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Despite significant advancements in automatic speech recognition (ASR) technology, even the best performing ASR systems are inadequate for speakers with impaired speech. This inadequacy may be, in part, due to the challenges associated with acquiring a sufficiently diverse training sample of disordered speech. Speakers with dysarthria, which refers to a group of divergent speech disorders secondary to neurologic injury, exhibit highly variable speech patterns both within and across individuals. This diversity is currently poorly characterized and, consequently, difficult to adequately represent in disordered speech ASR corpora. In this paper, we consider the variable expressions of dysarthria within the context of established clinical taxonomies (e.g., Darley, Aronson, and Brown dysarthria subtypes). We also briefly consider past and recent efforts to capture this diversity quantitatively using speech analytics. Understanding dysarthria diversity from the clinical perspective and how this diversity may impact ASR performance could aid in (1) optimizing data collection strategies for minimizing bias; (2) ensuring representative ASR training sets; and (3) improving generalization of ASR across users and performance for difficult-to-recognize speakers. Our overarching goal is to facilitate the development of robust ASR systems for dysarthric speech using clinical knowledge.

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MOTIVATION: The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging. Its importance lies in the fact that they constitute the crucial conceptual entities in biomedicine. Their recognition and normalization remains a challenging task because of widespread gene name ambiguities within species, across species, with common English words and with medical sublanguage terms. RESULTS: We present GeNo, a highly competitive system for gene name normalization, which obtains an F-measure performance of 86.4% (precision: 87.8%, recall: 85.0%) on the BioCreAtIvE-II test set, thus being on a par with the best system on that task. Our system tackles the complex gene normalization problem by employing a carefully crafted suite of symbolic and statistical methods, and by fully relying on publicly available software and data resources, including extensive background knowledge based on semantic profiling. A major goal of our work is to present GeNo's architecture in a lucid and perspicuous way to pave the way to full reproducibility of our results. AVAILABILITY: GeNo, including its underlying resources, will be available from www.julielab.de. It is also currently deployed in the Semedico search engine at www.semedico.org.

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Natural language processing of real-world documents requires several low-level tasks such as splitting a piece of text into its constituent sentences, and splitting each sentence into its constituent tokens to be performed by some preprocessor (prior to linguistic analysis). While this task is often considered as unsophisticated clerical work, in the life sciences domain it poses enormous problems due to complex naming conventions. In this paper, we first introduce an annotation framework for sentence and token splitting underlying a newly constructed sentence- and token-tagged biomedical text corpus. This corpus serves as a training environment and test bed for machine-learning based sentence and token splitters using Conditional Random Fields (CRFs). Our evaluation experiments reveal that CRFs with a rich feature set substantially increase sentence and token detection performance.

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