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Alan Medlar
University of Helsinki
23Publications
7H-index
135Citations
Publications 23
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#1Naihui Zhou (Iowa State University)H-Index: 2
#2Yuxiang Jiang (IU: Indiana University Bloomington)H-Index: 2
Last.Iddo Friedberg (Iowa State University)H-Index: 21
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The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experiment...
4 CitationsSource
#1Chien-yu Huang (Edin.: University of Edinburgh)
#2Arlene Casey (Edin.: University of Edinburgh)
Last.Alan Medlar (UH: University of Helsinki)H-Index: 7
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Scientific literature search engines typically index abstracts instead of the full-text of publications. The expectation is that the abstract provides a comprehensive summary of the article, enumerating key points for the reader to assess whether their information needs could be satisfied by reading the full-text. Furthermore, from a practical standpoint, obtaining the full-text is more complicated due to licensing issues, in the case of commercial publishers, and resource limitations of public ...
Source
#1Dhruv Tripathi (Edin.: University of Edinburgh)
#2Alan Medlar (UH: University of Helsinki)H-Index: 7
Last.Dorota Glowacka (UH: University of Helsinki)H-Index: 12
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Retrieval systems based on machine learning require both positive and negative examples to perform inference, which is usually obtained through relevance feedback. Unfortunately, explicit negative relevance feedback is thought to have poor user experience. Instead, systems typically rely on implicit negative feedback. In this study, we confirm that, in the case of binary relevance feedback, users prefer giving positive feedback (and implicit negative feedback) over negative feedback (and implici...
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#1Alan Medlar (UH: University of Helsinki)H-Index: 7
#2Liisa Holm (UH: University of Helsinki)H-Index: 54
Background Protein homology search is an important, yet time-consuming, step in everything from protein annotation to metagenomics. Its application, however, has become increasingly challenging, due to the exponential growth of protein databases. In order to perform homology search at the required scale, many methods have been proposed as alternatives to BLAST that make an explicit trade-off between sensitivity and speed. One such method, SANSparallel, uses a parallel implementation of the suffi...
1 CitationsSource
Oct 17, 2018 in CIKM (Conference on Information and Knowledge Management)
#1Alan Medlar (UH: University of Helsinki)H-Index: 7
#2Dorota Glowacka (Edin.: University of Edinburgh)H-Index: 1
Search activities involving knowledge acquisition, investigation and synthesis are collectively known as exploratory search. Exploratory search is challenging for users, who may be unable to formulate search queries, have ill-defined search goals or may even struggle to understand search results. To ameliorate these difficulties, reinforcement learning-based information retrieval systems were developed to provide adaptive support to users. Reinforcement learning is used to build a model of user ...
2 CitationsSource
#1Alan Medlar (Edin.: University of Edinburgh)H-Index: 7
#2Petri Törönen (UH: University of Helsinki)H-Index: 18
Last.Liisa Holm (UH: University of Helsinki)H-Index: 54
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9 CitationsSource
#1Petri Törönen (UH: University of Helsinki)H-Index: 18
#2Alan Medlar (Edin.: University of Edinburgh)H-Index: 7
Last.Liisa Holm (UH: University of Helsinki)H-Index: 54
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14 CitationsSource
#1Tuomas Aivelo (UH: University of Helsinki)H-Index: 5
#2Alan Medlar (UH: University of Helsinki)H-Index: 7
Last.Jukka Jernvall (UH: University of Helsinki)H-Index: 44
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Sympatric species are known to host the same parasites species. Nevertheless, surveys examining parasite assemblages in sympatric species are rare. To understand how parasite assemblages in sympatric host species differ in a given locality, we used a noninvasive identification method based on high-throughput sequencing. We collected fecal samples from sympatric species in Ranomafana National Park, Madagascar, from September to December in 2010, 2011, and 2012 and identified their parasites by me...
1 CitationsSource
#1Mehmet Tekman (UCL: University College London)H-Index: 6
#2Alan Medlar (UH: University of Helsinki)H-Index: 7
Last.Horia C. Stanescu (UCL: University College London)H-Index: 21
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Motivation: Haplotype reconstruction is an important tool for understanding the aetiology of human disease. Haplotyping infers the most likely phase of observed genotypes conditional on constraints imposed by the genotypes of other pedigree members. The results of haplotype reconstruction, when visualized appropriately, show which alleles are identical by descent despite the presence of untyped individuals. When used in concert with linkage analysis, haplotyping can help delineate a locus of int...
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#1Alan MedlarH-Index: 7
#2Petri TörönenH-Index: 18
Last.Liisa HolmH-Index: 54
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