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How AI Is Being Used In The Fight Against The Wuhan Coronavirus

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Artificial intelligence is being leveraged in the fight against the Wuhan Coronavirus. Artificial intelligence as being employed by researchers track the spread of the disease and to research potential treatments for the virus.

The Wuhan Coronavirus manifested in China in December, and in the two months since then it has spread across China and to other parts of the globe. It’s still unknown just how contagious the virus is and how quickly the virus could spread, although there are currently more than 40,000 confirmed cases within China. In order to get a better understanding of how the virus might spread and how fast the virus can spread, researchers are employing machine learning algorithms focused on data pulled from social media sites and other parts of the web.

Over the course of the past week,  the rate of infection seems to have decreased somewhat, but it’s unclear if the disease is falling under control or if new cases are becoming harder to detect.  While other countries around the world have only seen a few cases of coronavirus, in comparison to China, the world health community remains concerned about the virus’s ability to spread. Researchers are trying to get ahead of the viruses’ spread by using machine learning and big data collected from the internet.

As reported by Wired, an international team of researchers have extracted data from various parts of the internet, including posts from doctors and medical groups, public health channels, social media posts, and news reports, compiling a database of text that might relate to the coronavirus.  The researchers then analyze the data for signs that the virus could be spreading outside of China’s borders, making use of machine learning techniques in order to find relevant patterns in the data that could hint at how the virus is behaving.

The researchers sift through social media posts looking for potential symptoms of coronavirus, centering their search on regions where doctors think cases may manifest. The social media posts are processed using natural language processing techniques, techniques which can distinguish between posts where a person mentions their own symptoms versus someone saying symptom-related words in another context (such as discussing news about the coronavirus).

According to Alessandro Vespignani, as Wired reported, Northeastern University professor and expert contagion analyst, argues that even with advanced machine learning techniques it’s often difficult to track the spread of the virus because the characteristics of the virus are still somewhat unknown, and most social media posts are from media companies and currently about the outbreak in China. However, Vesignani believes that if the virus ever did take hold in the US it would become easier to monitor thanks to more posts concerning the virus.

Despite the challenge in gaining relevant information about the potential behavior of the coronavirus, the model created by the researchers does seem to be reasonably effective at finding clues within a large sea of social media posts. The model used by the researchers was able to find evidence of a viral outbreak on December 30th, although it took time to determine just how serious the situation would become. Crowdsourced information could improve the effectiveness of disease tracking models even further, as it enables the more efficient collection of relevant data regarding the virus. As an example, an analysis of data crowdsourced by Chinese physicians suggests that people younger than 15 years of age are more resilient to the virus.

Artificial intelligence can also be combined with data collected from mobile devices to build models that can potentially predict the direction a virus is spreading as well as the rate of a spread. For instance, Researchers from University of Southampton used mobile data to determine the path that the virus may have taken as it moved out of Wuhan in the days following its manifestation. Other researchers analyzed data collected by Tencent, a Chinese mobile app developer, and found that the restrictions imposed by the Chinese government potentially reduce the virus’ spread, buying vital time to develop a plan of attack.

As Fortune reported, the startup Insilico Medicine has made use of artificial intelligence to identify molecules that could potentially treat the coronavirus. Insilico’s AI identified thousands of possible drug molecules over the course of four days. Insilico explained that the 100 most promising candidates will be synthesized and all of their research on molecular structures will be published for other researchers to take advantage of. Medical researchers and companies are fast-tracking the development and testing of treatments, with the US-based biotech company Gilead planning to start the immediate testing of a new antiviral drug within the Wuhan region.

After Insilico decided to begin researching treatments, it focused its research on an enzyme called 3C-like protease. The coronavirus relies on this enzyme to reproduce and spread. According to Insilico, it decided on this specific enzyme because it’s quite similar to other viral proteases whose structures have already been documented, and because Shanghai Tech University had developed a model of the 2019-nCoV 3C-like protease. In the span of four days Insilico was able to generate hundreds of thousands of candidate molecules and choose only the hundred or so that were most likely to be useful. The results of the research were recently published in the repository bioRxiv and on Insilico’s website.

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Blogger and programmer with specialties in Machine Learning and Deep Learning topics. Daniel hopes to help others use the power of AI for social good.

Healthcare

New Advancements in AI for Clinical Use

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Researchers from Radboudumc helped advance artificial intelligence (AI) in the clinical setting after demonstrating how AI can diagnose problems similar to a doctor, while also showing how it reaches the diagnosis. AI already plays a role in this environment, being utilized to quickly detect abnormalities that could be labeled as a disease by experts.

AI in the Clinical Setting

Artificial intelligence has been increasingly used in the diagnosis of medical imaging. What was traditionally done by a doctor studying an X-ray or biopsy to identify abnormalities can now be done with AI. Through the use of deep learning, these systems can diagnose by themselves, oftentimes being just as accurate or even better than human doctors.

The systems are not perfect, however. One of the issues is that the AI does not demonstrate how it is analyzing the images and reaching a diagnosis. Another problem is that they do not do anything extra, meaning they stop once reaching a specific diagnosis. This could lead to the system missing some abnormalities even when there is a correct diagnosis.

In this scenario, the human doctor is better at observing the patient, X-ray, or other images overall.

Advancements in the AI 

These problems for AI in the clinical setting are now being addressed by researchers. Christina González Gonzalo is a Ph.D. candidate at the A-eye Research and Diagnostic Image Analysis Group of Radboudumc. 

González Gonzalo developed a new method for the diagnostic AI by utilizing eye scans that found abnormalities of the retina. The specific abnormalities can be easily found by human doctors and AI, and they often are found in groups. 

In the case of the AI system, it would diagnose one or a few of the abnormalities and stop, demonstrating one of the downsides of using such a system. In order to address this, González Gonzalo developed a process where the AI goes over the picture multiple times. When it does this, it learns to ignore the places that it had already covered, which allows it to discover new ones. On top of that, the AI also highlights suspicious areas, making the whole diagnostic process more transparent for humans to observe. 

This new method is different from the traditional AI systems used in these settings, which base their diagnosis on one assessment of the eye scan. Now, researchers can see how the new AI system reached its diagnosis.

In order to ignore the already detected abnormalities, the AI system digitally fills them with healthy tissue from around the abnormalities. The diagnosis is then made based on all of the assessment rounds being added together. 

The study found that this new system improved the sensitivity of the detection of diabetic retinopathy and age-related macular degeneration by 11.2+/-2.0%. 

This new system could really change how AI is used when diagnosing diseases based on abnormalities, and the biggest advancement is the new transparency that it can demonstrate when undergoing this process. This transparency is what will allow even more future corrections and advancements, with the end-goal being an AI system that could diagnose problems much more accurately and faster than the best human experts within the field. All of this could also lead to a more trustworthy system, possibly resulting in the widespread adoption of it within the larger field.

 

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Naheed Kurji, Co-Founder, President and CEO of Cyclica – Interview Series

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Naheed Kurji is the President and CEO of Cyclica, a Toronto-based biotechnology company that leverages artificial intelligence and computational biophysics to reshape the drug discovery process. Cyclica provides the pharmaceutical industry with an integrated, holistic, and end-to-end enabling platform that enhances how scientists design, screen, and personalize medicines for patients, and has recently been named by Deep Knowledge Analytics as one of the top 20 AI in Pharma companies globally

Cyclica leverages artificial intelligence and computational biophysics to reshape the drug discovery process. Can you discuss in what way AI is used in this process?

Technology has played a critical role in drug discovery dating back to the ’80s. However, the drug discovery and development process  is still very inefficient, time consuming and expensive, costing more than 2 billion dollars over 12 years. The poor efficiency often results in high rates of attrition and failure to meet drug safety and efficacy milestones. Researchers are aware of this and they are actively seeking tools to holistically understand the qualities that define the best drugs in order to develop safer and more effective medicines

Recent advances in cloud computing, AI and biophysics have created an opportunity to gain deep insight from the vast amounts of biochemical, biological, healthcare and patient data that are now available in order to better understand disease. These advances have also enabled medicinal chemists to enhance the design of novel therapies and use AI to drive greater predictive insights earlier in the drug development process. At Cyclica we have developed proprietary deep-learning engines, MatchMaker and POEM to support the drug design process. MatchMaker predicts how chemical compounds and drugs interact with multiple proteins, known as polypharmacology. We found the combination of both a knowledge-based and structure-based approach yielded the greatest predictive accuracy and performance. POEM (Pareto-Optimal Embedded Modeling), is a parameter-free supervised learning approach for building drug property prediction models and addresses several limitations of other ML approaches, resulting in less overfitting and increased interpretability.

At Cyclica, we are using AI to provide scientists with a robust and validated platform to accelerate decision-making and hypothesis generation in order to increase the overall efficiency of the drug discovery process and to reduce the number of downstream failures.

 

Cyclica has designed the Ligand Design and Ligand Express platform, what is this precisely?

We are the first company to approach computational polypharmacology (an appreciation that drugs interact with multiple targets) with an integrated drug discovery platform that interrogates molecular interactions on a proteome-wide scale. Our platform is comprised of two key pieces, Ligand Express, our first generation off-target profiling and target deconvolution platform, and Ligand Design, our next generation single and multi-targeted in silico drug design technology. Ligand Express and Ligand Design are powered by two internally built, validated, and patented machine learning and deep learning engines: MatchMaker and POEM. Rooted deeply in protein biophysics, MatchMaker is a deep learning drug-target interaction engine that generalizes across both data-rich and data-poor targets (see validation notes here and here). POEM, a machine learning technology implemented for Absorption, Distribution, Metabolism, and Excretion (ADME) property prediction, is a novel, parameter-free approach to model building.

All taken together, Ligand Design and Ligand Express offer a powerful end to end AI-augmented drug discovery platform for the design of advanced, chemically novel lead-like molecules that simultaneously prioritizes compounds based on their polypharmacological profile, effectively minimizing undesirable off-target effects. Our differentiated platform opens new opportunities for drug discovery, including multi-targeted and multi-objective drug design, lead optimization, ADMET-property prediction, target deconvolution, and drug repurposing. Driven by a diverse and highly-talented team with deep expertise across machine learning, computational biophysics/chemistry/biology, biochemistry, and medicinal chemistry, we are continuing to innovate through our robust R&D pipeline.

 

How important is decentralizing the discovery of medicine to the Cyclica business model?

Our vision is to decentralize the discovery of better medicines by combining our deep roots in Artificial Intelligence (AI) and protein biophysics with an innovative business model.  And at the very core of Cyclica’s ethos is the steadfast desire to help patients by advancing the discovery and development of better medicines by taking a holistic yet personalized approach.

To this end, we believe that the future of drug discovery is in the hands of innovative research institutions and emerging biotech companies (we wrote about this in Forbes here). Supporting our philosophy, in 2019 IQIVIA reported that emerging biopharma companies account for over 70% of the total R&D pipeline (up from 50% in 2003), and that these companies patented over 2/3 of new drugs in 2018 (up from 50% in 2010). While emerging biotech companies will lead innovation in drug discovery, big pharma will continue to invest in advancing late stage clinical trials and market penetration through their sales channels.

With our Series B funding, we will accelerate commercial plans to advance a growing pipeline of pre-clinical and clinical assets through an innovative decentralized partnership model. Our goal is to create and own hundreds of drug discovery programs across multiple therapeutic areas. These programs are created via spin outs and joint ventures (JVs) with top tier research institutions, facilitated largely through the Cyclica Academic Partnership Program (“CAPP”).

Propelled by a rapidly growing portfolio of more than 30 active and advancing drug discovery programs, we will continue to spark innovation through a combination of venture creation and partnerships with early-stage and emerging biotech companies. Recent partnerships include EntheogeniX Biosciences, NineteenGale Therapeutics, Rosetta Therapeutics, the Rare Diseases Medicine Accelerator, and two stealth JVs encompassing over 50 programs across multiple therapeutic areas. By executing on our decentralized business model, creating new companies through spin-outs and joint ventures and helping them scale, we are in effect creating the biotech pipeline of the future.

 

Many of your technologies are cloud-based, why is this so important?

Access to the cloud allows us to computationally scale the workflows that we are conducting, as well as benefit from regulated security infrastructure. Also, as an early stage company, the ability to get up and running with the cloud without the overhead of investing in our own hardware was critical for the financial viability in our early days. Looking forward, while much of our R&D work is done on the cloud, over the past couple of years we have become less cloud-dependent with the ability to run projects on single machines. We are also aiming to support private cloud installations since that’s something we feel our partners may desire. Technological advancements have made it possible to do on a personal laptop what used to take many machines on the cloud, but by continuing to utilize the cloud we are able to greatly expand the scope of the problems we are solving.

 

Cyclica often takes equity positions in companies that they partner with. Can you discuss the business reasoning behind this?

Smaller biotechnology companies and academic groups are generally overlooked by the market in terms of partnership opportunities. While they may not have the resources, infrastructure or facilities in comparison to mature big pharma counterparts, small biotechs are increasingly entering the spotlight with a combination of deep subject-matter expertise in specific indications and the benefits of a lean organization conducive to rapid innovation.

This led us to think on how we can engage with these smaller companies with an avant-garde strategy. We partner scientists in research organizations who are interested in spinning out a company or early stage biotech companies, and enable them with ourAI-augmented drug discovery platform through in kind contributions. In return, take equity into the companies and/or share in the ownership of the compounds and assets that are created and pursued. By sparking a surge of innovation through a combination of venture creation and partnerships, we can capture greater value and develop long-term relationships with our partners to address a spectrum of unmet medical needs to better the lives of patients.

 

Entheogenix Biosciences is a joint venture between Cyclica and ATAI Life Science. What exactly is Entheogenix Biosciences?

There is a unique opportunity for innovation in the neuropsychiatric landscape to better serve patients suffering from complex mental ailments. Current medicines and therapies that rely on single-targeted drug interventions often fall short, requiring patients to take multiple medications that may present potential safety issues as well as reduce medication adherence. We have partnered with ATAI Life Science to leverage their deep experience in mental health and psychedelics, while empowering them with our AI-augmented drug discovery platform to create not only new medicines, but the right ones to tackle mental ailments. Entheogenix Biosciences is one of the many joint ventures we have formed and is a testament to our belief in changing the paradigm in which mental health disorders are treated by bringing our disease agonistic, robust and scientifically validated computational platform into the hands of subject-matter experts and world-class scientists.

 

Is there anything else that you would like to share about Cyclica?

While we are very excited to share the announcement of our series B round of financing. We are just as eager to share the launch of the Cyclica Academic Partnership Program (CAPP) and new partnerships over the next few months.

Thank you for the interview. I look forward to following the future progress of Cyclica.

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Groundbreaking Research Shows How Sensors Can Be 3D Printed on Contracting Organs

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Major research has come out of the University of Minnesota that could have huge implications in healthcare. Mechanical Engineers and computer scientists have developed a new 3D printing technique that allows electronic sensors to be directly printed on organs that are expanding and contracting. 

The new technique uses motion capture technology like what is used to create movies, and besides having implications within the general field of healthcare, it could be specifically applied to diagnose and monitor the lungs of individuals with COVID-19. 

The research was published in Science Advances, a scientific journal published by the American Association for the Advancement of Science (AAAS). 

3D Printing Technique

The research is based on a 3D printing technique that was discovered two years ago. The technique was first used on a hand that rotated and moved left to right, with electronics directly printed on the skin of the hand. It has now been developed even further to work on organs such as the lungs or heart, which expand and contract, leading to a change in the shape or distortion. 

Michael McAlpine is a University of Minnesota mechanical engineering professor and senior researcher on the study.

“We are pushing the boundaries of 3D printing in new ways we never even imagined years ago,” said McAlpine. “3D printing on a moving object is difficult enough, but it was quite a challenge to find a way to print on a surface that was deforming as it expanded and contracted.”

Development and Future Applications

The researchers first used a balloon-like surface and a specialized 3D printer. They utilized motion capture tracking markers, like the ones used to create special effects in movies, in order to help the 3D printer adapt to the expansion and contraction movements on the surface. 

After using the balloon-like surface, the researchers tested it on an animal lung that was artificially inflated. It proved to be a success, and a soft hydrogel-based sensor was printed directly on the surface. 

According to McAlpine, this technology could be used in the future to print directly on a pumping heart.

“The broader idea behind this research, is that this is a big step forward to the goal of combining 3D printing technology with surgical robots,” said McAlpine. “In the future, 3D printing will not be just about printing but instead be part of a larger autonomous robotic system. This could be important for diseases like COVID-19 where health care providers are at risk when treating patients.

The research team also included lead author Zhijie Zhu, a mechanical engineering Ph.D. candidate at the University of Minnesota, as well as Hyun Soo Park, assistant professor in the University of Minnesota Department of Computer Science and Engineering. 

The work was supported by Medtronic and the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health.

 

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