A Comparison of Hybrid and End-to-End Models for Syllable Recognition

This paper presents a comparison of a traditional hybrid speech recognition system (kaldi using WFST and TDNN with lattice-free MMI) and a lexicon-free end-to-end (TensorFlow implementation of multi-layer LSTM with CTC training) models for German syllable recognition on the Verbmobil corpus. The results show that explicitly modeling prior knowledge is still valuable in building recognition systems. With a strong language model (LM) based on syllables, the structured approach significantly outperforms the end-to-end model. The best word error rate (WER) regarding syllables was achieved using kaldi with a 4-gram LM, modeling all syllables observed in the training set. It achieved 10.0% WER w.r.t. the syllables, compared to the end-to-end approach where the best WER was 27.53%. The work presented here has implications for building future recognition systems that operate independent of a large vocabulary, as typically used in a tasks such as recognition of syllabic or agglutinative languages, out-of-vocabulary techniques, keyword search indexing and medical speech processing.Comment: 22th International Conference of Text, Speech and Dialogue TSD201

Making sense of complexity in context and implementation: the Context and Implementation of Complex Interventions (CICI) framework.

BACKGROUND: The effectiveness of complex interventions, as well as their success in reaching relevant populations, is critically influenced by their implementation in a given context. Current conceptual frameworks often fail to address context and implementation in an integrated way and, where addressed, they tend to focus on organisational context and are mostly concerned with specific health fields. Our objective was to develop a framework to facilitate the structured and comprehensive conceptualisation and assessment of context and implementation of complex interventions. METHODS: The Context and Implementation of Complex Interventions (CICI) framework was developed in an iterative manner and underwent extensive application. An initial framework based on a scoping review was tested in rapid assessments, revealing inconsistencies with respect to the underlying concepts. Thus, pragmatic utility concept analysis was undertaken to advance the concepts of context and implementation. Based on these findings, the framework was revised and applied in several systematic reviews, one health technology assessment (HTA) and one applicability assessment of very different complex interventions. Lessons learnt from these applications and from peer review were incorporated, resulting in the CICI framework. RESULTS: The CICI framework comprises three dimensions-context, implementation and setting-which interact with one another and with the intervention dimension. Context comprises seven domains (i.e., geographical, epidemiological, socio-cultural, socio-economic, ethical, legal, political); implementation consists of five domains (i.e., implementation theory, process, strategies, agents and outcomes); setting refers to the specific physical location, in which the intervention is put into practise. The intervention and the way it is implemented in a given setting and context can occur on a micro, meso and macro level. Tools to operationalise the framework comprise a checklist, data extraction tools for qualitative and quantitative reviews and a consultation guide for applicability assessments. CONCLUSIONS: The CICI framework addresses and graphically presents context, implementation and setting in an integrated way. It aims at simplifying and structuring complexity in order to advance our understanding of whether and how interventions work. The framework can be applied in systematic reviews and HTA as well as primary research and facilitate communication among teams of researchers and with various stakeholders

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development

While gene expression dynamics have been extensively cataloged during hematopoietic differentiation in the adult, less is known about transcriptome diversity of human hematopoietic stem cells (HSCs) during development. To characterize transcriptional and post-transcriptional changes in HSCs during development, we leveraged high-throughput genomic approaches to profile miRNAs, lincRNAs, and mRNAs. Our findings indicate that HSCs manifest distinct alternative splicing patterns in key hematopoietic regulators. Detailed analysis of the splicing dynamics and function of one such regulator, HMGA2, identified an alternative isoform that escapes miRNA-mediated targeting. We further identified the splicing kinase CLK3 that, by regulating HMGA2 splicing, preserves HMGA2 function in the setting of an increase in let-7 miRNA levels, delineating how CLK3 and HMGA2 form a functional axis that influences HSC properties during development. Collectively, our study highlights molecular mechanisms by which alternative splicing and miRNA-mediated post-transcriptional regulation impact the molecular identity and stage-specific developmental features of human HSCs. Human hematopoietic stem cells (HSCs) display substantial transcriptional diversity during development. Here, we investigated the contribution of alternative splicing to such diversity by analyzing the dynamics of a key hematopoietic regulator, HMGA2. Next, we showed that CLK3, by regulating the splicing pattern of HMGA2, reinforces an HSC-specific program

Drug discovery for Diamond-Blackfan anemia using reprogrammed hematopoietic progenitors

Diamond-Blackfan anemia (DBA) is a congenital disorder characterized by the failure of erythroid progenitor differentiation, severely curtailing red blood cell production. Because many DBA patients fail to respond to corticosteroid therapy, there is considerable need for therapeutics for this disorder. Identifying therapeutics for DBA requires circumventing the paucity of primary patient blood stem and progenitor cells. To this end, we adopted a reprogramming strategy to generate expandable hematopoietic progenitor cells from induced pluripotent stem cells (iPSCs) from DBA patients. Reprogrammed DBA progenitors recapitulate defects in erythroid differentiation, which were rescued by gene complementation. Unbiased chemical screens identified SMER28, a small-molecule inducer of autophagy, which enhanced erythropoiesis in a range of in vitro and in vivo models of DBA. SMER28 acted through autophagy factor ATG5 to stimulate erythropoiesis and up-regulate expression of globin genes. These findings present an unbiased drug screen for hematological disease using iPSCs and identify autophagy as a therapeutic pathway in DBA.National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) (Grant R24-DK092760)National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) (Grant R24-DK49216)National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) (Grant U54DK110805)National Heart, Lung, and Blood Institute (Grant UO1-HL100001)National Heart, Lung, and Blood Institute (Grant U01HL134812)National Heart, Lung, and Blood Institute (Grant R01HL04880)National Institutes of Health (U.S.) (Grant R24OD017870-01

The Limits of Responsible Innovation: Exploring Care, Vulnerability and Precision Medicine

Drawing on insights from feminist and Science and Technology Studies writing on care and vulnerability, this paper will critically explore conceptualisations of responsibility, care and vulnerability in relation to contemporary approaches to Responsible Innovation (RI). Drawing on examples of some of the social and ethical challenges of precision medicine, we highlight the on-going, distributed and complex nature of innovation and responsibilities in relation to markets, patient and carer experience and data practices associated with these new technologies to highlight some of the limits of RI. We end by reflecting on the implications of our analysis for the social and ethical challenges of precision medicine and RI more generally

Familial thrombocytopenia due to a complex structural variant resulting in a WAC-ANKRD26 fusion transcript

Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleotide variants that prevent silencing of ANKRD26 expression during hematopoietic differentiation. Short-read whole-exome and genome sequencing approaches were unable to identify a causal variant in this family. Using long-read whole-genome sequencing, a large complex structural variant involving a paired-duplication inversion was identified. Through functional studies, we show that this structural variant results in a pathogenic gain-of-function WAC-ANKRD26 fusion transcript. Our findings illustrate how complex structural variants that may be missed by conventional genome sequencing approaches can cause human disease

Stochastic Modelling: From Pattern Classification to Speech Recognition and Language Translation

This paper gives an overview of the stochastic modelling approach to machine translation. Starting with the Bayes decision rule as in pattern classification and speech recognition, we show how the resulting system architecture can be structured into three parts: the language model probability, the string translation model probability and the search procedure that gener-ates the word sequence in the target language. We discuss the properties of the system components and report results on the translation of spoken dialogues in the VERBMOBIL project. The experience obtained in the VERB-MOBIL project, in particular a large-scale end-to-end evaluation, showed that the stochastic modelling approach resulted in significantly lower error rates than three competing translation approaches: the sentence error rate was 29 % in comparison with 52 % to 62% for the other translation approaches.

Identifying the need for good practices in Health Technology Assessment : summary of the ISPOR HTA Council Working Group Report on Good Practices in HTA

The systematic use of evidence to inform healthcare decisions, particularly health technology assessment (HTA), has gained increased recognition. HTA has become a standard policy tool for informing decision makers who must manage the entry and use of pharmaceuticals, medical devices, and other technologies (including complex interventions) within health systems, for example, through reimbursement and pricing. Despite increasing attention to HTA activities, there has been no attempt to comprehensively synthesize good practices or emerging good practices to support populationbased decision-making in recent years. After the identification of some good practices through the release of the ISPOR Guidelines Index in 2013, the ISPOR HTA Council identified a need to more thoroughly review existing guidance. The purpose of this effort was to create a basis for capacity building, education, and improved consistency in approaches to HTA-informed decision-making. Our findings suggest that although many good practices have been developed in areas of assessment and some other key aspects of defining HTA processes, there are also many areas where good practices are lacking. This includes good practices in defining the organizational aspects of HTA, the use of deliberative processes, and measuring the impact of HTA. The extent to which these good practices are used and applied by HTA bodies is beyond the scope of this report, but may be of interest to future researchers