2 posts tagged “Analysis”

Update and results – the Patient Voice Analysis study

Posted April 27th, 2015 by

About a year ago, the PatientsLikeMe Parkinson’s disease (PD) community started something totally different: a study to compare the sound of their voices to their self-reported PD Rating Scale (PDRS) on PatientsLikeMe. It’s called the Patient Voice Analysis (PVA), and we teamed up with you, Max Little, Ph.D. and Sage Bionetworks to get it done.

A little bit of background
Dr. Little had done some earlier work and compared the voice signals of people who were living with PD to those of people who were not, but we wanted to take that to the next level. With their PDRS, they shared how Parkinson’s was affecting them, and we were able to match their self-reported scores to the sound of their voice.

By matching a PDRS to voice samples, we might develop the ability to predict PDRS scores (which takes a few minutes to complete) by using the voice test (which only takes a few seconds). We might also be able to detect more subtle changes in people’s Parkinson’s through their voice than we can through the PDRS. This is what Dr. Little is working toward, and all the voice samples you donated will help make it happen.

Community results, starting with the basics
Who took part, from where, and how many PDRS scores could we match to voice recordings?

  • Most of the recordings came from the U.S. (81%), with others coming from the U.K. (12%), Canada (5%) and some from Australia and New Zealand, too.
  • 677 of you recorded 851 voice samples
    • Since our original goal was 500 samples, you blew that out of the water!
  • 114 of you took the test two or more times, and one community member even contributed 10 recordings!
    • For those that took part more than once, we can start to examine how your symptoms changed over time.

Why voice recording quality matters
For the PVA study, you were able to use your landlines, cell phones, even Skype or Voice-Over-Internet-Protocol (VoIP) to submit your voice samples. The recording quality varies depending on which type of call you used, occasionally creating technical issues in analyzing the voice samples.

For example, if you’re using a cell phone in a busy restaurant, your microphone will automatically get louder so that the person you’re talking to can hear your voice better and without distortion. But that also changes the loudness of the background noise. In this study, that automatic change could actually affect the quality of the voice recording, so we have to identify where this has been an issue and find ways to overcome it.

Partly because of this, we’re still analyzing the voice samples in detail. We’re looking for subtle markers of Parkinson’s, such as fluctuations in volume, pitch and breathiness. We’re also training intelligent algorithms to identify when the quality of the voice recording is strong enough so we can develop a consistent and repeatable process.

You be the researcher
To give you some idea of what we are looking for in these voice recordings, we wanted to share a couple with you. The first is someone living with severe Parkinson’s, who scores 55 on the PDRS. You can probably hear the noticeable tremor in pitch, and the occasional short breaks in voicing.

The second is a recording of someone with mild Parkinson’s, who has a very low PDRS score of 1.

Can you hear the subtle drift in pitch? This is, most likely, indistinguishable from normal pitch drift. Subtle pitch variations such as this are one of the kinds of symptoms that algorithms attempt to identify from these voice recordings, and they contribute towards making the PDRS prediction.

So, what’s next?
At this stage, the PVA project is still just a research tool and isn’t quite ready for clinical or diagnostic use. We’re still working on analyzing the data to compare the severity of voice patterns to the reported severity of Parkinson’s disease. But in the meantime, if you’re looking to share more info with your doctor, the most useful tool is your PDRS score on your PatientsLikeMe profile. It contains items that make sense to a neurologist. If your clinic has access to speech and language pathologists, they would also have the ability to map any vocal issues you may be experiencing as part of your Parkinson’s.

As we continue to evolve the tools, we hope to provide individual level feedback and information for clinicians. But before that can happen, we want to make sure that the data quality is high enough to support drawing clinical conclusions.

Share this post on Twitter and help spread the word for Parkinson’s.


Open funding for open science to accelerate ALS research: An interview with Prize4Life CEO Shay Rishoni

Posted January 6th, 2015 by

Just about a year ago, we teamed up with Sage Bionetworks and TED Fellow Dr. Max Little for an ongoing Parkinson’s disease (PD) project called the Patient Voice Analysis (PVA).

 

The big idea: combine data from two sources – phone-based voice recordings and patient reported data from PatientsLikeMe’s Parkinson’s Disease Rating Scale (PDRS). Then, make the de-identified data sets available to the broader research community on Sage Bionetworks’ cloud-based computational research platform (http://www.synapse.org) to develop new tools to track PD disease progression.

We were overwhelmed by the response from the PatientsLikeMe PD community. More than 650 members provided 851 voice samples, and 779 of those were matched to the PDRS symptom data entered.

 

What’s next for open science?

Sage Bionetworks is working with the distributed DREAM community and ALS non-profit Prize4Life on another open science challenge alongside called the ALS Stratification DREAM Challenge. How does it all fit together?

The “Fund the Prize” campaign is the first of its kind effort to make the path for accelerating drug development completely open – the patient data is open access, the research is open, global and collaborative, and the funding is crowd-based.

The ALS Stratification Challenge, opening in Spring 2015, will be a worldwide cloud-based competition designed to spur the development of quantitative solutions that can identify which ALS patients’ disease will progress rapidly and which will progress more slowly. Prize4Life provides the largest ALS clinical trials database in the world. Sage Bionetworks and DREAM have created a synergistic competition concept and cloud-based computing platform that includes forums, webinars and a “leaderboard” that shows whose model is working best.

The individual or team with the best solution wins the prize – a $37,000 donation that the Challenge is asking everyone to help raise through the INDIEGOGO “Fund The Prize” campaign. The prize will help incentivize innovators from around the world to take part, and 100% of every donation goes towards the prize.

Helping spread the word

Prize4Life CEO Shay Rishoni is a 48 year-old dad of two boys and was an Ironman triathlete before being diagnosed with ALS in August 2011. Within three months he saw his ability to use his arms weaken considerably while no other body parts were affected. Less than two years later he was completely paralyzed and breathing with a ventilator. We caught up with him to help spread the word and learn more about the Challenge, why he thinks the prize is so important and why he works so hard.

Can you tell us a little about your own journey with ALS?

I was diagnosed with ALS 3.5 years ago, when I was 45 years old, a CEO of a company, an Ironman, a pilot, a military colonel (in res.) and a family man with two young sons. Given all of that, receiving a diagnosis of ALS was of course not what I had planned! But I knew that like everything else in life, I will make sure to stay true to myself and my values nonetheless- to stay positive, active and entrepreneurial. That meant in my public life to fight for the development of treatments- and a cure!- for ALS, for current patients like me, but mostly for future patients. In my private life, as a husband, as a friend and as a father to fight to feel and know that Life is Good, and winning is a way of life. Although by now I am fully paralyzed, I believe that as long as I dream up plans and then work to make them happen, I am invincible.

You can see more of me explaining it in this video of my TED talk.

How did you become involved with Prize4Life and the ALS Stratification Dream Challenge?

I first learned about Prize4Life from its founder, Avi Kremer, who is also an ALS patient. Avi was diagnosed with ALS 10 years ago, as a 29 years old Harvard Business school student striving to make finding a cure for ALS a viable business. He was the recipient of the 2011 Israeli Prime minister award for innovation and entrepreneurship in the non-profit sector. I was inspired by his strength, courage and sophistication, and with Prize4Life model and important work and I knew that this is a framework with which I will do important meaningful things for ALS research, and I become the CEO in 2013.

One such important thing is the ALS Stratification Dream challenge. I think it’s a unique and highly innovative initiative. From a patient perspective it addresses a critical question- How can patients with a rare disease create meaningful solutions for their own illness? And the answer is by engaging as many stakeholders as possible. The “Fund the Prize” campaign is the first of its kind effort to make the path for accelerating drug development completely open- the patient data is open access, the research is open, global and collaborative, and the funding is crowd-based. It builds on Prize4Life’s database of ALS patients- the largest ALS clinical trials database in the world. Sage Bionetworks and DREAM, our collaborators, have created a synergistic competition concept and cloud-based computing platform to allow a planetary republic to use the data. Together we will get computational solutions that will tell us why patients are so diverse- from Lou Gehrig’s succumbing to the disease within two years to Stephen Hawking’s 50 years odyssey with ALS. The Challenge, opening in Spring, 2015, will be a worldwide cloud-based competition designed to spur the development of computer algorithms that effectively predict which ALS patients will experience rapid disease progression and which patients will live longer.

Why do you think the prize model is so important?

Prize4Life’s prize model is inspired by similar programs such as X-prize for space travel, demonstrated to foster meaningful research. These programs allow bringing awareness and new minds into a field and generate measurable results for well-defined goals. Prize4Life wants to bring all these benefits to ALS- awareness, new minds and measurable, highly needed, results.

Prize4Life aspires to span broad fields of innovation for their importance for ALS: we gave a $1M prize for a medical device that serves as a biomarker for ALS, another prize for developing algorithms that can predict disease progression and we are running a prize for a druggable cure. We believe that biologists, chemists, engineers, clinicians, software developers and all citizen scientists can bring a meaningful change in ALS.

Prize4Life and DREAM have already demonstrated the power of open Challenges to advance ALS disease research. The first ALS Challenge, conducted in 2012 when Prize4Life’s open ALS patient database contained data from about 1,000 patients, leveraged insights from over 1,000 solvers from 63 countries to identify novel methods that have the potential to reduce the costs of ALS drug development by millions of dollars. The winning approaches are now being used in the development of several ALS treatments, and are described in a recent article in Nature Biotechnology (here is coverage by Science news).

Why do you work so hard?

Because I have a lot to accomplish. (“If not me than who? If not now than when?”) ALS is still an orphan disease, still is relatively unknown, and we still see tremendous potential to realize- computer scientists can create solutions for better treatments and care, engineers can create better assistive technology, biologists can create better drugs… I believe everyone can be part of the victory over ALS.

What’s one thing about ALS that you think everyone should know?

That we, the ALS patients, even when we can no longer speak, still have a voice. That we still have big dreams and still work to make them happen, and if enough people will work together, we will win the fight over ALS.

…and that ALS patients can love and be loved.

How do you see open science evolving in the future?

I think open science will only become more important in fostering innovative research ideas from diverse communities. It will allow everyone to be part of the solutions, and that means many more solutions!

Where can someone make a donation to help fund the prize?

“Fund the Prize- Solving ALS Together” is a crowdfunding campaign (running now on Indiegogo.com) and intended to provide the prize money for the Challenge and thereby to bring together renowned scientists worldwide and drive innovation. The crowdfunding will run until January 22, 2015.

Share this post on Twitter and help spread the word for Fund the Prize and ALS.