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Alan Medlar
University of Helsinki
Information retrievalExploratory searchComputer scienceGeneticsBiology
27Publications
9H-index
221Citations
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Publications 26
Newest
#1Alan Medlar (UH: University of Helsinki)H-Index: 9
#2Dorota Glowacka (UH: University of Helsinki)H-Index: 12
Source
#1Naihui Zhou (Iowa State University)H-Index: 4
#2Yuxiang JiangH-Index: 4
Last. Iddo Friedberg (Iowa State University)H-Index: 23
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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 experimen...
24 CitationsSource
#1Naihui Zhou (Iowa State University)H-Index: 4
#2Yuxiang Jiang (IU: Indiana University)H-Index: 4
Last. Iddo Friedberg (Iowa State University)H-Index: 23
view all 167 authors...
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...
11 CitationsSource
#1Chien-yu Huang (Edin.: University of Edinburgh)
#2Arlene Casey (Edin.: University of Edinburgh)
Last. Alan Medlar (UH: University of Helsinki)H-Index: 9
view all 4 authors...
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: 9
Last. Dorota Glowacka (UH: University of Helsinki)H-Index: 12
view all 3 authors...
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...
Source
Oct 17, 2018 in CIKM (Conference on Information and Knowledge Management)
#1Alan Medlar (UH: University of Helsinki)H-Index: 9
#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 (UH: University of Helsinki)H-Index: 9
#2Liisa Holm (UH: University of Helsinki)H-Index: 56
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
#1Petri Törönen (UH: University of Helsinki)H-Index: 19
#2Alan Medlar (Edin.: University of Edinburgh)H-Index: 9
Last. Liisa Holm (UH: University of Helsinki)H-Index: 56
view all 3 authors...
: The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses ...
42 CitationsSource
#1Alan Medlar (Edin.: University of Edinburgh)H-Index: 9
#2Petri Törönen (UH: University of Helsinki)H-Index: 19
Last. Liisa Holm (UH: University of Helsinki)H-Index: 56
view all 3 authors...
: We present AAI-profiler, a web server for exploratory analysis and quality control in comparative genomics. AAI-profiler summarizes proteome-wide sequence search results to identify novel species, assess the need for taxonomic reclassification and detect multi-isolate and contaminated samples. AAI-profiler visualises results using a scatterplot that shows the Average Amino-acid Identity (AAI) from the query proteome to all similar species in the sequence database. Taxonomic groups are indicate...
20 CitationsSource
#1Tuomas Aivelo (UH: University of Helsinki)H-Index: 6
#2Alan Medlar (UH: University of Helsinki)H-Index: 9
Last. Jukka Jernvall (UH: University of Helsinki)H-Index: 45
view all 5 authors...
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
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