LE-MDCAP: A Computational Model to Prioritize Causal miRNA–Disease Associations

MicroRNAs (miRNAs) are associated with various complex human diseases and some miRNAs can be directly involved in the mechanisms of disease. Identifying disease-causative miRNAs can provide novel insight in disease pathogenesis from a miRNA perspective and facilitate disease treatment. To date, various computational models have been developed to predict general miRNA–disease associations, but few models are available to further prioritize causal miRNA–disease associations from non-causal associations. Therefore, in this study, we constructed a Levenshtein-Distance-Enhanced miRNA–Disease Causal Association Predictor (LE-MDCAP), to predict potential causal miRNA–disease associations. Specifically, Levenshtein distance matrixes covering the sequence, expression and functional miRNA similarities were introduced to enhance the previous Gaussian interaction profile kernel-based similarity matrix. LE-MDCAP integrated miRNA similarity matrices, disease semantic similarity matrix and known causal miRNA–disease associations to make predictions. For regular causal vs. non-disease association discrimination task, LF-MDCAP achieved area under the receiver operating characteristic curve (AUROC) of 0.911 and 0.906 in 10-fold cross-validation and independent test, respectively. More importantly, LE-MDCAP prominently outperformed the previous MDCAP model in distinguishing causal versus non-causal miRNA–disease associations (AUROC 0.820 vs. 0.695). Case studies performed on diabetic retinopathy and hsa-mir-361 also validated the accuracy of our model. In summary, LE-MDCAP could be useful for screening causal miRNA–disease associations from general miRNA–disease associations.

Predicting Variant-Driven Multi-Wave Pattern of COVID-19 via a Machine Learning Analysis of Spike Protein Mutations

Never before such a vast amount of data, including genome sequencing, has been collected for any viral pandemic than for the current case of COVID-19. This offers the possibility to trace the virus evolution and to assess the role mutations play in its spread within the population, in real time. To this end, we focused on the Spike protein for its central role in mediating viral outbreak and replication in host cells. Employing the Levenshtein distance on the Spike protein sequences, we designed a machine learning algorithm yielding a temporal clustering of the available dataset. From this, we were able to identify and define emerging persistent variants that are in agreement with known evidences. Our novel algorithm allowed us to define persistent variants as chains that remain stable over time and to highlight emerging variants of epidemiological interest as branching events that occur over time. Hence, we determined the relationship and temporal connection between variants of interest and the ensuing passage to dominance of the current variants of concern. Remarkably, the analysis and the relevant tools introduced in our work serve as an early warning for the emergence of new persistent variants once the associated cluster reaches 1% of the time-binned sequence data. We validated our approach and its effectiveness on the onset of the Alpha variant of concern. We further predict that the recently identified lineage AY.4.2 (‘Delta plus’) is causing a new emerging variant. Comparing our findings with the epidemiological data we demonstrated that each new wave is dominated by a new emerging variant, thus confirming the hypothesis of the existence of a strong correlation between the birth of variants and the pandemic multi-wave temporal pattern. The above allows us to introduce the epidemiology of variants that we described via the Mutation epidemiological Renormalisation Group (MeRG) framework.

Combining word embeddings to extract chemical and drug entities in biomedical literature

Background Natural language processing (NLP) and text mining technologies for the extraction and indexing of chemical and drug entities are key to improving the access and integration of information from unstructured data such as biomedical literature. Methods In this paper we evaluate two important tasks in NLP: the named entity recognition (NER) and Entity indexing using the SNOMED-CT terminology. For this purpose, we propose a combination of word embeddings in order to improve the results obtained in the PharmaCoNER challenge. Results For the NER task we present a neural network composed of BiLSTM with a CRF sequential layer where different word embeddings are combined as an input to the architecture. A hybrid method combining supervised and unsupervised models is used for the concept indexing task. In the supervised model, we use the training set to find previously trained concepts, and the unsupervised model is based on a 6-step architecture. This architecture uses a dictionary of synonyms and the Levenshtein distance to assign the correct SNOMED-CT code. Conclusion On the one hand, the combination of word embeddings helps to improve the recognition of chemicals and drugs in the biomedical literature. We achieved results of 91.41% for precision, 90.14% for recall, and 90.77% for F1-score using micro-averaging. On the other hand, our indexing system achieves a 92.67% F1-score, 92.44% for recall, and 92.91% for precision. With these results in a final ranking, we would be in the first position.

Word Search on the "SITUK" Application Using the Levenshtein Distance Algorithm

Integrated System for Online Competency Certification Test (SITUK) is an application used to carry out the assessment process (competency certification) at LSP (Lembaga Sertifikasi Profesional) UPN (University of Pembangunan Nasional) “Veteran” Jawa Timur, each of which is followed by approximately five hundred (500) assessments. Thus the data stored is quite a lot, so to find data using a search system. Often, errors occur in entering keywords that are not standard spelling or typos. For example, the keyword "simple," even though the default spelling is "simple." Of course, the admin will get incomplete information, and even the admin fails to get information that matches the entered keywords. To overcome the problems experienced in conducting data searches on the SITUK application, we need a string search approach method to maximize the search results. One of the algorithms used is Levenshtein which can calculate the distance of difference between two strings. Implementation of the Levenshtein algorithm on the data search system in the SITUK application has been able to overcome the problem of misspelling keywords with the mechanism of adding, inserting, and deleting characters.

Quantifying graphemic variation via large text corpora

The use of some basic computer science concepts could expand the possibilities of (manual) graphematic text corpus analysis. With these it can be shown that graphematic variation decreases constantly in printed German texts from 1600 to 1900. While the variability is continuously lesser on a text-internal level, it decreases faster for the whole available writing system of individual decades. But which changes took place exactly? Which types of variation went away more quickly, which ones persisted? How do we deal with large amounts of data which cannot be processed manually anymore? Which aspects are of special importance or go missing while working with a large textual base? The use of a measurement called entropy quantifies the variability of the spellings of a given word form, lemma, text or subcorpus, with few restrictions but also less details in the results. The difference between two spellings can be measured via Damerau-Levenshtein distance. To a certain degree, automated data handling can also determine the exact changes that took place. Afterwards, these differences can be counted and ranked. As data source the German Text Archive of the Berlin-Brandenburg Academy of Sciences and Humanities is used. It offers for example orthographic normalization – which is extremely useful –, preprocessing of parts of speech and lemmatization. As opposed to many other approaches the establishment of today’s normed spellings is not seen as the aim of the developments and is therefore not the focus of the research. Instead, the differences between individual spellings are of interest. Afterwards intra- and extralinguistic factors which caused these developments should be determined. These methodological findings could subsequently be used for improving research methods in other graphematic fields of interest, e. g. computer-mediated communication.

Automatic RadLex coding of Chinese structured radiology reports based on text similarity ensemble

Background Standardized coding of plays an important role in radiology reports’ secondary use such as data analytics, data-driven decision support, and personalized medicine. RadLex, a standard radiological lexicon, can reduce subjective variability and improve clarity in radiology reports. RadLex coding of radiology reports is widely used in many countries, but translation and localization of RadLex in China are far from being established. Although automatic RadLex coding is a common way for non-standard radiology reports, the high-accuracy cross-language RadLex coding is hardly achieved due to the limitation of up-to-date auto-translation and text similarity algorithms and still requires further research. Methods We present an effective approach that combines a hybrid translation and a Multilayer Perceptron weighting text similarity ensemble algorithm for automatic RadLex coding of Chinese structured radiology reports. Firstly, a hybrid way to integrate Google neural machine translation and dictionary translation helps to optimize the translation of Chinese radiology phrases to English. The dictionary is made up of 21,863 Chinese–English radiological term pairs extracted from several free medical dictionaries. Secondly, four typical text similarity algorithms are introduced, which are Levenshtein distance, Jaccard similarity coefficient, Word2vec Continuous bag-of-words model, and WordNet Wup similarity algorithms. Lastly, the Multilayer Perceptron model has been used to synthesize the contextual, lexical, character and syntactical information of four text similarity algorithms to promote precision, in which four similarity scores of two terms are taken as input and the output presents whether the two terms are synonyms. Results The results show the effectiveness of the approach with an F1-score of 90.15%, a precision of 91.78% and a recall of 88.59%. The hybrid translation algorithm has no negative effect on the final coding, F1-score has increased by 21.44% and 8.12% compared with the GNMT algorithm and dictionary translation. Compared with the single similarity, the result of the MLP weighting similarity algorithm is satisfactory that has a 4.48% increase compared with the best single similarity algorithm, WordNet Wup. Conclusions The paper proposed an innovative automatic cross-language RadLex coding approach to solve the standardization of Chinese structured radiology reports, that can be taken as a reference to automatic cross-language coding.

Food Ingredients Similarity Based on Conceptual and Textual Similarity

Open Food Facts provides a database of food products such as product names, compositions, and additives, where everyone can contribute to add the data or reuse the existing data. The open food facts data are dirty and needs to be processed before storing the data to our system. To reduce redundancy in food ingredients data, we measure the similarity of ingredient food using two similarities: the conceptual similarity and textual similarity. The conceptual similarity measures the similarity between the two datasets by its word meaning (synonym), while the textual similarity is based on fuzzy string matching, namely Levenshtein distance, Jaro-Winkler distance, and Jaccard distance. Based on our evaluation, the combination of similarity measurements using textual and Wordnet similarity (conceptual) was the most optimal similarity method in food ingredients.

3GOLD: Optimized Levenshtein distance for clustering third-generation sequencing data

Background:Third-generation sequencing offers some advantages over next-generation sequencing predecessors, but with the caveat of harboring a much higher error rate. Clustering-related sequences is an essential task in modern biology. To accurately cluster sequences rich in errors, error type and frequency need to be accounted for. Levenshtein distance is a well-established mathematical algorithm for measuring the edit distance between words and can specifically weight insertions, deletions and substitutions. However, there are drawbacks to using Levenshtein distance in a biological context and hence have rarely been used for this purpose. We present novel modifications to the Levenshtein distance algorithm to optimize it for clustering error-rich biological sequencing data.Results: We successfully introduced a bidirectional frameshift allowance with end-user determined accommodation caps combined with weighted error discrimination. Furthermore, our modifications dramatically improved the computational speed of Levenstein distance. For simulated ONT MinION and PacBio Sequel datasets, the average clustering sensitivity for 3GOLD was 41.45% (S.D. 10.39) higher than Sequence-Levenstein distance, 52.14% (S.D. 9.43) higher than Levenshtein distance, 55.93% (S.D. 8.67) higher than Starcode, 42.68% (S.D. 8.09) higher than CD-HIT-EST and 61.49% (S.D. 7.81) higher than DNACLUST. For biological ONT MinION data, 3GOLD clustering sensitivity was 27.99% higher than Sequence-Levenstein distance, 52.76% higher than Levenshtein distance, 56.39% higher than Starcode, 48% higher than CD-HIT-EST and 70.4% higher than DNACLUST.Conclusion:Our modifications to Levenshtein distance have improved its speed and accuracy compared to the classic Levenshtein distance, Sequence-Levenshtein distance and other commonly used clustering approaches on simulated and biological third-generation sequenced datasets. Our clustering approach is appropriate for datasets of unknown cluster centroids, such as those generated with unique molecular identifiers as well as known centroids such as barcoded datasets. A strength of our approach is high accuracy in resolving small clusters and mitigating the number of singletons.