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01/05/2019 - AI3SD Semantics and Knowledge Learning for Chemical Design Workshop - Solent Conference Centre, Southampton

posted 3 Jan 2019, 08:42 by Samantha Kanza   [ updated 30 Apr 2019, 06:40 ]
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Designing chemicals, discovering new drugs, discovering materials and indeed all aspects of scientific discovery are all tasks that are highly data driven, and semantic web technologies are key to enabling researchers to deal with high levels of data in a useful and meaningful way. Semantic technologies facilitate representing data in a formal, structured, and interoperable way, and enable data to be reasoned over to infer potential relationships. In this workshop we seek to explore the ways in which semantic web technologies can be used to drive predictions in chemical design, including using Machine Learning and other AI techniques to exploit semantic links in knowledge graphs and linked datasets. There will be several keynote talks, an expert panel chaired by Professor Jeremy Frey, and a chance for breakout discussions. Lunch will be provided and the day will end with networking drinks.

Keynote Speakers
  • Dr Colin Bachelor - Colin Batchelor is a theoretical chemist by training, and now works at the Royal Society of Chemistry. He started as a technical editor before moving over to work on Project Prospect and ChemSpider before joining the Data Science team. He has published on natural language processing for chemistry, ontologies and cheminformatics.

  • Dr Age Chapman - Age is an Associate Professor of Computer Science at the University of Southampton, Co-Director of the ECS Centre for Health Technologies, and is part of the Web and Internet Science(WAIS) Research Group. Her research is in the area of database systems, focusing on using data appropriately and effectively. This involves solving problems that span the areas of databases, information discovery and retrieval, provenance and algorithmic accountability.

  • Dr Nicholas Gibbins - Nick is an Associate Professor in Computer Science at the University of Southampton and is part of the Web and Internet Science (WAIS) Research Group. His primary research interests are in the Semantic Web, Hypertext and Distributed Information Systems.

  • Professor Jonathan Goodman - Jonathan is a Professor of Chemistry and Director of Studies of Chemistry at the University of Cambridge, where he also serves as the Academic Dean. His research focuses on experimental and computational chemistry.

  • Dr Alexandra Simperler - Alexandra is a freelance consultant who works with Dr Gerhard Goldbeck of Goldbeck Consulting on the H2020 EU project European Materials Modelling Council (EMMC). She is interested in finding holistic solutions to ingrate materials modelling deeper into industrial workflows.

Keynote Abstracts
  • You did WHAT? - Dr Age Chapman: During scientific research and experimentation, information is discovered, generated, processed, analysed and disseminated. Rinse. Repeat. At each point, a user must understand what happened previously to the data and what impact that may have on their current work. During this talk, I will describe the notion of provenance, the history of creation and modification of data. This talk will provide an overview of how provenance can be used to support trust, the tools available for its capture and manipulation in various different scientific settings. I will then move on to describe how provenance provides a backbone for reasoning over choices made and their impact on results.

  • The Semantic Web at 20: Lessons from two decades of developing linked data applications - Dr Nicholas Gibbins: The Resource Description Framework, the first of the technologies that underpin the Semantic Web, became a W3C recommendation in February 1999. Since that date, a large and vibrant research community has grown up around the Semantic Web, yet widespread visibility of Semantic Web technologies has been slower than the early hype would have had us believe. In this talk, I examine the growth of the Semantic Web, assess its technological maturity, and examine likely future developments.

  • Challenging Chemistry: Solving Molecular Problems - Professor Jonathan Goodman: The power of AI is changing the way that chemistry is done, but chemistry is far from being solved. What is holding us back? Creating a new molecule or a necessary, but unknown, transformation is a demanding problem. Successes and surprises in predicting how molecules should behave can be used to try to discover the limits of our knowledge and the best ways to solve molecular problems.

  • Semantics vs. Statistics in Chemistry – Dr Colin Bachelor: Since the late 1990s, natural language processing (NLP) has seen a massive shift from high-precision, low-recall systems based on small sets of hand-written rules, to methods based on the statistical analysis of large corpora. The field of chemoinformatics, likewise, is dominated by statistical and machine-learning approaches. More recently deep learning methods have had surprising success in aspects of natural language processing, image processing and board games. Conversely, pharmaceutical companies have been engaging more and more with Semantic Web technologies, which are largely built around the sorts of hand-written systems that NLP has moved away from this century. In this talk I cover how we have applied both sorts of systems at the Royal Society of Chemistry and their strengths and weaknesses.

  • EMMO (European Materials & Modelling Ontology): semantic knowledge organisation for applied sciences - Dr Alexandra Simperler: Semantic knowledge organisation refers to the organisation of information about a given domain providing not just data but some level of detail regarding meaning and logic. The European Materials & Modelling Ontology (EMMO), developed within the EMMC is a multidisciplinary effort aimed at providing a standard representational framework for materials and their modelling. An introduction to semantic knowledge organisation and the EMMO will be provided. In the advent of digitalisation, the aim is to come up with tool to build a ‘digital twin’ of a material, representing its key traits at different levels of granularity and its changes over time. Likewise, potential materials models (electronic, atomistic, mesoscopic and continuum) relate to granularity perspectives of the material. EMMO hence provides the basis for progress beyond syntactically based scripted workflows and reach true (semantic) interoperability between models. Therefore, solutions should be found that are based on semantic approaches with metadata backed up by an ontology framework. It will be discussed, how EMMC supports efforts to achieve interoperability of materials models and by establishing open standards for the integration of different codes (e.g. academic and commercial, open and close source), referred to as the Open Simulation Platform (OSP). The work presented is based on the efforts of Gerhard Goldbeck (Goldbeck Consulting, Emanuele Ghedini (University of Bologna), Jesper Friis (SINTEF), Adham Hashibon (Fraunhofer IWM), and Georg J. Schmitz (ACCESS).

The programme for the day is as follows:
  • 10:00-10:30: Coffee & Registration
  • 10:30-11:00: Welcome Introduction – Professor Jeremy Frey
  • 11:00-11:30: You did WHAT? – Dr Age Chapman
  • 11:30-12:00: Keynote - Dr Nick Gibbins
  • 12:00-12:30: Challenging Chemistry: Solving Molecular Problems – Professor Jonathan Goodman
  • 12:30-13:30: Lunch
  • 13:30-14:00: Semantics vs. Statistics in Chemistry - Dr Colin Bachelor
  • 14:00-15:00: Breakout Discussions
  • 15:00-15:30: Coffee & Report Back
  • 15:30-16:00: EMMO (European Materials & Modelling Ontology): semantic knowledge organisation for applied sciences - Dr Alexandra Simperler
  • 16:00-17:00: Panel Discussions chaired by Professor Jeremy Frey
  • 17:00-18:00: Drinks Reception

1. Who should attend? 
Anyone with an interest in Semantic Web Technologies (either in their own right or as a technology to be used in conjunction with Artificial Intelligence or Machine Learning), Scientific Discovery, Chemical Design, Knowledge learning for Scientific Discovery. We welcome members from academia, industry and government. We are always looking to grow our Network+ and bring in people with a wealth of experience in the many different subject areas that are needed so that we can form interdisciplinary partnerships and work together to further the field of Scientific Discovery.

2. What will I get out of it? 
You will be able to network with likeminded people who have research interests that complement yours. You will hear a range of thought-provoking talks about different aspects of semantics and knowledge learning for chemical design, and have the opportunity to both discuss this subject area with other members of the workshop, and address questions and raise areas of discussion to our expert panel. Members of the Network Executive Group will also be in attendance so you will be able to find out more about our Network and the opportunities we have available including funding opportunities and the types of events we will be running (e.g. workshops, conferences and hackathons). 

3. What are the aims of the workshop? 
This workshop is aiming to help the Network+ to drive progress in this area and facilitate collaboration by introducing people to make new interdisciplinary teams, and to produce new grant applications. To achieve this we may commission literature reviews, papers, or small scale investigations to test out new ideas. We welcome ideas and suggestions about how to go forward in this area and how best to achieve our aims.

4. What are the themes of the workshop? 
This workshop will begin by covering the topics of semantic web technologies, from their conception to the state of the available semantic web tools of today, alongside best practices of research data management with a strong focus of provenance. The workshop will then segway into the application of these technologies to chemistry in the form of creating chemistry ontologies, and using semantic web and AI technologies to make advances in chemical discovery.