In the past decade, the Healthcare and Life Sciences industry has enjoyed a boon in technological and scientific advancement. New insights and possibilities are revealed almost daily. At Google Cloud, driving innovation in cloud computing is in our DNA. Our team is dedicated to sharing ways Google Cloud can be used to accelerate scientific discovery. For example, the recent announcement of AlphaFold2 showcases a scientific breakthrough, powered by Google Cloud, that will promote a quantum leap in the field of proteomics. In this blog, we’ll review another omics use case, single-cell analysis, and how Google Cloud’s Dataproc and NVIDIA GPUs can help accelerate that analysis.

The Need for Performance in Scientific Analysis

The ability to understand the causal relationship between genotypes and phenotypes is one of the long-standing challenges in biology and medicine. Understanding and drawing insights from the complexity of biological systems abounds from the actual code of life (DNA) through to expression of genes (RNA) to translation of gene transcripts into proteins that function in different pathways, cells, and tissues within an organism. Even the smallest of changes in our DNA can have large impacts on protein expression, structure, and function, which ultimately drives development and response – at both cellular and organism levels. And, as the omics space becomes increasingly data- and compute-intensive, research requires an adequate informatics infrastructure. An infrastructure that scales with growing data demands, enables a diverse range of resource-intensive computational activities, and is affordable and efficient – reducing data bottlenecks and enabling researchers to maximize insight. 

But where do all these data and compute challenges come from and what makes scientific study so arduous? The layers of biological complexity begin to be made apparent immediately when looking at not just the genes themselves, but their expression. Although all the cells in our body share nearly identical genotypes, our many diverse cell types (e.g. hepatocytes versus melanocytes) express a unique subset of genes necessary for specific functions, making transcriptomics a more powerful method of analysis by allowing researchers to map gene expression to observable traits. Studies have shown that gene expression is heterogeneous, even in similar cell types. Yet, conventional sequencing methods require DNA or RNA extracted from a cell population. The development of single-cell sequencing was pivotal to the omics field. Single-cell RNA sequencing has been critical in allowing scientists to study transcriptomes across large numbers of individual cells. 

Despite its potential, and the increasing availability of single-cell sequencing technology, there are several obstacles: an ever increasing volume of high-dimensionality data, the need to integrate data across different types of measurements (e.g. genetic variants, transcript and protein expression, epigenetics) and across samples or conditions, as well as varying levels of resolution and the granularity needed to map specific cell types or states. These challenges present themselves in a number of ways including background noise, signal dropouts requiring imputation, and limited bioinformatics pipelines that lack statistical flexibility. These and other challenges result in analysis workflows that are very slow, prohibiting the iterative, visual, and interactive analysis required to detect differential gene activity. 

Accelerating Performance

Cloud computing can help not only with data challenges, but with some of the biggest obstacles: scalability, performance, and automation of analysis. To address several of the data and infrastructure challenges facing single-cell analysis, NVIDIA developed end-to-end accelerated single-cell RNA sequencing workflows that can be paired with Google Cloud Dataproc, a fully-managed service for running open source frameworks like Spark, Hadoop, and RAPIDS. The Jupyter notebooks that power these workflows include examples using samples like human lung cells and mouse brains cells and demonstrate acceleration between CPU-based processing compared to GPU-based workflows. 

Google Cloud Dataproc powers the NVIDIA GPU-based approach and demonstrates data processing capabilities and acceleration, which in turn have the potential of delivering considerable performance gains.  When paired with RAPIDS, practitioners can accelerate data science pipelines on NVIDIA GPUs, reducing operations like data loading, processing, and training from hours to seconds. RAPIDS abstracts the complexities of accelerated data science by building upon popular Python and Java libraries effortlessly. When applying RAPIDS and NVIDIA accelerated compute to single-cell genomics use cases, practitioners can churn through analysis of a million cells in only a few minutes.

Give it a Try

The journey to realizing the full potential of omics is long; but through collaboration with industry experts, customers, and partners like NVIDIA, Google Cloud is here to help shine a light on the road ahead. To learn more about the notebook provided for single-cell genomic analysis, please take a look at NVIDIA’s walkthrough. To give this pattern a try on Dataproc, please visit our technical reference guide.

The game of baseball has no shortage of statistics — from batting average to exit velocity, strikeouts to wins above replacement. Among all sports, Major League Baseball (MLB) arguably contains the most analytical and data-driven participants and fan base. Subconsciously or viscerally, players and managers on the field and those following from anywhere are constantly assessing and making decisions based off of game play trends and expectations — whether a batter will come through with a hit in an important situation, when a pitcher should be pulled. Less analyzed, however, is what leads fans to become engaged with certain players or teams, and what factors drive their love of the game. This is the motivation behind the problem being posed by Major League Baseball in their Kaggle competition for Player Digital Engagement Forecasting. Can you use machine learning to deconstruct baseball fandom?

This competition asks you to predict measures of digital engagement for each active player on a daily basis during the MLB season. So, how large was the surge in fan interest after Joe Musgrove threw the first no-hitter in Padres history? Is Shohei Ohtani’s engagement higher when he pitches well, when he hits a monster home run…or when he does both? You’re provided a wealth of game, team and player information – detailed stats, awards, rosters, and transaction information – as well as social and digital engagement data as your inputs. Data scientists will recognize this as an exciting forecasting problem with both traditional regression and time series components, where having this input data just prior to the prediction date is critical to determining which players will receive the most engagement. 

With so many variables in the game, there are an endless number of vectors which could possibly influence fan engagement. Eleven-time All-Star Miguel Cabrera delighted fans by hitting the first home run of the season – in the snow! Occasionally a lesser-known player like Musgrove or Carlos Rodón “wins the day” with an unlikely no-hitter. And sometimes just getting traded to an iconic franchise like the Yankees generates a ton of fan interest, like it did for Rougned Odor in early April.

As these examples show, a player’s digital engagement can be pretty dynamic during the season, with many different potential contributors to who is “trending” on a given day. How can you use data to uncover which factors are the most influential of engagement with each player’s digital content?

Ready to play ball? Check out the competition on Kaggle for all the details. $50,000 in prizes is up for grabs in two prize categories. The code competition puts your machine learning skills to the test, to see who can build the most accurate forecasting models to predict daily digital engagement for every active player. You’ll have until July 31st to build your models and then be evaluated on a future time frame, which will determine the winners. For data visualization and exploration experts out there, the explainability prizes give you an opportunity to analyze more broadly which factors, even those outside of what we’re providing directly, most influence digital engagement. You’ll be evaluated on how well you can use what the data is telling you to support your findings.

And if you’re looking to get started, we’ve provided an introductory video and some notebook tutorials, including a starting point for harnessing the power of Vertex AI through tools including Cloud Notebooks, Explainable AI, and Vizier. 

With the second half of the season upon us, it’s an exciting time to be an MLB fan. With this Kaggle competition, it’s also a perfect opportunity to use data science to help understand baseball fandom and potentially earn some of your own accolades in the process. Step up to the plate!

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