Webinar: Fusion methodology for point clouds deep learning

Speaker: Fauzy Othman, Heriot-Watt University, Edinburgh
Date: 30 May 2022
Time: 15:00 – 16:00
Venue: Online

Fauzy is a PhD student working with Phil Bartie, Oliver Lemon, and Ben Kenwright. During the weekly SWeL meeting, Fauzy will be giving his first year progression presentation.

Abstract: This project aspires to address gaps in autonomous detection in aerial surveillance on ground objects. There are existing point cloud deep learning techniques, however many are having gaps in accuracy of detection and not developed for objects which are of interest to energy industry surveillance work. Hence the aim is to improve accuracy of object detection by exploring deep learning architecture, focusing on point cloud data manipulation and fusion methods. This Year 1 presentation covers literature review and initial implementation works.

Biohackathon 2018 -Paris

Last November I had the privilege to be one of 150 participants at the Biohackathon organised by ELIXIR. The hackathon was organised into 29 topics, many of which were related to Bioschemas and one directly focused on Bioschemas. For the Bioschemas topic we had up to 30 people working around three themes. The first theme […]

Bioschemas at the Biohackathon

Last November I had the privilege to be one of 150 participants at the Biohackathon organised by ELIXIR. The hackathon was organised into 29 topics, many of which were related to Bioschemas and one directly focused on Bioschemas. For the Bioschemas topic we had up to 30 people working around three themes.

The first theme was to implement markup for the various life sciences resources present. Representatives from ELIXIR Core Data Resources and node resources from the UK and Switzerland were there to work on this thanks to the staff exchange and travel fund. By the end of the week we had new live deploys for 11 additional resources and examples for many more.

The second theme was to refine the types and profiles that Bioschemas has been developing based on the experiences of deploying the markup. Prior to the hackathon, Bioschemas had moved from a minimal Schema.org extension of a single BioChemEntity type to collection of types for the different life science resources, e.g. Gene, Protein, and Taxon. Just before the hackathon a revised set of types and profiles were released. This proved to be useful for discussion, but it very quickly became clear that there was need for further refinement. During the hackathon we started new profiles for DNA, Experimental Studies, and Phenotype, and the Chemical profile was split into MolecularEntity and ChemicalSubstance. Long discussions were held about the types and their structure with early drafts for 17 types being proposed. These are now getting to a state where they are ready for further experimentation.

The third theme was to develop tooling to support Bioschemas. Due to the intensity of the discussions on the types and profiles, there was no time to work on this topic. However, the prototype Bioschemas Generator was extensively tested during the first theme and improvements fed back to the developer. There were also refinements made to the GoWeb tool.

Overall, it was a very productive hackathon. The venue proved to be very conducive to fostering the right atmosphere. During the evenings there were opportunities to socialise or carry on the discussions. Below are two of the paintings that were produced during one of the social activities that capture the Bioschemas discussions.

And there was the food. Wow! Wonderful meals, three times a day.

ISWC 2018

ISWC 2018 Trip Report Keynotes There were three amazing and inspiring keynote talks, all very different from each other. The first was given by Jennifer Golbeck (University of Maryland). While Jennifer did her PhD on the Semantic Web in the early days of social media and Linked Data, she now focuses on user privacy and […]

ISWC 2018 Trip Report

Keynotes

There were three amazing and inspiring keynote talks, all very different from each other.

The first was given by Jennifer Golbeck (University of Maryland). While Jennifer did her PhD on the Semantic Web in the early days of social media and Linked Data, she now focuses on user privacy and consent. These are highly relevant topics to the Semantic Web community and something that we should really be considering when linking people’s personal data. While the consequences of linking scientific data might not be as scary, there are still ethical issues to consider if we do not get it right. Check out her TED talk for an abridged version of her keynote.

She also suggested that when reading a companies privacy policy, you should replace the work “privacy” with “consent” and see how it seems then.

The talk also struck an accord with the launch of the SOLID framework by Tim Berners-Lee. There was a good sales pitch of the SOLID framework from Ruben Verborgh in the afternoon of the Decentralising the Semantic Web Workshop.

The second was given by Natasha Noy (Google). Natasha talked about the challenges of being a researcher and engineering tools that support the community. Particularly where impact may only be detect 6 to 10 years down the line. She also highlighted that Linked Data is only a small fraction of the data in the world (the tip of the iceberg), and it is not appropriate to expect all data to become Linked Data.

Her most recent endeavour has been the Google Dataset Search Tool. This has been a major engineering and social endeavour; getting schema.org markup embedded on pages and building a specialist search tool on top of the indexed data. More details of the search framework are in this blog post. The current search interface is limited due to the availability of metadata; most sites only make title and description available. However, we can now start investigating how to return search results for datasets and what additional data might be of use. This for me is a really exciting area of work.

Later in the day I attended a talk on the LOD Atlas, another dataset search tool. While this gives a very detailed user interface, it is only designed for Linked Data researchers, not general users looking for a dataset.

The third keynote was given by Vanessa Evers (University of Twente, The Netherlands). This was in a completely different domain, social interactions with robots, but still raised plenty of questions for the community. For me the challenge was how to supply contextualised data.

Knowledge Graph Panel

The other big plenary event this year was the knowledge graph panel. The panel consisted of representatives from Microsoft, Facebook, eBay, Google, and IBM, all of whom were involved with the development of Knowledge Graphs within their organisation. A major concern for the Semantic Web community is that most of these panelists were not aware of our community or the results of our work. Another concern is that none of their systems use any of our results, although it sounds like several of them use something similar to RDF.

The main messages I took from the panel were

  • Scale and distribution were key

  • Source information is going to be noisy and challenging to extract value from

  • Metonymy is a major challenge

This final point connects with my work on contextualising data for the task of the user [1, 2] and has reinvigorated my interest in this research topic.

Final Thoughts

This was another great ISWC conference, although many familiar faces were missing.

There was a great and vibrant workshop programme. My paper [3] was presented during the Enabling Open Semantic Science workshop (SemSci 2018) and resulted in a good deal of discussion. There were also great keynotes at the workshop from Paul Groth (slides) and Yolanda Gil which I would recommend anyone to look over.

I regret not having gone to more of the Industry Track sessions. The one I did make was very inspiring to see how the results of the community are being used in practice, and to get insights into the challenges faced.

The conference banquet involved a walking dinner around the Monterey Bay Aquarium. This was a great idea as it allowed plenty of opportunities for conversations with a wide range of conference participants; far more than your standard banquet.

Here are some other takes on the conference:

I also managed to sneak off to look for the sea otters.

[1] [doi] Colin R. Batchelor, Christian Y. A. Brenninkmeijer, Christine Chichester, Mark Davies, Daniela Digles, Ian Dunlop, Chris T. A. Evelo, Anna Gaulton, Carole A. Goble, Alasdair J. G. Gray, Paul T. Groth, Lee Harland, Karen Karapetyan, Antonis Loizou, John P. Overington, Steve Pettifer, Jon Steele, Robert Stevens, Valery Tkachenko, Andra Waagmeester, Antony J. Williams, and Egon L. Willighagen. Scientific Lenses to Support Multiple Views over Linked Chemistry Data. In The Semantic Web – ISWC 2014 – 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part I, page 98–113, 2014.
[Bibtex]
@inproceedings{BatchelorBCDDDEGGGGHKLOPSSTWWW14,
abstract = {When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over the data with no way of varying the notion of equivalence to be applied.
In this paper, we present an approach to enable applications to choose the equivalence criteria to apply between datasets. Thus, supporting multiple dynamic views over the Linked Data. For chemical data, we show that multiple sets of links can be automatically generated according to different equivalence criteria and published with semantic descriptions capturing their context and interpretation. This approach has been applied within a large scale public-private data integration platform for drug discovery. To cater for different use cases, the platform allows the application of different lenses which vary the equivalence rules to be applied based on the context and interpretation of the links.},
author = {Colin R. Batchelor and
Christian Y. A. Brenninkmeijer and
Christine Chichester and
Mark Davies and
Daniela Digles and
Ian Dunlop and
Chris T. A. Evelo and
Anna Gaulton and
Carole A. Goble and
Alasdair J. G. Gray and
Paul T. Groth and
Lee Harland and
Karen Karapetyan and
Antonis Loizou and
John P. Overington and
Steve Pettifer and
Jon Steele and
Robert Stevens and
Valery Tkachenko and
Andra Waagmeester and
Antony J. Williams and
Egon L. Willighagen},
title = {Scientific Lenses to Support Multiple Views over Linked Chemistry
Data},
booktitle = {The Semantic Web - {ISWC} 2014 - 13th International Semantic Web Conference,
Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part {I}},
pages = {98--113},
year = {2014},
url = {http://dx.doi.org/10.1007/978-3-319-11964-9_7},
doi = {10.1007/978-3-319-11964-9_7},
}
[2] [doi] Alasdair J. G. Gray. Dataset Descriptions for Linked Data Systems. IEEE Internet Computing, 18(4):66–69, 2014.
[Bibtex]
@article{Gray14,
abstract = {Linked data systems rely on the quality of, and linking between, their data sources. However, existing data is difficult to trace to its origin and provides no provenance for links. This article discusses the need for self-describing linked data.},
author = {Alasdair J. G. Gray},
title = {Dataset Descriptions for Linked Data Systems},
journal = {{IEEE} Internet Computing},
volume = {18},
number = {4},
pages = {66--69},
year = {2014},
url = {http://dx.doi.org/10.1109/MIC.2014.66},
doi = {10.1109/MIC.2014.66},
}
[3] Alasdair J. G. Grayg. Using a Jupyter Notebook to perform a reproducible scientific analysis over semantic web sources. In Enabling Open Semantic Science, Monterey, California, USA, 2018. Executable version: https://mybinder.org/v2/gh/AlasdairGray/SemSci2018/master?filepath=SemSci2018%20Publication.ipynb
[Bibtex]
@InProceedings{Gray2018:jupyter:SemSci2018,
abstract = {In recent years there has been a reproducibility crisis in science. Computational notebooks, such as Jupyter, have been touted as one solution to this problem. However, when executing analyses over live SPARQL endpoints, we get different answers depending upon when the analysis in the notebook was executed. In this paper, we identify some of the issues discovered in trying to develop a reproducible analysis over a collection of biomedical data sources and suggest some best practice to overcome these issues.},
author = {Alasdair J G Grayg},
title = {Using a Jupyter Notebook to perform a reproducible scientific analysis over semantic web sources},
OPTcrossref = {},
OPTkey = {},
booktitle = {Enabling Open Semantic Science},
year = {2018},
OPTeditor = {},
OPTvolume = {},
OPTnumber = {},
OPTseries = {},
OPTpages = {},
month = oct,
address = {Monterey, California, USA},
OPTorganization = {},
OPTpublisher = {},
note = {Executable version: https://mybinder.org/v2/gh/AlasdairGray/SemSci2018/master?filepath=SemSci2018%20Publication.ipynb},
url = {http://ceur-ws.org/Vol-2184/paper-02/paper-02.html},
OPTannote = {}
}

Congratulations Qianru Zhou

This morning Qianru Zhou successfully her PhD thesis “Ontology-driven knowledge based autonomic management for telecommunication networks: Theory, implementation and applications”, receiving minor corrections. Congratulations!
Supervisors: …

This morning Qianru Zhou successfully her PhD thesis “Ontology-driven knowledge based autonomic management for telecommunication networks: Theory, implementation and applications”, receiving minor corrections. Congratulations!

Supervisors:

External examiner: James Irvine (University of Strathclyde)

Internal examiner: Mauro Dragone (Engineering and Physical Sciences)

 

Bioschemas Samples Hackathon

Last week the Bioschemas Community hosted a workshop. The focus of the meeting was to get web resources describing biological samples to embed Schema.org mark up in their pages. The embedded mark up will enable the web resources to become more discoverable, and therefore the biological samples also. I was not able to attend the […]

Last week the Bioschemas Community hosted a workshop. The focus of the meeting was to get web resources describing biological samples to embed Schema.org mark up in their pages. The embedded mark up will enable the web resources to become more discoverable, and therefore the biological samples also.

I was not able to attend the event but Justin Clark-Casey has written this blog post summarising the event.

NAR Database Paper

The new year started with a new publication, an article in the 2018 NAR Database issue about the IUPHAR Guide to Pharmacology Database. Simon D. Harding, Joanna L. Sharman, Elena Faccenda, Chris Southan, Adam J. Pawson, Sam Ireland, Alasdair J. G. Gray, Liam Bruce, Stephen P. H. Alexander, Stephen Anderton, Clare Bryant, Anthony P. Davenport, […]

The new year started with a new publication, an article in the 2018 NAR Database issue about the IUPHAR Guide to Pharmacology Database.

  • Simon D. Harding, Joanna L. Sharman, Elena Faccenda, Chris Southan, Adam J. Pawson, Sam Ireland, Alasdair J. G. Gray, Liam Bruce, Stephen P. H. Alexander, Stephen Anderton, Clare Bryant, Anthony P. Davenport, Christian Doerig, Doriano Fabbro, Francesca Levi-Schaffer, Michael Spedding, Jamie A. Davies, and {NC-IUPHAR}. The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. Nucleic Acids Research, 46(D1):D1091-D1106, 2018. doi:10.1093/nar/gkx1121
    [BibTeX] [Abstract] [Download PDF]

    The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been ‘forked’ from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.

    @Article{Harding2018-GTP,
    abstract = {The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been ‘forked’ from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.},
    author = {Harding, Simon D and Sharman, Joanna L and Faccenda, Elena and Southan, Chris and Pawson, Adam J and Ireland, Sam and Gray, Alasdair J G and Bruce, Liam and Alexander, Stephen P H and Anderton, Stephen and Bryant, Clare and Davenport, Anthony P and Doerig, Christian and Fabbro, Doriano and Levi-Schaffer, Francesca and Spedding, Michael and Davies, Jamie A and , {NC-IUPHAR}},
    title = {The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY},
    journal = {Nucleic Acids Research},
    year = {2018},
    volume = {46},
    number = {D1},
    pages = {D1091-D1106},
    month = jan,
    OPTnote = {},
    OPTannote = {},
    url = {http://dx.doi.org/10.1093/nar/gkx1121},
    doi = {10.1093/nar/gkx1121}
    }

My involvement came from Liam Bruce’s honours project. Liam developed the RDB2RDF mappings that convert the existing relational content into an RDF representation. The mappings are executed using the Morph-RDB R2RML engine.

To ensure that we abide by the FAIR data principles, we also generate machine processable metadata descriptions of the data that conform to the HCLS Community Profile.

Below is an altmetric donut so you can see what people are saying about the paper.

Seminar: PhD Progression Talks

A double bill of PhD progression talks (abstracts below):

Venue: 3.07 Earl Mountbatten Building, Heriot-Watt University, Edinburgh

Time and Date: 11:15, 8 May 2017

Evaluating Record Linkage Techniques

Ahmad Alsadeeqi

Many computer algorithms have been developed to automatically link historical records based on a variety of string matching techniques. These generate an assessment of how likely two records are to be the same. However, it remains unclear how to assess the quality of the linkages computed due to the absence of absolute knowledge of the correct linkage of real historical records – the ground truth. The creation of synthetically generated datasets for which the ground truth linkage is known helps with the assessment of linkage algorithms but the data generated is too clean to be representative of historical records.

We are interested in assessing data linkage algorithms under different data quality scenarios, e.g. with errors typically introduced by a transcription process or where books can be nibbled by mice. We are developing a data corrupting model that injects corruptions into datasets based on given corruption methods and probabilities. We have classified different forms of corruptions found in historical records into four types based on the effect scope of the corruption. Those types are character level (e.g. an f is represented as an s – OCR Corruptions), attribute level (e.g. gender swap – male changed to female due to false entry), record level (e.g. missing records due to different reasons like loss of certificate), and group of records level (e.g. coffee spilt over a page, lost parish records in fire). This will give us the ability to evaluate record linkage algorithms over synthetically generated datasets with known ground truth and with data corruptions matching a given profile.

Computer-Aided Biomimetics: Knowledge Extraction

Ruben Kruiper

Biologically inspired design concerns copying ideas from nature to various other domains, e.g. natural computing. Biomimetics is a sub-field of biologically inspired design and focuses specifically on solving technical/engineering problems. Because engineers lack biological knowledge the process of biomimetics is non-trivial and remains adventitious. Therefore, computational tools have been developed that aim to support engineers during a biomimetics process by integrating large amounts of relevant biological knowledge. Existing tools work apply NLP techniques on biological research papers to build dedicated knowledge bases. However, these existing tools impose an engineering view on biological data. I will talk about the support that ‘Computer-Aided Biomimetics’ tools should provide, introducing a theoretical basis for further research on the appropriate computational techniques.

Smart Descriptions & Smarter Vocabularies (SDSVoc) Report

In December 2016 I presented at the Smart Descriptions and Smarter Vocabularies workshop on the Health Care and Life Sciences Community Profile for describing datasets, and our validation tool (Validata). Presentations included below. The purpose of the workshop was to understand current practice in describing datasets and where the DCAT vocabulary needs improvement. Phil Archer has written a very […]

In December 2016 I presented at the Smart Descriptions and Smarter Vocabularies workshop on the Health Care and Life Sciences Community Profile for describing datasets, and our validation tool (Validata). Presentations included below.

The purpose of the workshop was to understand current practice in describing datasets and where the DCAT vocabulary needs improvement. Phil Archer has written a very comprehensive report covering the workshop. A charter is being drawn up for a W3C working group to develop the next iteration of the DCAT vocabulary.

Research Blog: Facilitating the discovery of public datasets

Google are doing some interesting work on making datasets, in particular scientific datasets, more discoverable with schema.org markup. This is closely related to the bioschemas community project.
Source: Research Blog: Facilitating the discovery of pu…

Google are doing some interesting work on making datasets, in particular scientific datasets, more discoverable with schema.org markup. This is closely related to the bioschemas community project.

Source: Research Blog: Facilitating the discovery of public datasets