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AI and Machine Learning Revolutionizing Healthcare
Artificial intelligence (AI) and machine learning (ML) are rapidly transforming the healthcare landscape, bringing about a new era of personalized, efficient, and data-driven care. These technologies are revolutionizing various aspects of healthcare, from diagnosis and treatment to drug discovery and patient management. Diagnosis and Treatment: AI and ML algorithms are being used to analyze medical images, such as X-rays, CT scans, and MRIs, with unprecedented accuracy. This allows for earlier and more accurate diagnosis of diseases like cancer, heart disease, and neurological disorders. Additionally, AI-powered systems can analyze patient data, including medical history, lab results, and genetic information, to predict the risk of developing certain diseases and recommend personalized treatment plans. Drug Discovery and Development: AI and ML are playing a crucial role in accelerating drug discovery and development. These technologies can analyze vast amounts of data to identify potential drug targets and predict the efficacy and safety of new drugs. This can significantly reduce the time and cost of bringing new drugs to market. Patient Management and Monitoring: AI-powered chatbots and virtual assistants are being used to provide patients with 24/7 support and information. These systems can answer patients' questions, schedule appointments, and even monitor their health status remotely. Additionally, AI algorithms can analyze patient data to identify those at risk of complications or readmission, allowing for early intervention and improved outcomes. Administrative Tasks and Workflow Optimization: AI and ML can automate many administrative tasks in healthcare, such as scheduling appointments, processing claims, and managing medical records. This frees up healthcare professionals to focus on providing direct patient care. Additionally, AI-powered systems can analyze data to identify inefficiencies in workflows and suggest improvements, leading to increased efficiency and cost savings. Challenges and Ethical Considerations: Despite the numerous benefits, AI and ML in healthcare also present challenges and ethical considerations. Data privacy and security are critical concerns, as AI systems rely on vast amounts of patient data. Additionally, ensuring fairness and avoiding bias in AI algorithms is crucial to prevent discrimination and ensure equitable access to healthcare. Conclusion: AI and ML are revolutionizing healthcare, offering the potential to improve patient outcomes, reduce costs, and increase efficiency. However, it is important to address the challenges and ethical considerations associated with these technologies to ensure their responsible and equitable implementation. As AI and ML continue to evolve, the future of healthcare promises to be more personalized, data-driven, and accessible than ever before.
Excel Template
Hi, I would like a suggestion on how to create an excel sheet to monitor sample reception monthly and yearly. I would like to include variables such as total samples received monthly, number of samples tested, number of positive and the district the samples were received from. I am not really a tech guru but I follow instructions. Thanks
How Social Support Programs Impact Healthcare Accessibility in South Africa
How have Sassa Grants impacted poverty alleviation and social welfare in South Africa? Join the conversation to share your insights, experiences, and analysis of the role SASSA plays in supporting vulnerable populations across the country.AI-powered tool predicts gene activity in cancer cells from biopsy images
To determine the type and severity of a cancer, pathologists typically analyze thin slices of a tumor biopsy under a microscope. But to figure out what genomic changes are driving the tumor's growth -; information that can guide how it is treated -; scientists must perform genetic sequencing of the RNA isolated from the tumor, a process that can take weeks and costs thousands of dollars. Now, Stanford Medicine researchers have developed an artificial intelligence-powered computational program that can predict the activity of thousands of genes within tumor cells based only on standard microscopy images of the biopsy. The tool, described online in Nature Communications Nov. 14, was created using data from more than 7,000 diverse tumor samples. The team showed that it could use routinely collected biopsy images to predict genetic variations in breast cancers and to predict patient outcomes. This kind of software could be used to quickly identify gene signatures in patients' tumors, speeding up clinical decision-making and saving the health care system thousands of dollars." Olivier Gevaert, PhD, professor of biomedical data science and senior author of the paper The work was also led by Stanford graduate student Marija Pizuria and postdoctoral fellows Yuanning Zheng, PhD, and Francisco Perez, PhD. Driven by genomics Clinicians have increasingly guided the selection of which cancer treatments -; including chemotherapies, immunotherapies and hormone-based therapies -; to recommend to their patients based on not only which organ a patient's cancer affects, but which genes a tumor is using to fuel its growth and spread. Turning on or off certain genes could make a tumor more aggressive, more likely to metastasize, or more or less likely to respond to certain drugs. However, accessing this information often requires costly and time-consuming genomic sequencing. Gevaert and his colleagues knew that the gene activity within individual cells can alter the appearance of those cells in ways that are often imperceptible to a human eye. They turned to artificial intelligence to find these patterns. The researchers began with 7,584 cancer biopsies from 16 different of cancer types. Each biopsy had been sliced into thin sections and prepared using a method known as hematoxylin and eosin staining, which is standard for visualizing the overall appearance of cancer cells. Information on the cancers' transcriptomes -; which genes the cells are actively using -; was also available. A working model After the researchers integrated their new cancer biopsies as well as other datasets, including transcriptomic data and images from thousands of healthy cells, the AI program -; which they named SEQUOIA (slide-based expression quantification using linearized attention) -; was able to predict the expression patterns of more than 15,000 different genes from the stained images. For some cancer types, the AI-predicted gene activity had a more than 80% correlation with the real gene activity data. In general, the more samples of any given cancer type that were included in the initial data, the better the model performed on that cancer type. "It took a number of iterations of the model for it to get to the point where we were happy with the performance," Gevaert said. "But ultimately for some tumor types, it got to a level that it can be useful in the clinic." Gevaert pointed out that doctors are often not looking at genes one at a time to make clinical decisions, but at gene signatures that include hundreds of different genes. For instance, many cancer cells activate the same groups of hundreds of genes related to inflammation, or hundreds of genes related to cell growth. Compared with its performance at predicting individual gene expression, SEQUOIA was even more accurate at predicting whether such large genomic programs were activated. To make the data accessible and easy to interpret, the researchers programmed SEQUOIA to display the genetic findings as a visual map of the tumor biopsy, letting scientists and clinicians see how genetic variations might be distinct in different areas of a tumor. Predicting patient outcomes To test the utility of SEQUOIA for clinical decision making, Gevaert and his colleagues identified breast cancer genes that the model could accurately predict the expression of and that are already used in commercial breast cancer genomic tests. (The Food and Drug Administration-approved MammaPrint test, for instance, analyzes the levels of 70 breast-cancer-related genes to provide patients with a score of the risk their cancer is likely to recur.) "Breast cancer has a number of very well-studied gene signatures that have been shown over the past decade to be highly correlated with treatment responses and patient outcomes," Gevaert said. "This made it an ideal test case for our model." SEQUOIA, the team showed, could provide the same type of genomic risk score as MammaPrint using only stained images of tumor biopsies. The results were repeated on multiple different groups of breast cancer patients. In each case, patients identified as high risk by SEQUOIA had worse outcomes, with higher rates of cancer recurrence and a shorter time before their cancer recurred. The AI model can't yet be used in a clinical setting -; it needs to be tested in clinical trials and be approved by the FDA before it's used in guiding treatment decisions -; but Gevaert said his team is improving the algorithm and studying its potential applications. In the future, he said, SEQUOIA could reduce the need for expensive gene expression tests. "We've shown how useful this could be for breast cancer, and we can now use it for all cancers and look at any gene signature that is out there," he said. "It's a whole new source of data that we didn't have before." Scientists from Roche Diagnostics were also authors of the paper. Funding for this research was provided by the National Cancer Institute (grant R01 CA260271), a fellowship of the Belgian American Educational Foundation, a grant from Fonds Wetenschappelijk Onderzoek-Vlaanderen, the Fulbright Spanish Commission and Ghent University
"Enhancing Service Delivery at NSFAS through Microsoft Technologies"
By integrating Microsoft technologies, NSFAS can streamline application processes, enhance communication with applicants, and automate administrative tasks, resulting in improved efficiency, transparency, and service delivery to students in need.
Did Microsoft make an effort to lift poverty in South Africa?
What specific initiatives has Microsoft undertaken to address poverty in South Africa, and how do these efforts compare with government programs like SASSA and other social assistance initiatives aimed at alleviating poverty and promoting economic empowerment?Introducing Scalable and Enterprise-Grade Genomics Workflows in Azure ML
Genomics workflows are essential in bioinformatics as they help researchers analyse and interpret vast amounts of genomic data. However, creating a consistent and repeatable environment with specialized software and complex dependencies can be challenging, making integration with CI/CD tools difficult, too. Azure Machine Learning (Azure ML) is a cloud-based platform that provides a comprehensive set of tools and services for developing, deploying, and managing machine learning models. Azure ML offers great repeatability and auditability features natively that not many workflow solutions offer. It provides a highly integrated and standardised environment for running workflows, ensuring that each step is executed in a consistent and reproducible manner. This feature is particularly useful for genomics workflows that require the use of multiple tools and software packages of certain versions with specific dependencies. In this blog post, we will show how Azure ML can run genomics workflows efficiently and effectively, in addition to being an end-to-end platform for machine learning model training and deployment. Figure 1 illustrates an example of such a workflow. Figure 1: A sample genomics workflow running in Azure ML, consisting of 3 steps. A reference genome input dataset flows into the indexer step, while the sequence quality step gets its data from a folder of DNA sequences (".fastq" files). Azure ML has comprehensive audit and logging capabilities that track and record every step of the workflow, ensuring traceability and repeatability. One of the critical features of Azure ML to achieve these capabilities is its support for users to be able to specify Docker and Conda environments for each workflow step, which guarantees consistent environment execution. These environments can be versioned and centrally shared. Workflow steps within pipelines then can refer to a particular environment. Figure 2 shows one such environment, bwa, version "5". As we make modifications in the environment definition, the new version will be registered as "6", however, we will still be able to continue to use older versions. Figure 2: An example Azure ML environment, defining a Docker image containing the BWA bioinformatics software package. This is the 5th version of this environment registered under the name, "bwa". Like environments, Azure ML supports user created pipeline components that can be centrally registered for reuse in other pipelines, also versioned, and with an audit log of their usage. Runs are logged together with standard out and error streams generated by the underlying processes, automatically. MLflow logging and adding custom tags to all assets and runs are supported, too. This feature ensures that the results are consistent and reproducible, saving users’ time. An example versioned component is shown in Figure 3. Figure 3: An Azure ML component named "BWA Indexer". It is a self-contained, re-usable, versioned piece of code that does one step in a machine learning pipeline: running the bwa indexer command, in this instance. Versioning is not limited to environments and pipeline components. Another essential feature of Azure ML is its support for versioning all input datasets and genomic data, including overall pipeline input, and as well as intermediate step and final outputs, if needed. This feature enables users to keep track of dataset changes and ensure that the same version is used consistently across different runs of the workflow, or in others. There are many genomics workflow engines which are very good with multiple parallel execution when it comes to processing files in parallel. However, Azure ML parallel steps support parallel running both at the file-level (one by one, or 3 files at a time etc) and at the file chunk-level (50 MB of data per process, or 20 KB of text per node etc) where appropriate as supported by the consuming application, enabling the processing of large genomic datasets efficiently across elastic compute clusters that can auto-scale. Pipelines can even also run locally on your laptop for test/development phases, and of course support powerful CPU and GPU-based VMs, low priority or on-demand compute clusters, Spark engines, and other compute targets such as Azure Kubernetes, making it flexible for different use cases. Azure ML has integrations with Azure DevOps and GitHub Actions for CI/CD, making it easy to deploy and manage genomics workflows in a production environment, which in turn makes GenomicsOps possible. Well established pipelines ready for "production use" can be published, and called on-demand or from other Azure services including the Azure Data Factory and Synapse. This means we can create a schedule for running pipelines automatically, or whenever data become available. Thanks to its Python SDK, command line utility (az cli, ml extension), REST-API, and user-friendly UI, it makes it possible to develop pipelines and initiate pipeline runs from any preferred means, also providing easy monitoring and management of workflows. That said, event-based triggers and notifications are also supported. For instance, one can set up an email alert that will be triggered whenever a genomics pipeline finishes execution. As compute and storage are de-coupled, any pipeline input or output stored in an Azure ML datastore or blob storage can also be accessed by Azure ML’s Jupyter Notebooks for any upstream or downstream analysis. Azure ML is a managed PaaS service, making it an accessible and easy to set up platform for genomics researchers and bioinformaticians. Additionally, it has a Visual Studio Code integration for local development and has a workspace concept for managing pipeline projects, enabling collaboration, and Azure role-based access control (RBAC). In conclusion, Azure ML comes with advanced security features, including AD authentication, public & private endpoints, subscription-based event triggers, storage backed by the Azure Storage Service that comes with encryption at rest and in transit, and application insights, making it a reliable and already proven enterprise platform that can also be natively used for genomics research. For a more detailed tutorial that shows how to set up and run the example workflow shown in Figure 1, as well as for all the source code for creating the aforementioned sample environments and components, please check out this GitHub repository: truehand/azureml-genomics (github.com)
