Researchers from Carnegie Mellon University (CMU) have created the first robotically driven experimentation system to determine the effects of a large number of drugs on many proteins, reducing the number of necessary experiments by 70%.
The model, presented in the journal eLife, uses an approach that could lead to accurate predictions of the interactions between novel drugs and their targets, helping reduce the cost of drug discovery.
“Biomedical scientists have invested a lot of effort in making it easier to perform numerous experiments quickly and cheaply,” says lead author Armaghan Naik, a Lane Fellow in CMU’s Computational Biology Department.
“However, we simply cannot perform an experiment for every possible combination of biological conditions, such as genetic mutation and cell type. Researchers have therefore had to choose a few conditions or targets to test exhaustively, or pick experiments themselves. The question is which experiments do you pick?”
Naik says that careful balance between performing experiments that can be predicted confidently and those that cannot is a challenge for humans, as it requires reasoning about an enormous amount of hypothetical outcomes at the same time.
To address this problem, the research team has previously described the application of a machine learning approach called “active learning”. This involves a computer repeatedly choosing which experiments to do, in order to learn efficiently from the patterns it observes in the data. The team is led by senior author Robert F. Murphy, Professor at the Ray and Stephanie Lane Center for Computational Biology, and Head of CMU’s Computational Biology Department.
While their approach had only been tested using synthetic or previously acquired data, the team’s current model builds on this by letting the computer choose which experiments to do. The experiments were then carried out using liquid-handling robots and an automated microscope.
The learner studied the possible interactions between 96 drugs and 96 cultured mammalian cell clones with different, fluorescently tagged proteins. A total of 9,216 experiments were possible, each consisting of acquiring images for a given cell clone in the presence of a given drug. The challenge for the algorithm was to learn how proteins were affected in each of these experiments, without performing all of them.
The first round of experiments began by collecting images of each clone for one of the drugs, totaling 96 experiments. Images were represented by numerical features that captured the protein’s location in the cell.
At the end of each round, all experiments that passed quality control were used to identify phenotypes (patterns in the location of a protein) that may or may not have related to a previously characterized drug effect.
A novelty of this work was for the learner to identify potentially new phenotypes on its own as part of the learning process. To do this, it clustered the images to form phenotypes. The phenotypes were then used to form a predictive model, so the learner could guess the outcomes of unmeasured experiments. The basis of the model was to identify sets of proteins that responded similarly to sets of drugs, so that it could predict the same prevailing trend in the unmeasured experiments.
The learner repeated the process for a total of 30 rounds, completing 2,697 out of the 9,216 possible experiments. As it progressively performed the experiments, it identified more phenotypes and more patterns in how sets of proteins were affected by sets of drugs.
Using a variety of calculations, the team determined that the algorithm was able to learn a 92% accurate model for how the 96 drugs affected the 96 proteins, from only 29% of the experiments conducted.
“Our work has shown that doing a series of experiments under the control of a machine learner is feasible even when the set of outcomes is unknown. We also demonstrated the possibility of active learning when the robot is unable to follow a decision tree,” explains Murphy.
“The immediate challenge will be to use these methods to reduce the cost of achieving the goals of major, multi-site projects, such as The Cancer Genome Atlas, which aims to accelerate understanding of the molecular basis of cancer with genome analysis technologies.”
The Latest on: Machine learning
via Google News
The Latest on: Machine learning
- AI for Executives: How Machine Learning Is Impacting the Next Generation Workforceon September 6, 2019 at 1:30 pm
The term “artificial” doesn’t really do the next generation, with the attitude of “how we will get things done,” justice. Artificial refers to a machine doing the work rather than a human, and the ...
- Snapshot of the Emerging ICT Led Innovations in Artificial Intelligence, Machine Learning, Analytics, and Computer Visionon September 6, 2019 at 8:29 am
DUBLIN, Sept. 6, 2019 /PRNewswire/ -- The "Recent Innovations in Information Technology, Computing, and Communications" report has been added to ResearchAndMarkets.com's offering. This provides a ...
- HubSpot Leverages Machine Learning to Remove Duplicate Content, Expands Its Sales Hubon September 6, 2019 at 3:52 am
To share a press release or news update, please email our Features Editor, Ameya at: [email protected] "We get hundreds of suggestions from our customers every year for new features and ...
- Machine learning may augment diagnostics of kidney diseaseon September 6, 2019 at 12:42 am
Two new studies reveal that modern machine learning--a branch of artificial intelligence in which systems learn from data, identify patterns, and make decisions--may augment traditional diagnostics of ...
- This AI & Machine Learning Mastery Bundle is 99% off at only $19on September 5, 2019 at 8:46 am
From Tesla's self-driving cars to Apple's Siri, AI is powering the future of tech, and it's in your best interest to keep pace if you want to stay relevant in your field. Covering the building blocks ...
- Global Machine Learning as a Service Market Market by Emerging Trends, Share, Growth Rate, Opportunities And Market Forecast To 2023on September 5, 2019 at 3:00 am
Sep 05, 2019 (AmericaNewsHour) -- Machine learning has become a disruptive trend in the technology industry with computers learning to accomplish tasks without being explicitly programmed. The ...
- Reduction of false alarms in the intensive care unit using an optimized machine learning based approachon September 5, 2019 at 2:03 am
This work attempts to reduce the number of false alarms generated by bedside monitors in the intensive care unit (ICU), as a majority of current alarms are false. In this study, we applied methods ...
- How YACHT Used Machine Learning to Create Their New Albumon September 5, 2019 at 2:00 am
This story originally appeared on Ars Technica, a trusted source for technology news, tech policy analysis, reviews, and more. Ars is owned by WIRED's parent company, Condé Nast. “I know this isn’t ...
- Machine Learning and AI are Transforming Employee Workloads for all the Right Reasonson September 4, 2019 at 3:44 pm
Advancements in technologies such as machine learning and artificial intelligence are growing in the workplace – to the benefit of employees who are able to work more efficiently and intelligently ...
- New Study Shows EarlySign's Machine Learning Algorithm Can Predict Which Cardiac Patients are at High-Risk Following Dischargeon September 4, 2019 at 6:37 am
Peer-Reviewed Study Suggests AI Solution can be More Effective than Traditional Models to Identify Patients at Risk of Death or Readmission for Congestive Heart Failure TEL AVIV, Israel and ...
via Bing News