̽��ֱ�� of Cambridge - Karolinska Institutet

AI system may accelerate search for cancer discoveries

sc604 — Tue, 27 Nov 2018 12:09:25 +0000

̽��ֱ��system, called LION LBD and developed by computer scientists and cancer researchers at the ̽��ֱ�� of Cambridge, has been designed to assist scientists in the search for cancer-related discoveries. It is the first literature-based discovery system aimed at supporting cancer research. ̽��ֱ��results are reported in the journal Bioinformatics.

Global cancer research attracts massive amounts of funding worldwide, and the scientific literature is now so huge that researchers are struggling to keep up with it: critical hypothesis-generating evidence is now often discovered long after it was published.

Cancer is a complex class of diseases that are not completely understood and are the second-leading cause of death worldwide. Cancer development involves changes in numerous chemical and biochemical molecules, reactions and pathways, and cancer research is being conducted across a wide variety of scientific fields, which have variability in the way that they describe similar concepts.

“As a cancer researcher, even if you knew what you were looking for, there are literally thousands of papers appearing every day,” said Professor Anna Korhonen, Co-Director of Cambridge’s Language Technology Lab who led the development of LION LBD in collaboration with Dr Masashi Narita at Cancer Research UK Cambridge Institute and Professor Ulla Stenius at Karolinska Institutet in Sweden. “LION LBD uses AI to help scientists keep up-to-date with published discoveries in their field, but could also help them make new discoveries by combining what is already known in the literature by making connections between sources that may appear to be unrelated.”

̽��ֱ��‘LBD’ in LION LBD stands for Literature-Based Discovery, a concept developed in the 1980s which seeks to make new discoveries by combing pieces of information from disconnected sources. ̽��ֱ��key idea behind the original version of LBD is that concepts that are never explicitly linked in the literature may be indirectly linked through intermediate concepts.

̽��ֱ��design of the LION LBD system allows real-time search to discover indirect associations between entities in a database of tens of millions of publications while preserving the ability of users to explore each mention in its original context.

“For example, you may know that a cancer drug affects the behaviour of a certain pathway, but with LION LBD, you may find that a drug developed for a totally different disease affects the same pathway,” said Korhonen.

LION LBD is the first system developed specifically for the needs of cancer research. It has a particular focus on the molecular biology of cancer and uses state-of-the-art machine learning and natural language processing techniques, in order to detect references to the hallmarks of cancer in the text. Evaluations of the system have demonstrated its ability to identify undiscovered links and to rank relevant concepts highly among potential connections.

̽��ֱ��system is built using open data, open source and open standards, and is available as an interactive web-based interface or a programmable API.

̽��ֱ��researchers are currently working on extending the scope of LION-LBD to include further concepts and relations. They are also working closely with cancer researchers to help and improve the technology for end users.

̽��ֱ��system was developed in collaboration with ̽��ֱ�� of Cambridge Language Technology Lab, Cancer Research UK Cambridge Institute, and Karolinska Institutet in Sweden, and was funded by the Medical Research Council.

Reference:
Sampo Pyysalo et al. ‘LION LBD: a Literature-Based Discovery System for Cancer Biology.’ Bioinformatics (2018). DOI: 10.1093/bioinformatics/bty845

Searching through the mountains of published cancer research could be made easier for scientists, thanks to a new AI system.

As a cancer researcher, even if you knew what you were looking for, there are literally thousands of papers appearing every day

Anna Korhonen

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Skin cancer cells from a mouse show how cells attach at contact points

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Cancer Core Europe: institutes unite across Europe to tackle cancer

lw355 — Fri, 26 Sep 2014 08:04:10 +0000

̽��ֱ��consortium of European cancer centres will link cancer programmes on a huge scale to help the joint monitoring of patients and the development of next-generation clinical trials.

Cancer Core Europe, launched today, brings together the Cambridge Cancer Centre, the Gustave Roussy Cancer Campus Grand Paris (Villejuif, France), the Karolinska Institutet (Stockholm, Sweden), the Netherlands Cancer Institute (Amsterdam, ̽��ֱ��Netherlands), the Vall d’Hebron Institute of Oncology (Barcelona, Spain), and the German Cancer Research Center and its National Center for Tumor Diseases (Heidelberg, Germany).

Professor Carlos Caldas, from the ̽��ֱ�� of Cambridge’s Department of Oncology and Cancer Research UK Cambridge Institute, has played a leading role in establishing the new collaboration. Cancer is a strategic research initiative within the ̽��ֱ��, and with around 150 research group leaders and 100 clinicians currently undertaking basic, translational or clinical cancer research, Cambridge has substantial expertise to offer the consortium.

Across the Cancer Core Europe consortium as a whole, ever year around 60,000 newly diagnosed cancer patients are seen, 300,000 cancer treatments are delivered, about 1,000,000 outpatient visits are performed, and around 1,500 clinical trials are conducted.

̽��ֱ��consortium’s goal of linking scientific discovery from bench to bedside includes the creation of a virtual ‘e-hospital’ to enable joint research programs. Four areas of data will be linked across the partnership: electronic medical records that will ease the exchange of patient information according to clinical trial protocols; molecular imaging and diagnostics to enable comparable monitoring of patients; a clinical trial infrastructure that will eventually allow one of the six centres to sponsor trials across the consortium; and the development of innovative next generation clinical trials.

“This initiative brings together outstanding cancer centres across Europe in a visionary way,” said Patrick Maxwell, Regius Professor of Physic and Head of the School of Clinical Medicine. “Our understanding of cancer is increasing faster than ever before, and over the next decade or so I believe that this will lead to a revolution in how physicians treat patients. This network will lead that revolution.”

Cancer Core Europe will be able to support the full spectrum of research required to address the continuum between cancer research and cancer care, as well as provide a unique environment to train the next generation of talents in innovative translational and clinical oncology.

“There is little doubt that this partnership will bring new insights into, and opportunities to address, the critical issues we all face in caring for patients with cancer, and we are absolutely delighted, and incredibly excited to be part of it,” said Dr Keith McNeil, Chief Executive of Cambridge ̽��ֱ�� Hospitals.

Susan Galbraith, Head of Oncology at Astra Zeneca, added: “ ̽��ֱ��development of Cancer Core Europe is exciting. ̽��ֱ��understanding of the science that drives cancer growth is leading to rapid and significant changes in how we need to approach the diagnosis, monitoring and treatment of patients with cancer. If we are to be successful in bringing revolutionary new treatment regimens to patients quickly it will require this kind of collaboration across cancer centres. AZ Oncology looks forward to also collaborating with Cancer Core Europe to help deliver this revolutionary vision.”

Launched today (26 September), Cancer Core Europe brings together six cancer centres – including the Cambridge Cancer Centre at the ̽��ֱ�� of Cambridge – to link cancer research through to cancer care.

Our understanding of cancer is increasing faster than ever before, and over the next decade or so I believe that this will lead to a revolution in how physicians treat patients. This network will lead that revolution.

Patrick Maxwell

John Stingl, CRUK Cambridge Institute

Breast cells grown in the laboratory for research on which cells in the breast form tumours

Examples of the expertise that Cambridge brings to the Cancer Core Europe partnership

• An established and growing early phase clinical trials team already collaborating on innovative national and international clinical trials. ̽��ֱ��POSEIDON trial , co-led by Cambridge in collaboration with the Netherlands Cancer Institute and the Vall d'Hebron Cancer Centre in Barcelona, is assessing the effectiveness of combining Tamoxifen and the Genentech inhibitor GDC0032 in patients with ER+ breast cancer. ̽��ֱ��BET inhibitor trial is a phase I/II open-label, dose escalation study to investigate the safety, pharmacokinetics, pharmacodynamics and clinical activity of a BET-family inhibitor (GSK525762) in patients with relapsed, refractory haematologic malignancies.

• Pioneering development of the technology to analyse circulating tumour DNA. This technique has exciting potential application in the form of a ‘liquid biopsy’ from a simple blood sample that could be used in future for the early diagnosis of cancer and for monitoring how a tumour is responding to treatment.

• Novel magnetic resonance imaging methods, such as hyperpolarised C13 MRI, are being developed to detect how tumours are responding to treatment within hours rather than days, which will in future enable patients to be given the best personalised treatment for their cancer as soon as possible.

• ̽��ֱ��Joint Clinical Information System (JCIS) records key cancer data items and tracks treatment pathways for all patients with cancer at Addenbrooke’s Hospital and the use of electronic health records such as EPIC, recently launched at Addenbrooke’s, will enhance the ability to treat and monitor patients.

• ̽��ֱ��MRC Biostatistics Unit in Cambridge is one of the largest groups of biostatisticians in Europe and has established itself as an internationally acclaimed centre for research in biostatistics and a major centre for training and knowledge transfer. A particular area of expertise is the design and analysis of randomised trials, specifically to give them the flexibility to adapt as trial data emerges and to be used to plan the extent and scope of the next phase of research.

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