Current STRATiGRAD PhD student Sam Cooper was on the winning team at this weekend’s Pistoia Alliance deep learning hackathon, which aimed to put together deep/machine learning researchers with scientists working in the pharmaceutical industry to promote collaborations between the fields.
At the event, a series of challenges and datasets were put forward by companies in the Pistoia Alliance. Teams were then tasked with developing innovative machine learning solutions to these challenges. Sam speaks below about his experience.
What problem were you trying to solve?
We worked on a challenge put forward by Janssen in which we had to predict the activity of a drug across 7 different biological assays given its activity in thousands of other assays. However, drugs were very rarely active and as such the data was very sparse. Such data represents a real challenge to machine learning algorithms.
What was your winning solution?
To solve this challenge we developed a neural network using functions specifically designed for very sparse data, which enabled us to predict the results of the assay more accurately than everyone else. This was helped by the fact we specially configured a cloud computing server provided by Microsoft Azure for the event to train the network using graphics cards, which can train neural networks thousands of times faster rate than the processors used on standard servers and desktop computers.
What do you plan to do with the prize money?
Have a nice relaxing weekend away that doesn’t involve programming!
Find out more about the work of Dr Veronique Azuara and Rute Tomaz in an interview following their latest paper to be published in Development last week – Jmjd2c facilitates the assembly of essential enhancer-protein complexes at the onset of embryonic stem cell differentiation.
Congratulations to Jack Leese (UG student BSc Surgery and Anaesthesia) who has been awarded the Young Investigator Prize at the Winter Meeting of the Anatomical Society for his presentation of the research conducted as part of his BSc Surgery and Anaesthesia project (supervised by Professor Ceri Davies).
The prize is awarded for research conducted as an undergraduate or a PhD student and must be presented within 1 year of graduation. His talk was entitled An Investigation of the anatomy of the Infrapatellar Fat Pad: a cadaveric study.
Congratulations to Dr Catherine Van Der Straeten (Senior Clinical Scientist in Translational Musculoskeletal Science and Technology) who has become the new Deputy Chair of the METADAC Big Data Initiative. The METADAC is a multi-agency multi-study, designed to establish an independent mechanism for the efficient and effective governance of access to biosamples and health-related data from several leading UK cohort studies. Launched in June 2015, the METADAC also seeks to provide a scalable mechanism to enable additional cohorts to be included in the future, thus relieving the need for each to produce structures, policies and guidelines at considerable additional expense.
The Deputy Chair of the METADAC is a voting member of the Committee, with additional responsibilities. Dr Van Der Straeten will bring bio-medical expertise to complement the current Chair’s social scientific background and has a strong history in the field of genetic and medical research in longitudinal studies. As part of her former job, Dr Van Der Straeten was the Medical Director of the Biobank at Ghent University Hospital, and has an extensive track record in clinical research.
Dr Van Der Straeten has also been appointed as the Surgery Subspecialty (Orthopaedics) Lead for Northwest London as part of the NIHR CRN. Thorough both positions she aims to use her influence and expertise to make a difference and help create new opportunities for the Department.
Congratulations to Professor Daqing Ma (Professor of Anaesthesia), who received an Outstanding Award from the Chinese Society of Anaesthesiology and Chinese Journal of Anesthesiology, Beijing, China, in December 2016, for his special contribution to the development and excellent achievement in Anesthesiology.
On November 29th, Imperial inaugurated the International Phenome Centre Network (IPCN), at the WISH conference in Doha. Building on the best-practices established at the MRC-NIHR National Phenome Centre, the IPCN will promote global harmonisation in the field of metabolic phenotyping, and using the data sets generated, conduct research to inform global public health policies and the development of new therapies.
Dame Sally Davies, the UK’s Chief Medical Officer stated:
Phenomic research really is one of the next medical frontiers which can advance our understanding of a whole raft of diseases and conditions. The way we treat autism, cancers, mental health, stroke, obesity, metabolic diseases and type 2 diabetes could all be revolutionised by research in this area. It is also really good for work to cross international boundaries to find ways of tackling the biggest global public health challenges facing us today faster.
Congratulations to Professor Ian Wilson who was awarded the Martin Medal, from the Chromatographic Society which recognises scientists who have made outstanding contributions to the advancement of separation science. Professor Wilson received the medal from Dr Tony Edge of the Chromatographic Society in the closing ceremony of the 31st International Symposium on Chromatography (ISC), which was held from the 28th August to the 1st of September 2016, at the University of Cork, Ireland.
The Nobel Prize in Chemistry 1952 was awarded jointly to Archer John Porter Martin and Richard Laurence Millington Synge “for their invention of partition chromatography”. In 1978 Prof Martin gave permission for the Chromatographic Society (Society currently celebrating its 60th Anniversary Year) to associate his name with the Martin Medal.
Members of the All Party Parliamentary Group (APPG) for Ovarian Cancer including Sharon Hodgson MP (Chair) and Mark Durkan MP visited the Imperial Ovarian Cancer Action Research Centre (OCARC) last week, together with representatives from Ovarian Cancer Action, to learn about some of the ovarian research being carried out at Imperial. After some good discussion around ovarian cancer screening, genetic testing and strategies for early detection and diagnosis, the group had a tour of the OCARC labs and discussion with some of the scientists.
The Department was delighted to welcome more than 175 staff and students to the Surgery and Cancer Departmental Staff meeting held yesterday. Prof Regan chaired the meeting and Prof Nicholson gave a brief overview of the Department, covering some recent successes as well as opportunities for the future.
The agenda then moved to a much more interactive phase with participants responding to questions on the real-time polling software Mentimeter, ably compered by Toby Athersuch. Via people’s online devices staff answered questions about the culture of the Department.
Paul Strutton then spoke about his role as mental health champion for the Department and provided a very informative overview of the College and Department support available for staff and students. Covering the Departmental mentoring scheme, staff support scheme, health and wellbeing and parents network.
After a break everyone moved to their allocated colour table to engage in table discussions led by Kate Hardy, covering topis of communications, behaviour and networking. Each table was presented with a question relating to one of these topics and asked to discuss the issue and come up with possible solutions.
The results of the Mentimeter questions were then presented by Ana Costa-Pereira via visuals generated through the Mentimeter software.
In concluding the meeting – Jeremy and Lesley led the Department’s response and indicated their enthusiasm for many of the ideas generated and their commitment to implementing actionable ideas. Visuals from the Mentimeter questions and a report of the outcomes of the table discussions will be circulated shortly and there will be more updates from this meeting as actionable items are implemented.
We’d welcome any thoughts you have about how the afternoon worked for you – What was good? What was bad? What would you like to see next time? Please send comments to firstname.lastname@example.org.
Congratulations to Professor Elaine Holmes who has made it on to the 2016 Analytical Scientist Power List. Read more about Prof Holmes passions, pivotal moment and prediction for the future on her power list profile.
Congratulations to Computation and Systems Medicine PhD student Liza Selly who won the 2016 Max Perutz Science Writing Prize (run by MRC). From over 120 entries Liza won the prize for her piece on the negative effects of brake dust emissions on human health and the economy. To read more on Liza’s work please see the MRC blog post on Braking perceptions of traffic pollution.
Prof Anthony Gordon was invited to give a plenary talk entitled “Levosimendan for the Prevention of Acute Organ Dysfunction in Sepsis” in the “Hot Topics” session at the European Society of Intensive Care Medicine annual conference in Milan on October 5th 2016. The presentation was accompanied by a simultaneous publication in the New England Journal of Medicine.
Congratulations to Helen Laycock and Harriet Kemp, two Clinical Research Fellows working in Pain Research, who together have won best poster prize in the clinical science category at the World Congress on Pain which took place last month in Yokohama Japan. The winning poster was selected as one of three prize winners from over 2000 posters submitted.
Read an Interview with Professor Naomi Chayen, head of the Crystallization Group in Computational and Systems Medicine, winner of prestigious awards, including Innovator of the Year, and nicknamed the ‘Crystallization Guru’.
Prof Naomi Chayen talks about her career and the work her lab is doing to help advance the crystallization field.
Huge congratulations go to Professor Paul Abel (Prof of Urology) who has won the Associate Dean’s Award, a newly created prize to celebrate individuals who have dedicated themselves to teaching.
Prof Abel was recognised for his many years of teaching at the School of Medicine and overall dedication to students, many of which spoke extremely highly of his teaching and recognised him as an inspiratory educator.
The Associate Dean’s award will be presented at the School of Medicine’s Teaching Excellence ceremony in November and comes with a prize of £250.
Congratulations to two of our HPB Surgeons at Hammersmith Hospital, Mr Duncan Spalding and Mr Madhava Pai who have come top in student feedback for Year 6 Senior Surgery at Imperial for the last academic year. The overall score for the Hammersmith Hospital and teacher scores are top amongst 9 hospitals to which Imperial Year 6 senior surgery students are posted.