About Abalone Bio

Abalone Bio is an innovative drug discovery company specializing in antibody drugs that activate challenging drug targets to treat disease affecting millions of patients. Their proprietary Functional Antibody Selection Technology (FAST) platform interrogates large antibody libraries with engineered yeast cells and generates vast amounts of data on the functional activity of hundreds of millions of antibodies, going beyond the binding and inhibition focus of traditional antibody discovery methods. These large-scale activity datasets uniquely power protein large language models to unlock new therapies for untreated patients.

Abalone Bio's FAST platform was generating gigabytes of data with millions of data points, far more than traditional drug discovery methods. However, they were only able to analyze a fraction of this data, focusing on the strongest signals and potentially missing valuable insights hidden in the rest of the dataset.

 "We were generating an unprecedented amount of data, but we were only scratching the surface of its potential. We needed a way to unlock the hidden value in our datasets."

Recognizing the potential of machine learning to unlock hidden value in their data, Abalone Bio turned to Coiled. They needed a flexible, scalable solution that could:

1. Handle large datasets (10-20 million sequences)
2. Support the entire machine learning lifecycle, from exploration to production
3. Offer cloud provider flexibility to avoid vendor lock-in
4. Provide robust support for data science tools like Dask
5. Accelerating and extending the capabilities of a small computational biology team

Why Coiled?

Abalone Bio chose Coiled for several key reasons:

1. Flexibility: Coiled's cloud-agnostic approach and ability to integrate with a variety of modern machine learning tools allowed Abalone Bio to iterate quickly and maintain flexibility in their infrastructure choices.
2. Scalability: Coiled easily scaled to handle Abalone Bio's growing datasets, from 1 million to 20 million sequences, making it easy to accelerate model training across NVIDIA GPUs on the cloud.
3. Full Lifecycle Support: Coiled offered a number of developer-friendly tools for every stage of development, from prototyping  in a notebook to production-ready deployments.
4. Dask Integration: Coiled's strong support for Dask and ability to integrate with the broader Python ecosystem aligned well with Abalone Bio's data processing needs.
5. Responsive Support: The Coiled team provided timely, personalized support, crucial for Abalone Bio's small data science team.

“Coiled support is like traveling first class.” 

Results + Impact

Coiled made it easy for Abalone Bio to train their protein LLMs at scale on GPU-accelerated hardware to identify drug target-activating antibodies. This integration of machine learning, powered by Coiled, has had a significant impact on Abalone Bio's operations and value proposition:

1. Increased Hit Rate: The ML model found 30 promising antibody candidates where traditional methods only identified one.
2. Expanded Platform Capabilities: Machine learning is now a core part of Abalone Bio's FAST platform, enhancing their value proposition to partners and investors.
3. Accelerated Discovery: The automated ML pipeline, running on Coiled's infrastructure, has become a push-button solution for analyzing new antibody selections.
4. Novel Antibody Generation: Coiled enables Abalone Bio to use generative models to design entirely new antibodies, expanding their discovery potential beyond naturally occurring antibodies.

 "Coiled has transformed our approach to drug discovery. Machine learning is no longer an add-on to our platform—it's become an integral part of our value proposition."

Looking Ahead

With Coiled as a crucial part of their ML operations, Abalone Bio is well-positioned to continue pushing the boundaries of antibody discovery. They're currently working on discovering and developing drugs for therapeutic areas ranging from metabolic disease, cancer, and inflammation. Using the Coiled platform, Abalone Bio has developed anti-inflammatory candidates that treat neuropathic pain and fibrosis in animal models and in human tissue samples, and uncovered activator antibodies for its pharma partners.

The scalability and flexibility offered by Coiled will allow Abalone Bio to continue expanding their computational capabilities as they tackle ever more complex challenges in drug discovery.

"As we look to the future, we're excited about the possibilities that Coiled opens up for us. Their platform gives us the confidence to tackle increasingly complex computational challenges, knowing we have the scalability and support to back up our ambitions."