Google Releases AI Tool for Pathology

by Jondavid Klipp | Apr 15, 2024 | AI, Digital Pathology

Google Releases AI Tool for Pathology

Google has released a free cloud-based tool (“Path Foundation”) that
transforms digitized slide images into numerical data that researchers
can use to create AI tools for pathology. “This is a landmark for us,” says
David Steiner, MD, PhD, Clinical Research Scientist at Google. Based on feedback to Path Foundation, Google will make decisions toward developing commercial AI tools for pathologists.

For more than seven years, Google has employed a team of clinical research scientists based in Mountain View, California and London, England, tasked with developing AI software tools for radiology and pathology. Below is a summary of LE’s interview with Google’s David Steiner, MD, PhD, Clinical Research Scientist.

How can labs and pathologists use Path Foundation?

Commercial labs and academic medical centers, for example, can use Path Foundation to convert patches of their digitized slide images into numerical vectors, known as embeddings. These embeddings capture important features and patterns contained in digitized slide images which are learned by Path Foundation during its training on millions of pathology images. After the embeddings for each image are collected, this data can be used to train and create custom algorithms for a range of tasks such as identifying tissue type, tumors, or performing quality assurance on digitized images.

What’s the benefit of using a “Foundation” model to analyze content in images?
Leveraging the embeddings from Path Foundation requires less data and computational resources than traditional methods, giving researchers a big head start toward developing their own algorithms.

In contrast, traditional methods such as strongly supervised deep learning models require more resources because every task requires fresh training in its own unique deep learning model and many labeled images for each category of interest.

The foundation model is similar to that of seasoned guitar player quickly learning a new song by ear. Because the guitar player has already built up a foundation of skill and understanding, they can quickly pick up the patterns and groove of a new song.

Where did you get the digitized images to train Path Foundation on?
We used 20,000 whole-slide images, covering millions of image patches, from a variety of sources, including the National Cancer Institute’s Cancer Genome Atlas, as well as academic medical centers and some private pathology labs.

What is the user roadmap to getting started with Path Foundation?
After filling out the access form, users can run a small demo notebook that walks them through how to train a tumor classifier. To use Path Foundation on their own task (i.e., identifying tissue type) they would need to collate a set of digital pathology images with accompanying labels. The user would then upload these images and labels into Google Cloud.

From there, the users can adapt the demo notebook to call the Path Foundation API on their uploaded images. Using the existing code in the demo notebook they would then train a model to classify their images based on the labels and evaluate its performance on a held-out part of
the dataset not used to train the model. In the future we hope to make it even easier to use Path Foundation and the embeddings directly in your pathology slide viewer with no coding required.

We’re offering Path Foundation free to users on github.com/Google-Health.

Do labs that use Path Foundation need to share their digitized images or the results of their research with Google?
They don’t need to share the images or the results of their research with Google. They do need to have their images stored in Google Cloud (in their own private or institution account), but these are kept private to the user and not accessible by Google. In addition, when the images are sent to the Path Foundation model to compute the embeddings, they are not saved or stored by Google.

Any plans to develop commercial AI software tools like Ibex, Paige or PathAI?
Yes. Path Foundation represents a landmark toward that end.

What is the next step for your research team in terms of developing AI tools for pathologists?
We’ll take feedback on users from Path Foundation to understand key-use cases and how to make the tool better and easier to use. We’ll also explore how these embeddings might be used with large language and large multimodal models (LLMs & LMMs). And then we plan to develop useful approaches and models for working with whole slide images (WSIs), in addition to the “patch-based” models and applications that this current tool represents.

Has Google completed any studies related to AI-assisted diagnostic tools for cancer?
Yes. We have published several studies in peer-reviewed journals.

Most recently, we published a study that used AI to predict immunotherapy outcomes from digitized slide images in non-small cell lung cancer (Cancer Research, vol. 84, 2024).

In 2023, we published a paper that showed how AI can be used for clinical decision-making in colorectal cancer (Nature Communications Medicine, vol. 3, 2023). And, in 2022, we published a study that used AI for diagnosis and Gleason Grading of prostate cancer (Nature Medicine, vol. 28, 2022).

We have also published studies focusing on AI models for breast cancer.

Will AI algorithms eventually replace pathologists?
AI will make pathologists better rather than replace them. Initially, AI will be used to automate repetitive tasks such as locating the image patches that pathologists should focus their eyes on. Eventually, AI could be used to query images. Pathologists and researchers may someday be able to
type in specific questions and get AI answers about an image.

Is there the potential to integrate pathology and radiology image data using AI?
I’m excited to explore this and do see the promise in bringing these two specialties together. I believe the combination will yield more than the sum of the parts. Google does have a team of research scientists working on AI tools for radiology. And we did introduce an AI tool for chest x-rays (CXR Foundation) in July 2022.

FDA Final LDT Rule Could be Published Soon

by Jondavid Klipp | Mar 18, 2024 | ACLA, CLFS, FDA, Lab Developed Tests (LDT)

FDA Final LDT Rule Could be Published Soon

On March 1, the FDA submitted its final rule for LDT regulation to
the White House’s Office of Information and Regulatory Affairs
(OIRA). This is a perfunctory last step before the final rule is published
in the Federal Register. This could occur as soon as April 1. This will be
the most impactful new regulatory change for laboratories since PAMA
completely overhauled the Medicare CLFS in 2018.

FDA FINAL LDT RULE COULD BE PUBLISHED SOON

OIRA (pronounced “oh-eye-rah”) is a statutory part of the Office of Management and Budget within the Executive Office of the President. OIRA is responsible for reviewing all federal regulations (i.e., the Executive Branch’s administrative actions) to ensure they meet all statutory requirements. OIRA is currently headed by Richard Revesz, Administrator, who was appointed by President Biden and confirmed by the U.S. Senate in late 2022.

“OIRA reviewed the proposed rule in record time, so it is reasonable to expect that the review of the final rule will not be protracted. I would not be surprised if OIRA completes its review in 30 days and FDA publishes the final rule in the federal register in the first week of April,” according to attorney Sheila Walcoff, Chief Executive at the IVD consulting firm Goldbug Strategies (Gaithersburg, MD).

Typically, a final rule will specify an effective date of 30 or 60 days after the publication date, adds Walcoff.

Once a final rule is published it will be difficult to overturn.

Last Chance to Sway OIRA Against Regulation

OIRA staff held nine teleconferences with organizations advocating both for and against FDA LDT regulation last year. OIRA is next scheduled to meet with The Association for Diagnostics and Laboratory Medicine (ADLM — formerly AACC) on March 18. ADLM, which represents approximately 8,000 members, including clinical labs and IVD manufacturers, has steadfastly
opposed FDA regulation of LDTs. This could be the last chance that the lab industry has to sway OIRA against rubber-stamping the final rule.

Expected Legal Challenge

A final rule is almost guaranteed to trigger a lawsuit from lab trade groups, which will argue that the FDA does not have the authority to regulate LDTs.
The American Clinical Laboratory Assn. (ACLA — Washington, DC) seems to be gearing up for a lawsuit to the impending final rule. In a statement, ACLA President Susan Van Meter said:

ACLA has significant concerns about the legality and impact of FDA unilaterally imposing an ill-fitting medical device scheme on laboratory-developed testing services, which are professional services and not medical products. Should the agency promulgate a final rule, ACLA will assess its options at that time; but we continue to urge the agency to withdraw the proposed rule and reengage on advancing appropriate legislation.

Could a New Trump Administration Put the Kibosh on LDT Regulation?

As a component of OMB, OIRA is part of the Executive Office of the President and helps ensure that covered agencies’ rules reflect the President’s policies and priorities.

The FDA is moving quickly because the national election in November could result in a new administration opposed to LDT regulation. A new President could, immediately upon taking office, prevent a proposed rule from being finalized, according to long-time lab regulation expert Dennis
Weissman (Falls Church, VA).

However, Weissman says that changing or canceling a final rule is much more difficult. Once a federal rule has been finalized a new administration would be required to undergo the formal rulemaking process (i.e., opportunity for public comment on a proposal followed by final rule) to change or repeal all or part of a final rule.

In addition to this administrative action, Congress could also take legislative action to overturn a final rule, notes Weissman.

New Market Research Report on U.S. Clinical Laboratory Market

by Jondavid Klipp | Dec 21, 2023 | Laboratory Economics, Laboratory Market Research, Laboratory Outlook

New Market Research Report on U.S. Clinical Laboratory Market

Laboratory Economics has just released The U.S. Clinical Laboratory Industry Forecast & Trends 2023-2025. With this special report, you can
tap into 100+ pages of proprietary market research that reveals critical
data and information about key business trends affecting the U.S.
laboratory testing market.

The report reveals that the U.S. laboratory testing market represented
an estimated $125 billion of revenue in 2023 with a long-term annual
growth rate of 3-4%. Growth is currently being driven almost entirely by
increased PCR-based microbiology testing.

The U.S. laboratory testing market faces unprecedented challenges,
including the post-pandemic employee wage inflation, greater utilization
management and claims denials by private payers and persistent
reimbursement pressure. Despite these challenges, the U.S. lab industry
has shown persistent growth.

“The adoption of new higher-priced PCR-based test panels for respiratory
viruses, UTIs and STDs is helping to offset price and volume pressure on
routine clinical lab tests,” according to Jondavid Klipp, President of
Laboratory Economics.

The report includes:

More than 100 charts and graphs
U.S. lab market size and growth rates for 2012-2025
Detailed estimates for market subsets like hospital-based labs,
independent labs, and physician-office-based labs
In-depth analysis of the PCR-based testing market size, growth rate,
and highest-volume laboratories
Top 50 hospital outreach labs by Medicare CLFS and PFS payments
Detailed reimbursement rate information from Medicare CLFS, Aetna,
Cigna, UnitedHealthcare, etc.
Comprehensive lab M&A valuation metrics by revenue and EBITDA
Results from Laboratory Economics Clinical Lab Trends Surveys from
2014 through 2023
The biggest challenges and opportunities for labs

Laboratory companies highlighted include:

ACL Laboratories
ARUP Laboratories
Exact Sciences
Fulgent Genetics
Labcorp
Mayo Clinic Laboratories
Myriad Genetics
NeoGenomics
Northwell Health Labs
OPKO/BioReference Labs
PathAI/Poplar Healthcare
PathGroup
Quest Diagnostics
Sonic Healthcare

The U.S. Clinical Laboratory Industry: Forecast & Trends 2023-2025 is
published by Laboratory Economics (www.laboratoryeconomics.com), an
independent market research firm focused exclusively on the business of
pathology and laboratory medicine.

FDA Won’t Extend Comment Period on LDT Regs

by Jondavid Klipp | Nov 14, 2023 | ACLA, CAP, FDA, Lab Developed Tests (LDT)

FDA Won’t Extend Comment Period on LDT Regs

The FDA has announced that its standard 60-day comment period for its proposed regulation of laboratory-developed test (LDTs) will not be extended past December 4. Several trade groups, including CAP and ACLA, had requested to stretch the comment period to 120 days. An extension would have potentially delayed implementation of the rule while giving Congress more time to pass LDT reform legislation. The FDA has indicated that a final rule could be published as early as April 1, 2024.

The FDA estimates that there are approximately 12,000 U.S. labs performing high-complexity testing and that 10% of these are marketing LDTs. These 1,200 labs are currently offering 80,400 LDTs and 7,776 new LDTs are coming to the market each year. The FDA estimates that labs will generate $28.6 billion of revenue from LDTs in 2023.

One of the biggest concerns is the FDA’s capacity to review and process as many as 80,000+ LDT applications over the next few years. For example, the FDA gave marketing authorization to a grand total of only 765 medical devices, including lab tests, in 2022, according to the FDA’s Center for Devices and Radiological Health 2022 Annual Report. The FDA’s ability to process tens of thousands of LDT applications in a timely manner, even with the help of third-party reviewers, is doubtful.

During an October 24 call with investors, Jim Davis, Chief Executive of Quest Diagnostics, said that Quest agrees with the long-standing assertion of the American Clinical Laboratory Assn. (ACLA), “that the FDA does not have the statutory authority to unilaterally regulate LDTs under its existing medical device authority.” Davis noted that by volume, LDTs account for less than 10% of Quest’s overall testing business. Quest performs the majority of its LDT testing at three ISO-certified labs, including San Juan Capistrano, CA; Chantilly, VA; and Lewisville, TX.

On an October 26 conference call, Labcorp CEO Adam Schechter said that LDTs account for less than 5% of Labcorp’s volume and less than 10% of its testing revenue. “If you look at the rigor that we go through with our laboratory-developed tests, we think we do the vast majority of what they [FDA] would be asking for anyway.” Schechter said FDA regulation could have unintended consequences. LDTs “are sometimes the most important test for new specialty areas. And getting those tests to patients quickly is what’s most important.”

One group in favor of LDT regulation is AdvaMed (Washington, DC), whose members include Abbott, BD, Bio-Rad Laboratories, bioMerieux, Hologic, Illumina and Roche. “We like the rule….This is really about making sure there’s a level playing field when you’re talking about diagnostics tests and having everything go through a similar pathway,” said AdvaMed CEO Scott Whitaker at an October 10 press conference. “Either you raise the regulatory standard, or you lower the regulatory standard, but you do it across the board without stifling innovation,” he said.

The last major effort by the FDA to formally regulate LDTs came in October 2014, when the agency issued draft guidance. But after collecting comments and facing two years of stiff opposition, the agency chose not to issue final guidance. One of the strongest critics was ACLA, which challenged the FDA’s authority over the tests by filing a citizen petition and making clear its intent to sue if necessary.

Pathologist Job Openings Remain Near Record-High

by Jondavid Klipp | Oct 17, 2023 | Digital Pathology, Pathology Consultants

Pathologist Job Openings Remain Near Record-High

The biggest online job board for pathologists, PathologyOutlines.com, currently has 705 pathologist jobs listed. That’s near the site’s all-time record of 706 pathologist job ads reached in February 2022. Prior to 2020, the average number of job openings was between 300 and 400.

Rich Cornell, President and Founder of the life sciences recruiting firm Santé Consulting (St. Louis, MO), says it’s important for labs to understand that the shortage is not going away soon. Cornell says, “Labs must establish an internal sense of urgency in the hiring process in order to hire effectively in this market. The total actual number of U.S. pathologist openings is currently closer to 1,000 when including jobs that are not advertised on PathologyOutlines.com. The biggest competition exists for jobs in the subspecialties in highest demand: cytopathology, hematopathology and gastrointestinal.

According to Cornell, only about 600 pathologist residents and fellows graduate each year. A large percentage of those graduates will require visa sponsorship, but only about 1/3 of visa requests will likely get accepted. In other words, the market is out of balance and will continue this way for the next several years, says Cornell.

So what should labs do in this tight job market? Cornell says it boils down to these two things:

1. The interview-to-hire ratio has changed. Pathology practices should expect to interview an average of five candidates in order to successfully hire one pathologist. That’s the new average.

2. Young millennial pathologists (age 27-42 years) are seeking low stress working environments and a quick interview timeframe. They expect offers within 48 hours after an interview. The timng and pace of your offer are crucial once the interview takes place.

How are other labs advertising for pathologist openings in light of this severe shortage? Here are some recent examples from PathologyOutlines.com:

$100K Sign-On Bonus
A large independent pathology practice in Connecticut is offering $100,000 sign-on bonuses in an effort to hire one or more full-time surgical pathologists with subspecialty training in gastrointestinal pathology, breast or hematopathology. The annual salary range is highly competitive with four weeks vacation. Current fellows, pathologists straight out of fellowships and experienced pathologists are encouraged to apply.

22 Pathologists Needed at HCA Healthcare
HCA Healthcare has ads for 22 pathologist job openings—mostly for its hospitals in Florida, Georgia and Texas. HCA Healthcare is offering sign-on bonuses of up to $30,000. Other organizations with a large number of job ads include Sonic Healthcare (21 pathologist openings), Rutgers New Jersey Medical School (11 openings) and Northwell Health in New York (10 openings).

Cornell says that many groups are struggling because of their hiring process, or lack thereof. “We recently worked with a large healthcare system with more than 20 pathologists. They needed four additional pathologists to handle their workload volume increases. However, their internal process prevented them from being successful. They would take 4 weeks to make an offer once the interview had occurred. Candidates would lose interest because they were left waiting for too long after they were interviewed. Younger candidates expect feedback from employers immediately following the interview.”