Hack For Kids With NF
By: Seyma Tas
Tags: NLP, Image Classification, Healthcare Ai, Data Science, Software Development

Hack For Kids With NF

The Children’s tumor foundation called for healthcare startups, developers, and hackathon enthusiasts to develop solutions for neurofibromatosis on Aug 7, 2020. Hack for NF took place October 2 — November 13, 2020.

I learned about the event from my career coach at Flatiron School. We made a team of 2 data scientists, Eunjoo Byeon and Seyma Tas, 2 software developers, Enrique Pittaluga and Gabriel Joseph and 1 designer Joelle Hagen. When we met for the first time as a team, we had only 14 days until the deadline. We had to be well organized because we didn’t have time to make a single mistake. We started to collect as much domain knowledge as we could about NF.

Here is a very brief summary of what we learned:

What is NF?

Neurofibromatosis(NF) is a set of genetic disorders that develop tumors anywhere in the nervous system (brain and spinal cord) throughout the body.

There are three types of NF: NF1, NF2, and Schwannomatosis.

Neurofibromatosis(NF) is a rare disease that a lot of people have. Yes, this is an irony! NF1 is seen in one of every 3000 births. That means there are more than 100,000 NF1 patients in the US. This is a huge number for a rare disease!

NF2 and Schwannomatosis are less common than NF1, they are seen about one in every 40,000 births. They can cause severe pain and many other symptoms in adults.

What causes NF?

Almost half of the NF patients inherit the disorder from an affected parent, while the other half has no family history, meaning that new cases appear through changes in the genes.

What are the NF symptoms?

There are a lot of NF symptoms. Some of them are headaches, hearing and vision loss, chronic severe pain, balance difficulties, bone deformities, skin lesions, heart and blood vessel problems, and learning disabilities.

Because there is an abundance of symptoms, patients will need an app to track them. This was our team’s starting point.

Kids with NF1

My team decided to focus on kids because NF1 has more diverse symptoms than NF2 and Schwannomatosis and is seen in children. It can be hard to explain a kid diagnosed with a rare genetic disease that has no certain treatment.

If a patient can keep track of all of her symptoms for many years, she can have a very valuable record of how the illness is evaluating. The doctors or researchers can use these records to make a provision for hearing or vision loss, bone deformities, etc. In addition, this data can be used for NF research.

However, the disease has tons of symptoms that are needed to be tracked and stored. We decided to turn this problem into a positive experience. We created AVI!

Meet AVI

Image by Joelle Hagen, AVI

AVI is a virtual pet that grows if the child logs entries regularly. If the log is neglected AVI becomes sad and decreases in size.

NLP

By using natural language processing(NLP) we are able to get the necessary data to observe the symptoms. The pet asks a simple question: How are you feeling today? The kid answers either by writing or by speaking.

Image by Joelle Hagen, NLP Model

Image Recognition

NF1 symptoms can appear on the skin in many different ways. It is difficult for parents to keep track of all of the skin lesions for many years because there are a lot of them and they appear at different ages. Our image classification algorithm makes this job easier. A parent takes a picture of a skin lesion, the deep learning algorithm classifies the lesion as a cafe au lait spot(flat, light brown spots on the skin), a freckling, or a neurofibroma(soft, pea-sized bumps on or under the skin) and keeps records of numbers, locations, and appearance dates of all the lesions.

One more function of image recognition in the project is something that parents can not do. The algorithm keeps the sizes of the cafe au lait spots and reports the change in the area of the spot.

With the help of the AVI app, parents and doctors have a chance to observe and record even a tiny change on a patient’s skin.

In the long term, the app provides an archive for families to store all information including symptoms, MRI imaging, images of skin marks, bumps, cafe au lait spots, and more details about their kid’s illness.

Other Projects

There were 23 excellent projects at the hackathon. I admire the effort and sacrifice all the hackathon participants put into the projects. NF Care, MaLIGNANT, NFMatrix, Pocket Audiologist, Pharmacom, NF Terminator, NF personalized Health, CentralPoint, MyNF… The projects’ three-minute presentations can be watched from the link below.

Results

Our project AVI won the first prize, the incubation prize, and a grant to continue the project.

NF-Matrix won the second prize, the incubation prize, and a grant to continue the project.

Self-updating Causal Models to Accelerate Discovery in NF won the third prize.

Veometrics, Gene network, AVI, and Cutaneous Neurofibromas Drug Discovery also won incubation prizes.

About the organization

At this hackathon, we had infinite support from the Children’s Tumor Foundation. We felt ourselves in a community even if all the hackathon was virtual. We were able to reach out to organizers and ask questions through Hack For NF Slack workspace and got very fast and clear answers.

We had 56 mentors including data scientists, software developers, patients, parents, researchers, and doctors. They were all willing to help us. They shared their valuable domain knowledge, experiences, and expertise with our team modestly.

Children’s Tumor Foundation organized webinars every week to make the participants engage the community and share the recent research about NF illness.

Thanks

I should especially thank:

Dan Webster for sharing his computer vision studies and his insights about the focus of the project,

Bill Riter for helping us to understand the patient side of the disease,

Frank Buono, for helping us to form the latest version of the features we include in the app,

Barbara Gallagher and Salvatore La Rosa, and Lucas for the organization and their help at every level of the project.

Useful links

A Brief Information About NF

Children’s Tumor Foundation:

News about the 2020 NF hackathon:

Conclusion

It is obvious that we can’t solve complicated problems like NF on our own. However, if we join the tiny pieces efforts together with the help of patients, parents, guardians, researchers, and all the NF community, we can help kids and adults increase their quality of life and the researchers to obtain the data for the solution of NF disease.

From my point of view, it is very satisfying to build an app to make an impact on the lives of kids with a very complicated and rare disease. My team could never make a project without the help of the Children’s Tumor Foundation. Hopefully, other research communities for rare diseases will be inspired by CTF’s Hack for NF!