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Drug response prediction by inferring pathway-response associations with Kernelized Bayesian Matrix Factorization

arXiv.org Machine Learning

A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially valuable in oncology, where molecular and genetic heterogeneity of the cells has a major impact on the response. However, the prediction task is extremely challenging, raising the need for methods that can effectively model and predict drug responses. In this study, we propose a novel formulation of multi-task matrix factorization that allows selective data integration for predicting drug responses. To solve the modeling task, we extend the state-of-the-art kernelized Bayesian matrix factorization (KBMF) method with component-wise multiple kernel learning. In addition, our approach exploits the known pathway information in a novel and biologically meaningful fashion to learn the drug response associations. Our method quantitatively outperforms the state of the art on predicting drug responses in two publicly available cancer data sets as well as on a synthetic data set. In addition, we validated our model predictions with lab experiments using an in-house cancer cell line panel. We finally show the practical applicability of the proposed method by utilizing prior knowledge to infer pathway-drug response associations, opening up the opportunity for elucidating drug action mechanisms. We demonstrate that pathway-response associations can be learned by the proposed model for the well known EGFR and MEK inhibitors.


First Surgical Robot from Secretive Startup Auris Cleared for Use

IEEE Spectrum Robotics

The U.S. Food and Drug Administration (FDA) has just approved the first medical robot from Auris Surgical, a stealthy startup led by the co-founder of industry leader Intuitive Surgical, makers of the widely-used da Vinci robot. The teleoperated ARES robot (the acronym stands for Auris Robotic Endoscopy System), was cleared by the FDA at the end of May, and could now be used for diagnosing and treating patients. Auris, which describes itself only as a "technology company based in Silicon Valley," was previously thought to be working on a robotic microsurgical system designed to remove cataracts, and the company has in fact filed several patent applications along those lines. However, an investigation by IEEE Spectrum suggests that the company has greater ambitions, including, according to current and former employees, "building the next generation of surgical robots… capable of expanding the applicability of robotics to a broad spectrum of medical procedures." A close reading of recent patent applications filed by Auris scientists shows that the company is focusing on so-called endolumenal (or endoluminal) surgery.


Machine Learning & AI Is Revamping The Health-Care Start-Up World

#artificialintelligence

Just after teaming up with one of my new partner for an upcoming healthcare Start-up, being thrilled once more, start writing my today's post. Since this healthcare start-up project will be using Machine learning and Artificial Intelligence. So I thought, it will be valuable to share my thoughts through this content with you all especially who are going to start healthcare start-ups and also for those who are planned to use AI and Machine learning to their healthcare projects. As I previously mentioned one of my preferred area is to work with healthcare projects and start-ups in my previous writing "Artificial Intelligence Is Using Dynamic Phases of Healthcare Start-Ups". So I always feel snug to discourse this area.


Groups, Hospitals Enlist AI for Radiology

#artificialintelligence

Radiologists may not think about video game components helping them do their work. But graphic processing units (GPU), the computing power behind video games, have been in radiology equipment for years. "You'd be hard pressed to find diagnostic instruments like CT, MRI, and ultrasound, that don't have GPU embedded in them for real time reconstruction," said Kimberly Powell, senior director of industry business development at the technology company NVIDIA. Now GPU processing technology is being applied to deep learning, also known as machine learning and artificial intelligence. Computer algorithms able to detect an intracranial hemorrhage?


Soon You'll Swallow Origami Pills and Get Magnetic Colonoscopies

WIRED

This might be a tough pill to swallow, but the future of medicine is all about ingestible sensors. Things like cameras to scope out your bowels and electronics that detect if you've taken your medicine (recently FDA-approved, by the way). Researchers at MIT have developed a frozen gizmo made of pig intestine that you drop down the hatch. As it thaws in your stomach, it unfolds. Using a magnetic field, a doctor could theoretically lead the device to something you've gone and swallowed but really shouldn't have--batteries aren't as tasty as they look--and hurry the offending object out of your system.


What is Machine Learning?

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"Given an example of presence and absence of a specific concept, computers would use storage to memorize examples exactly as they appear from a shallow learning concept – classic memorization," Dreyer said. Humans adjust neural weighting to solve for current and future examples, so we don't have to see a future example to know what something is. If you show a computer a picture of a bunch of oranges and then show it an apple, the computer wouldn't know what the apple was because it hadn't seen it before. Humans exploit deep learning by classifying new objects, recognizing faces, and recognizing language, Dreyer said. We see examples every day of facial recognition technology (for example, used by Facebook and Twitter).


Critical Care

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Identification of patients with overt cardiorespiratory insufficiency or at high risk of impending cardiorespiratory insufficiency is often difficult outside the venue of directly observed patients in highly staffed areas of the hospital, such as the operating room, intensive care unit (ICU) or emergency department. And even in these care locations, identification of cardiorespiratory insufficiency early or predicting its development beforehand is often challenging. The clinical literature has historically prized early recognition of cardiorespiratory insufficiency and its prompt correction as being valuable at minimizing patient morbidity and mortality while simultaneously reducing healthcare costs. Recent data support the statement that integrated monitoring systems that create derived fused parameters of stability or instability using machine learning algorithms, accurately identify cardiorespiratory insufficiency and can predict their occurrence. In this overview, we describe integrated monitoring systems based on established machine learning analysis using various established tools, including artificial neural networks, k?nearest neighbor, support vector machine, random forest classifier and others on routinely acquired non?invasive and invasive hemodynamic measures to identify cardiorespiratory insufficiency and display them in real?time with a high degree of precision.


UPMC CIO on docs and robots: It's not man vs. machine, it's man vs. man and machine - MedCity News

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The experimental Smart Tissue Autonomous Robot (STAR) recently sewed a piglet's gut together using a computer program and camera-based guidance, overseen by a team of doctors and computer scientists from the Children's National Health System in Washington DC and Johns Hopkins University. The procedure took 50 minutes, as opposed to 8 minutes when performed by a surgeon, but (unfortunately for doctors) resulted in more evenly spaced sutures and less leakage from the gut. And with iterative improvements, it's likely that the time difference can be shrunk. Meanwhile, FDA-approved robotic surgery on humans is making strides as well, though it requires a surgeon to operate the mechanical arm. The potential treatment paradigm, highlighted by The Economist this month, raises questions about whether patients will trust robots with their lives, and who is liable if something goes wrong. Another question robots pose: Are doctors in line for a string of layoffs?


Qardio's smart medical devices will now share data with your doctor

PCWorld

The future of health care is wearable devices that transmit our vitals to our physicians. Instead of self-reported data, which is often inaccurate (no offense, but your memory just kind of sucks), doctors will have real numbers to form the basis for diagnoses and treatment plans. In the wake of Apple's CareKit launch, connected medical device maker Qardio is launching a platform to share health data from its hardware with your doctor. QardioArm is a medical-grade smart blood pressure monitor that can send data to your doctor. The company has two FDA-approved products for consumers: the smart blood pressure monitor QardioArm and wireless scale QardioBase.


Behold.ai launches artificially intelligent medical software to find abnormalities faster

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Jeet Raut's mom was told she no longer had breast cancer. But it turned out to be a false diagnosis and she had to undergo further treatment. She's okay now, but that medical mistake could have cost her life and it gave Raut the idea to build a better way to catch medical abnormalities in the body. He and his co-founder Peter Wakahiu Njenga created Behold.ai to speed up the process of finding cancers and minimize human error. "The idea behind Behold.ai is to increase efficiency," Raut told TechCrunch.