Bringing Bio Foundation Models to the Fingertips of Scientists

June 4, 2024.

Luxinnovation, the University of Luxembourg and LuxProvide are jointly managing the Luxembourg National Competence Centre in High-Performance Computing (HPC). Its mission is to promote the use of HPC linked to computing, data analytics and artificial intelligence and to support stakeholders such as industry – including SMEs and startups – academia and public administration to navigate the national and european HPC ecosystem.

Luxembourg has a unique HPC infrastructure that is open to companies as well as to researchers. The Luxembourg National Competence Centre in HPC offers a wide portfolio of services to help you to set up and implement your HPC-enabled projects.

Challenge
Solution
Business Impact
Benefits

Helical builds the first open-source platform for researchers, biologists & developers to explore bio foundation models, and build cutting-edge applications to accelerate drug development. As a Luxembourg-based startup, we are driving innovation in the biotech industry. Specializing in harnessing the power of Generative AI for Genomics and Transcriptomics, Helical empowers biotech firms through intelligent genomics data collection, scientific feedback incorporation, and scalable model fine-tuning. Helical democratizes the use of bio foundation models, enabling organizations to build scalable processes to fine-tune and use the models for specific biological applications and research objectives. We develop proprietary AI algorithms to extract the most of these bio foundation models and bring human feedback into the process to enhance the efficiency of the different drug discovery processes (among others).

Technical/Scientific Challenge

Bio Foundation Models have been trained on thousands of genomes or RNA which enables them to extract important features from biological data. These models will enable a new range of applications, but they are different from traditional AI methods, requiring a dedicated IT infrastructure and optimized frameworks to run. From training, fine-tuning to the usage of the models in different workflows, all of these processes are not readily available for scientists to use within their applications. With the HPC these models can be democratized and put to work.

Solution

Using the HPC enabled Helical to use the necessary computational power to develop and use the bio foundation models for different applications such as biomarker discovery. Working with large AI models has been made easier through the resources of the HPC. Additionally, the high data throughputs allowed Helical to run various optimizations for large datasets to improve the applications that are developed as part of their platform. To test and deploy their models, Helical uses the HPC and its resources to investigate how bio foundation models can be hosted and made easily available for scientists to query them. Making these models available to bioinformaticians will be crucial to enable a new range of bio applications.

Business Impact

Through LuxProvide, Helical was able to start developing its platform on a much larger scale by being able to use a wide range of bio foundation models directly with the distributed network of GPU nodes. Reducing the development time is important for Helical which in turn will accelerate the number of new applications that can be enabled. In a first phase, Helical focused on biomarker discovery with RNA sequencing data. Using the Jupyterlabs interface on the HPC enabled for quick development cycles and the batch jobs will enable Helical to do optimizations on a larger scale in the future. Additionally, Helical is deploying AI methods to further enhance outcomes for the biological applications it is developing. For these methods, larger clusters of nodes will result in more precise and better solutions, giving the algorithms more computational power which they are able to leverage to scale well.

This strategic partnership with LuxProvide signifies a significant step forward in advancing genomics research and innovation. By combining Helical’s cutting-edge capabilities with LuxProvide’s state-of-the-art infrastructure, we aim to revolutionize genomics, unlocking new frontiers in healthcare and biotechnology. Together, Helical and LuxProvide are poised to drive transformative progress in understanding and leveraging the intricate complexities of the biological world.

Benefits

Quicker turnaround times through faster inference
Development of a high-performance oriented platform for bio
Large Scale Optimization which was not possible before enabling better results

Success story # Highlights

Keywords: Genomics, Bio Foundation Models, Platform
Industry sector: Biotechnology, Bioinformatics, Healthcare, Crop Sciences
Technology: HPC, Generative AI, Evolutionary Algorithms

This project has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 951732. The JU receives support from the European Union’s Horizon 2020 research andinnovation programme and Germany, Bulgaria, Austria, Croatia, Cyprus, the Czech Republic, Denmark, Estonia, Finland, Greece, Hungary, Ireland, Italy, Lithuania, Latvia, Poland, Portugal, Romania, Slovenia, Spain, Sweden, the United Kingdom, France, the Netherlands, Belgium, Luxembourg, Slovakia, Norway, Switzerland, Turkey, Republic of North Macedonia, Iceland, Montenegro.