AWS Partner Network (APN) Blog
AWS AI Backend Developed by Avahi Enables WittGen Biotechnology to Help Fight Cancer
By Nirav Shah, Principal Solutions Architect – AWS
By Jack Singh, CEO – Avahi Technologies
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| Avahi Technologies |
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Enabling companies to leverage technology to take on life’s biggest challenges is one of the more rewarding aspects of working in the IT sector. Avahi Technologies and Amazon Web Services (AWS) experienced this during an engagement with WittGen Biotechnologies, which is based in Berkeley and founded in 2022.
Avahi is an AWS Specialization Partner and AWS Marketplace Seller that helps customers drive change and compete at speed by leveraging a cloud-first strategy. Specializing in startups, Avahi offers a team of certified cloud, data, and software engineering experts who excel at architecting and operating secure and automated solutions built on AWS.
In this post, we present how Avahi and AWS teamed up to enable the WittGen artificial intelligence (AI) platform to help the healthcare industry fight cancer. The company had previously developed an algorithm that profiles and categorizes tumor cell phenotypes by integrating multimodal single-cell data. This helps researchers and clinicians deal with high heterogeneity, which strictly limits cancer research.
The AI frontend interface developed by WittGen also provides a method for cancer researchers to disentangle the inter-tumor and intra-tumor heterogeneity of transcriptome profiles. The platform analyzes tumor DNA samples and produces genomic data, which helps with cancer research and enables clinicians to manage cases more effectively so they can improve patient outcomes and drug responsiveness.
Frontend Interface Requires Scalable Backend
WittGen develops high-resolution, single-cell profiling software to help researchers and clinicians treat cancer patients. Analyzing solid tumor RNA sequencing data (focusing on heterogeneity analysis), the company’s machine learning (ML) algorithm curates sequenced patient single-cell datasets.
The platform technology then predicts, characterizes, and categorizes tumor cell phenotypes and the genetic molecular subtypes of cancer—thus disentangling the intra-tumor heterogeneity of transcriptome profiles.
After designing an on-premises platform, WittGen needed specialized expertise and more resources to move the solution to the cloud so it could scale and go to market as quickly as possible.
WittGen Co-Founders Yun Rhie, Minwoo Jung, and Minjun Kim wanted to develop an AI backend in the cloud to set up the platform as a software-as-a-service (SaaS) offering. They also wanted to leverage the cloud for the necessary computing power and to be able to scale services to handle the projected growth in user demand as the platform went live.
Key challenges of the project included:
- Investors wanting new service to go to market quickly.
- Internal technical resources already stretched beyond capacity.
- ML algorithm required backend coding.
- Platform required expanded compute capacity and scalability.
“The customers of our platform—researchers, oncologists and pathologists—are not familiar with coding to run analyses, so we needed to set up a machine learning engine in the cloud for them to use,” explains Jung. “As a small startup, we did not have backend developers on staff, so we did not have the resource bandwidth to get it done on time to satisfy our investors who were looking for us to go to market quickly. Building a cloud infrastructure was also something we were not familiar with.”
Avahi Solves Cloud Migration Challenges
WittGen had already established a cloud environment with AWS and knew AWS could deliver the required application performance and security. As WittGen qualified for an AWS funding program covering the cost of developing the cloud environment, the next step was to find a partner with the necessary infrastructure and AI backend expertise.
After meeting Avahi as a potential partner, it didn’t take long for WittGen to realize the Avahi team could do the job. “Once we described our platform concept, they instantly understood what researchers and clinicians would need to use our service,” says Rhie. “Comprehending a complex technology offering so quickly does not always happen when working with third-party developers—but the Avahi team was in sync with our vision right away.”
Soon after the two companies met, Avahi produced a backend schema and AWS architecture to support the platform to confirm the designs were on target with what WittGen wanted.
“It took them just a few days and matched our requirements exactly,” adds Jung. “We could see that partnering with Avahi would be just like collaborating with our own internal team—and that gave us confidence early in the relationship.”
Solution Architecture Provides Proofpoint for the Healthcare Industry
The image below shows the AWS infrastructure Avahi designed and built to support the WittGen platform. It includes a portal researchers can log into to save DNA and genomic data pertaining to cancer patients on Amazon Simple Storage Service (Amazon S3).
Figure 1 – Architecture diagram for WittGen BioTechnologies.
Each time a request comes in, a WittGen data officer pre-processes the data on an Amazon Elastic Compute Cloud (Amazon EC2) server to perform quality control and format the data for machine learning analysis. The AWS Batch service then uses the containerized ML model to run computing jobs in Amazon DynamoDB and saves the analysis output to Amazon S3.
Clinicians can then log into the portal to view and download the results as they consider treatments for their cancer patients.
The platform relies on Amazon CloudWatch to monitor the performance of all compute resources and AWS services. Avahi also applied security controls, such as Amazon Cognito and AWS Identity and Access Management (IAM) to ensure access to the platform is limited to authorized users.
The value Avahi delivered by designing and deploying the AI platform is demonstrated on the WittGen website. The company displays the schema image to prove the strength of the platform to the healthcare industry.
New Platform Accelerates Time to Market
During the project, WittGen was impressed by Avahi’s approach to working with a startup company. “As is the case with most technology startups, our platform plans changed quickly as we were working with Avahi,” says Yung. “Avahi realizes this often happens with startups, and they overcome this obstacle by communicating frequently. When we needed a new schema to sync with our changes, they jumped right in and made it happen.”
In addition to the platform change, Avahi helped WittGen realize it needed to migrate the pre-processing function from on-premises machines to the AWS cloud—where it’s easier to access more RAM and scale other compute resources to format the data for analysis. The extra memory is needed because there’s no special code for the pre-processing since the datasets submitted by researchers differ significantly, and the file sizes are often 50GB or more.
“Setting up the pre-processing function in the cloud was not easy, but Avahi managed to do it,” says Jung. “This is also an example of how they proactively recommend ways for us to improve our platform. Their approach differs from many partners who just sit back and only do what you ask them to do.”
Key results of the project included:
- Provides expertise and resource bandwidth to design and implement AWS environment.
- Accelerates timeline for bringing new service to market.
- Enhances the reliability and performance of the AI platform.
- Establishes necessary security controls for compliance with healthcare regulations.
By partnering with Avahi, WittGen accelerated how quickly the AI platform for cancer research will go to market—expected sometime in 2023. “Providing a service sooner—that the healthcare industry can use to treat people with cancer—is the biggest win,” says Jung. “From an operating standpoint, it also gives us a stronger position to secure more funding.”
Adds Rhie, “The security controls Avahi applied are also critical—helping us demonstrate our platform complies with HIPAA regulations. This is a must, given the sensitive patient information we process. We appreciate Avahi’s expertise in ensuring AWS environments are secure and compliant to go along with their ability to design the infrastructure and code the machine learning backend.”
WittGen also realized the way Avahi designed the infrastructure and AI backend allows its application to run more reliably and faster for the researchers and clinicians using the system. Because Avahi created an infrastructure-as-code (IaC) environment, each time WittGen needs to add a new feature or apply a fix to the code, the change can be made quickly—with minimal or no downtime for the platform.
A Partner Equally Driven Towards Success
At the conclusion of the project, Avahi provided WittGen with the implementation code and explained how to maintain the infrastructure and make changes to the AI backend when necessary. “This is not something partners always offer,” says Avahi Co-Founder Yun Rhie. “They sometimes hold onto the code, hoping you will need to keep coming back for more services. Avahi has given us the option to handle things on our own.”
Looking ahead, WittGen won’t hesitate to reach out to Avahi again if extensive development is needed on the platform or to tune the AWS environment as the customer base grows and user demand spikes.
“Avahi is the ideal partner in that we don’t look at them as a partner,” says Avahi Co-Founder Minwoo Jung. “They are an integral part of our team and want to us succeed as much as we do.”
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Avahi Technologies – AWS Partner Spotlight
Avahi Technologies is an AWS Specialization Partner that offers a team of certified cloud, data, and software engineering experts who excel at architecting and operating secure and automated solutions built on AWS.