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We present a simple tool for extracting text and markup information from printouts of (not only) scientific documents. While the heavy-lifting OCR is done by off-the-shelf tesseract, our focus is on detection, extraction, and basic categorization of color-highlighted text sections, as well as on providing a framework for downstream processing of extraction results. The tool can be useful for document analysis tasks that must, or benefit from being able to, use printed paper.
We describe a simple procedure for the automatic creation of word-level alignments between printed documents and their respective full-text versions. The procedure is unsupervised, uses standard, off-the-shelf components only, and reaches an F-score of 85.01 in the basic setup and up to 86.63 when using pre- and post-processing. Potential areas of application are manual database curation (incl. document triage) and biomedical expression OCR.
We introduce a novel scientific document processing task for making previously inaccessible information in printed paper documents available to automatic processing. We describe our data set of scanned documents and data records from the biological database SABIO-RK, provide a definition of the task, and report findings from preliminary experiments. Rigorous evaluation proved challenging due to lack of gold-standard data and a difficult notion of correctness. Qualitative inspection of results, however, showed the feasibility and usefulness of the task.
pyMMAX2 is an API for processing MMAX2 stand-off annotation data in Python. It provides a lightweight basis for the development of code which opens up the Java- and XML-based ecosystem of MMAX2 for more recent, Python-based NLP and data science methods. While pyMMAX2 is pure Python, and most functionality is implemented from scratch, the API re-uses the complex implementation of the essential business logic for MMAX2 annotation schemes by interfacing with the original MMAX2 Java libraries. pyMMAX2 is available for download at http://github.com/nlpAThits/pyMMAX2.
The demo presents a minimalist, off-the-shelf AND tool which provides a fundamental AND operation, the comparison of two publications with ambiguous authors, as an easily accessible HTTP interface. The tool implements this operation using standard AND functionality, but puts particular emphasis on advanced methods from natural language processing (NLP) for comparing publication title semantics.
We present WOMBAT, a Python tool which supports NLP practitioners in accessing word embeddings from code. WOMBAT addresses common research problems, including unified access, scaling, and robust and reproducible preprocessing. Code that uses WOMBAT for accessing word embeddings is not only cleaner, more readable, and easier to reuse, but also much more efficient than code using standard in-memory methods: a Python script using WOMBAT for evaluating seven large word embedding collections (8.7M embedding vectors in total) on a simple SemEval sentence similarity task involving 250 raw sentence pairs completes in under ten seconds end-to-end on a standard notebook computer.
Data sets of publication meta data with manually disambiguated author names play an important role in current author name disambiguation (AND) research. We review the most important data sets used so far, and compare their respective advantages and shortcomings. From the results of this review, we derive a set of general requirements to future AND data sets. These include both trivial requirements, like absence of errors and preservation of author order, and more substantial ones, like full disambiguation and adequate representation of publications with a small number of authors and highly variable author names. On the basis of these requirements, we create and make publicly available a new AND data set, SCAD-zbMATH. Both the quantitative analysis of this data set and the results of our initial AND experiments with a naive baseline algorithm show the SCAD-zbMATH data set to be considerably different from existing ones. We consider it a useful new resource that will challenge the state of the art in AND and benefit the AND research community.
We present a supervised machine learning AND system which tackles semantic similarity between publication titles by means of word embeddings. Word embeddings are integrated as external components, which keeps the model small and efficient, while allowing for easy extensibility and domain adaptation. Initial experiments show that word embeddings can improve the Recall and F score of the binary classification sub-task of AND. Results for the clustering sub-task are less clear, but also promising and overall show the feasibility of the approach.
This paper introduces LRTwiki, an improved variant of the Likelihood Ratio Test (LRT). The central idea of LRTwiki is to employ a comprehensive domain specific knowledge source as additional “on-topic” data sets, and to modify the calculation of the LRT algorithm to take advantage of this new information. The knowledge source is created on the basis of Wikipedia articles. We evaluate on the two related tasks product feature extraction and keyphrase extraction, and find LRTwiki to yield a significant improvement over the original LRT in both tasks.