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MotivationTo understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficiently from sizable databases. One way to organize existing knowledge on cancer is to utilize the widely accepted framework of the Hallmarks of Cancer. These hallmarks refer to the alterations in cell behaviour that characterize the cancer cell.ResultsWe created an extensive Hallmarks of Cancer taxonomy and developed automatic text mining methodology and a tool (CHAT) capable of retrieving and organizing millions of cancer-related references from PubMed into the taxonomy. The efficiency and accuracy of the tool was evaluated intrinsically as well as extrinsically by case studies. The correlations identified by the tool show that it offers a great potential to organize and correctly classify cancer-related literature. Furthermore, the tool can be useful, for example, in identifying hallmarks associated with extrinsic factors, biomarkers and therapeutics targets.Availability and implementationCHAT can be accessed at: http://chat.lionproject.net. The corpus of hallmark-annotated PubMed abstracts and the software are available at: http://chat.lionproject.net/aboutSupplementary information Supplementary data are available at Bioinformatics online.

Motivation The overwhelming size and rapid growth of the biomedical literature make it impossible for scientists to read all studies related to their work, potentially leading to missed connections and wasted time and resources. Literature-based discovery (LBD) aims to alleviate these issues by identifying implicit links between disjoint parts of the literature. While LBD has been studied in depth since its introduction three decades ago, there has been limited work making use of recent advances in biomedical text processing methods in LBD. Results We present LION LBD, a literature-based discovery system that enables researchers to navigate published information and supports hypothesis generation and testing. The system is built with a particular focus on the molecular biology of cancer using state-of-the-art machine learning and natural language processing methods, including named entity recognition and grounding to domain ontologies covering a wide range of entity types and a novel approach to detecting references to the hallmarks of cancer in text. LION LBD implements a broad selection of co-occurrence based metrics for analyzing the strength of entity associations, and its design allows real-time search to discover indirect associations between entities in a database of tens of millions of publications while preserving the ability of users to explore each mention in its original context in the literature. Evaluations of the system demonstrate its ability to identify undiscovered links and rank relevant concepts highly among potential connections. Availability and implementation The LION LBD system is available via a web-based user interface and a programmable API, and all components of the system are made available under open licenses from the project home page http://lbd.lionproject.net. Supplementary information Supplementary data are available at Bioinformatics online.

Objective In recent years numerous studies have achieved promising results in Alzheimer’s Disease (AD) detection using automatic language processing. We systematically review these articles to understand the effectiveness of this approach, identify any issues and report the main findings that can guide further research. Materials and Methods We searched PubMed, Ovid, and Web of Science for articles published in English between 2013 and 2019. We performed a systematic literature review to answer 5 key questions: (1) What were the characteristics of participant groups? (2) What language data were collected? (3) What features of speech and language were the most informative? (4) What methods were used to classify between groups? (5) What classification performance was achieved? Results and Discussion We identified 33 eligible studies and 5 main findings: participants’ demographic variables (especially age ) were often unbalanced between AD and control group; spontaneous speech data were collected most often; informative language features were related to word retrieval and semantic, syntactic, and acoustic impairment; neural nets, support vector machines, and decision trees performed well in AD detection, and support vector machines and decision trees performed well in decline detection; and average classification accuracy was 89% in AD and 82% in mild cognitive impairment detection versus healthy control groups. Conclusion The systematic literature review supported the argument that language and speech could successfully be used to detect dementia automatically. Future studies should aim for larger and more balanced datasets, combine data collection methods and the type of information analyzed, focus on the early stages of the disease, and report performance using standardized metrics.

simon.baker@cl.cam.ac.uk.

Research that has explored public enthusiasm for cancer screening has suggested that the public may be overly enthusiastic about being screened with certain tests, and this has been attributed, in part, to lack of knowledge about the risks and benefits. In this article the authors considered the possibility that some people may be enthusiastic about screening even when they are informed and also accept that the test unquestionably does not save lives. Two studies were conducted, one that involved a nationally representative U.S. sample and another that involved an online convenience sample. All participants were asked whether they would want to receive a hypothetical screening test for breast (women) or prostate (men) cancer that does not reduce the chance of cancer death or extend the length of life. Over half of participants wanted to receive the described screening test. Many people did not believe that cancer screening might not save lives, yet screening preferences were not due to disbelief alone. Results further suggested that cancer worry, reassurance, and a desire for health information explained variance in preferences for unbeneficial screening, adjusting for beliefs about screening benefits, perceptions of screening risks, family history, perceptions of cancer risk, and demographics. (PsycINFO Database Record

Supply chains are increasingly global, complex and multi-tiered. Consequently, companies often struggle to maintain complete visibility of their supply network. This poses a problem as visibility of the network structure is required for tasks like effectively managing supply chain risk. In this paper, we discuss automated supply chain mapping as a means of maintaining structural visibility of a company's supply chain, and we use Deep Learning to automatically extract buyer-supplier relations from natural language text. Early results show that supply chain mapping solutions using Natural Language Processing and Deep Learning could enable companies to a) automatically generate rudimentary supply chain maps, b) verify existing supply chain maps, or c) augment existing maps with additional supplier information. KEYWORDSsupply chain management; supply chain map; natural language processing; text mining; supply chain visibility; supply chain mining; deep learning; machine learning CONTACT P. Wichmann.

Most existing systems for subcategorization frame (SCF) acquisition rely on supervised parsing and infer SCF distributions at type, rather than instance level. These systems suffer from poor portability across domains and their benefit for NLP tasks that involve sentence-level processing is limited. We propose a new unsupervised, Markov Random Field-based model for SCF acquisition which is designed to address these problems. The system relies on supervised POS tagging rather than parsing, and is capable of learning SCFs at instance level. We perform evaluation against gold standard data which shows that our system outperforms several supervised and type-level SCF baselines. We also conduct task-based evaluation in the context of verb similarity prediction, demonstrating that a vector space model based on our SCFs substantially outperforms a lexical model and a model based on a supervised parser 1 .