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Motivation Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction and question answering. Manually labeling training data for the BioNER task is costly, however, due to the significant domain expertise required for accurate annotation. The resulting data scarcity causes current BioNER approaches to be prone to overfitting, to suffer from limited generalizability, and to address a single entity type at a time (e.g. gene or disease). Results We therefore propose a novel all-in-one (AIO) scheme that uses external data from existing annotated resources to enhance the accuracy and stability of BioNER models. We further present AIONER, a general-purpose BioNER tool based on cutting-edge deep learning and our AIO schema. We evaluate AIONER on 14 BioNER benchmark tasks and show that AIONER is effective, robust, and compares favorably to other state-of-the-art approaches such as multi-task learning. We further demonstrate the practical utility of AIONER in three independent tasks to recognize entity types not previously seen in training data, as well as the advantages of AIONER over existing methods for processing biomedical text at a large scale (e.g. the entire PubMed data). Availability and implementation The source code, trained models and data for AIONER are freely available at https://github.com/ncbi/AIONER. [ABSTRACT FROM AUTHOR]

Motivation DNA methylation plays an important role in epigenetic modification, the occurrence, and the development of diseases. Therefore, identification of DNA methylation sites is critical for better understanding and revealing their functional mechanisms. To date, several machine learning and deep learning methods have been developed for the prediction of different DNA methylation types. However, they still highly rely on manual features, which can largely limit the high-latent information extraction. Moreover, most of them are designed for one specific DNA methylation type, and therefore cannot predict multiple methylation sites in multiple species simultaneously. In this study, we propose iDNA-ABT, an advanced deep learning model that utilizes adaptive embedding based on Bidirectional Encoder Representations from Transformers (BERT) together with transductive information maximization (TIM). Results Benchmark results show that our proposed iDNA-ABT can automatically and adaptively learn the distinguishing features of biological sequences from multiple species, and thus perform significantly better than the state-of-the-art methods in predicting three different DNA methylation types. In addition, TIM loss is proven to be effective in dichotomous tasks via the comparison experiment. Furthermore, we verify that our features have strong adaptability and robustness to different species through comparison of adaptive embedding and six handcrafted feature encodings. Importantly, our model shows great generalization ability in different species, demonstrating that our model can adaptively capture the cross-species differences and improve the predictive performance. For the convenient use of our method, we further established an online webserver as the implementation of the proposed iDNA-ABT. Availability and implementation Our proposed iDNA-ABT and data are freely accessible via http://server.wei-group.net/iDNA%5fABT and our source codes are available for downloading in the GitHub repository (https://github.com/YUYING07/iDNA%5fABT). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Biomedical literature is growing at a rate that outpaces our ability to harness the knowledge contained therein. To mine valuable inferences from the large volume of literature, many researchers use information extraction algorithms to harvest information in biomedical texts. Information extraction is usually accomplished via a combination of manual expert curation and computational methods. Advances in computational methods usually depend on the time-consuming generation of gold standards by a limited number of expert curators. Citizen science is public participation in scientific research. We previously found that citizen scientists are willing and capable of performing named entity recognition of disease mentions in biomedical abstracts, but did not know if this was true with relationship extraction (RE). Results In this article, we introduce the Relationship Extraction Module of the web-based application Mark2Cure (M2C) and demonstrate that citizen scientists can perform RE. We confirm the importance of accurate named entity recognition on user performance of RE and identify design issues that impacted data quality. We find that the data generated by citizen scientists can be used to identify relationship types not currently available in the M2C Relationship Extraction Module. We compare the citizen science-generated data with algorithm-mined data and identify ways in which the two approaches may complement one another. We also discuss opportunities for future improvement of this system, as well as the potential synergies between citizen science, manual biocuration and natural language processing. Availability and implementation Mark2Cure platform: https://mark2cure.org ; Mark2Cure source code: https://github.com/sulab/mark2cure ; and data and analysis code for this article: https://github.com/gtsueng/M2C%5frel%5fnb. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Automatic biomedical named entity recognition (BioNER) is a key task in biomedical information extraction. For some time, state-of-the-art BioNER has been dominated by machine learning methods, particularly conditional random fields (CRFs), with a recent focus on deep learning. However, recent work has suggested that the high performance of CRFs for BioNER may not generalize to corpora other than the one it was trained on. In our analysis, we find that a popular deep learning-based approach to BioNER, known as bidirectional long short-term memory network-conditional random field (BiLSTM-CRF), is correspondingly poor at generalizing. To address this, we evaluate three modifications of BiLSTM-CRF for BioNER to improve generalization: improved regularization via variational dropout, transfer learning and multi-task learning. Results We measure the effect that each strategy has when training/testing on the same corpus ('in-corpus' performance) and when training on one corpus and evaluating on another ('out-of-corpus' performance), our measure of the model's ability to generalize. We found that variational dropout improves out-of-corpus performance by an average of 4.62%, transfer learning by 6.48% and multi-task learning by 8.42%. The maximal increase we identified combines multi-task learning and variational dropout, which boosts out-of-corpus performance by 10.75%. Furthermore, we make available a new open-source tool, called Saber that implements our best BioNER models. Availability and implementation Source code for our biomedical IE tool is available at https://github.com/BaderLab/saber. Corpora and other resources used in this study are available at https://github.com/BaderLab/Towards-reliable-BioNER. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Summary The rapid progresses of high-throughput sequencing technology-based omics and mass spectrometry-based proteomics, such as data-independent acquisition and its penetration to clinical studies have generated increasing number of proteomic datasets containing hundreds to thousands of samples. To analyze these quantitative proteomic datasets and other omics (e.g. transcriptomics and metabolomics) datasets more efficiently and conveniently, we present a web server-based software tool ProteomeExpert implemented in Docker, which offers various analysis tools for experimental design, data mining, interpretation and visualization of quantitative proteomic datasets. ProteomeExpert can be deployed on an operating system with Docker installed or with R language environment. Availability and implementation The Docker image of ProteomeExpert is freely available from https://hub.docker.com/r/lifeinfo/proteomeexpert. The source code of ProteomeExpert is also openly accessible at http://www.github.com/guomics-lab/ProteomeExpert/. In addition, a demo server is provided at https://proteomic.shinyapps.io/peserver/. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Summary Recent whole-brain mapping projects are collecting increasingly larger sets of high-resolution brain images using a variety of imaging, labeling and sample preparation techniques. Both mining and analysis of these data require reliable and robust cross-modal registration tools. We recently developed the mBrainAligner, a pipeline for performing cross-modal registration of the whole mouse brain. However, using this tool requires scripting or command-line skills to assemble and configure the different modules of mBrainAligner for accommodating different registration requirements and platform settings. In this application note, we present mBrainAligner-Web, a web server with a user-friendly interface that allows to configure and run mBrainAligner locally or remotely across platforms. Availability and implementation mBrainAligner-Web is available at http://mbrainaligner.ahu.edu.cn/ with source code at https://github.com/reaneyli/mBrainAligner-web. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Functional imaging at single-neuron resolution offers a highly efficient tool for studying the functional connectomics in the brain. However, mainstream neuron-detection methods focus on either the morphologies or activities of neurons, which may lead to the extraction of incomplete information and which may heavily rely on the experience of the experimenters. Results We developed a convolutional neural networks and fluctuation method-based toolbox (ImageCN) to increase the processing power of calcium imaging data. To evaluate the performance of ImageCN, nine different imaging datasets were recorded from awake mouse brains. ImageCN demonstrated superior neuron-detection performance when compared with other algorithms. Furthermore, ImageCN does not require sophisticated training for users. Availability and implementation ImageCN is implemented in MATLAB. The source code and documentation are available at https://github.com/ZhangChenLab/ImageCN. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Single-molecule localization microscopy allows studying the dynamics of biomolecules in cells and resolving the biophysical properties of the molecules and their environment underlying cellular function. With the continuously growing amount of data produced by individual experiments, the computational cost of quantifying these properties is increasingly becoming the bottleneck of single-molecule analysis. Mining these data requires an integrated and efficient analysis toolbox. Results We introduce TRamWAy, a modular Python library that features: (i) a conservative tracking procedure for localization data, (ii) a range of sampling techniques for meshing the spatio-temporal support of the data, (iii) computationally efficient solvers for inverse models, with the option of plugging in user-defined functions and (iv) a collection of analysis tools and a simple web-based interface. Availability and implementation TRamWAy is a Python library and can be installed with pip and conda. The source code is available at https://github.com/DecBayComp/TRamWAy. [ABSTRACT FROM AUTHOR]

Summary We present GeoBoost2, a natural language-processing pipeline for extracting the location of infected hosts for enriching metadata in nucleotide sequences repositories like National Center of Biotechnology Information's GenBank for downstream analysis including phylogeography and genomic epidemiology. The increasing number of pathogen sequences requires complementary information extraction methods for focused research, including surveillance within countries and between borders. In this article, we describe the enhancements from our earlier release including improvement in end-to-end extraction performance and speed, availability of a fully functional web-interface and state-of-the-art methods for location extraction using deep learning. Availability and implementation Application is freely available on the web at https://zodo.asu.edu/geoboost2. Source code, usage examples and annotated data for GeoBoost2 is freely available at https://github.com/ZooPhy/geoboost2. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation: Automated annotation of neuroanatomical connectivity statements from the neuroscience literature would enable accessible and large-scale connectivity resources. Unfortunately, the connectivity findings are not formally encoded and occur as natural language text. This hinders aggregation, indexing, searching and integration of the reports. We annotated a set of 1377 abstracts for connectivity relations to facilitate automated extraction of connectivity relationships from neuroscience literature. We tested several baseline measures based on co-occurrence and lexical rules. We compare results from seven machine learning methods adapted from the protein interaction extraction domain that employ part-of-speech, dependency and syntax features.Results: Co-occurrence based methods provided high recall with weak precision. The shallow linguistic kernel recalled 70.1% of the sentence-level connectivity statements at 50.3% precision. Owing to its speed and simplicity, we applied the shallow linguistic kernel to a large set of new abstracts. To evaluate the results, we compared 2688 extracted connections with the Brain Architecture Management System (an existing database of rat connectivity). The extracted connections were connected in the Brain Architecture Management System at a rate of 63.5%, compared with 51.1% for co-occurring brain region pairs. We found that precision increases with the recency and frequency of the extracted relationships.Availability and implementation: The source code, evaluations, documentation and other supplementary materials are available at http://www.chibi.ubc.ca/WhiteText.Contact: paul@chibi.ubc.caSupplementary information: Supplementary data are available at Bioinformatics Online. [ABSTRACT FROM AUTHOR]

Summary: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987.Availability: The library and web services are implemented in Java and the sources are available from http://gnat.sourceforge.net.Contact: jorg.hakenberg@roche.com [ABSTRACT FROM AUTHOR]