student, prof),and member(person, project). IE Methods - There are a variety of approaches to constructing IE systems. One approach is to manually develop information extraction rules by encoding patterns (e.g. regular expressions) that reliably identify the desired entities or relations. For example, the Suiseki system [8] extracts information on interacting proteins from biomedical text using manually developed patterns. However, due to the variety of forms and contexts in which the desired information can appear, manually developing patterns is very difficult and tedious and rarely results in robust systems. Consequently, supervised machine- learning methods trained on human annotated corpora has become the most successful approach to developing robust IE systems [14]. A variety of learning methods have been applied to IE. One approach is to automatically learn pattern-based extraction rules for identifying each type of entity or relation. For example, our previously developed system, Rapier [12; 13], learns extraction rules consisting of three parts: 1) a pre-filler pattern that matches the text immediately preceding the phrase to be extracted, 2) a filler pattern that matches the phrase to be extracted, and 3) a post-filler pattern that matches the text immediately following the filler. Patterns are expressed in an enhanced regular-expression language, similar to that used in Perl [72]; and a bottom-up relational rule learner is used to induce rules from a corpus of labeled training examples. In Wrapper Induction [37] and Boosted Wrapper Induction (BWI) [30], regular-expression- type patterns are learned for identifying the beginning and ending of extracted phrases. Inductive Logic Programming (ILP) [45] has also been used to learn logical rules for identifying phrases to be extracted from a document [29]. An alternative general approach to IE is to treat it as a sequence labeling task in which each word (token) in the document is assigned a label (tag) from a fixed set of alternatives. For example, for each slot, X, to be extracted, we include a token label BeginX to mark the beginning of a filler for X and InsideX to mark other tokens in a filler for X. Finally, we include the label Other for tokens that are not included in the filler of any slot. Given a sequence labeled with these tags, it is easy to extract the desired fillers. One approach to the resulting sequence labeling problem is to use a statistical sequence model such as a Hidden Markov Model (HMM) [57] or a Conditional Random Field (CFR) [38]. Several earlier IE systems used generative HMM models [4; 31]; however, discriminately-trained CRF models have recently been shown to have an advantage over HMM’s [54; 65]. In both cases, the mode Figure 3: Sample Extraction Rule Learned by Rapier a supervised training corpus and then an efficient dynamic programming method based on the Viterbi algorithm [71] is used to determine the most probable tagging of a complete test document. Another approach to the sequence labeling problem for IE is to use a standard feature-based inductive classifier to predict the label of each token based on both the token itself and its surrounding context. Typically, the context is represented by a set of features that include the one or two tokens on either side of the target token as well as the labels of the one or two preceding tokens (which will already have been classified when labeling a sequence from left to right). Using this general approach, IE systems
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have been developed that use many different trained classifiers such as decision trees [3], boosting [15], memory-based learning (MBL) [43], support-vector machines (SVMs) [40], maximum entropy (MaxEnt) [17], transformation-based learning (TBL)[68] and many others
[64].
Many IE systems simply treat text as a sequence of un- interpreted tokens; however, many others use a variety of other NLP tools or knowledge bases. For example, a number of systems preprocess the text with a part-of- speech (POS) tagger (e.g. [18; 9]) and use words’ POS (e.g. noun, verb, adjective) as an extra feature that can be used in hand- written patterns [8], learned extraction rules [13], or induced classifiers [64]. Several IE systems use phrase chunkers (e.g. [59]) to identify potential phrases to extract [64; 73]. Others use complete syntactic parsers (e.g. [21]), particularly those which try to extract relations between entities by examining the synactic relationship between the phrases describing the relevant entities [24; 61]. Some use lexical semantic databases, such as Word Net [28], which provide word classes that can be used to define more general extraction patterns [13]. As a sample extraction pattern, Figure 3 shows a rule learned by Rapier [13] for extracting the transaction amount from a newswire concerning a corporate acquisition. This rule extracts the value “undisclosed” from phrases such as “sold to the bank for an undisclosed amount” or “paid Honeywell an undisclosed price”. The pre-filler pattern matches a noun or proper noun (indicated by the POS tags ’nn’ and ’pn’, respectively) followed by at most two other unconstrained words. The filler pattern matches the word “undisclosed” only when its POS tag is “adjective.” The post-filler pattern matches any word in WordNet’s semantic class named “price”.
3. FUTURE RESEARCH
Information extraction remains a challenging problem with many potential avenues for progress. In section, we discussed mining knowledge from extracted data; this discovered knowledge can itself be used to help improve extraction. The predictive relationships between different slot fillers discovered by KDD can provide additional clues about what information should be extracted from a document. For example, suppose we discover the rule “MySQL language” “Database area”. If the IE system extracted “MySQL language” but failed to extract “Database area”, we may want to assume there was an extraction error and add “Database” to the area slot. We have developed methods for using mined knowledge to improve the recall of extraction but not the precision [48; 52]. McCallum and Jensen [41] propose using probabilistic graphical models to unify IE and KDD; however, actual results on this approach are a goal of on-going research. Most IE systems are developed by training on human annotated corpora; however, constructing corpora sufficient for training accurate IE systems is a burdensome chore. One approach is to use active learning methods to decrease the amount of training data that must be annotated by selecting only the most informative sentences or passages to give to human annotators. We presented an initial approach to active learning for IE [70]; however, more research is needed to explore methods for reducing the demand for supervised training data in IE. Another approach to reducing demanding corpus-building requirements is to develop unsupervised learning methods for building IE systems. Although some work has been done in this area [19; 36], this is another promising area for future research. Developing semi-supervised learning methods for IE is a related research direction in which there has been only a limited amount of work [62]. With respect to handling textual variation when mining extracted data, it would be nice to see experimental comparisons of the two approaches mentioned in section ; i.e. automated data cleaning versus mining “soft matching” rules from “dirty” data. Do both approaches discover equally accurate knowledge with similar computational efficiency? When mining “soft-matching” rules, our current methods use a fixed, predetermined similarity metric for matching rule antecedents to variable text data. However, we have developed adaptive learned similarity metrics for data cleaning and “deduping’ [6]. It would be interesting to use such learned similarity metrics when discovering “soft- matching” rules since judging the similarity of textual strings is often domain dependent.
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4. CONCLUSIONS
In this paper we have discussed two approaches to using natural-language information extraction for text mining. First, one can extract general knowledge directly from text. As an example of this approach, we reviewed our project which extracted a knowledge base of 6,580 human protein interactions by mining over 750,000 Medline abstracts. Second, one can first extract structured data from text documents or web pages and then apply traditional KDD methods to discover patterns in the extracted data. As an example of this approach, we reviewed our work on the DiscoTEX system and its application to Amazon book descriptions and computer-science job postings and resumes. Research in information extraction continues to develop more effective algorithms for identifying entities and relations in text. By exploiting the lastest techniques in human-language technology and computational linguistics and combining them with the latest methods in machine learning and traditional data mining, one can effectively mine useful and important knowledge from the continually growing body of electronic documents and web pages.
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