Named entity recognition aims at extracting named entities from unstructured text. A recent trend of named entity recognition is finding approximate matches in the text with respect to a large dictionary of known entities, as the domain knowledge encoded in the dictionary helps to improve the extraction performance. In this paper, we study the problem of approximate dictionary matching with edit distance constraints. Compared to existing studies using token-based similarity constraints, our problem definition enables us to capture typographical or orthographical errors, both of which are common in entity extraction tasks yet may be missed by token-based similarity constraints. Our problem is technically challenging as existing approaches based on q-gram filtering have poor performance due to the existence of many short entities in the dictionary. Our proposed solution is based on an improved neighborhood generation method employing novel partitioning and prefix pruning techniques. We also propose an efficient document processing algorithm that minimizes unnecessary comparisons and enumerations and hence achieves good scalability. We have conducted extensive experiments on several publicly available named entity recognition datasets. The proposed algorithm outperforms alternative approaches by up to an order of magnitude.

Efficient approximate entity extraction with edit distance constraints

Plants have been used as a source of medicine since historic times and several commercially important drugs are of plant-based origin. The traditional approach towards discovery of plant-based drugs often times involves significant amount of time and expenditure. These labor-intensive approaches have struggled to keep pace with the rapid development of high-throughput technologies. In the era of high volume, high-throughput data generation across the biosciences, bioinformatics plays a crucial role. This has generally been the case in the context of drug designing and discovery. However, there has been limited attention to date to the potential application of bioinformatics approaches that can leverage plant-based knowledge. Here, we review bioinformatics studies that have contributed to medicinal plants research. In particular, we highlight areas in medicinal plant research where the application of bioinformatics methodologies may result in quicker and potentially cost-effective leads toward finding plant-based remedies.

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Bioinformatics opportunities for identification and study of medicinal plants

The significant growth in the volume of electronic biomedical data in recent decades has pointed to the need for approximate string matching algorithms that can expedite tasks such as named entity recognition, duplicate detection, terminology integration, and spelling correction. The task of source integration in the Unified Medical Language System (UMLS) requires considerable expert effort despite the presence of various computational tools. This problem warrants the search for a new method for approximate string matching and its UMLS-based evaluation. This paper introduces the Longest Approximately Common Prefix (LACP) method as an algorithm for approximate string matching that runs in linear time. We compare the LACP method for performance, precision and speed to nine other well-known string matching algorithms. As test data, we use two multiple-source samples from the Unified Medical Language System (UMLS) and two SNOMED Clinical Terms-based samples. In addition, we present a spell checker based on the LACP method. The Longest Approximately Common Prefix method completes its string similarity evaluations in less time than all nine string similarity methods used for comparison. The Longest Approximately Common Prefix outperforms these nine approximate string matching methods in its Maximum F1 measure when evaluated on three out of the four datasets, and in its average precision on two of the four datasets.

/pdf/mapping-biological-entities-using-the-longest-approximately-1vhqe9fhxd.pdf

Mapping biological entities using the longest approximately common prefix method

Improving hash-q exact string matching algorithm with perfect hashing for DNA sequences.

Pattern matching is widely used in various fields such as information retrieval, natural language processing (NLP), data mining and network security. In Uyghur (a typical agglutinative, low-resource language with complex morphology, spoken by the ethnic Uyghur group in Xinjiang, China), research on pattern matching is also ongoing. Due to the language characteristics, the pattern matching using characters and words as basic units has insufficient performance. There are two problems for pattern matching: (1) vowel weakening and (2) morphological changes caused by suffixes. In view of the above problems, this paper proposes a Boyer–Moore-U (BM-U) algorithm and a retrievable syllable coding format based on the syllable features of the Uyghur language and the improvement of the Boyer–Moore (BM) algorithm. This algorithm uses syllable features to perform pattern matching, which effectively solves the problem of weakening vowels, and it can better match words with stem shape changes. Finally, in the pattern matching experiments based on character-encoded text and syllable-encoded text for vowel-weakened words, the BM-U algorithm precision, recall, F1-measure and accuracy are improved by 4%, 55%, 33%, 25% and 10%, 52%, 38%, 38% compared to the BM algorithm.

https://www.mdpi.com/2078-2489/11/5/248/pdf

Research on Uyghur Pattern Matching Based on Syllable Features

Text-based search is widely used for biomedical data mining and knowledge discovery. Character errors in literatures affect the accuracy of data mining. Methods for solving this problem are being explored. This work tests the usefulness of the Smith–Waterman algorithm with affine gap penalty as a method for biomedical literature retrieval.Names ofmedicinal herbs collected fromherbalmedicine literatures arematchedwith those frommedicinal chemistry literatures by using this algorithm at different string identity levels (80–100%). The optimum performance is at string identity of 88%, at which the recall and precision are 96.9% and 97.3%, respectively. Our study suggests that the Smith–Waterman algorithm is useful for improving the success rate of biomedical text retrieval. 2004 Elsevier Ltd. All rights reserved.

/pdf/assessment-of-approximate-string-matching-in-a-biomedical-5b7gy1s5ms.pdf

Z.R. Lia

Papers

Assessment of approximate string matching in a biomedical text retrieval problem