Category Archives: Machine Learning
How AI and Machine Learning Are Revolutionizing Prostate Cancer … – UroToday
Read the Full Video Transcript
Alicia Morgans: Hi. I'm so excited to be here today with Professor Tamara Lotan, who is joining me from Johns Hopkins University. Thank you so much for being here.
Tamara Lotan: Great. Thanks for having me.
Alicia Morgans: Wonderful. Tamara, you are a pathologist. And we don't get to interview a lot of pathologists on UroToday, so I'm really excited to talk with you and really about the overlap of pathology and urologic oncology, and specifically how this has evolved in a really digitized and even AI type of world. Can you tell me a little bit about the progress that's been made in pathology and what we should be on the lookout for now as we're thinking about modern-day pathology?
Tamara Lotan: Yeah, these are great questions. I always start by telling people pathology has really not changed for the last hundred years or so. The way we practice, we use the same kind of microscopes, small updates. We still take the tissue and fix it in fixative and process it and cut it onto glass slides. Been doing this exactly the same way for a hundred years. So I think that the rise of digital pathology is really exciting, and that really is a step where we then take the glass slide and scan it so that we have a digital representation of that that we can look at on a computer screen. And then most importantly, use it now to apply all kinds of algorithms, especially machine learning or artificial intelligence algorithms, to try to augment the diagnoses that until now we've just been making by eye through the microscope. We can now make with some additional machine learning techniques that really, I think, augment our ability to make diagnoses and also to predict how patients are going to do in the future.
Alicia Morgans: Well, that's certainly really exciting. I wonder if you can walk us through some use cases. What are situations where we might actually see this?
Tamara Lotan: Yeah. Prostate cancer has really been a test case for the use of digital pathology from the beginning, I think because it's a very high volume practice, looking at prostate biopsies, for example. And a lot of what we do with prostate biopsies is semi-quantitative where we identify the cancer and then grade it by deciding what percent pattern 3, 4, 5 we think is in the tumor. And we know that humans don't do that very well by eye visually. We can only get to a certain accuracy visually, whereas a machine learning type algorithm where we can teach the machine to recognize these different patterns that the tumor cells are making and then quantify the relative proportions of those patterns can do that much more accurately.
We know when humans compare, if I grade a prostate cancer case and I compare to my colleague, probably only agreement, we say CAPA values is how we typically do the metric of agreement. And it's usually between 0.4 and 0.6, which is at most moderate agreement. And most clinicians, I think, have had that experience where they see a case that's seen at their institution. Outside institution, you get slight disagreements. So the hope, I think, is that these algorithms will help us for diagnosis, but then maybe most importantly for grading so that we can really standardize grading. Institutions that don't have urologic pathologists who have had a lot of extra training and maybe have higher inter-observer agreement in terms of grading are not available at all institutions, and certainly not internationally in many areas of the world. So if you had an algorithm that can do this more accurately and represent what a urologic pathologist would interpret on the slide, that would really equalize access to care.
So I think that's very exciting. And also just ensure a consistency in terms of grading, which we know is really the most important prognostic parameter in prostate cancer.
Alicia Morgans: I couldn't agree more. And it's so critical that I tell second opinions that come to see me in my clinic that perhaps even more than what I say is that second opinion by the pathology group, because understanding the risk based on the Gleason score, of course, is the way that we really need to personalize treatment and make those decisions in the localized disease setting. So what's another use case? Where else might we see the use of this?
Tamara Lotan: I think one exciting area in prostate is thinking about how we can go beyond Gleason grading. As you mentioned, Gleason grading is such a powerful prognostic parameter, but it actually was developed in the '60s based on I think only 300 or so cases in one VA hospital. So it's amazing that it performs as well as it does, but there's no question we can probably do even better than Gleason grading in terms of coming up with a totally novel system that predicts patient outcomes.
So I think another exciting use case is to think about training algorithms on large, large data sets where we know exactly how each patient did. And we can ask the computer to look at this totally agnostic to any human grading system and come up with features that are associated with prognosis and a totally novel prognostic prediction algorithm. And I think those kind of data sets may even improve on Gleason grading when we can do that, not just with 300 cases like Dr. Gleason did, but now with thousands and thousands of cases, much more diverse data sets, for example as well.
Alicia Morgans: Is something like that in the works right now, is that something that we should be on the lookout from Lotan, et al?
Tamara Lotan: Yeah. We and many other groups, I think, are working on developing exactly these algorithms. One challenge has been to just get enough cases that have these very high quality clinical annotations and also have whole slide images available. But yes, many groups are working on putting together those data sets and maybe even sharing them across institutions. So we really have multi-institutional data sets, which are especially critical in digital pathology.
Alicia Morgans: That'll be really exciting because not only will that help, I think, make the diagnostic process more equitable. It will be fast because you can run it through those kinds of tests in a really quick manner and get an answer to a patient, to a clinician to really get moving on a treatment plan.
Tamara Lotan: Yeah, a hundred percent. It also doesn't exhaust any tissue. This is using just the original diagnostic H&E or hematoxylin, eosin stain. So you don't have to worry about using tissue that you may then want to preserve for future genomic assays and things like that.
Alicia Morgans: Great. So what's another use case as we continue to pepper you with these questions?
Tamara Lotan: Yeah, sure. I think another great use case is a long prediction of response to therapy. So there already are some companies working in this space and academic groups also studying large data sets from clinical trials, for example, to try to predict. Does this patient need hormonal therapy in addition to radiation, for example, or perhaps they would respond just to radiation alone? So I think these, we're going to see more and more predictive biomarkers coming out from AI or deep learning algorithms that are using just the diagnostic pathology images, and that'll be very exciting.
Another area I think that is definitely growing is thinking about how we can maybe triage patients for downstream sequencing. We know, although we recommend patients have germline and somatic sequencing if they're high risk, in some cases, not everyone is getting that sequencing even nationally, certainly not internationally. So if we had, for example, machine learning algorithms that can look at these diagnostic tissue samples and say, "This patient has a 90% risk of having," for example, "a BRCA2 mutation," then we could really flag those cases that we think need sequencing especially and make sure that that happens in those cases.
Alicia Morgans: That would be incredibly powerful because I think if clinicians, particularly those busy clinicians who are maybe in a community setting where they see so many patients in a day from all different types of cancer and don't necessarily know the specifics of this test or that test for their prostate cancer patients, that would be just a wonderful way to raise a flag and say, "Make sure you get germline and somatic testing for this patient." That's great.
Tamara Lotan: Yeah, a hundred percent. I think that's very exciting.
Alicia Morgans: All of this excitement I think needs to be couched with our understanding of the limitations and the challenges that the field faces. And what are those?
Tamara Lotan: So probably the biggest challenge in terms of uptake, I think, in most pathology labs is the cost. So digital pathology is really not budget-neutral. It's adding cost at least right now because we still have to prepare the tissue in exactly the same way we would to just look at it using a glass slide under the microscope. But then we need an additional step where we buy often very expensive scanning, digital scanner machines often costing several hundreds of thousands of dollars. And if you're going to do the throughput of a very large pathology lab, you might spend millions and millions of dollars on this equipment. And then even more than that, that's a fixed cost, but even more than that is the cost of storing these images. So they're huge images actually compared to radiology images. A typical digital pathology image for a single slide might be three gigabytes or something like that. So you end up terabytes, petabytes of data and the expense of that, which just accumulates over the years. In labs like ours, which are producing a million slides a year, it becomes astronomical.
So I think a lot of groups are thinking about how to store images similar to our radiology colleagues where you have some that are immediately accessible and some that are in a colder kind of storage that reduces cost, for example, and hoping that the cost for storage goes down over time. But I think that what's really going to drive uptake is if we have these compelling use cases. So if pathologists are saying, "I really want a digital pathology practice in my group because I feel like that will make my Gleason grading more reproducible," if a clinician like yourself says, "I want you to put a test online that predicts the outcome of my patient better than grading alone," that hopefully will drive investment by big health systems in this technology.
Alicia Morgans: I agree. Once certain groups are doing it, then other groups will follow, and so on down the line. This is really, really important. So if you have to look back and think about digital pathology, these AI algorithms, machine learning, what would your message be to listeners as they try to think more deeply about pathology and the way that it intersects with our care of patients with GU malignancies?
Tamara Lotan: I think this is an incredibly exciting time. I think we're really at the precipice of this revolution in how we practice pathology, and we're only going to become more accurate, more reproducible, and more equitable across all kinds of care settings. So I think that's a super exciting part of being a pathologist right now. Many pathologists or many, I would say, non-pathologists say to pathologists, "Oh, you must be scared. You won't have a job in the future. You're going to be replaced by machines." But I think pathologists really look forward to this because I think this will take away the most menial parts of our job where we're just screening things and replace it with a much more efficient process and really allow us to focus on the things that are most exciting and that require all of that medical knowledge that we've accrued over the years to apply to our patient samples. So we're really looking forward, I think, to the future, and I think it's a very exciting time for the field.
Alicia Morgans: Well, I could not agree more, and I really look forward to seeing the bright future that is the new wave of pathology in GU oncology but also of course, I'm sure across the spectrum of cancers and perhaps even beyond. And I thank you so much for sharing your knowledge today, for your time, and for your expertise.
Tamara Lotan: Thanks so much for having me.
Go here to see the original:
How AI and Machine Learning Are Revolutionizing Prostate Cancer ... - UroToday
Researchers boost vaccines and immunotherapies with machine learning to drive more effective treatments – Phys.org
This article has been reviewed according to ScienceX's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility:
fact-checked
peer-reviewed publication
trusted source
proofread
close
Small molecules called immunomodulators can help create more effective vaccines and stronger immunotherapies to treat cancer.
But finding the molecules that instigate the right immune response is difficult the number of drug-like small molecules has been estimated to be 1060, much higher than the number of stars in the visible universe.
In a potential first for the field of vaccine design, machine learning guided the discovery of new immune pathway-enhancing molecules and found one particular small molecule that could outperform the best immunomodulators on the market. The results are published in the journal Chemical Science.
"We used artificial intelligence methods to guide a search of a huge chemical space," said Prof. Aaron Esser-Kahn, co-author of the paper who led the experiments. "In doing so, we found molecules with record-level performance that no human would have suggested we try. We're excited to share the blueprint for this process."
"Machine learning is used heavily in drug design, but it doesn't appear to have been previously used in this manner for immunomodulator discovery," said Prof. Andrew Ferguson, who led the machine learning. "It's a nice example of transferring tools from one field to another."
Immunomodulators work by changing the signaling activity of innate immune pathways within the body. In particular, the NF-B pathway plays a role in inflammation and immune activation, while the IRF pathway is essential in antiviral response.
Earlier this year, the PME team conducted a high-throughput screen that looked at 40,000 combinations of molecules to see if any affected these pathways. They then tested the top candidates, finding that when those molecules were added to adjuvantsingredients that help boost the immune response in vaccinesthe molecules increased antibody response and reduced inflammation.
To find more candidates, the team used these results combined with a library of nearly 140,000 commercially available small molecules to guide an iterative computational and experimental process.
Graduate student Yifeng (Oliver) Tang used a machine learning technique called active learning, which blends both exploration and exploitation to efficiently navigate the experimental screening through molecular space. This approach learns from the data previously collected and finds potential high-performing molecules to be tested experimentally while also pointing out areas that have been under-explored and may contain some valuable candidates.
The process was iterative; the model pointed out potential good candidates or areas in which it needed more information, and the team conducted a high-throughput analysis of those molecules and then fed the data back into the active learning algorithm.
close
After four cycles and ultimately sampling only about 2% of the librarythe team found high-performing small molecules that had never been found before. These top-performing candidates improved NF-B activity 110%, elevated IRF activity by 83%, and suppressed NF-B activity by 128%.
One molecule induced a three-fold enhancement of IFN- production when delivered with what's called a STING (stimulator of interferon genes) agonist. STING agonists promote stronger immune responses within tumors and are a promising treatment for cancer.
"The challenge with STING has been that you can't get enough immune activity in the tumor, or you have off-target activity," Esser-Kahn said. "The molecule we found outperformed the best published molecules by 20 percent."
They also found several "generalists"immunomodulators capable of modifying pathways when co-delivered with agonists, chemicals that activate cellular receptors to produce a biological response. These small molecules could ultimately be used in vaccines more broadly.
"These generalists could be good across all vaccines and therefore could be easier to bring to market," Ferguson said. "That's quite exciting, that one molecule could play a multifaceted role."
To better understand the molecules found by machine learning, the team also identified common chemical features of the molecules that promoted desirable behaviors. "That allows us to focus on molecules that have these characteristics, or rationally engineer new molecules with these chemical groups," Ferguson said.
The team expects to continue this process to search for more molecules and hope others in the field will share datasets to make the search even more fruitful. They hope to screen molecules for more specific immune activity, like activating certain T-cells, or find a combination of molecules that gives them better control of the immune response.
"Ultimately, we want to find molecules that can treat disease," Esser-Kahn said.
A team from the Pritzker School of Molecular Engineering (PME) at The University of Chicago tackled the problem by using machine learning to guide high-throughput experimental screening of this vast search space.
More information: Yifeng Tang et al, Data-driven discovery of innate immunomodulators via machine learning-guided high throughput screening, Chemical Science (2023). DOI: 10.1039/D3SC03613H
Journal information: Chemical Science
See the original post:
Researchers boost vaccines and immunotherapies with machine learning to drive more effective treatments - Phys.org
New Amazon AI initiative includes scholarships, free AI courses – About Amazon
Artificial intelligence (AI) is the most transformative technology of our generation. If we are going to unlock the full potential of AI to tackle the worlds most challenging problems, we need to make AI education accessible to anyone with a desire to learn.
Thats why Amazon is announcing AI Ready, a new commitment designed to provide free AI skills training to 2 million people globally by 2025. To achieve this goal, were launching new initiatives for adults and young learners, and scaling our existing free AI training programsremoving cost as a barrier to accessing these critical skills.
The three new initiatives are:
The need for an AI-savvy workforce has never been greater. A new study by AWS and research firm Access Partnership found the following:
Amazon is launching AI Ready to help those with a desire to learn about AI and benefit from the tremendous opportunity ahead. The following initiatives are designed to open opportunities to those in the workforce today as well as the future generation.
To support professionals in the workplace, were announcing eight new, free AI and generative AI courses open to anyone and aligned to in-demand jobs. There is something for everyone with courses ranging from foundational to advanced and for business leaders as well as technologists. These courses augment the 80+ free and low-cost AI and generative AI courses and resources provided through AWS.
Through the AWS Generative AI Scholarship, AWS will provide Udacity scholarships, valued at more than $12 million, to more than 50,000 high school and university students from underserved and underrepresented communities globally.
We want to help as many students as possible. Eligible students can take the new Udacity course Introducing Generative AI with AWS for free. The course, which was designed by AI experts at AWS, introduces students to foundational generative AI concepts and guides them through a hands-on project. Upon successful course completion, students earn a certificate from Udacity to showcase their knowledge to future employers.
Amazon is kicking off a new collaboration between Amazon Future Engineer and Code.org to launch Hour of Code Dance Party: AI Edition. During this hour-long introduction to coding and AI, students will create their own virtual music video set to hit songs from artists including Miley Cyrus, Harry Styles, and more.
Students will code their virtual dancers choreography and use emojis as AI prompts to generate animated backgrounds. The activity will give participants an introduction to generative AI, including learning about large language models and how they are used to power the predictive analytics responsible for creating new images, text, and more.
Hour of Code will take place globally during Computer Science Education Week, December 410, engaging students and teachers in kindergarten through 12th grade. Additionally, AWS is providing up to $8 million in AWS Cloud computing credits to Code.org, which runs on AWS, to further support Hour of Code.
Amazons new AI Ready commitment is in addition to AWSs commitment to invest hundreds of millions of dollars to provide free cloud computing skills training to 29 million people by 2025, which has already trained more than 21 million people.
Excerpt from:
New Amazon AI initiative includes scholarships, free AI courses - About Amazon
RoboGarden and University of Northern British Columbia partner on … – Canadian Manufacturing
CALGARY RoboGarden a cloud-based publisher that works on interactive, AI-driven digital skills learning experiences announces a new collaboration with University of Northern British Columbia Continuing Studies to offer its singular Machine Learning and Artificial Intelligence (AI) Bootcamp experience to the UNBC CS workforce upskilling and lifelong learning community.
New Organization for Economic Cooperation and Development (OECD) surveys of employers and workers in the manufacturing and finance sectors of seven countries shed new light on the impact that Artificial Intelligence has on the workplace. The findings suggest that both workers and their employers are generally very positive about the impact of AI on performance and working conditions. However, there are also concerns, including job loss. The surveys show that both training and worker consultation are associated with better outcomes for workers.
This unique learning program was developed with career progression and earning potential in mind, geared toward providing students with access to an industry with an average base pay of over $88k per year. Prior programming experience or credentials are not required. Instead, the Bootcamp meets students on their terms, encouraging them to transfer their prior studies and life experiences into industry-informed Machine Learning and AI projects. Delivered online via the designed in Calgary RoboGarden learning platform, students work through 10 progressive learning modules, offering an experience as engaging as it is enriching, and culminating in RoboGardens signature Capstone project. Coupled with live-virtual instructor sessions, this learning experience disrupts the typical education style to provide students with industry expert instructors and curated content to deliver outcomes for what is needed in the workforce now, and in the future.
We know that the Canadian economy across sectors is transforming rapidly with the introduction of Artificial Intelligence and Machine Learning-based tools, services and solutions, said Dr. Mohamed Elhabiby, Co-Founder and President of RoboGarden. It gives me great pleasure to know that were equipping the Canadian workforce with the skillsets they need to innovate and succeed in this new AI-driven era. The students well be teaching in partnership with our amazing collaborators at University of Northern British Columbia Continuing Studies, will complete the program ready to contribute with high-demand skills, bringing with them practical, future-minded learnings from our world-class instructors and curriculum.
Part of reimagining how we educate and learn to meet the challenges of a rapidly changing world is through collaboration. Our partnership with RoboGarden to deliver this online, instructor-supported Machine Learning and AI Digital Workforce Upskilling Bootcamp will provide residents in northern British Columbia with the most up-to-date tools and resources in this field, says UNBC Continuing Studies Interim Manager Stacey Linton. This innovative partnership will empower our learners with the cutting-edge knowledge and skills to meet the emerging needs of the workforce, both at home and further afield.
Continued here:
RoboGarden and University of Northern British Columbia partner on ... - Canadian Manufacturing
The last Machine Learning curriculum you will ever need! – Medium
Your decision to embark on a new AI journey is commendable, and at this stage, I assume youve already solidified your commitment, driven by a compelling reason. The crucial first step is to anchor yourself to this motivation let it serve as the key to unlocking your untapped potential and surmounting any challenges ahead.
Now that youve set your course, you venture online in search of valuable resources. However, what you likely didnt anticipate was navigating through a myriad of courses that often exhibit substantial topic overlap. Its a common challenge faced by many beginners, and truth be told, even seasoned professionals can find themselves entangled in the complexity of choices at times.
Luckily, I am here to help. However, there are a few things that you need to remember.
Embarking on the path of learning is akin to setting out on a journey, not a sprint. Frequently, I receive inquiries such as, How soon until I secure my first job? or What projects should I showcase on my Resume for an internship? I empathize with these queries, having navigated those uncertainties myself. However, to truly comprehend AI and harness its potential for your aspirations, impatience is not your ally. While it might be tempting to expedite the process by combining various tools to achieve quick results, the essence of learning AI lies in embracing the journey. Along this path, challenges will arise that demand a profound understanding of AI principles for long-term success.
Broadening your understanding of machine learning requires a multi-faceted approach. Delve into the intricacies of AI topics by tapping into a variety of resources. Whether its diverse instructors, a range of courses, insightful books, research papers, or thought-provoking blogs immersing yourself in multiple perspectives is the key. This comprehensive exploration not only deepens your insights but also equips you with a well-rounded understanding of artificial intelligence.
Resist the urge to dive into a multitude of courses or topics simultaneously. Opt for a focused approach master one concept thoroughly before venturing into the next. This sequential immersion ensures a solid foundation and a more effective learning experience.
Theory, while essential, is only a fraction of the learning journey. The true grasp of concepts comes from hands-on implementation. Remember, knowledge solidifies when you actively engage with it. Trust the process, invest time in implementing solutions, and solve real-world problems. The insights gained from practical application far exceed those acquired through lengthy lectures, forming the bedrock of profound understanding.
The realization struck me post-industry immersion: thriving in the AI domain demands more than just technical acumen. While AI knowledge is crucial, its only the tip of the iceberg. To navigate the dynamic landscape, supplement your expertise with a toolkit that extends beyond AI algorithms embrace essential software tools like GitHub and Docker. Expand your programming language repertoire, hone your paper-reading skills, delve into cloud computing intricacies, and grasp project management essentials. You will require good writing and documentation skills. The key lies in adaptability; remaining flexible and prepared for the demands of the evolving AI industry.
The rest is here:
The last Machine Learning curriculum you will ever need! - Medium
Digital staffing company Aya Healthcare picks up Winnow AI to … – FierceHealthcare
Digital staffing company Aya Healthcare acquired Winnow AI to bolster its physician recruitment capabilities as the industry grapples with a historic provider shortage.
Winnow AI is a data-science-driven recruiting solution that identifies predictive matches and referral connections for each open role at a provider organization. The startup combines artificial intelligence with business intelligence to help organizations tap into a unique source of passive physicians who are likely to relocate to their region.
Winnow AI launched just two years ago to "unlock a better approach to physician recruiting," Ray Guzman, co-founder of Winnow AI and CEO of SwitchPoint Ventures, wrote in a LinkedIn post.
"The speed at which Winnow gained traction demonstrated that it was solving a huge pain point, one that demanded disruption of the status quo. Were delighted that Aya has the same massive vision for Winnow that we do, and we look forward to innovating and growing together," Guzman wrote.
Financial details of the deal were not disclosed.
Aya Healthcare, with more than 7,000 global employees, operates adigital staffing platform that providesevery component of healthcare-focused labor services, including travel nursing and allied health, per diem, permanent staff hiring, interim leadership, locum tenens and nonclinical professionals, according to the company. Ayas software suite includes vendor management, float pool technology, provider services and predictive analytics.
The Winnow AI acquisition marks Aya Healthcare's third M&A deal in five months as the company works to build up its AI capabilities for staffing, hiring and retention.
In July, Aya Healthcare picked upFlexwise Health, a company that offers technology to forecast gaps in patient demand and staffing levels. Its aim is to assist hospitals in optimizing resource allocation and cost.
A few weeks later, the company acquiredPolaris AI, a machine learning platform that predicts future patient volume and staffing levels in clinical settings. Polaris utilizes proprietary machine learning algorithms to intelligently inform staffing needs and provide tools for systems to effectively distribute internal resources and plan alternative schedules.
With its latest deal, Winnow AI will operate within Ayas Provider Solutions division. The company says the startup's capabilities complement its DocCafe brand, aphysician talent acquisition platform with the nations largest pool of active job seekers. Ayas Provider Solutions division will now be able to offer both active and passive job seeker recruitment platforms. The division also enables healthcare organizations to hire locum providers and manage their provider recruitment and engagement through Aya Connect, according to the company.
Were able to help healthcare organizations effectively fill their open provider positions by offering Winnow AI to identify passive job seekers and DocCafe to effectively recruit active physician job seekers, said Alan Braynin, president and CEO of Aya Healthcare, in a statement. This acquisition is an example of our never-ending quest to deliver innovative solutions to our clients that create greater efficiencies, generate cost savings, and improve access to care for the communities they serve.
Winnows AI predicts which physicians are likely to change jobs and where they are most likely to relocate. These insights equip medical leaders and in-house recruiters to drive novel candidate options and referrals and to create perfectly aligned provider teams, leading to faster, more efficient physician recruitment, the company said.
"Winnow AI offers a more targeted approach to building all-star teams by pinpointing candidates who match the profiles of a companys best doctors, Guzman said in a statement. "Ayas ability to scale Winnows innovative solution will help healthcare companies dramatically improve their ability to attract, hire, and retain the best-fit providers for their organizations.
Companies tackling the physician and nursing workforce shortage are attracting big money from investors. There's been a lot of funding activity around startups offering tools and platforms aimed at making it easier to find, fill and upskill for healthcare jobs. According to Pitchbook, asample list of 17 funded startups tied to the space collectively raised more than $700 million from June 2021 to June 2022.
As of June 2022, those companies, including Trusted Health, IntelyCare andNomad Health, raised over $1.15 billion.
Two years ago, Aya Healthcare acquiredVizient's Contract Labor Management business unit and transitioned it to Vaya Workforce Solutions. That business operates as a vendor-neutral workforce solutions provider covering whole-house contract labor needs.
Excerpt from:
Digital staffing company Aya Healthcare picks up Winnow AI to ... - FierceHealthcare
Ethnic disparity in diagnosing asymptomatic bacterial vaginosis … – Nature.com
Dataset
The dataset was originally reported by Ravel et al.16. The study was registered at clinicaltrials.gov under ID NCT00576797. The protocol was approved by the institutional review boards at Emory University School of Medicine, Grady Memorial Hospital, and the University of Maryland School of Medicine. Written informed consent was obtained by the authors of the original study.
Samples were taken from 394 asymptomatic women. 97 of these patients were categorized as positive for BV, based on Nugent score. In the preprocessing of the data, information about community group, ethnicity, and Nugent score was removed from the training and testing datasets. Ethnicity information was stored to be referenced later during the ethnicity-specific testing. 16S rRNA values were listed as a percentage of the total 16S rRNA sample, so those values were normalized by dividing by 100. pH values ranged on a scale from 1 to 14 and were normalized by dividing by 14.
Each experiment was run 10 times, with a different random seed defining the shuffle state, to gauge variance of performance.
Four supervised machine learning models were evaluated. Logistic regression (LR), support vector machine (SVM), random forest (RF), and Multi-layer Perceptron (MLP) models were implemented with the scikit-learn python library. LR fits a boundary curve to separate the data into two classes. SVM finds a hyperplane that maximizes the margin between two classes. These methods were implemented to test whether boundary-based models can perform fairly among different ethnicities. RF is a model that creates an ensemble of decision trees and was implemented to test how a decision-based model would classify each patient. MLP passes information along nodes and adjusts weights and biases for each node to optimize its classification. MLP was implemented to test how a neural network-based approach would perform fairly on the data.
Five-fold stratified cross validation was used to prevent overfitting and to ensure that each ethnicity has at least two positive cases in the test folds. Data were stratified by a combination of ethnicity and diagnosis to ensure that each fold has every representation from each group with comparable distributions.
For each supervised machine learning model, hyper parameter tuning was performed by employing a grid search methodology from the scikit-learn python library. Nested cross validation with 4 folds and 2 repeats was used as the training subset of the cross validation scheme.
For Logistic Regression, the following hyper-parameters were tested: solver (newton-cg, lbfgs, liblinear) and the inverse of regularization strength C (100, 10, 1.0, 0.1, 0.01).
For SVM, the following hyper-parameters were tested: kernel (polynomial, radial basis function, sigmoid) and the inverse regularization parameter C (10, 1.0, 0.1, 0.01).
For Random Forest, the following hyper-parameters were tested: number of estimators (10, 100, 1000) and maximum features (square root and logarithm to base 2 of the number of features).
For Multi-layer perceptron, the following hyper-parameters were tested: hidden layer size (3 hidden layers of 10,30, and 10 neurons and 1 hidden layer of 20 neurons), solver (stochastic gradient descent and Adam optimizer), regularization parameter alpha (0.0001, or .05), and learning rate (constant and adaptive).
The models were evaluated using the following metrics: balanced accuracy, average precision, false positive rate (FPR), and false negative rate (FNR). Balanced accuracy was chosen to better capture the practical performance of the models while using an unbalanced dataset. Average precision is an estimate of the area under the precision recall curve, similar to AUC which is the area under the ROC curve. The precision-recall curve is used instead of a receiver operator curve to better capture the performance of the models on an unbalanced dataset39. Previous studies with this dataset reveal particularly good AUC scores and accuracy, which is to be expected with a highly unbalanced dataset.
The precision-recall curve was generated using the true labels and predicted probabilities from every fold of every run to summarize the overall precision-recall performance for each model. Balanced accuracy and average precision were computed using the corresponding functions found in the sklearn.metrics package. FPR and FNR were calculated computed and coded using Equations below39.
Below are the equations for the metrics used to test the Supervised Machine Learning models:
$${Precision}=frac{{TP}}{{TP}+{FP}}$$
(1)
$${Recall}=frac{{TP}}{{TP}+{FN}}$$
(2)
$${Balanced},{Accuracy}=frac{1}{2}left(frac{{TP}}{{TP}+{FN}}+frac{{TN}}{{TN}+{FP}}right)$$
(3)
$${FPR}=frac{{FP}}{{FP}+{TN}}$$
(4)
$${FNR}=frac{{FN}}{{FN}+{TP}}$$
(5)
where TP is the number of true positives, TN is the number of true negatives, FP is the number of false positives, and FN is the number of false negatives.
$${Average},{Precison}=sum _{n}left({R}_{n}-{R}_{n-1}right){P}_{n}$$
(6)
where R denotes recall, and P denotes precision.
The performance of the models were tested against each other as previously stated. Once the model made a prediction, the stored ethnicity information was used to reference which ethnicity each predicted label and actual label belonged to. These subsets were then used as inputs for the metrics functions.
To see how training on data containing one ethnicity affects the performance and fairness of the model, an SVM model was trained on subsets that each contained only one ethnicity. Information on which ethnicity each datapoint belonged to was not given to the models.
To increase the performance and accuracy of the model, several feature selection methods were used to reduce the 251 features used to train the machine learning models. These sets of features were then used to achieve similar or higher accuracy with the machine learning models used. The feature selection methods used included the ANOVA F-test, two-sided T-Test, Point Biserial correlation, and the Gini impurity. The libraries used for these feature selection tests were the statistics and scikit learn packages in Python. Each feature test was performed with all ethnicities, then only the white subset, only Black, only Asian, and only Hispanic.
The ANOVA F-Test was used to select 50 features with the highest F-value. The function used calculates the ANOVA F-value between the feature and target variable using variance between groups and within the groups. The formula used to calculate this is defined as:
$$F=frac{{SSB}/(k-1)}{{SSW}/(n-k)}$$
(7)
Where k is the number of groups, n is the total sample size, SSB is the variance between groups, and SSW is the sum of variance within each group. The two-tailed T-Test was used to compare the BV negative versus BV positive groups rRNA data against each other. The two-tailed T-Test is used to compare the means of two independent groups against each other. The null hypothesis in a two-tailed T-Test is defined as the means of the two groups being equal while the alternative hypothesis is that they are not equal. The dataset was split up into samples that were BV negative and BV positive which then compared the mean of each feature against each other to find significant differences. A p-value <0.05 allows us to reject the null hypothesis that the mean between the two groups is the same, indicating there is a significant difference between the positive and negative groups for each feature. Thus, we use a p-value of less than 0.05 to select important features. The number of features selected were between 40 and 75 depending on the ethnicity group used. The formula for finding the t-value is defined as:
$$t=frac{left({bar{x}}_{1}-{bar{x}}_{2}right)}{sqrt{frac{({{s}_{1}})^{2}}{{n}_{1}}+frac{({{s}_{2}})^{2}}{{n}_{2}}}}$$
(8)
({bar{{rm{x}}}}_{1,2}) being the mean of the two groups. ({{rm{s}}}_{1,2}) as the standard deviation of the two groups. ({{rm{n}}}_{1,2}) being the number of samples in the two groups. The p-value is then found through the t-value by calculating the cumulative distribution function. This defines probability distribution of the t-distribution by the area under the curve. The degrees of freedom are also needed to calculate the p-value. They are the number of variables used to find the p-value with a higher number being more precise. The formulas are defined as:
$${rm{df}}={n}_{1}+{n}_{2}{{{-}}}2$$
(9)
$${p}=2* left(1-{rm{CDF}}left(left|tright|,{rm{df}}right)right)$$
(10)
where ({df}) denotes the degrees of freedom and ({{rm{n}}}_{1,2}) being the number of samples in the group. The Point Biserial correlation test is used to compare categorical against continuous data. For our dataset was used to compare the categorical BV negative or positive classification against the continuous rRNA bacterial data. Each feature has a p-value and correlation value associated with it which was then restricted by an alpha of 0.2 and further restricted by only correlation values >0.5 showing a strong correlation. The purpose of the alpha value is to indicate the level of confidence of a p-value being significant. An alpha of 0.2 was chosen because the Point Biserial test tends to return higher p-values. This formula is defined as:
$${{r}}_{{pb}}=frac{left({M}_{1}-{M}_{0}right)}{{rm{s}}},sqrt{{pq}}$$
(11)
where M1 is the mean of the continuous variable for the categorical variable with a value of 1; M0 is the mean of the continuous variable for the categorical variable with a value of 0; s denotes the standard deviation of the continuous variable; p is the proportion of samples with a value of 1 to the sample set; and q is the proportion of samples with a value of 0 to the sample set.
Two feature sets were made from the Point Biserial test. One feature set included only the features that were statistically significant using a p-value of <0.2 which returned 60100 significant features depending on the ethnicity set used. The second feature set included features that were restricted by a p-value<0.2 and greater than a correlation value of 0.5. This second feature set contained 815 features depending on the ethnicity set used.
Features were also selected using Gini impurity. Gini impurity defines the impurity of the nodes which will return a binary split at a node. It will calculate the probability of misclassifying a randomly chosen data point. The Gini impurity model fitted a Random Forest model with the dataset and took the Gini scores for each feature based on the largest reduction of Gini impurity when splitting nodes. The higher the reduction of Gini value, the impurity after the split, the more important the feature is used in predicting the target variable. The Gini impurity value varies between 0 and 1. Using Gini, the total number of features were reduced to 310 features when using the ethnicity-specific sets and 20 features when using all ethnicities. The formula is defined as:
$${Gini}=1-sum {{p}_{i}}^{2}$$
(12)
where ({{rm{p}}}_{{rm{i}}}) is the proportion of each class in the node. The five sets of selected features from each of the five ethnicities were used to train a model using four supervised machine learning algorithms (LR, MLP, RF, SVM) with the full dataset using our nested cross-validation schemed as previously described. All features were selected using the training sets only, and they were applied to the test sets after being selected for testing. Five-fold stratified cross validation was used for each model to gather including means and confidence intervals.
Originally posted here:
Ethnic disparity in diagnosing asymptomatic bacterial vaginosis ... - Nature.com
The Role of Machine Learning in Precision Synthesis – The Medicine Maker
With the aim to overcome key barriers to applying machine learning (ML) to real experiments and processes for example, the fact that ML typically struggles with sparse data (data with gaps) our latest project, in partnership with the Centre for Process Innovation (CPI) and with funding from Innovate UK, focuses on the potential for ML to act as a catalyst for manufacturing oligonucleotide therapeutics. We are improving predictive modelling tools, experimental program design, optimal process parameter discovery, and target output identification.
Oligonucleotides are difficult to manufacture particularly at scale.They are large, complex molecules that require a multi-stage synthetic process, interleaved with significant purification and analysis stages. The presence of impurities or small variations in reaction conditions and process steps can make significant differences to the structure, yield, and quality of the end product. Synthesis is expensive, meaning that experimental data is often sparse, and research teams would prefer to extract as much value as they can from the data that exists. Alongside these common industry problems, oligonucleotide manufacturing also has significant sustainability challenges; namely, large amounts of waste produced, poor atom economy, and low use of renewable feedstocks.
For these reasons, oligonucleotide manufacturing is an ideal target for ML, which can help detect subtle, non-linear relationships in multi-parameter data that might otherwise be missed. I expect ML to help research teams better understand the key factors driving oligonucleotide manufacturing processes, leading to improved design and control of these processes.
The importance of oligonucleotide therapies cannot be understated. Despite significant advances in medicine, there is still a large gap between the number of diseases and disorders that are druggable with approved therapies. Oligonucleotide therapies represent a relatively new and innovative approachwith the potential to treat a wide range of diseases, including rare genetic disorders, certain types of cancer, and neurodegenerative conditions.The high specificity of oligonucleotides and their ability to target gene mutations or protein expression means that they are a form of personalized medicine, with fewer off-target effects and, potentially, fewer side effects than small molecules. Given the promise, many companies within the pharma industry are either investing heavily in platform R&D to progress oligonucleotide pipelines or forming partnerships and collaborationsto advance these to commercialization.
Going back to ML adoption in this space, oligonucleotides will likely suffer the same challenges seen in other modalities and sectors. Traditional ML methods and algorithms require large, high-quality datasets for training. And as noted, In oligonucleotide manufacturing it is challenging to obtaining sufficient data especially for highly complex and nonlinear proprietary processes. Over-simplified models may not provide meaningful insights.Building models that can generalize across different data formats and processes for different pharma companies will also be challenging. As will the integration of ML solutions into existing manufacturing systems, where it is important to work seamlessly with automation and control systems. The final barriers to adoption are simply inertia or a lack of knowledge and understanding of ML technologies.
Certainly, a small number of specialist companies have made progress in addressing the manufacturing challenges of oligonucleotides, but their insights and models are often proprietary (and pharma is an industry where knowledge is not widely shared). As with many challenges, collaboration is likely key; pre-competitive projects could combine expertise, with ML models acting as a vehicle for capturing and sharing knowledge among the collaborating organizations. This way, what is learnt can be shared to accelerate progress and drive innovation.
And in my view, its absolutely worth it! A somewhat consistent rule of thumb for ML technology when applied to the DoE is a reduction of around 5080 percent in the number of experiments required to achieve a given objective.Furthermore, it could generate new insights and guide informed decision making. Yes, its speculative but the effective use of ML could drive two- to five-fold reductions in the problematic process development phase of bringing new oligonucleotides to market.
CEO and co-founder of Intellegens, a machine learning (ML) software company, focused on research-intensive industries such as chemicals, life sciences, and materials. Originally a spinout from the University of Cambridge, Intellegens worked alongside automotive giant Rolls Royce in a research project to extract more value from rare experimental and process data to optimize the design of a new superalloy.
Continue reading here:
The Role of Machine Learning in Precision Synthesis - The Medicine Maker
Looking beyond the AI hype: Delivering real value for financial … – Fintech Nexus News
If a financial institution looks beyond the hype of AI and tempers its expectations, it can use AI to deliver measurable business results. Thats been the experience of Amounts director of decision science Garrett Laird.
Given the interest in Chat GPT and related tools, the recent buzz around AI is understandable. Like many in fintech, Laird reminds the excited that AI has been around in such forms as machine learning for years. Avant has used machine learning in credit underwriting for at least a decade.
Its not a silver bullet, Laird said. It does some things really, really well. But it wont solve all your problems, especially in our space.
Financial products are highly regulated, right? These new LLMs (large language models) are entirely unexplainable; theyre pretty much true black-box models, so they limit the applications and use cases.
Laird sees clear use cases in outlier detection and unsupervised learning. He credits the current AI fervor with igniting interest in LLMs. As businesses look for ways to deploy LLMs, they are also looking at other AI types.
Regulations prevent AI from being used everywhere in financial services. Laird cited the many protected classifications that dictate how and where advertisements and solicitations can be sent. If your AI model cannot explain why one customer got an offer while another did not, youre asking for trouble.
Machine learning can be used to become more compliant because you can empirically describe why youre making the decisions youre making, Laird said. When there are humans making decisions everyone has their implicit biases, and those are hard to measure or even know what they are.
With algorithms and machine learning, you can empirically understand if a model is biased and in what ways and then you can control for that. While there are many restrictions on one side, I think many things were doing with machine learning and AI benefit consumers from a discrimination and compliance perspective.
Laird said the training models depend on what their systems are used for. Fraud models must be updated quickly and often with third-party sources, historical information and consumer data.
This is one area where machine learning helps. Machine learning operations can ensure proper validations are completed. They prevent it from picking up discriminatory data or information from protected classes.
Laird said an industry cliche is that 90% of machine learning work is data preparation. That has two parts: having relevant data and ensuring it is accessible in real time so it can make valuable business decisions.
While credit provision might not bring the same urgency as fraud, Laird also advises considering how it can benefit from AI. Credit models must have strong governance and risk management processes in place. They need good data sets. Lenders require a thorough understanding of their customers, which, in the case of mortgages, can take years.
Getting access to the right data is a huge challenge, and then making sure its the right population, Laird said. Thats a trend the industry is moving in: product-specific but also customer-base-specific modelling.
The direction were headed is like the democratization of machine learning for credit underwriting where you have models that are very catered to your very unique situation. That challenges many banks because it takes a lot of human capital. Having it takes a lot of data, and its not something you have overnight.
Also read:
AI lowers the entry barrier for fraudsters by providing sophisticated tools and allowing them to communicate in better-quality English. Combatting them also involves AI as one of many layers.
However, AI is used differently with different fraud types. First-party fraudsters can evade identity checks, which introduce friction for legitimate customers.
Third-party fraud brings challenges to supervised models. Those models are based on learnings from previous cases of such fraud. Their characteristics are identified, and models are developed. AI can help to identify those patterns quickly.
However, the process is never-ending because systems must quickly adjust as fraudsters determine how to beat mitigation challenges. Laird said he focuses on that by deploying velocity checks.
We put a lot of mental effort into identifying ways to pick up on these clusters of bad actors, Laird said. And there are many ways you can do that. A couple of the interesting ones that we employ are velocity checks. A lot of times, a fraud ring will exhibit similar behaviors. They might be applying from a certain geography, have the same bank theyre applying from, or have similar device data. They might use VOIP, any number of like attributes.
Laird said some institutions also use unsupervised learning. They might not have specific targets, but they can detect patterns using clustering algorithms. If a population starts defaulting or claiming fraud, the algorithms can identify similar behaviors that need further scrutiny.
Recent financial sector turbulence lends itself to rising deposit-related fraud. If a banks defences are sub-par, they could find themselves vulnerable to fraud that is already happening.
That is probably a problem thats already starting to rear its head and will only get worse, Laird suggested. I think with all of the movement in deposits that happened this past spring, with SVB and all the other events, there was a mad rush of deposit opening.
And with that, two things always happen. Theres an influx of volume. It makes it easier for fraudsters to slip through the cracks. Also, many banks saw that as an opportunity and probably either rushed solutions out or reduced some of their defences. We think theres probably a lot of dormant, recently opened deposit accounts that are probably in the near future going to be utilized as vehicles for bust-out fraud.
Laird returned to case-specific modelling as a significant emerging trend. FICO and Vantage are good models many use, but theyre generic for everything from mortgages to credit cards and personal loans. Casting a wide net limits accuracy, and given increased competition, more bespoke models are a must.
I can go on Credit Karma and get 20 offers with two clicks of a button, or I can go to 100 different websites and get an offer without impacting my credit, Laird observed. If youre trying to compete with that, if your pricing is just based on a FICO score or Vantage score, youre going to get that 700 FICO customer thats trending towards 650, whereas someone with a more advanced credit model is going to get that 700 thats trending towards 750.
Laird is eagerly watching developments following the Consumer Financial Protection Bureaus recent announcement on open banking. Financial institutions must make their banking data available.
Thats a modelling goldmine, Laird said. Financial institutions had an advantage in lending to their customer bases because only they can access that information. Now that its publicly available, that data can be used by all financial institutions to make underwriting decisions. Laird said its mission-critical for financial institutions to have good solutions.
Financial institutions generally take conservative approaches to AI. Most have used Generative AI for internal efficiencies, not direct customer interactions. That time will come but in limited capacities.
Laird reiterated his excitement about the renewed interest in machine learning. He believes they are well-suited to address the problems.
Im excited that theres that renewed interest in investment and an appetite for starting to leverage AI for fraud, Laird said. Its been there for a while.
I think the increased focus on credit underwriting is another one that I get really excited about because with the new open banking regulations coming out, I think financial institutions that dont embrace it are going to get left behind. Theyre going to be adversely selected; theyre not going to be able to remain competitive. It behooves everyone to start thinking about it and understanding ways to leverage that from not just the traditional fraud focuses but increasingly on the credit side.
Tony is a long-time contributor in the fintech and alt-fi spaces.A two-time LendIt Journalist of the Year nominee and winner in 2018, Tony has written more than 2,000 original articles on the blockchain, peer-to-peer lending, crowdfunding, and emerging technologies over the past seven years.He has hosted panels at LendIt, the CfPA Summit, and DECENT's Unchained, a blockchain exposition in Hong Kong. Email Tony here.
Read this article:
Looking beyond the AI hype: Delivering real value for financial ... - Fintech Nexus News
Applications of Semi-supervised Learning part4(Machine Learning … – Medium
Author : Gaurav Sahu, Olga Vechtomova, Issam H. Laradji
Abstract : This work tackles the task of extractive text summarization in a limited labeled data scenario using a semi-supervised approach. Specifically, we propose a prompt-based pseudolabel selection strategy using GPT-4. We evaluate our method on three text summarization datasets: TweetSumm, WikiHow, and ArXiv/PubMed. Our experiments show that by using an LLM to evaluate and generate pseudolabels, we can improve the ROUGE-1 by 1020% on the different datasets, which is akin to enhancing pretrained models. We also show that such a method needs a smaller pool of unlabeled examples to perform better
2.Semi-supervised machine learning model for Lagrangian flow state estimation (arXiv)
Author : Reno Miura, Koji Fukagata
Abstract : In recent years, many researchers have demonstrated the strength of supervised machine learning for flow state estimation. Most of the studies assume that the sensors are fixed and the high-resolution ground truth can be prepared. However, the sensors are not always fixed and may be floating in practical situations for example, in oceanography and river hydraulics, sensors are generally floating. In addition, floating sensors make it more difficult to collect the high-resolution ground truth. We here propose a machine learning model for state estimation from such floating sensors without requiring high-resolution ground-truth data for training. This model estimates velocity fields only from floating sensor measurements and is trained with a loss function using only sensor locations. We call this loss function as a semi-supervised loss function, since the sensor measurements are utilized as the ground truth but high-resolution data of the entire velocity fields are not required. To demonstrate the performance of the proposed model, we consider Stokes second problem and two-dimensional decaying homogeneous isotropic turbulence. Our results reveal that the proposed semi-supervised model can estimate velocity fields with reasonable accuracy when the appropriate number of sensors are spatially distributed to some extent in the domain. We also discuss the dependence of the estimation accuracy on the number and distribution of sensors.
Read the rest here:
Applications of Semi-supervised Learning part4(Machine Learning ... - Medium