Today, to accelerate research in the bio-pharma space, from the creation of treatments for diseases to the production of new synthetic biomaterials, we are announcing a new Vertex AI solution that demonstrates how to use Vertex AI Pipelines to run DeepMind’s AlphaFold protein structure predictions at scale.

Once a protein’s structure is determined and its role within the cell is understood, scientists can develop drugs that can modulate the protein function based on its role in the cell. DeepMind, an AI research organization within Alphabet, created the AlphaFold system to advance this area of research by helping data scientists and other researchers to accurately predict protein geometries at scale.

In 2020, in the Critical Assessment of Techniques for Protein Structure Prediction (CASP14) experiment, DeepMind presented a version of AlphaFold that predicted protein structures so accurately, experts declared the “protein-folding problem” solved. The next year, DeepMind open sourced the AlphaFold 2.0 system. Soon after, Google Cloud released a solution that integrated AlphaFold with Vertex AI Workbench to facilitate interactive experimentation. This made it easier for many data scientists to efficiently work with AlphaFold, and today’s announcement builds on that foundation.

Last week, AlphaFold took another significant step forward when DeepMind, in partnership with the European Bioinformatics Institute (EMBL-EBI), released predicted structures for nearly all cataloged proteins known to science. This release expands the AlphaFold database from nearly 1 million structures to over 200 million structures—and potentially increases our understanding of biology to a profound degree. Between this continued growth in the AlphaFold database and the efficiency of Vertex AI, we look forward to the discoveries researchers around the world will make.

In this article, we’ll explain how you can start experimenting with this solution, and we’ll also survey its benefits, which include offering lower costs through optimized selection of hardware, reproducibility through experiment tracking, lineage and metadata management, and faster run time through parallelization.

Background for running AlphaFold on Vertex AI

Generating a protein structure prediction is a computationally intensive task. It requires significant CPU and ML accelerator resources and can take hours or even days to compute. Running inference workflows at scale can be challenging—these challenges include optimizing inference elapsed time, optimizing hardware resource utilization, and managing experiments.Our new Vertex AI solution is meant to address these challenges.

To better understand how the solution addresses these challenges, let’s review the AlphaFold inference workflow:

1. Feature preprocessing. You use the input protein sequence (in the FASTA format) to search through genetic sequences across organisms and protein template databases using common open source tools. These tools include JackHMMER with MGnify and UniRef90, HHBlits with Uniclust30 and BFD, and HHSearch with PDB70. The outputs of the search (which consist of multiple sequence alignments (MSAs) and structural templates) and the input sequences are processed as inputs to an inference model. You can run the feature preprocessing steps only on a CPU platform. If you’re using full-size databases, the process can take a few hours to complete.
2. Model inference. The AlphaFold structure prediction system includes a set of pretrained models, including models for predicting monomer structures, models for predicting multimer structures, and models that have been fine-tuned for CASP. At inference time, you independently run the five models of a given type (such as monomer models) on the same set of inputs. By default, one prediction is generated per model when folding monomer models, and five predictions are generated per model when folding multimers. This step of the inference workflow is computationally very intensive and requires GPU or TPU acceleration.
3. (Optional) Structure relaxation. In order to resolve any structural violations and clashes that are in the structure returned by the inference models, you can perform a structure relaxation step. In the AlphaFold system, you use the OpenMM molecular mechanics simulation package to perform a restrained energy minimization procedure. Relaxation is also very computationally intensive, and although you can run the step on a CPU-only platform, you can also accelerate the process by using GPUs.

The Vertex AI solution

The AlphaFold batch inference with the Vertex AI solution lets you efficiently run AlphaFold inference at scale by focusing on the following optimizations:

• Optimizing inference workflow by parallelizing independent steps.
• Optimizing hardware utilization (and as a result, costs) by running each step on the optimal hardware platform. As part of this optimization, the solution automatically provisions and deprovisions the compute resources required for a step.
• Describing a robust and flexible experiment tracking approach that simplifies the process of running and analyzing hundreds of concurrent inference workflows.

The following diagram shows the architecture of the solution.

The solution encompasses the following:

A strategy for managing genetic databases. The solution includes high-performance, fully managed file storage. In this solution, Cloud Filestore is used to manage multiple versions of the databases and to provide high throughput and low-latency access.

An orchestrator to parallelize, orchestrate, and efficiently run steps in the workflow. Predictions, relaxations, and some feature engineering can be parallelized. In this solution, Vertex AI Pipelines is used as the orchestrator and runtime execution engine for the workflow steps.

Optimized hardware platform selection for each step. The prediction and relaxation steps run on GPUs, and feature engineering runs on CPUs. The prediction and relaxation steps can use multi-GPU node configurations. This is especially important for the prediction step because the memory usage is approximately quadratic with the number of residues. Therefore, predicting a large protein structure can exceed the memory of a single GPU device.

Metadata and artifact management. The solution includes management for running and analyzing experiments at scale. In this solution, Vertex AI Metadata is used to manage metadata and artifacts.

The basis of the solution is a set of reusable Vertex AI Pipelines components that encapsulate core steps in the AlphaFold inference workflow: feature preprocessing, prediction, and relaxation. In addition to those components, there are auxiliary components that break down the feature engineering step into tools, and helper components that aid in the organization and orchestration of the workflow.

The solution includes two sample pipelines: the universal pipeline and a monomer pipeline. The universal pipeline mirrors the settings and functionality of the inference script in the AlphaFold Github repository. It tracks elapsed time and optimizes compute resources utilization. The monomer pipeline further optimizes the workflow by making feature engineering more efficient. You can customize the pipeline by plugging in your own databases.

Next steps

To learn more and to try out this solution, check our GitHub repository, which contains the components and universal and monomer pipelines. The artifacts in the repository are designed so that you can customize them. In addition, you can integrate this solution into your upstream and downstream workflows for further analysis. To learn more about Vertex AI, visit our product page.

Acknowledgements

We would like to thank the following people for their collaboration: Shweta Maniar, Sampath Koppole, Mikhail Chrestkha, Jasper Wang, Alex Burdenko, Meera Lakhavani, Joan Kallogjeri, Dong Meng (NVIDIA), Mike Thomas (NVIDIA), and Jill Milton (NVIDIA).

Finally and most importantly, we would like to thank our Solution Manager Donna Schut for managing this solution from start to finish. This would not have been possible without Donna.

Data science can be applied to business problems to improve practices and help to strengthen customer satisfaction. In this blog, we address how the addition of Looker extends the value of your Google Cloud investments to help you understand your customer journey, unlock value from first-party data, and optimize existing cloud infrastructure.    

Data is a powerful tool 

While everyone doesn’t need to understand the nuts and bolts of data technologies, most people do care about the value data can create for them — how it can help them do their jobs better. Within the data space, we are seeing a trend of ongoing failure to make data accessible to “humans” –   the industry still hasn’t figured out how to put data into the hands of people when and where they need it, how they need it. 

What if everyone in your organization could analyze data at scale, and make more-informed, fact-based decisions?   Data and insights derived from data are valuable but only if your users see it.  We think Looker helps solve that. 

Solutions tell a larger story of how it all fits together 

Across all verticals and industries,  businesses benefit from knowing and understanding their customers better. Many business goals are to increase revenue by improving product recommendations and pricing optimization, improving the user experience through targeted marketing and personalization, and reducing churn while improving retention rates.  To help reach  these goals, key strategies should focus on understanding customer needs, their motivations, likes and dislikes, and using all available data – in other words, put yourself in the shoes of your customer.    

Our goal with Looker solutions is to offer the right level of out-of-box support that allows customers to get to value quickly, while maintaining the necessary flexibility. We aim to offer a library of data-driven solutions that accelerate data projects. Many solutions include Looker Blocks (pre-built pieces of code that accelerate data exploration environments) and Actions (custom integrations) that get customers up and running quickly and lets you build business-friendly access points for Google Cloud functionality like BQML, App Engine and Cloud Functions.  

Below, you’ll find a sampling of the newest Looker solutions. 

Listening to customers by looking at the data

Looker’s solution for Contact Center AI (CCAI), helps businesses gain a deeper understanding and appreciation of their customers’ full journey by unlocking insights from all their company’s first-party data. Call centers can converse naturally with customers and deliver outstanding experiences by leveraging artificial intelligence. CCAI‘s newest product —CCAI Insights — reviews conversations support agents are having, finding and annotating the data with the important information, and identifying the calls that need review. We’ve partnered with the product teams at CCAI to build Looker’s Block for CCAI Insights, which sets you on the path to integrating the advanced insights into your first-party data in Looker, overlaying business data with the customer experience.

Businesses can better understand contact center experiences and take immediate action when necessary to make sure the most valuable customers receive the best service. 

Realizing full business value of First-Party data

Looker for Google Marketing Platform (GMP) provides marketers the power to unlock the value of their company’s first-party data to more effectively target audiences.  The Looker Blocks and Actions for GMP offer interactive data exploration, slices of data with built-in ML predictions and activation paths back to the GMP.  This strategic solution continues to evolve with the Looker Action for Google Ads (Customer Match), the Looker Action for Google Analytics (Data Import) and the Looker Block for Google Analytics 4 (GA4).

• The Looker Action for Customer Match allows marketers to send segments and audiences based on first-party data directly into Google Ads. Reach users cross-device and across the web’s most powerful channels such as Display, Video, YouTube, and Gmail.  The entire process is performed within a single screen in Looker, and is able to be completed in a few minutes by a non-technical user. 
• The Looker Action for Data Import can be used to enhance user segmentation and remarketing audiences in Google Analytics by taking advantage of user information accessible in Looker, such as in CRM systems or transactional data warehouses.
• The Looker Block for Google Analytics 4 (GA4) expands the solution’s support with out-of-the-box dashboards and pre-baked BigQuery ML models for the newest version of Google Analytics.The Looker Block offers up reports with flexible configuration capabilities to unlock custom insights beyond the standard GA reporting. Customize audience segments, define custom goals to track and share these reports with teams who do not have access to the GA console.

From clinical notes to patient insights at scale

Taking a look at the Healthcare vertical, the Looker Healthcare NLP API Block serves as a critical bridge between existing care systems and applications hosted on Google Cloud providing a managed solution for storing and accessing healthcare data in Google Cloud. The Healthcare NLP API uses natural language models to extract healthcare information from medical text,  rapidly unlocking insights from unstructured medical text and providing medical providers with simplified access to intelligent insights.  Healthcare providers, payers, and pharma companies can quickly understand the context and relationships of medical concepts within the text, such as medications, procedures, conditions, clinical history, and begin to link this to other clinical data sources for downstream AI/ML.   

Specifically, the natural language processing (NLP) Patient View (pictured below) allows you to review a single selected patient of interest, surfacing their clinical notes history over time. It informs clinical diagnosis with family history insights, which is not currently captured in claims, and captures additional procedure coding for revenue cycle purposes.

The dashboard below shows the NLP Term View which allows users to focus on chosen medical terms across the entire patient population in the dataset so they can start to view trends and patterns across groups of patients. 

This data can be used to: 

• Enhance patient matching for clinical trials 
• Identify re-purposed medications
• Drive advancements for research in cancer and rare diseases
• Identify how social determinants of health impact access to care

Managing Costs Across Clouds

Effective cloud cost management is important for reasons beyond cost control — it provides you the ability to reduce waste and predictably forecast both costs and resource needs. Looker’s solution for Cloud Cost Management offers quick access to necessary reporting and clear insights into cloud expenditures and utilization. 

This solution brings together billing data from different cloud providers in a phased approach: get up and running quickly with Blocks optimized for where the data is today (Google Cloud, AWS or Azure) as you work towards more sophisticated analysis for cross-platform planning and even cloud spend optimization with the mapping of tags, labels and cost centers across clouds.

The Looker Cloud Cost Management solution provides operational teams struggling to monitor, understand, and manage the costs and needs associated with their cloud technology with a comprehensive view into what, where and why they are spending money.

Making better decisions with Looker-powered data

Leading companies are discovering ways to get value from all of that data beyond displaying it in a report or a dashboard. They want to enable everyone to make better decisions but that’s only going to happen if everyone can ask questions of the data, and get reliable, correct answers without using outdated or incomplete data and without waiting for it. People and systems need to have data available to them in the way that makes the most sense for them at that moment.  

It’s clear that successful data-driven organizations will lead their respective segments not because they use data to create reports, but because they use it to power data experiences tailored to every part of the business, including employees, customers, operational workflows, products and services.   

As people’s way of experiencing data has evolved, more than ever before, dashboards alone are not enough. You can use data as fuel for data-driven business workflows, and to power digital experiences that improve customer engagement, conversions, and advocacy. 

From Nov. 9 – 11th, Looker is hosting its annual conference JOIN, where we’ll be showing new features, including how we help to:

• Build data experiences at the speed of business
• Accelerate the business value with packaged experiences 
• Unleash more insights for more people in the right way – Deliver data experiences at scale

There is no cost to attend JOIN.  Register here and learn how Looker helps organizations build and deliver custom data-driven experiences that goes beyond just reports and dashboards, scales and grows with your business, allows developers to build innovative data products faster, and ensures data reaches everyone.

It’s simply amazing to witness how some of our systems integrators employ Google Cloud solutions to drive innovation in ways we at Google may never have considered—especially in healthcare.  According to analyst firm MarketsandMarkets, the market for the Cloud in healthcare is projected to grow 43% between 2020 and 2025 to nearly $65 billion, fueled by the need for better technology infrastructures and faster digital transformation.  

Healthcare and life sciences communities are looking to Google Cloud and its Service engagement model partners to improve collaboration and activate the power of medical data.  These transformations deliver robust data analytics and bring a much deeper perspective into health epidemics like COVID-19 to help save lives.

In the healthcare and life sciences industry, our Google Cloud partners and customers provide constant energy and inspiration–and are the magic in some key healthcare innovations globally.  

Let me show you how they are solving real-world business challenges.

Improving collaboration in Healthcare

Cloudbakers and Comanche County Memorial Hospital transitioned 2,000 employees to Google Workspace to improve collaboration, reduce costs, and increase security. By implementing a system that requires less maintenance while enabling mobile access to data and true collaboration, Comanche County Memorial Hospital saves $175,000 annually on licenses and helps medical professionals spend more time with patients.

“We chose Google Workspace because it cost a quarter of what we were paying previously, offers the kind of modern features that healthcare facilities need, and gave us data security and peace of mind.” —James Wellman, CIO, Comanche County Memorial Hospital

Accessing previously locked down medical data

Google Cloud and Quantiphi supported advances in cloud-based machine learning services to reduce infrastructure costs, unlock new paths of treatment, and dramatically reduce the amount of time it takes to evaluate scanned imagery following a stroke.  John Hopkins University BIOS Division has been working on medical imaging to accelerate insights from scans on approximately 500 patients from 2,500 hours to 90 minutes, and lead to more accurate decision-making for brain injury patients that will ultimately improve medical outcomes.  

“We’ve aligned closely with the goal of showing that a cloud-based, AI-driven approach is robust and that it can be performed while protecting personal PHI. In terms of costs, the cloud has definitely reduced some of the traditional financial demands of our research.” —Daniel F. Hanley, Jr., M.D., Director, Johns Hopkins University BIOS Division

Improving data access with the flexibility of Google Cloud

With the help of MediaAgility, TRIARQ migrated to Google Cloud to modernize their platform, build new applications, and expand their global footprint.  With BigQuery, TRIARQ can now consolidate all transactional data, past and present, into a single location to report on specific insights and predict future data from e-prescriptions to complex revenue-cycle data and value-base analysis.

“The future of this industry will need to be a global one, and we can no longer be stuck in legacy systems if we want to survive. Having a team that is passionate about supporting us in this journey is definitely a plus point.”—Yaw Kwakye, Co-founder and Chief Architect, TRIARQ

Increasing visibility to COVID-19 outbreaks for actionable insights

As part of its response to the COVID-19 pandemic, HCA Healthcare chose to work with Google Cloud and SADA to create a national portal that increases visibility into outbreaks in 3,100 counties across the country in just 8 weeks.  Now, the portal generates 30,000 new analytical views each day that can help inform private and public sector decision making for reopenings, closures, hot spots, and many other population health management activities. 

“This project required deep knowledge of AI, and consumer-facing platforms, as well as healthcare. Google brought together the ideal combination of product, people, and partners. Google Cloud’s healthcare-specific products along with SADA’s expertise in the healthcare IT space made this partnership the perfect choice to move quickly and intelligently.”—Dr. Edmund Jackson, Chief Data Officer, HCA Healthcare

We’re committed to building the technology, resources, and services through Partner Advantage to help our partners address this opportunity.  Looking for a solution focused partner in your region who has achieved Expertise and/or Specialization in your industry?  Search our Global Partner Directory.  Not yet a Google Cloud partner? Visit Partner Advantage and learn how to become one today!

Over the last two years, we’ve seen a significant uptick in the number of people using messaging to connect with businesses. Whether it was checking hours of operation, verifying what was in stock, or scheduling a pick-up, the pandemic caused a significant shift in consumer behavior.

• 45% of users are spending more time on messaging services because of the pandemic 
• 85% of consumers would like to message brands directly

With the rise in demand for messaging, consumers expect communication with businesses to be  speedy, simple, and convenient. For businesses, keeping up with customer inquiries can be a labor-intensive process, and offering 24/7 support outside of store hours can be costly.  

To help businesses seamlessly deliver helpful, timely, and engaging conversations with customers when and where they need help, we introduced AI-powered Business Messages.

https://youtube.com/watch?v=fcgP3RHjBLY%3Fenablejsapi%3D1%26

What is AI-powered Business Messages?

With AI-powered Business Messages, you can connect with your customers in their moment of need, in the places they’re looking for answers—such as Google Search, Google Maps, or any brand-owned channel. For instance, check out how Walmart customers in the US are able to receive real-time information on product availability, straight from a search results page.

People turn to Google when they are searching for answers to their questions, looking to buy something, or trying to accomplish a particular task with one of our many tools. In fact, 68% of all online experiences begin with a search engine.

At Google, we know how important it is for interactions with a brand to be personalized, helpful, and simple. With AI-powered Business Messages, customers are able to chat with virtual agents that understand, interact, and respond in natural ways.

We are also combining smart automation with the ability for customers to chat with live agents when it’s really needed. This approach saves your customers precious time, while also saving you money. And with Business Messages automatically handling many customer inquiries in the background, businesses have the option to distribute their human customer service agents to address other needs. 

Getting started with conversational AI is easy with Bot-in-a-Box

We know it can be difficult to get started with AI. That’s why we are utilizing existing Google AI tools like Dialogflow—part of Google Cloud Contact Center AI—to create the capability within Google’s Business Messages called Bot-in-a-Box, which makes getting started with Conversational AI easy. Bot-in-a-Box allows for fast and effective adoption of automation for businesses of all sizes. 

Enabling Business Messages with Bot-in-a-Box can be as simple as leveraging an existing customer FAQ document you already have, whether it’s from a web page or an internal document. And since the conversational AI is powered by Business Messages and Dialogflow working together, your chat bot is able to understand and respond to customer questions automatically without the need to write code. 

Bot-in-a-Box also supports other critical journeys like “Custom Intents.” That means that your bot is able to understand the different ways customers express a similar question and respond accurately by using machine learning capabilities.

Finding success 

In April 2021, Wake County courthouses in North Carolina partnered with Tango Technology to implement Business Messages when it became apparent that being able to provide the public and attorneys with around-the-clock access to information would significantly reduce the pressure on courthouse staff. Using Bot-in-a-Box, Tango Technology was able to customize a solution for Wake County Courthouse, Justice Center, and Clerk of Superior Court in just four days.

“With the combination of Google’s Business Messages, GCP, and Dialogflow, we were able to spin up an AI-driven bot for the courts in days. And the technology stack allows us to continually improve by adding functionality in an agile process.”— Mike Lotz, Co-Founder, Tango Technology

With Business Messages, North Carolina courthouses saw a 37% decrease in the call volume handled by courthouse staff.  With 398,298 fewer phone calls during the first year of operation, the AI-based messages helped Wake County Courthouse work more efficiently and productively.

We’ve seen many brands benefiting from AI-powered Business Messages. For instance, Levi’s saw a 30% increase in off-hours shoppers and surpassed 85% customer satisfaction scores after implementing Business Messages. They also drove 30x more store-related questions than Levi’s website chat. 

Bring Google’s conversational AI to your storefront with Business Messages

Google’s Business Messages makes it easier for businesses of all sizes to engage their existing or potential customers in a virtual conversation, when and where they need it. 

To learn more, watch our Cloud Next session here or visit us at g.co/businessmessages. We have specialized services to help you get started  and can share the wisdom of our channel partners and dedicated experts who specialize in unleashing the potential of conversational AI.

Organizations that collect geospatial data can use that information to understand their operations, help make better business decisions, and power innovation. Traditionally, organizations have required deep GIS expertise and tooling in order to deliver geospatial insights. In this post, we outline some ways that geospatial data can be used in various business applications. 

Assessing environmental risk 

Governments and businesses involved in insurance underwriting, property management, agriculture technology, and related areas are increasingly concerned with risks posed by environmental conditions. Historical models that predict natural disasters like pollution, flooding, and wildfires are becoming less accurate as real-world conditions change. Therefore, organizations are incorporating real-time and historical data into a geospatial analytics platform and using predictive modeling to more effectively plan for risk and to forecast weather.

Selecting sites and planning expansion

Businesses that have storefronts, such as retailers and restaurants, can find the best locations for their stores by using geospatial data like population density to simulate new locations and to predict financial outcomes. Telecom providers can use geospatial data in a similar way to determine the optimal locations for cell towers. A site selection solution can combine proprietary site metrics with publicly-available data like traffic patterns and geographic mobility to help organizations make better decisions about site selection, site rationalization, and expansion strategy.

Planning logistics and transport

For freight companies, courier services, ride-hailing services, and other companies that manage fleets, it’s critical to incorporate geospatial context into business decision-making. Fleet management operations include optimizing last-mile logistics, analyzing telematics data from vehicles for self-driving cars, managing precision railroading, and improving mobility planning. Managing all of these operations relies extensively on geospatial context. Organizations can create a digital twin of their supply chain that includes geospatial data to mitigate supply chain risk, design for sustainability, and minimize their carbon footprint. 

Understanding and improving soil health and yield

AgTech companies and other organizations that practice precision agriculture can use a scalable analytics platform to analyze millions of acres of land. These insights help organizations understand soil characteristics and help them analyze the interactions among variables that affect crop production. Companies can load topography data, climate data, soil biomass data, and other contextual data from public data sources. They can then combine this information with data about local conditions to make better planting and land-management decisions. Mapping this information using geospatial analytics not only lets organizations actively monitor crop health and manage crops, but it can help farmers determine the most suitable land for a given crop and to assess risk from weather conditions.

Managing sustainable development

Geospatial data can help organizations map economic, environmental, and social conditions to better understand the geographies in which they conduct business. By taking into account environmental and socio-economic phenomena like poverty, pollution, and vulnerable populations, organizations can determine focus areas for protecting and preserving the environment, such as reducing deforestation and soil erosion. Similarly, geospatial data can help organizations design data-driven health and safety interventions. Geospatial analytics can also help an organization meet its commitments to sustainability standards through sustainable and ethical sourcing. Using geospatial analytics, organizations can track, monitor, and optimize the end-to-end supply chain from the source of raw materials to the destination of the final product.

What’s next

Google Cloud provides a full suite of geospatial analytics and machine learning capabilities that can help you make more accurate and sustainable business decisions without the complexity and expense of managing traditional GIS infrastructure. Get started today by learning how you can use Google Cloud features to get insights from your geospatial data, see Geospatial analytics architecture.

Acknowledgements: We’d like to thank Chad Jennings, Lak Lakshmanan, Kannappan Sirchabesan, Mike Pope, and Michael Hao for their contributions to this blog post and the Geospatial Analytics architecture.