Professor Aaron Quigley new SICSA Director

Congratulations to Professor Aaron Quigley who has been appointed as the new Director of SICSA. Aaron, the Chair of Human Computer Interaction co-founded SACHI, the St Andrews Computer Human Interaction research group and served as its director from 2011-2018.

In his volunteer roles he is the ACM SIGCHI Vice President for Conferences (on the ACM SIGCHI Executive Committee), member of the ACM Europe Council Conferences Working Group, a board member of ScotlandIS and an ACM Distinguished Speaker. Aaron will be general co-chair for the ACM CHI conference in Asia in 2021.

For more information about Professor Quigley, please see https://aaronquigley.org.

Juho Rousu: Predicting Drug Interactions with Kernel Methods

Event details

  • When: 30th April 2019 14:00 - 15:00
  • Where: Cole 1.33a
  • Format: Seminar

Title:
Predicting Drug Interactions with Kernel Methods

Abstract:
Many real world prediction problems can be formulated as pairwise learning problems, in which one is interested in making predictions for pairs of objects, e.g. drugs and their targets. Kernel-based approaches have emerged as powerful tools for solving problems of that kind, and especially multiple kernel learning (MKL) offers promising benefits as it enables integrating various types of complex biomedical information sources in the form of kernels, along with learning their importance for the prediction task. However, the immense size of pairwise kernel spaces remains a major bottleneck, making the existing MKL algorithms computationally infeasible even for small number of input pairs. We introduce pairwiseMKL, the first method for time- and memory-efficient learning with multiple pairwise kernels. pairwiseMKL first determines the mixture weights of the input pairwise kernels, and then learns the pairwise prediction function. Both steps are performed efficiently without explicit computation of the massive pairwise matrices, therefore making the method applicable to solving large pairwise learning problems. We demonstrate the performance of pairwiseMKL in two related tasks of quantitative drug bioactivity prediction using up to 167 995 bioactivity measurements and 3120 pairwise kernels: (i) prediction of anticancer efficacy of drug compounds across a large panel of cancer cell lines; and (ii) prediction of target profiles of anticancer compounds across their kinome-wide target spaces. We show that pairwiseMKL provides accurate predictions using sparse solutions in terms of selected kernels, and therefore it automatically identifies also data sources relevant for the prediction problem.

References:
Anna Cichonska, Tapio Pahikkala, Sandor Szedmak, Heli Julkunen, Antti Airola, Markus Heinonen, Tero Aittokallio, Juho Rousu; Learning with multiple pairwise kernels for drug bioactivity prediction, Bioinformatics, Volume 34, Issue 13, 1 July 2018, Pages i509–i518, https://doi.org/10.1093/bioinformatics/bty277

Short Bio:
Juho Rousu is a Professor of Computer Science at Aalto University, Finland. Rousu obtained his PhD in 2001 form University of Helsinki, while working at VTT Technical Centre of Finland. In 2003-2005 he was a Marie Curie Fellow at Royal Holloway University of London. In 2005-2011 he held Lecturer and Professor positions at University of Helsinki, before moving to Aalto University in 2012 where he leads a research group on Kernel Methods, Pattern Analysis and Computational Metabolomics (KEPACO). Rousu’s main research interest is in learning with multiple and structured targets, multiple views and ensembles, with methodological emphasis in regularised learning, kernels and sparsity, as well as efficient convex/non-convex optimisation methods. His applications of interest include metabolomics, biomedicine, pharmacology and synthetic biology.

PhD viva success: Evan Brown

Congratulations to Evan Brown, who successfully defended his thesis today. He is pictured with Internal examiner Dr Tristan Henderson and external examiner Professor Chris Marsden, Professor of Internet Law at the University of Sussex.

Evan’s PhD research on using corpus linguistics to build collaborative legal research tools was supervised by Professor Aaron Quigley.

Distinguished Speaker: Australia, Columbia and Thailand

This Saturday Professor Aaron Quigley will deliver a keynote talk on Global Human Computer Interaction at the Thai SIGCHI Symposium in Bangkok. This is the first symposium of the Bangkok ACM SIGCHI Chapter which aims to connect the Thai UX and HCI communities together with those beyond their borders. This talk is part of the Distinguished Speaker Program (DSP) of the Association for Computing Machinery (ACM).

In May, Professor Quigley will travel to Melbourne and Sydney Australia as part of the ACM DSP program. First, he will deliver a talk on the Future of Interaction at the Melbourne Knowledge Week followed by a “fireside chat” and panel in the University of Melbourne and finally a seminar in the University of Sydney. His talks will cover a number of areas of research he explores with his colleagues and students in SACHI, the St Andrews Computer Human Interaction research group.

In August, Aaron has been invited to deliver a keynote at the 5th Workshop on ICTs for improving Patients Rehabilitation Research Techniques in Popayán, Colombia. This talk will focus on some of Aaron’s more recent, and unpublished research, in augmenting interactions in AR and his older work on technology for rehabilitation and older people.

Professor Quigley is currently on sabbatical in the National University of Singapore but he will attend the CHI 2019 conference in Glasgow this May with SACHI colleagues and graduate students presenting their latest research.

Tom Kelsey appointed Associate Editor of Human Reproduction Update

Arne Sunde, the incoming Editor-in-Chief, has appointed Tom Kelsey as Associate Editor of Human Reproduction Update.

Human Reproduction Update is the leading journal in Reproductive Medicine, with an Impact Factor of 11.852. The journal publishes comprehensive and systematic review articles in human reproductive physiology and medicine, and is published on behalf of the European Society of Human Reproduction and Embryology (ESHRE). The Associate Editor system at Human Reproduction Update has been in place since the beginning of 2001 and it has a significant positive effect on the quality and dynamism of the journal.

In the ISI JCR Global Ranking for 2017, Human Reproduction Update is ranked first of 29 journals in Reproductive Biology, and first of 82 journals in Obstetrics & Gynecology.

Tom Kelsey has published extensively in Human Reproduction Update and its sister journals Human Reproduction (impact factor 4.949) and Molecular Human Reproduction (impact factor 3.449). He is also Associate Editor for the Open Access journals Frontiers in Endocrinology and Frontiers in Physiology. He is a regular reviewer for these journals and also the British Medical Journal, BMJ Open, Health Education Journal, Nature Scientific Reports, PLOS One, Mathematical Medicine and Biology, Systems Biology in Reproductive Medicine, and the European Journal of Obstetrics & Gynecology and Reproductive Biology.

Professors Quigley and Kitamura to co-chair ACM CHI 2021 in Asia

Professors Quigley and Kitamura

Professor Aaron Quigley and Professor Yoshifumi Kitamura (Tohoku University, Japan) have been appointed the general co-chairs for the ACM CHI conference on Human Factors in Computing Systems in Asia in 2021.  CHI is hosted by the ACM SIGCHI, the Special Interest Group on Computer-Human Interaction

The ACM CHI Conference on Human Factors in Computing Systems is the premier international conference for the field of Human-Computer Interaction (HCI). This flagship conference is generally considered the most prestigious in the field of HCI and attracts thousands of international attendees annually.

 

CHI provides a place where researchers and practitioners can gather from across the world to discuss the latest HCI topics. It has been held since 1982 and this is only the second time CHI will be held in Asia.  CHI 2020 will be held in Hawaii while CHI 2019 will be held in Glasgow next May. The location for CHI 2021 will be announced to the global research community during CHI 2019.

This week Professor Quigley was invited to present at the Third ACM SIGCHI Asian Symposium hosted in the Research Institute of Electrical Communication at Tohoku University, Sendai. The ACM SIGCHI Asian Development committee organised this event to bring together early career researchers, students and more from multiple countries in the Asia-Pacific region to discuss ideas that can lead to innovations and to inspire us all. The event served to  develop connections and regional/local societies through promoting collaboration among Asian-Pacific HCI researchers and practitioners. Professor Quigley will be spending his upcoming sabbatical in Asia.  

Job vacancies: Interdisciplinary Data Scientists

The Schools of Medicine and Computer Science are seeking to appoint three highly motivated data scientists with a passion for computer vision and deep learning, and specifically their application to medical imaging. The data scientists will be based in the Schools of Computer Science and Medicine at the University of St Andrews and will work on a national Innovate UK funded initiative to create a pan Scotland Industrial Centre for AI Research in Digital Diagnostics (iCAIRD).

The successful candidates will have the opportunity to work alongside and learn from clinicians, industrial experts from Philips Healthcare and academics to help develop artificial intelligence solutions for the automatic reporting of cancer diagnoses in endometrial and cervical cancer. The main duties of the role will involve being an active member of an interdisciplinary team of scientists to help develop deep learning algorithms, within industry standard guidelines, to analyse patient samples in a manner that allows rapid clinical transfer. This work will therefore have the opportunity to impact both patient welfare and relieve pathologist work burden.

Applicants should have experience in machine learning, demonstrable experience in computer programming languages and an interest in the medical applications of computer science. The candidates would benefit from a track record in scientific writing and working in interdisciplinary teams as well as experience in computer vision.

The posts are full time and over a period of 36 months.
Closing Date: 18 January 2019

Find out more about the vacancies further particulars on the recruitment website.

PhD viva success: Julian Petford

Congratulations to Julian Petford, who successfully defended his thesis today. He is pictured with internal examiner Professor Aaron Quigley and external examiner Dr Jason Alexander, from Lancaster University. Julian’s PhD research in Full Coverage Displays for Non-Immersive Applications was supervised by Dr Miguel Nacenta.

Image courtesy of Wendy Boyter