| 1. |
- Su, Zhan, et al.
(author)
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Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
- 2012
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:10
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Journal article (peer-reviewed)abstract
- Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (Pcombined=4.09×10(-9); odds ratio (OR)=1.21, 95% confidence interval (CI)=1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (Pcombined=2.74×10(-10); OR=1.14, 95% CI=1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus.
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| 2. |
- Maxwell, Tania L., et al.
(author)
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Global dataset of soil organic carbon in tidal marshes
- 2023
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In: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
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Journal article (peer-reviewed)abstract
- Tidal marshes store large amounts of organic carbon in their soils. Field data quantifying soil organic carbon (SOC) stocks provide an important resource for researchers, natural resource managers, and policy-makers working towards the protection, restoration, and valuation of these ecosystems. We collated a global dataset of tidal marsh soil organic carbon (MarSOC) from 99 studies that includes location, soil depth, site name, dry bulk density, SOC, and/or soil organic matter (SOM). The MarSOC dataset includes 17,454 data points from 2,329 unique locations, and 29 countries. We generated a general transfer function for the conversion of SOM to SOC. Using this data we estimated a median (± median absolute deviation) value of 79.2 ± 38.1 Mg SOC ha−1 in the top 30 cm and 231 ± 134 Mg SOC ha−1 in the top 1 m of tidal marsh soils globally. This data can serve as a basis for future work, and may contribute to incorporation of tidal marsh ecosystems into climate change mitigation and adaptation strategies and policies.
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| 3. |
- Dobnik, Simon, 1977, et al.
(author)
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A Model for Attention-Driven Judgements in Type Theory with Records
- 2016
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In: JerSem: The 20th Workshop on the Semantics and Pragmatics of Dialogue. J. Hunter, M. Simons, and M. Stone (eds.). New Brunswick, NJ USA, July 16–18 2016.. - 2308-2275.
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Conference paper (peer-reviewed)abstract
- This paper makes three contributions to the discussion on the applicability of Type Theory with Records (TTR) to embodied dialogue agents. First, it highlights the problem of type assignment or judgements in practical implementations which is re- source intensive. Second, it presents a judgement control mechanism, which con- sists of grouping of types into clusters or states by their thematic relations and selec- tion of types following two mechanisms inspired by the Load Theory of selective attention and cognitive control (Lavie et al., 2004), that addresses this problem. Third, it presents a computational frame- work, based on Bayesian inference, that offers a basis for future practical exper- imentation on the feasibility of the pro- posed approach.
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| 4. |
- Dobnik, Simon, 1977, et al.
(author)
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Atention-driven Perceptual Classification and Reasoning
- 2016
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In: The Sixth Swedish language technology conference (SLTC), Umeå University, 17-18 November, 2016, (ed. Björklund, Johanna and Stymne, Sara). - Umeå : Umeå University.
-
Conference paper (peer-reviewed)abstract
- One of the central challenges for embodied and situated agents with limited memory and processing resources is how to process and react to a large amount of information that they receive continuously through their sensors. Secondly, a model of infor- mation fusion is also required: how perceptual and linguistic/conceptual information interact and drive their reasoning. We present a computational model for perceptual classification in probabilistic Type Theory with Records (TTR), a formal meaning representation layer for such agents. The model is based on the cognitive notion of attention.
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| 5. |
- Dobnik, Simon, 1977, et al.
(author)
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Back to the Future: Logic and Machine Learning
- 2017
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In: Conference on Logic and Machine Learning in Natural Language (LaML).
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Conference paper (other academic/artistic)abstract
- In this paper we argue that since the beginning of the natural language processing or computational linguistics there has been a strong connection between logic and machine learning. First of all, there is something logical about language or linguistic about logic. Secondly, we argue that rather than distinguishing between logic and machine learning, a more useful distinction is between top-down approaches and data-driven approaches. Examining some recent approaches in deep learning we argue that they incorporate both properties and this is the reason for their very successful adoption to solve several problems within language technology.
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| 6. |
- Dobnik, Simon, 1977, et al.
(author)
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Changing perspective: Local alignment of reference frames in dialogue
- 2015
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In: Proceedings of SemDial 2015 (goDIAL): The 19th Workshop on the Semantics and Pragmatics of Dialogue. Christine Howes and Staffan Larsson (eds.). Gothenburg, 24–26 August 2015. - 2308-2275. ; , s. 24-32
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Conference paper (peer-reviewed)
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| 7. |
- Dobnik, Simon, 1977, et al.
(author)
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Changing perspective: Local alignment of reference frames in dialogue
- 2015
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In: The 6th annual CLT workshop. Tollered, 20-22 October, 2015.
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Conference paper (other academic/artistic)abstract
- In this paper we examine how people negotiate, interpret and repair the frame of reference (FoR) in free dialogues discussing spatial scenes. We describe a pilot study in which participants are given different perspectives of the same scene and asked to locate several objects that are only shown on one of their pictures. This task requires participants to coordinate on FoR in order to identify the missing objects. Preliminary results indicate that conversational participants align locally on FoR but do not converge on a global frame of reference. Misunderstandings lead to clarification sequences in which participants shift the FoR. These findings have implications for situated dialogue systems.
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| 8. |
- Dobnik, Simon, 1977, et al.
(author)
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Exploration of functional semantics of prepositions from corpora of descriptions of visual scenes
- 2014
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In: Proceedings of the Workshop on Vision and Language 2014 (VL'14), 25th International Conference on Computational Linguistics (COLING 2014), Dublin, 23rd August 2014. ; , s. 33-37
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Conference paper (peer-reviewed)abstract
- We present a method of extracting functional semantic knowledge from corpora of descriptions of visual scenes. Such knowledge is required for interpretation and generation of spatial descriptions in tasks such as visual search. We identify semantic classes of target and landmark objects related by each preposition by abstracting over WordNet taxonomy. The inclusion of such knowledge in visual search should equip robots with a better, more human-like spatial cognition.
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| 9. |
- Dobnik, Simon, 1977, et al.
(author)
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Exploring the Functional and Geometric Bias of Spatial Relations Using Neural Language Models
- 2018
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In: Proceedings of SpLU 2018 at NAACL-HLT 2018, June 6, 2018 New Orleans, Louisiana / Parisa Kordjamshidi, Archna Bhatia, James Pustejovsky, Marie-Francine Moens (eds.). - New Orleans, Louisiana, USA : Association of Computational Linguistics (ACL). - 9781948087216
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Conference paper (peer-reviewed)abstract
- The challenge for computational models of spatial descriptions for situated dialogue systems is the integration of information from different modalities. The semantics of spatial descriptions are grounded in at least two sources of information: (i) a geometric representation of space and (ii) the functional interaction of related objects that. We train several neural language models on descriptions of scenes from a dataset of image captions and examine whether the functional or geometric bias of spatial descriptions reported in the literature is reflected in the estimated perplexity of these models. The results of these experiments have implications for the creation of models of spatial lexical semantics for human-robot dialogue systems. Furthermore, they also provide an insight into the kinds of the semantic knowledge captured by neural language models trained on spatial descriptions, which has implications for image captioning systems.
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| 10. |
- Dobnik, Simon, 1977, et al.
(author)
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Investigating the role of priming and alignment of perspective in dialogue
- 2013
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In: Proceedings of the 17th Workshop on the Semantics and Pragmatics of Dialogue, Amsterdam, 16–18 December 2013, Amsterdam. - 2308-2275. ; 17, s. 182-184
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Conference paper (other academic/artistic)abstract
- We examine the alignment of the primed frame of reference (FoR) for spatial descriptions over several utterances of a situated dialogue. We confirm the tendency of FoR alignment and that the intrinsic FoR is the most popular one independent of the priming.
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