Assessment of approximate string matching in a biomedical text retrieval problem

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

Exact string matching algorithms involve finding all occurrences of a pattern P in a text T. These algorithms have been extensively studied in computer science, primarily because of their applications in various fields such as text search and computational biology. The main goal of exact string matching algorithms is to find all pattern matches correctly within the shortest possible time frame. Although hash-based string matching algorithms run fast, there are shortcomings, such as hash collisions. In this study, a novel hash function has been proposed that eliminates hash collisions for DNA sequences. It provides us perfect hashing and produces hash values in a time-efficient manner. We have proposed two exact string matching algorithms based on the proposed hash function. In the first approach, we replace the traditional Hash-q algorithm's hash function with the proposed one. In the second approach, we improved the first approach by utilizing the shift size indicated at the (m-1)^th entry in the good suffix shift table when an exact matching is found. In these approaches, we eliminate the need to compare the last q characters of the pattern and text. We have included six algorithms from the literature in our evaluations. E. Coli and Human Chromosome1 datasets from the literature and a synthetic dataset produced randomly are utilized for comparisons. The results show that the proposed approaches achieve better performance metrics in terms of the average runtime, the average number of character comparisons, and the average number of hash comparisons.

Research on Uyghur Pattern Matching Based on Syllable Features

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.

A fuzzy-match search engine for physician directories

Background

A search engine to find physicians’ information is a basic but crucial function of a health care provider’s website. Inefficient search engines, which return no results or incorrect results, can lead to patient frustration and potential customer loss. A search engine that can handle misspellings and spelling variations of names is needed, as the United States (US) has culturally, racially, and ethnically diverse names.

Objective

The Marshfield Clinic website provides a search engine for users to search for physicians’ names. The current search engine provides an auto-completion function, but it requires an exact match. We observed that 26% of all searches yielded no results. The goal was to design a fuzzy-match algorithm to aid users in finding physicians easier and faster.

Methods

Instead of an exact match search, we used a fuzzy algorithm to find similar matches for searched terms. In the algorithm, we solved three types of search engine failures: “Typographic”, “Phonetic spelling variation”, and “Nickname”. To solve these mismatches, we used a customized Levenshtein distance calculation that incorporated Soundex coding and a lookup table of nicknames derived from US census data.

Results

Using the “Challenge Data Set of Marshfield Physician Names,” we evaluated the accuracy of fuzzy-match engine–top ten (90%) and compared it with exact match (0%), Soundex (24%), Levenshtein distance (59%), and fuzzy-match engine–top one (71%).

Conclusions

We designed, created a reference implementation, and evaluated a fuzzy-match search engine for physician directories. The open-source code is available at the codeplex website and a reference implementation is available for demonstration at the datamarsh website.

Mapping biological entities using the longest approximately common prefix method

Background

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.

Results

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.

Conclusions

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.

Bioinformatics opportunities for identification and study of medicinal plants

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.