Operationalizing AI powered medical imaging pipeline for cohort building
Authors: Jared Erwin, Senior Software Engineer, HLS Nursing AI and Data Platform, Faculty UW School of Medicine Manoj Kumar, Director, HLS - Data & AI HLS Frontiers AI Alberto Santamaria-Pang, Principal Applied Data Scientist, HLS Frontiers AI and Adjunct Faculty, Johns Hopkins Medicine Overview In Part 1, of this series, we showed how natural language could be used to define medical imaging cohorts and retrieve relevant studies in seconds instead of months. That proof-of-concept demonstrated the value of the idea — but not how to make it repeatable, or production-ready. This post focuses on how we turned that prototype into a production-oriented Azure Machine Learning pipeline — to scale execution and produce clear, versioned artifacts that could drive an interactive cohort exploration UI. If you're building ML pipelines for medical imaging, or any domain where data is large, messy, and locked behind access controls, we hope our experience saves you time. From scripts to a pipeline: Why Azure ML components? The original hackathon implementation consisted of notebooks and scripts that required careful manual execution. To make the system repeatable and auditable, we standardized it using Azure ML pipelines. Azure ML pipelines gave us: Componentized execution — each processing step is a self-contained unit with defined inputs, outputs, and dependencies Parallel branches — steps that don't depend on each other run concurrently Reproducibility — every run is versioned and logged with full lineage Compute flexibility — run on CPU for metadata extraction, GPU for model inference, without manual orchestration The pipeline architecture The pipeline consists of 5 python components arranged in a DAG with two parallel branches: [0]scans a DICOM directory and extracts metadata from headers — study/series UIDs, modality, body part, slice counts. [1]classifies each series by anatomy and orientation using a multi-tier strategy (more on this below). [2] and [3] form the search pipeline: anatomy labels are converted to natural language text templates, then encoded with BiomedCLIP into a FAISS vector index. [4]generates 2D UMAP coordinates from the embeddings for the interactive scatter plot visualization in the UI. The image depicts a flowchart detailing the process of DICOM metadata extraction, anatomy classification, visualization enrichment, and text template generation, followed by the creation of a FAISS vector index. Components 2 and 4 run in parallel after component 1 completes, saving roughly 10-15% of total execution time. It's a modest gain for a single run, but it adds up when iterating on pipeline parameters. [1] Anatomy classification, integrating MedImageInsight The Anatomy classification component in the pipeline relies on MedImageInsight (MI2). MedImageInsight is Microsoft's foundation model for medical image understanding, available through the Azure AI Foundry model catalog. Unlike generative models, MedImageInsight is an embedding model — it maps medical images and text into a shared 1024-dimensional vector space, enabling tasks like classification and similarity search by comparing image embeddings against text label embeddings. Given a DICOM image, we compare its embedding against candidate labels (e.g., "Brain", "Chest", "Abdomen") to determine the body part, scan orientation, and other imaging characteristics through zero-shot classification. We also may get directly annotated anatomy from component 0, the DICOM metadata extractor component. We can combine both data points to build our final search index. [2] [3] FAISS index construction As an input to the FAISS index, we first run component 2, the text template generator. This component takes the metadata and anatomy information from components 0 and 1 and feeds them into 5 different agents with different instructions on how to describe the DICOM study. This results in textual descriptions which some variation, referred to as text templates, which can be indexed in the next component The FAISS index builder (component 3) uses BiomedCLIP to encode all text templates into 512-dimensional vectors: MODEL_NAME = "hf-hub:microsoft/BiomedCLIP-PubMedBERT_256-vit_base_patch16_224" @torch.no_grad() def encode(self, texts: List[str], batch_size: int = 256) -> np.ndarray: embeddings = [] for i in range(0, len(texts), batch_size): batch = texts[i:i+batch_size] tokens = self.tokenizer(batch).to(self.device) batch_embeddings = self.model.encode_text(tokens) batch_embeddings = F.normalize(batch_embeddings, dim=-1) # L2 normalize embeddings.append(batch_embeddings.cpu().numpy()) return np.vstack(embeddings) We L2-normalize all vectors and use faiss.IndexFlatIP (inner product), which is equivalent to cosine similarity on normalized vectors. For our current dataset sizes (thousands of series), flat indexing is fast enough. For hospital-scale datasets with millions of images, we might switch to IndexIVFFlat or IndexHNSW for approximate nearest neighbor search. In the cohort explorer app, a user will enter a natural language query, which is then converted to embeddings using the same BiomedCLIP model. This allows a search using the FAISS index to find relevant DICOM studies. [4] Visualization: making embeddings explorable The scatter plot in the UI is often the first thing users interact with. It needs to show meaningful clusters without requiring users to understand dimensionality reduction. Component 4 takes the embeddings from component 1 and projects them to 2D with UMAP: umap = UMAP( n_components=2, n_neighbors=10, # Balances local vs. global structure min_dist=0.5, # Prevents over-clustering metric='cosine', # Matches our embedding similarity metric random_state=42 # Reproducible layouts ) coordinates_2d = umap.fit_transform(features) Each point in the scatter plot corresponds to a single DICOM series produced by the pipeline, with color, grouping, and hover metadata derived directly from the JSON artifacts emitted by components 1 and 4. Each pipeline run produces a small set of well-defined artifacts — metadata tables, embedding vectors, UMAP coordinates, and the FAISS index — which are consumed directly by the cohort exploration UI. The cohort explorer application can reload or switch between datasets. The diagram is a screen capture of an Azure ML pipeline. It includes 5 pipeline components along with connecting arrows showing incoming and outgoing data, including the final outputs of the pipeline. Pipeline execution: time, cost, and what we learned Here's what a typical pipeline run looks like for a dataset of ~4,500 DICOM series: Component Task Approximate Time (CPU) Approximate Time (GPU) 0 - DICOM Metadata Extractor Scan files, extract headers 5-10 min 5-10 min 1 - Anatomy Classification Classify anatomy/orientation 90-120 min 5-10 min 2 - Text Template Generator Generate 5 templates per series 5-10 min 5-10 min 3 - FAISS Index Builder BiomedCLIP encoding + FAISS build 60-90 min 10-15 min 4 - Visualization Enrichment UMAP + color assignment 20-40 min 5-10 min Azure ML overhead Compute provisioning, env setup 5-10 min 5-10 min Total ~200-300 min ~30-50 min Key observations: Azure ML overhead is significant when doing quick iteration and testing. Compute provisioning, conda environment builds, and data mounting add several minutes before any component code runs. We first built each component as python code to run locally and debug before our first Azure ML run. This way we quickly iterated and avoided cost until we were ready. BiomedCLIP encoding dominates on CPU. Component 3 is the bottleneck. Moving to GPU compute for this component cuts encoding time roughly in half, but GPU clusters cost more. For a pipeline you run occasionally, CPU is fine. For frequent re-indexing, GPU pays for itself. Batch size tuning matters. The default BiomedCLIP batch size of 256 balances memory and throughput. On GPU, you can push to 512. On CPU with limited RAM, drop to 128. At Scale: 120,000 Images, CPU vs. GPU We ran the full pipeline against a larger dataset of ~120,000 images to understand how compute choice affects end-to-end time and cost: CPU Pipeline GPU Pipeline Pipeline compute time 4 days, 12 hours (108 hrs) 15 hours Pipeline compute cost ~$0.25/hr × 108 hrs = ~$27 ~$3.00/hr × 15 hrs = ~$45 MedImageInsight endpoint (MaaP on Standard_NC4as_T4_v3) ~$151 ~$21 Total estimated cost ~$178 ~$66 Both pipeline runs make the same ~120,000 classification calls to the MedImageInsight endpoint, but those calls are spread out over different time periods depending on how quickly and efficiently the pipeline can make the calls to MedImageInsight. The hourly cost for MedImageInsight on a Standard_NC4as_T4_v3 VM is ~$1.40/hr. Resulting in the estimated costs for MedImageInsight in the table above. GPU compute was roughly 7× faster at about 0.37× the total cost when endpoint costs are included. This was a key learning and clearly indicates the benefits of the more powerful compute resources. MedImageInsight can be deployed in two ways, depending on dataset size and operational needs. For smaller or infrequently processed datasets, we deploy MedImageInsight as a managed Azure ML online endpoint and invoke it from the pipeline. This keeps the pipeline simpler and avoids managing the MedImageInsight compute directly, while offering comparable performance at modest scale. For larger batch workloads, an alternative approach is to load MedImageInsight directly on the Azure ML pipeline’s GPU-backed compute. In this model, the pipeline handles both model loading and classification, eliminating per-request network round trips and the fixed cost of hosting a persistent endpoint. While this approach requires slightly longer pipeline run time, it becomes more cost‑effective at scale by avoiding endpoint overhead and improving throughput during bulk processing. Possible future enhancements Additional modalities: Extending the pipeline and classification to CT, X-ray, and ultrasound imaging, and build on the pattern for pathology images Image embeddings fusion: Combining MedImageInsight image embeddings with text embeddings for hybrid search Condition-aware search: Enabling queries about findings and conditions, not just imaging parameters The gap between a hackathon demo and a production system is where the real engineering happens. We hope sharing our journey helps others building similar systems. If you’re interested in partnering with us to work toward this goal or need access to the GitHub repo with the pipeline and UI code, contact authors through your Microsoft account team or reach out to Microsoft HLS AI frontier team The healthcare AI models in Microsoft Foundry are intended for research and model development exploration. The models are not designed or intended to be deployed in clinical settings as-is nor for use in the diagnosis or treatment of any health or medical condition, and the individual models' performances for such purposes have not been established. You bear sole responsibility and liability for any use of the healthcare AI models, including verification of outputs and incorporation into any product or service intended for a medical purpose or to inform clinical decision-making, compliance with applicable healthcare laws and regulations, and obtaining any necessary clearances or approvals.
Driving AI‑Powered Healthcare: A Data & AI Webinar and Workshop Series
Across these sessions, you’ll learn how healthcare organizations are using Microsoft Fabric, advanced analytics, and AI to unify fragmented data, modernize analytics, and enable intelligent, scalable solutions, from enterprise reporting to AI‑powered use cases. Whether you’re just getting started or looking to accelerate adoption, these sessions offer practical guidance, real‑world examples, and hands‑on learning to help you build a strong data foundation for AI in healthcare. Date Topic Details Location Registration Link May 6 Webinar: Microsoft Fabric Foundations - A Simple Path to Modern Analytics and AI Discover how Microsoft Fabric consolidates fragmented analytics into a single integrated data platform, making it easier to deliver trusted insights and adopt AI without added complexity. Virtual Register May 13 Webinar: Reduce BI Sprawl, Cut Cost and Build an AI-Ready Analytics Foundation Learn how Power BI enables enterprise BI consolidation, consistent metrics, and secure, scalable analytics that support both operational reporting and emerging AI use cases. Virtual Register May 19-20 In Person Workshop: Driving AI‑Powered Healthcare: Advanced Analytics, AI, and Real‑World Impact Attend this two‑day, in‑person event to learn how healthcare organizations use Microsoft Fabric to unify data, accelerate AI adoption, and deliver measurable clinical and operational value. Day 1 focuses on strategy, architecture, and real‑world healthcare use cases, while Day 2 offers hands‑on workshops to apply those concepts through guided labs and agent‑powered solutions. Chicago Register May 27 Webinar: Unified Data Foundation for AI & Analytics - Leveraging OneLake and Microsoft Fabric This session shows how organizations can simplify fragmented data architectures by using Microsoft Fabric and OneLake as a single, governed foundation for analytics and AI. Virtual Register June 3-4 In Person Workshop: Driving AI‑Powered Healthcare: Advanced Analytics, AI, and Real‑World Impact Attend this two‑day, in‑person event to learn how healthcare organizations use Microsoft Fabric to unify data, accelerate AI adoption, and deliver measurable clinical and operational value. Day 1 focuses on strategy, architecture, and real‑world healthcare use cases, while Day 2 offers hands‑on workshops to apply those concepts through guided labs and agent‑powered solutions. New York Register June 10 Webinar: From Data to Decisions: How AI Data Agents in Microsoft Fabric Redefine Analytics Join us to learn how Fabric Data Agents enable users to interact with enterprise data through AI‑powered, governed agents that understand both data and business context. Virtual Register June 23-24 In Person Workshop: Driving AI‑Powered Healthcare: Advanced Analytics, AI, and Real‑World Impact Attend this two‑day, in‑person event to learn how healthcare organizations use Microsoft Fabric to unify data, accelerate AI adoption, and deliver measurable clinical and operational value. Day 1 focuses on strategy, architecture, and real‑world healthcare use cases, while Day 2 offers hands‑on workshops to apply those concepts through guided labs and agent‑powered solutions. Dallas RegisterThe Agent Era Has Already Arrived in Healthcare. Are You Ready to Govern It?
Start here. Answer honestly. Right now, how many AI agents are running inside your organization? Who built them? Which patient data, claims information, or proprietary research are they configured to access? If your CISO walked into your office tomorrow and asked for a complete inventory of every agent in your enterprise, including each one's owner, the systems it is permitted to access, and the policies that govern how it operates, could you produce that inventory before lunch? When the analyst who built that clinical summarization agent moves to a new role next quarter, what happens to the agent? Does its access continue? Does anyone notice? If a regulator opened an audit tomorrow, could you prove that every AI agent operating in your environment is subject to the same lifecycle controls, identity standards, and data protection policies you apply to your human workforce? Could you disable a compromised agent enterprise-wide with a single click, the same way you would revoke a lost access credential? If those questions made you hesitate, you are not alone. Almost no healthcare or life sciences organization can answer them confidently today. And that gap is exactly where the next decade of risk, and the next decade of competitive advantage, will be decided. The quiet crisis nobody talks about yet Healthcare and life sciences leaders are caught in a paradox. You need AI to survive the operational pressures squeezing your organization from every direction. Physician burnout is at crisis levels, with 45.2% of US physicians reporting symptoms in recent Mayo Clinic research. Revenue cycle complexity continues to climb, and McKinsey now estimates that the cost to collect consumes 30 to 60 percent of net patient revenue at many provider organizations. Prior authorization backlogs delay care. Clinical trial timelines stretch into years. Documentation burden eats hours that belong to patients. So you started piloting Microsoft 365 Copilot. You experimented with agents in Copilot Studio. Maybe a clinical team built an agent to draft discharge summaries. A revenue cycle group spun up an agent to triage denials. A medical affairs team built one to comb through literature. Each one delivered value. Each one was approved on its own merits. And then a quiet thing happened. You lost track of how many agents you have. According to KPMG's AI Quarterly Pulse Survey, 88 percent of organizations are now exploring or piloting AI agents. IDC projects that 1.3 billion agents will be in operation by 2028. Inside your own walls, the number is climbing fast. Each new agent is a digital identity that authenticates into your environment, accesses your data, and executes work on behalf of your business. Most have no formal owner. Most have no documented access scope. Most have no decommissioning plan. Most have never been reviewed by Compliance. Microsoft's 2024 Data Security Index found that 84 percent of organizations lack confidence in their AI data security posture, and 40 percent have already experienced an AI related data security incident. That is not a future problem. That is a now problem. If shadow IT was the defining governance challenge of the last decade, agent sprawl is the defining challenge of this one. And in healthcare and life sciences, where ePHI, member PII, and proprietary clinical trial data are at stake, the consequences are not theoretical. They are existential. The reframe that changes everything Here is the counterintuitive truth that separates HLS organizations that scale AI from those stuck in pilot purgatory. Governance is not the brake on AI adoption. Governance is the accelerator. When security, identity, and agent oversight are engineered in from day one, your teams stop tiptoeing. They build with confidence because the guardrails are real. They expand into clinical use cases because Compliance trusts the foundation. They scale wall-to-wall because IT can prove every agent is accounted for. The organizations that lead with trust end up moving faster in the long run, not slower. This is the bet behind Microsoft Agent 365 and Microsoft 365 E7. What Agent 365 and Microsoft 365 E7 actually are Microsoft 365 E7, announced March 6, 2026 and now generally available, is the Frontier Suite. It is Microsoft's answer to a single question that every healthcare CIO, CISO, and COO is wrestling with: how do you run AI safely, at scale, across an entire organization? E7 is not another SKU on top of your existing stack. It is one cohesive platform that brings together four essential capabilities: Microsoft 365 E5 for your enterprise productivity, collaboration, and security foundation, including Microsoft Defender, Microsoft Purview, and Microsoft Intune. Microsoft 365 Copilot for AI grounded in your organizational data through Work IQ, embedded in the flow of work for clinicians, researchers, operations teams, and administrators. Microsoft Entra Suite for identity governance, Conditional Access, and Zero Trust network access, extended consistently across users, applications, and AI agents. Microsoft Agent 365 as the centralized control plane to observe, govern, and secure every AI agent, whether built by Microsoft, your internal teams, or external partners. Agent 365 is also available as a standalone capability. But the magic happens when it works alongside the rest of E7, because that is where AI, identity, security, and governance stop being separate disciplines and become one operating system for the agentic era. The mental model that unlocks everything: agents are first-class digital identities Here is the simplest way to understand what Agent 365 does. Microsoft 365 governs your enterprise identities. Agent 365 governs your agent identities. The same control plane disciplines apply to both. Think about the rigor you apply to any privileged identity in your environment, whether a service account, an API integration, or a third-party application connector. You issue it a unique identity in Microsoft Entra. You assign a human owner who is accountable. You scope its access to least privilege. You apply DLP, sensitivity labels, and Conditional Access. You monitor for anomalous behavior. You have a documented decommissioning path. Identities that no one watches over become identities that get exploited. Now ask yourself how the last AI agent in your environment was created. The honest answer at most organizations: someone opened Copilot Studio, pointed it at a SharePoint library of clinical protocols, gave it a name, and moved on. No documented owner. No access review. No retirement plan. Compliance was never consulted. You would never stand up a privileged service account that way. Yet that is exactly how most organizations are standing up the fastest-growing class of digital identities in their environment. Agent 365 closes that gap by extending the identity, security, and lifecycle controls you already trust for users and applications so they apply with the same rigor to AI agents. Every agent receives a unique Entra Agent ID, a first-class identity in Azure AD with the same governance primitives as any other privileged identity. Every agent has a designated human owner who is accountable for its scope and behavior. Access is granted explicitly through Conditional Access and policy templates, so each agent operates only against the resources its purpose requires. Microsoft Purview DLP and sensitivity labels govern which data the agent is permitted to read, generate, or share. Microsoft Defender monitors agent activity for anomalies and surfaces alerts the same way it does for any other identity-driven risk. Lifecycle rules flag or auto-retire agents that are dormant, orphaned, or risky, eliminating the unowned automations that quietly accumulate in every enterprise. This is not metaphor. It is the actual architecture. The fastest path to governing agents is to extend the identity infrastructure you already trust. The three pillars of Agent 365: Observe, Govern, Secure Pillar 1: Observe. Know what is actually happening. You cannot govern what you cannot see. The first job of Agent 365 is to give you complete, continuous visibility into every AI agent operating in your environment. The Agent Registry is the single authoritative inventory of every agent, whether built by Microsoft, custom developed by your team, deployed by a partner, or discovered as a shadow agent operating without oversight. Each entry shows the owner, purpose, capabilities, lifecycle status, and business context. Agent Analytics tracks adoption, quality, performance, and business impact. Agent Map visualizes how agents connect with other agents, people, tools, and data sources, surfacing dependencies and risk concentrations you would never spot in a spreadsheet. Real time monitoring flows directly into Microsoft Defender, so unusual agent behavior generates alerts the same way unusual user behavior does today. For a health system CISO, that means finally being able to answer the question: which agents are touching ePHI, and is every one of them authorized? For a life sciences compliance officer, it means audit ready visibility into every AI system operating across R&D, regulatory affairs, and commercial. For a payer operations leader, it means knowing which claims processing agents are actually delivering accuracy and throughput, and which are quietly underperforming. Pillar 2: Govern. Set the rules. Control the lifecycle. Visibility is the start. Control is what turns visibility into outcomes. Agent 365 ensures that every agent is approved, compliant, and accountable from creation through retirement. IT led onboarding workflows make sure each agent launches with the right identity, access, and ownership before it ever touches data. Policy templates enforce data handling, permission, and usage rules consistently from day one through Defender, Entra, and Purview. Rules based agent management gives admins an automated If This Then That interface. If an agent is unused for 90 days, auto retire it. If an agent is flagged as risky, block it and alert the security operations team. No human in the loop required for the routine cases, full alerting and override for the exceptions. Ownership enforcement requires every agent to have a designated human owner. When that owner leaves the organization, the platform flags the orphaned agent for bulk reassignment, so nothing operates without clear accountability. The Tools Gateway brokers and audits tool access for agents, enabling least privilege at the action level, not just the identity level. For HLS specifically, that translates to outcomes you can take to your board. A hospital CIO can ensure any agent touching Epic or Cerner goes through standardized approval. A pharma IT director can enforce that clinical trial matching agents only touch de identified data unless elevated permissions are explicitly granted and documented. A payer compliance team can automatically retire agents tied to a completed open enrollment campaign instead of letting them silently expand the attack surface. Pillar 3: Secure. Protect agents and data with the stack you already trust. The final pillar is what makes Agent 365 production grade for healthcare and life sciences. Security and compliance are not bolted on. They are the same proven Microsoft security stack you already run for your users, extended natively to agents. Microsoft Purview, your data security and compliance backbone: Data Security Posture Management for AI gives visibility into how agents interact with sensitive data and detects risky usage patterns. Data Loss Prevention stops agents from accessing or processing files labeled Highly Confidential, even when a user prompts them to. Sensitivity labels are inherited automatically by agent outputs, governing how data is viewed, extracted, or shared downstream. Insider Risk Management detects risky behavior by users interacting with agents, such as unusual prompt patterns or excessive access to sensitive data. Communication Compliance monitors AI driven interactions for regulatory or ethical violations and unauthorized disclosures. eDiscovery and Audit logs every agent interaction, giving legal, compliance, and IT teams the transparency required for HIPAA, GDPR, and FDA 21 CFR Part 11. Oversharing Assessments run weekly checks for sensitive data exposure across SharePoint sites and agent access patterns. Microsoft Entra, your identity control plane: Entra Agent ID gives every agent a unique identity in Azure AD, so Conditional Access, role based access, and risk based policies apply individually. Conditional Access for agents enforces policies like only allow this prior authorization agent to access claims data from approved devices and locations during business hours. Identity Governance provides access packages for agents with reduced scope permissions and least privilege defaults. Block at Scale lets you instantly disable all high-risk agents from Entra in a single action. Microsoft Defender, your threat protection layer: Security Posture Management identifies and remediates agent misconfigurations, such as agents running with no authentication. Threat Detection and Blocking monitors suspicious agent activity, generates alerts, and blocks unauthorized tool invocations. Threat Investigation and Hunting collects unified agent observability logs so SOC teams can forensically trace every action an agent took. One Click Kill Switch instantly disables any agent and surfaces the complete audit trail of every action it took before being stopped. For a hospital security operations team, that means the same DLP policies protecting patient records in email and Teams now protect agents that summarize clinical notes. For a life sciences data protection officer, it means agents accessing proprietary compound data respect the same sensitivity labels as human researchers. For a payer CISO, it means an anomalous claims agent can be killed in seconds, with a complete forensic record of every member record it touched. Why this only works as an integrated platform Individual capabilities are useful. Integration is what makes them transformative. Here is the contrast HLS leaders feel today versus what changes the moment E7 lights up. Without an integrated platform, you operate with: Fragmented tools for identity, security, compliance, and AI, each with its own console and its own gaps. No centralized agent inventory, forcing your IT and security teams to track bots and automations in spreadsheets. Inconsistent policy enforcement across agents, creating compliance gaps every audit team will eventually find. Blind spots where agents access data, invoke tools, or interact with other agents without any oversight. Manual triage when an incident hits, because nothing connects user identity, agent identity, and data classification in one view. With Microsoft 365 E7, you gain: A Unified Agent Registry providing a single source of truth for every agent, whether Microsoft built, custom developed, partner deployed, or shadow discovered. Entra Agent ID giving each agent a unique identity, so Conditional Access, role based access, and risk based policies apply at the individual agent level. Full lifecycle governance with standardized onboarding, periodic review, ownership transfers, auto retirement of dormant agents, and structured offboarding. Policy by design, where Purview DLP, sensitivity labels, and compliance rules extend to all agent interactions through pre built templates applied consistently from day one. One click disable to instantly freeze any agent, with Defender threat detection extended to agents and full audit trails for forensic investigation. Expanded threat coverage that addresses agent sprawl, overprivileged access, tool misuse, misconfiguration, and inter agent risk patterns no legacy tool was designed to see. Shared registry and controls that let IT, Security, and Compliance reference the same authoritative inventory across Defender, Entra, and Purview, eliminating the silos that slow incident response. This is the reason E7 exists as a platform, not a bundle. AI, identity, security, and governance stop being separate disciplines and start operating as one system. What this is actually worth: the Forrester numbers Microsoft commissioned Forrester to conduct a Total Economic Impact study of Microsoft 365 Copilot, published in March 2025. The composite organization in that study, modeled on real customer interviews, achieved: 132 percent three-year ROI with payback in under one year. 9 hours saved per Copilot user per month through automation of routine work like drafting, summarizing, and analysis. Up to 2.6 percent top line revenue lift through better qualified opportunities, improved win rates, and stronger retention in customer facing teams. 25 percent acceleration in new employee onboarding as new hires ramp faster on summarized institutional knowledge. Those are the verified numbers. The bigger story for HLS is what they look like when applied to clinical, claims, and research workflows where every reclaimed hour is an hour that goes back to patients, members, or science. AI is already defending AI The same agentic capabilities transforming clinical and operational workflows are now embedded in your security stack. Microsoft Security Copilot agents work alongside human analysts inside Defender, Entra, Purview, and Intune, accelerating threat response and absorbing the manual load that today drowns most security operations teams. Independent benchmarks back the impact. In a 162 admin randomized study published in 2025, the Conditional Access Optimization Agent in Microsoft Entra completed configuration tasks 43 percent faster and produced 48 percent more accurate Conditional Access policies than admins working without it. Security triage, alert investigation, and identity hygiene are following the same trajectory. For HLS security teams already stretched thin, that is hours reclaimed every week to focus on the threats that actually matter, with the same Agent 365 governance applying to the security agents themselves. The defenders are governed by the same rules as the workforce they defend. How HLS organizations are putting Agent 365 to work Here is how the value shows up across the three biggest HLS segments. For providers: reclaiming time for care The challenge: clinicians spend more time on documentation than on patients. Care coordination is fragmented. Burnout is gutting retention. The strategy: deploy agents that absorb administrative load while Agent 365 ensures every one of them respects ePHI boundaries. Clinical documentation agents integrated with Microsoft Dragon Copilot structure dictation against EHR requirements, apply billing codes, and flag missing elements before submission. Care coordination agents generate care plans, allocate tasks, and surface relevant patient context during multidisciplinary rounds, optimized for HL7 FHIR interoperability. Patient intake and scheduling agents built in Copilot Studio handle appointment booking, reminders, eligibility verification, and referral management. Handoff and shift summary agents pull from multiple systems to generate complete handoff summaries for nurses and physicians transitioning between shifts, reducing communication gaps that drive adverse events. The aha moment: applied across a 10,000 employee health system, nine hours per user per month is more than one million reclaimed hours a year. That is the equivalent of hundreds of full time clinicians, returned to direct patient care, with every agent governed under the same Conditional Access and DLP policies your IT team already manages today. For payers: transforming revenue cycle and member experience The challenge: prior auth backlogs delay care. Denial rates climb. Member services teams drown in volume. The strategy: agentic AI rewires the most expensive, most manual workflows in your operation while Agent 365 keeps every agent inside the lines on member PII. Prior authorization agents autonomously gather clinical documentation, cross reference medical policy, determine approval criteria, and route decisions, accelerating turnaround from days to hours. Claims processing agents automate billing and denial management. With cost to collect running 30 to 60 percent of net patient revenue at many organizations, even modest automation produces material margin recovery. Denial resolution and appeals agents analyze denial patterns, surface root causes, generate appeal documentation, and track success rates over time, turning a cost center into a continuous improvement engine. Member services agents integrated with Microsoft 365 Copilot Chat handle benefits inquiries, claims status, and self service triage, deflecting call volume and improving first contact resolution. Fraud detection and risk adjustment agents scan claims data for anomalies and optimize coding accuracy for Medicare Advantage and ACA populations. The aha moment: a payer CISO can disable an anomalous prior auth agent in one click and produce a complete forensic record of every member record it accessed, while Compliance simultaneously confirms the agent never violated DLP. That is regulatory readiness that legacy automation cannot deliver. For life sciences and pharma: accelerating discovery and commercialization The challenge: clinical trials take years. Regulatory submissions consume teams. Medical affairs cannot keep up with literature volume. The strategy: orchestrate agents across R&D, regulatory, medical, and commercial, with Agent 365 enforcing the data classification rules that proprietary IP and clinical data demand. Clinical trial matching agents scan patient profiles and eligibility criteria to surface trial opportunities, accelerating recruitment. Regulatory document preparation agents assemble submissions, cross reference data across modules, and ensure consistency in FDA, EMA, and global filings. Medical research and literature review agents powered by Microsoft GraphRAG retrieve research backed insights with verified source references, giving medical science liaisons trustworthy synthesis on demand. Pharmacovigilance agents monitor safety databases, flag potential adverse events, and generate timely case reports. Commercial insights and launch planning agents synthesize market data, payer policy, and HCP sentiment for sharper launch and field strategy. The aha moment: cutting even three months off a regulatory cycle on a single high revenue product can mean tens of millions in additional sales, while Purview sensitivity labels guarantee every agent accessing proprietary compound data respects the same data classification as your senior researchers. A phased path that actually works in regulated industries In regulated industries, a big bang AI rollout is a recipe for incidents. The HLS organizations getting this right are following a five-phase pattern that builds expertise and validates governance before scale. Establish. Form a cross-functional champion team across IT, Compliance, Clinical Operations, and Research. Define what risks you are mitigating and what outcomes you are unlocking. Inventory the agents already in flight. Configure. Stand up identity, DLP, and policy templates in Microsoft 365 Admin Center, Power Platform Admin Center, and Microsoft Purview. Enforce that any agent handling PHI runs in a secure environment with audit logging on by default. Pilot. Choose a small group of makers in a controlled environment. Start with non-critical workflows like internal reporting or scheduling before moving to clinical or member facing use cases. Run weekly reviews with Compliance and Security. Empower. Launch role specific training for clinicians, researchers, makers, and IT. Stand up a Center of Excellence to provide templates, best practices, and reusable patterns. Promote success stories internally to build momentum. Scale. Expand agent development across departments with governance as a guardrail, not a gate. Use pay as you go metering to track usage and optimize licensing. Refine policies continuously based on Purview signals and audit results. The strategic insight: organizations that lead with governance reach scale faster than those that lead with experimentation. Trust is the unlock, not the obstacle. Governance is a team sport Here is the pattern we see again and again. The HLS organizations that succeed with AI at scale are not the ones with the smartest IT shop or the boldest Compliance officer. They are the ones whose IT, Security, Compliance, Clinical, Research, and Operations leaders sit at the same table on agent strategy from week one. Agent 365 was designed for that table. The Agent Registry is the shared truth. Purview policies satisfy your Compliance officer. Entra controls reassure your CISO. The lifecycle workflows give your CIO confidence. The clinical and research outcomes give your COO and Chief Medical Officer the business case. Everyone gets the view they need from the same single source. Stand up an agent governance council. Meet every two weeks. Use the Agent Registry as your standing agenda. Make decisions in plain sight. The organizations that do this consistently outperform on both speed and safety. The ones that try to keep AI inside a single function fall behind on both. Who contributes what Think back to the mental model. You would never let a single function authorize, configure, and oversee a new privileged system on its own, not when it touches ePHI, claims, or proprietary research. Security, IT, Compliance, Clinical, and the relevant business owner all weigh in because the stakes are too high for any one seat to carry alone. Agent governance demands the same multidisciplinary scrutiny, and the council is where that happens. Each seat brings something the others cannot. CIO. Owns the agent strategy and the platform investment. Translates board-level AI ambition into an operating model the rest of the organization can execute against. CISO and Security Operations. Define agent identity standards, Conditional Access policies, and incident response playbooks. Without this seat, an anomalous agent touching ePHI becomes a breach instead of a contained event. Chief Compliance Officer and Privacy. Translate HIPAA, GDPR, FDA 21 CFR Part 11, and state regulations into Purview policies and audit requirements. This is the seat that keeps you out of an OCR investigation or a 483 letter. Chief Medical Officer and Clinical Operations. Validate that clinical agents are safe, accurate, and aligned with care standards. Own the clinical risk review for any agent that touches patient care, the same way you would for a new clinical protocol. Chief Research Officer or Head of R&D. Govern how agents interact with proprietary trial data, compound libraries, and scientific IP. The seat that protects the next decade of pipeline value. COO and Revenue Cycle Leadership. Prioritize the operational workflows where agents will move the needle on cost to collect, denial rates, and throughput, and own the business outcomes that justify the investment. Center of Excellence Lead. Maintains templates, reusable patterns, and maker enablement. Turns every council decision into a guardrail builders can actually use the next morning. Frontline champions. Clinicians, claims specialists, and researchers who pilot, give feedback, and carry credibility back to their peers. The seat that decides whether agents get adopted or quietly ignored. When every one of these voices is in the room, your governance council operates like a tumor board for AI. Different lenses, one shared decision, full accountability. That is how regulated industries make complex calls safely, and it is exactly the muscle Agent 365 was built to support. Seven questions to bring to your next leadership meeting If you want to know whether your organization is ready, run through these together. The places you hesitate are exactly where Agent 365 and E7 deliver the most value. Visibility. Do you know which AI agents, bots, and automations are running in your environment today, who built them, what they have access to, and whether they are still needed? Control. If someone on your team builds a new AI agent tomorrow, what is the actual process to make sure it is approved and secured? Or could they deploy it with wide open access? Security. What prevents an AI agent from reading or transmitting patient data it should not? Do you have a way to detect and stop a rogue or compromised agent? Accountability. Who owns the outputs of an AI agent's actions? What is the offboarding process when the agent or its creator leaves? Scale. Six months from now, you may have a hundred agents deployed across departments. Are your oversight and compliance structures ready for that volume? Cross-functional alignment. How are your IT, Security, and Compliance teams partnering on AI today? Governance is a team sport. Data readiness. How confident are you that your data estate is clean, labeled, and governed well enough for AI to surface accurate answers and not outdated or conflicting information? If you hesitated on even one of those, you have just identified where Agent 365 and Microsoft 365 E7 will pay for themselves the fastest. The path forward Here is the honest truth. The healthcare and life sciences organizations that lead in the next decade will not be the ones that adopted AI first. They will be the ones that adopted AI safely, compliantly, and at scale, with intelligence and trust woven into every layer. Microsoft Agent 365 and Microsoft 365 E7 give you the only integrated platform that brings AI, identity, security, and governance into one cohesive system, running in the flow of work you already use. This is not about adding another tool to your stack. It is about extending the investments you have already made in Microsoft 365, Entra, Defender, and Purview to cover the fastest-growing class of digital identities in your environment. The agent era has already arrived. The question is whether you will govern it with confidence or chase it with anxiety. We would love to help you lead. Take the next step Explore Microsoft Agent 365: The Control Plane for Agents Microsoft Entra Agent ID: aka.ms/EntraAgentID Learn more about Microsoft 365 E7, the Frontier Suite: Introducing Microsoft 365 E7 See Microsoft 365 Copilot in action: Microsoft 365 Copilot Read the Forrester TEI study: The Total Economic Impact of Microsoft 365 CopilotHealthcare Agent Orchestrator: Multi-agent Framework for Domain-Specific Decision Support
At Microsoft Build, we introduced the Healthcare Agent Orchestrator, now available in Azure AI Foundry Agent Catalog . In this blog, we unpack the science: how we structured the architecture, curated real tumor board data, and built robust agent coordination that brings AI into real healthcare workflows. Healthcare Agent Orchestrator assisting a simulated tumor board meeting. Introduction Healthcare is inherently collaborative. Critical decisions often require input from multiple specialists—radiologists, pathologists, oncologists, and geneticists—working together to deliver the best outcomes for patients. Yet most AI systems today are designed around narrow tasks or single-agent architectures, failing to reflect the real-world teamwork that defines healthcare practice. That’s why we developed the Healthcare Agent Orchestrator: an orchestrator and code sample built around Microsoft’s industry-leading healthcare AI models, designed to support reasoning and multidisciplinary collaboration -- enabling modular, interpretable AI workflows that mirror how healthcare teams actually work. The orchestrator brings together Microsoft healthcare AI models—such as MedImageParse for image recognition, CXRReportGen for automated radiology reporting, and MedImageInsight for retrieval and similarity analysis—into a unified, task-aware system that enables developers to build an agent that reflects real-word healthcare decision making pattern. This work was led by Yu (Aiden) Gu, Principal Applied Scientist at Microsoft Research, who conceived the study, defined the research direction, and led the design and development of the Healthcare Agent Orchestrator proof-of-concept. Healthcare Is Naturally Multi-Agent Healthcare decision-making often requires synthesizing diverse data types—radiologic images, pathology slides, genetic markers, and unstructured clinical narratives—while reconciling differing expert perspectives. In a molecular tumor board, for instance, a radiologist might highlight a suspicious lesion on CT imaging, a pathologist may flag discordant biopsy findings, and a geneticist could identify a mutation pointing toward an alternate treatment path. Effective collaboration in these settings hinges not on isolated analysis, but on structured dialogue—where evidence is surfaced, assumptions are challenged, and hypotheses are iteratively refined. To support the development of healthcare agent orchestrator, we partnered with a leading healthcare provider organization, who independently curated and de-identified a proprietary dataset comprising longitudinal patient records and real tumor board transcripts—capturing the complexity of multidisciplinary discussions. We provided guidance on data types most relevant for evaluating agent coordination, reasoning handoffs, and task alignment in collaborative settings. We then applied LLM-based structuring techniques to convert de-identified free-form transcripts into interpretable units, followed by expert review to ensure domain fidelity and relevance. This dataset provides a critical foundation for assessing agent coordination, reasoning handoffs, and task alignment in simulated collaborative settings. Why General-Purpose LLMs Fall Short for Healthcare Collaboration While general-purpose large language models have delivered remarkable results in many domains, they face key limitations in high-stakes healthcare environments: Precision is critical: Even small hallucinations or inconsistencies can compromise safety and decision quality Multi-modal integration is required: Many healthcare decisions involve interpreting and correlating diverse data types—images, reports, structured records—much of which is not available in public training sets Transparency and traceability matter: Users must understand how conclusions are formed and be able to audit intermediate steps The Healthcare Agent Orchestrator addresses these challenges by pairing general reasoning capabilities with specialized agents that operate over imaging, genomics, and structured EHRs—ensuring grounded, explainable results aligned with clinical expectations. Each agent contributes domain-specific expertise, while the orchestrator ensures coherence, oversight, and explainability—resulting in outputs that are both grounded and verifiable. Architecture: Coordinating Specialists Through Orchestration Healthcare Agent Orchestrator. Healthcare Agent Orchestrator’s multi-agent framework is built on modular AI infrastructure, designed for secure, scalable collaboration: Semantic Kernel: A lightweight, open-source development kit for building AI agents and integrating the latest AI models into C#, Python, or Java codebases. It acts as efficient middleware for rapidly delivering enterprise-grade solutions—modular, extensible, and designed to support responsible AI at scale. Model Context Protocol (MCP): an open standard that enables developers to build secure, two-way connections between their data sources and AI-powered tools. Magentic-One: Microsoft’s generalist multi-agent system for solving open-ended web and file-based tasks across domains—built on Microsoft AutoGen, our popular open-source framework for developing multi-agent applications. Each agent is orchestrated within the system and integrated via Semantic Kernel’s group chat infrastructure, with support for communication and modular deployment via Azure. This orchestration ensures that each model—whether interpreting a lung nodule, analyzing a biopsy image, or summarizing a genomic variant—is applied precisely where its expertise is most relevant, without overloading a single system with every task. The modularity of the framework also future-proofs: as new health AI models and tools emerge, they can be seamlessly incorporated into the ecosystem without disrupting existing workflows—enabling continuous innovation while maintaining clinical stability. Microsoft’s healthcare AI models at the Core Healthcare agent orchestrator also enables developers to explore the capabilities of Microsoft’s latest healthcare AI models: CXRReportGen: Integrates multimodal inputs—including current and prior X-ray images and report context—to generate grounded, interpretable radiology reports. The model has shown improved accuracy and transparency in automated chest X-ray interpretation, evaluated on both public and private data. MedImageParse 3 : A biomedical foundation model for imaging parsing that can jointly conduct segmentation, detection, and recognition across 9 imaging modalities. MedImageInsight 4 : Facilitates fast retrieval of clinically similar cases, supports disease classification across broad range of medical image modalities, accelerating second opinion generation and diagnostic review workflows. Each model has the ability to act as a specialized agent within the system, contributing focused expertise while allowing flexible, context-aware collaboration orchestrated at the system level. CXRReportGen is included in the initial release and supports the development and testing of grounded radiology report generation. Other Microsoft healthcare models such as MedImageParse and MedImageInsight are being explored in internal prototypes to expand the orchestrator’s capabilities across segmentation, detection, and image retrieval tasks. Seamless Integration with Microsoft Teams Rather than creating new silos, Healthcare Agent Orchestrator integrates directly into the tools clinicians already use—specifically Microsoft Teams. Developers are investigating how clinicians can engage with agents through natural conversation, asking questions, requesting second opinions, or cross-validating findings—all without leaving their primary collaboration environment. This approach minimizes friction, improves user experience, and brings cutting-edge AI into real-world care settings. Building Toward Robust, Trustworthy Multi-Agent Collaboration Think of the orchestrator as managing a secure, structured group chat. Each participant is a specialized AI agent—such as a ‘Radiology’ agent, ‘PatientHistory’ agent, or 'ClinicalTrials‘ agent. At the center is the ‘Orchestrator’ agent, which moderates the interaction: assigning tasks, maintaining shared context, and resolving conflicting outputs. Agents can also communicate directly with one another, exchanging intermediate results or clarifying inputs. Meanwhile, the user can engage either with the orchestrator or with specific agents as needed. Each agent is configured with instructions (the system prompt that guides its reasoning), and a description (used by both the UI and the orchestrator to determine when the agent should be activated). For example, the Radiology agent is paired with the cxr_report_gen tool, which wraps Microsoft’s CXRReportGen model for generating findings from chest X-ray images. Tools like this are declared under the agent’s tools field and allow it to call foundation models or other capabilities on demand—such as the clinical_trials tool 5 for querying ClinicalTrials.gov. Only one agent is marked as facilitator, designating it as the moderator of the conversation; in this scenario, the Orchestrator agent fills that role. Early observations highlight that multi-agent orchestration introduces new complexities—even as it improves specialization and task alignment. To address these emergent challenges, we are actively evolving the framework across several dimensions: Mitigating Error Propagation Across Agents: Ensuring that early-stage errors by one agent do not cascade unchecked through subsequent reasoning steps. This includes introducing critical checkpoints where outputs from key agents are verified before being consumed by others. Optimizing Agent Selection and Specialization: Recognizing that more agents are not always better. Adding unnecessary or redundant agents can introduce noise and confusion. We’ve implemented a systematic framework that emphasizes a few highly suited agents per task —dynamically selected based on case complexity and domain needs—while continuously tracking performance gains and catching regressions early. Improving Transparency and Hand-off Clarity: Structuring agent interactions to make intermediate outputs and rationales visible, enabling developers (and the system itself) to trace how conclusions were reached, catch inconsistencies early, and intervene when necessary. Adapting General Frameworks for Healthcare Complexity Generic orchestration frameworks like Semantic Kernel provide a strong foundation—but healthcare demands more. The stakes are higher, the data more nuanced, and the workflows require precision, traceability, and regulatory compliance. Here’s how we’ve extended and adapted these systems to help address healthcare demands: Precision and Safety: We introduced domain-aware verification checkpoints and task-specific agent constraints to reduce inappropriate tool usage—supporting more reliable reasoning. To help uphold the high standards required in healthcare, we defined two complementary metric systems (Check Healthcare Agent Orchestrator Evaluation for more details): Core Metrics: monitor health agents selection accuracy, intent resolution, contextual relevance, and information aggregation RoughMetric: a composite score based on ROUGE that helps quantify the precision of generated outputs and conversation reliability. TBFact: A modified version of RadFact 2 that measures factuality of claims in agents' messages and helps identifying omissions and hallucination Domain-Specific Tool Planning: Healthcare agents must reason across multimodal inputs—such as chest X-rays, CT slices, pathology images, and structured EHRs. We’ve customized Semantic Kernel’s tool invocation and planning modules to reflect clinical workflows, not generic task chains. These infrastructure-level adaptations are designed to complement Microsoft Healthcare AI models—such as CXRReportGen, MedImageParse, and MedImageInsight—working together to enable coordinated, domain-aware reasoning across complex healthcare tasks. Enabling Collaborative, Trustworthy AI in Healthcare Healthcare demands AI systems that are as collaborative, adaptive, and trustworthy as the clinical teams they aim to support. The Healthcare Agent Orchestrator is a concrete step toward that vision—pairing specialized health AI models with a flexible, multi-agent coordination framework, purpose-built to reflect the complexity of real clinical decision-making. By aligning with existing healthcare workflows and enabling transparent, role-specific collaboration, this system shows promise to empower clinicians to work more effectively—with AI as a partner, not a replacement. Healthcare Multi-Agent Orchestrator and the Microsoft healthcare AI models are intended for research and development use. Healthcare Multi-Agent Orchestrator and the healthcare AI models not designed or intended to be deployed in clinical settings as-is nor is it intended for use in the diagnosis or treatment of any health or medical condition, and its performance for such purposes has not been established. You bear sole responsibility and liability for any use of Healthcare Multi-Agent Orchestrator or the healthcare AI models, including verification of outputs and incorporation into any product or service intended for a medical purpose or to inform clinical decision-making, compliance with applicable healthcare laws and regulations, and obtaining any necessary clearances or approvals. 1 arXiv, Universal Abstraction: Harnessing Frontier Models to Structure Real-World Data at Scale, February 2, 2025 2 arXiv, MAIRA-2: Grounded Radiology Report Generation, June 6, 2024 3 Nature Method, A foundation model for joint segmentation, detection and recognition of biomedical objects across nine modalities, Nov 18, 2024 4 arXiv, Medimageinsight: An open-source embedding model for general domain medical imaging, Oct 9, 2024 5 Machine Learning for Healthcare Conference, Scaling Clinical Trial Matching Using Large Language Models: A Case Study in Oncology, August 4, 2023Can you use AI to implement an Enterprise Master Patient Index (EMPI)?
The Short Answer: Yes. And It's Better Than You Think. If you've worked in healthcare IT for any length of time, you've dealt with this problem. Patient A shows up at Hospital 1 as "Jonathan Smith, DOB 03/15/1985." Patient B shows up at Hospital 2 as "Jon Smith, DOB 03/15/1985." Patient C shows up at a clinic as "John Smythe, DOB 03/15/1985." Same person? Probably. But how do you prove it at scale — across millions of records, dozens of source systems, and data quality that ranges from pristine to "someone fat-fingered a birth year"? That's the problem an Enterprise Master Patient Index (EMPI) solves. And traditionally, it's been solved with expensive commercial products, rigid rule engines, and a lot of manual review. We built one with AI. On Azure. With open-source tooling. And the results are genuinely impressive. This post walks through how it works, what the architecture looks like, and why the combination of deterministic matching, probabilistic algorithms, and AI-enhanced scoring produces better results than any single approach alone. 1. Why EMPI Still Matters (More Than Ever) Healthcare organizations don't have a "patient data problem." They have a patient identity problem. Every EHR, lab system, pharmacy platform, and claims processor creates its own patient record. When those systems exchange data via FHIR, HL7, or flat files, there's no universal patient identifier in the U.S. — Congress has blocked funding for one since 1998. The result: Duplicate records inflate costs and fragment care history Missed matches mean clinicians don't see a patient's full medical picture False positives can merge two different patients into one record — a patient safety risk Traditional EMPI solutions use deterministic matching (exact field comparisons) and sometimes probabilistic scoring (fuzzy string matching). They work. But they leave a significant gray zone of records that require human review — and that queue grows faster than teams can process it. What if AI could shrink that gray zone? 2. The Architecture: Three Layers of Matching Here's the core insight: no single matching technique is sufficient. Exact matches miss typos. Fuzzy matches produce false positives. AI alone hallucinates. But layer them together with calibrated weights, and you get something remarkably accurate. Let's break each layer down. 3. Layer 1: Deterministic Matching — The Foundation Deterministic matching is the bedrock. If two records share an Enterprise ID, they're the same person. Full stop. The system assigns trust levels to each identifier type: Identifier Weight Why Enterprise ID 1.0 Explicitly assigned by an authority SSN 0.9 Highly reliable when present and accurate MRN 0.8 System-dependent — only valid within the same healthcare system Date of Birth 0.35 Common but not unique — 0.3% of the population shares any given birthday Phone 0.3 Useful signal but changes frequently Email 0.3 Same — supportive evidence, not proof The key implementation detail here is MRN system validation. An MRN of "12345" at Hospital A is completely unrelated to MRN "12345" at Hospital B. The system checks the identifier's source system URI before considering it a match. Without this, you'd get a flood of false positives from coincidental MRN collisions. If an Enterprise ID match is found, the system short-circuits — no need for probabilistic or AI scoring. It's a guaranteed match. 4. Layer 2: Probabilistic Matching — Where It Gets Interesting This is where the system earns its keep. Probabilistic matching handles the messy reality of healthcare data: typos, nicknames, transposed digits, abbreviations, and inconsistent formatting. Name Similarity The system uses a multi-algorithm ensemble for name matching: Jaro-Winkler (60% weight): Optimized for short strings like names. Gives extra credit when strings share a common prefix — so "Jonathan" vs "Jon" scores higher than you'd expect. Soundex / Metaphone (phonetic boost): Catches "Smith" vs "Smythe," "Jon" vs "John," and other sound-alike variations that string distance alone would miss. Levenshtein distance (typo detection): Handles single-character errors — "Johanson" vs "Johansn." These scores are blended, and first name and last name are scored independently before combining. This prevents a matching last name from compensating for a wildly different first name. Date of Birth — Smarter Than You'd Think DOB matching goes beyond exact comparison. The system detects month/day transposition — one of the most common data entry errors in healthcare: Scenario Score Exact match 1.0 Month and day swapped (e.g., 03/15 vs 15/03) 0.8 Off by 1 day 0.9 Off by 2–30 days 0.5–0.8 (scaled) Different year 0.0 This alone catches a category of mismatches that pure deterministic systems miss entirely. Address Similarity Address matching uses a hybrid approach: Jaro-Winkler on the normalized full address (70% weight) Token-based Jaccard similarity (30% weight) to handle word reordering Bonus scoring for matching postal codes, city, and state Abbreviation expansion — "St" becomes "Street," "Ave" becomes "Avenue" 5. Layer 3: AI-Enhanced Matching — The Game Changer This is where the architecture diverges from traditional EMPI solutions. OpenAI Embeddings (Semantic Similarity) The system generates a text embedding for each patient's complete demographic profile using OpenAI's text-embedding-3-small model. Then it computes cosine similarity between patient pairs. Why does this work? Because embeddings capture semantic relationships that string-matching can't. "123 Main Street, Apt 4B, Springfield, IL" and "123 Main St #4B, Springfield, Illinois" are semantically identical even though they differ character-by-character. The embedding score carries only 10% of the total weight — it's a signal, not a verdict. But in ambiguous cases, it's the signal that tips the scale. GPT-5.2 LLM Analysis (Intelligent Reasoning) For matches that land in the human review zone (0.65–0.85), the system optionally invokes GPT-5.2 to analyze the patient pair and provide structured reasoning: { "match_score": 0.92, "confidence": "high", "reasoning": "Multiple strong signals: identical last name, DOB matches exactly, same city. First name 'Jon' is a common nickname for 'Jonathan'.", "name_analysis": "First name variation is a known nickname pattern.", "potential_issues": [], "recommendation": "merge" } The LLM doesn't just produce a number — it explains why it thinks two records match. This is enormously valuable for the human reviewers who make final decisions on ambiguous cases. Instead of staring at two records and guessing, they get AI-generated reasoning they can evaluate. When LLM analysis is enabled, the final score blends traditional and LLM scores: Final Score = (Traditional Score × 0.8) + (LLM Score × 0.2) The LLM temperature is set to 0.1 for consistency — you want deterministic outputs from your matching engine, not creative ones. 6. The Graph Database: Modeling Patient Relationships Records and scores are only half the story. The real power comes from how the system stores and traverses relationships. We use Azure Cosmos DB with the Gremlin API — a graph database that models patients, identifiers, addresses, and clinical data as vertices connected by typed edges. (:Patient)──[:HAS_IDENTIFIER]──▶(:Identifier) │ ├──[:HAS_ADDRESS]──▶(:Address) │ ├──[:HAS_CONTACT]──▶(:ContactPoint) │ ├──[:LINKED_TO]──▶(:EmpiRecord) ← Golden Record │ ├──[:POTENTIAL_MATCH {score, confidence}]──▶(:Patient) │ └──[:HAS_ENCOUNTER]──▶(:Encounter) └──[:HAS_OBSERVATION]──▶(:Observation) Why a Graph? Three reasons: Candidate retrieval is a graph traversal problem. "Find all patients who share an identifier with Patient X" is a natural graph query — traverse from the patient to their identifiers, then back to other patients who share those same identifiers. In Gremlin, this is a few lines. In SQL, it's a multi-table join with performance that degrades as data grows. Relationships are first-class citizens. A POTENTIAL_MATCH edge stores the match score, confidence level, and detailed breakdown directly on the relationship. You can query "show me all high-confidence matches" without any joins. EMPI records are naturally hierarchical. A golden record (EmpiRecord) links to multiple source patients via LINKED_TO edges. When you merge two patients, you're adding an edge — not rewriting rows in a relational table. Performance at Scale Cosmos DB's partition strategy uses source_system as the partition key, providing logical isolation between healthcare systems. The system handles Azure's 429 rate-limiting with automatic retry and exponential backoff, and uses batch operations for bulk loads to avoid RU exhaustion. 7. FHIR-Native Data Ingestion The system ingests HL7 FHIR R4 Bundles — the emerging interoperability standard for healthcare data exchange. Each FHIR Bundle is a JSON file containing a complete patient record: demographics, encounters, observations, conditions, procedures, immunizations, medication requests, and diagnostic reports. The FHIR loader: Maps FHIR identifier systems to internal types (SSN, MRN, Enterprise ID) Handles all three FHIR date formats (YYYY, YYYY-MM, YYYY-MM-DD) Extracts clinical data for comprehensive patient profiles Uses an iterator pattern for memory-efficient processing of thousands of patients Tracks source system provenance for audit compliance This means the service can ingest data directly from any FHIR-compliant EHR — Epic, Cerner, MEDITECH, or Synthea-generated test data — without custom integration work. 8. The Conversational Agent: Matching via Natural Language Here's where it gets fun. The system includes a conversational AI agent built on the Azure AI Foundry Agent Service. It's deployed as a GPT-5.2-powered agent with OpenAPI tools that call the matching service's REST API. Instead of navigating a complex UI to find matches, a data steward can simply ask: "Search patients named Aaron" "Compare patient abc-123 with patient xyz-456" "What matches are pending review?" "Approve the match between patient A and patient B" The agent is integrated directly into the Streamlit dashboard's Agent Chat tab, so users never leave their workflow. Under the hood, when the agent decides to call a tool (like "search patients"), Azure AI Foundry makes an HTTP request directly to the Container App API — no local function execution required. Available Agent Tools Tool What It Does searchPatients Search patients by name, DOB, or identifier getPatientDetails Get detailed patient demographics and history findPatientMatches Find potential duplicates for a patient compareTwoPatients Side-by-side comparison with detailed scoring getPendingReviews List matches awaiting human decision submitReviewDecision Approve or reject a match getServiceStatistics MPI dashboard metrics This same tool set is also exposed via a Model Context Protocol (MCP) server, making the matching engine accessible from AI-powered IDEs and coding assistants. 9. The Dashboard: Putting It All Together The Patient Matching Service includes a full-featured Streamlit dashboard for operational management. Page What You See Dashboard Key metrics, score distribution charts, recent match activity Match Results Filterable list with score breakdowns — deterministic, probabilistic, AI, and LLM tabs Patients Browse and search all loaded patients with clinical data Patient Graph Interactive graph visualization of patient relationships using streamlit-agraph Review Queue Pending matches with approve/reject actions Agent Chat Conversational AI for natural language queries Settings Configure match weights, thresholds, and display preferences The match detail view provides six tabs that walk reviewers through every scoring component: Summary, Deterministic, Probabilistic, AI/Embeddings, LLM Analysis, and Raw Data. Reviewers don't just see a number — they see exactly why the system scored a match the way it did. 10. Azure Architecture The full solution runs on Azure: Service Role Azure Cosmos DB (Gremlin + NoSQL) Patient graph storage and match result persistence Azure OpenAI (GPT-5.2 + text-embedding-3-small) LLM analysis and semantic embeddings Azure Container Apps Hosts the FastAPI REST API Azure AI Foundry Agent Service Conversational agent with OpenAPI tools Azure Log Analytics Centralized logging and monitoring The separation between Cosmos DB's Gremlin API (graph traversal) and NoSQL API (match result documents) is intentional. Graph queries excel at relationship traversal — "find all patients connected to this identifier." Document queries excel at filtering and aggregation — "show me all auto-merge matches from the last 24 hours." 11. What We Learned AI doesn't replace deterministic matching. It augments it. The three-layer approach works because each layer compensates for the others' weaknesses: Deterministic handles the easy cases quickly and with certainty Probabilistic catches the typos, nicknames, and formatting differences that exact matching misses AI provides semantic understanding and human-readable reasoning for the ambiguous middle ground The LLM is most valuable as a reviewer's assistant, not a decision-maker. We deliberately keep the LLM weight at 20% of the final score. Its real value is the structured reasoning it produces — the "why" behind a match score. Human reviewers process cases faster when they have AI-generated analysis explaining the matching signals. Graph databases are naturally suited for patient identity. Patient matching is fundamentally a relationship problem. "Who shares identifiers with whom?" "Which patients are linked to this golden record?" "Show me the cluster of records that might all be the same person." These are graph traversal queries. Trying to model this in relational tables works, but you're fighting the data model instead of leveraging it. FHIR interoperability reduces integration friction to near zero. By accepting FHIR R4 Bundles as the input format, the service can ingest data from any modern EHR without custom connectors. This is a massive practical advantage — the hardest part of any EMPI project is usually getting the data in, not matching it. 12. Try It Yourself The Patient Matching Service is built entirely on Azure services and open-source tooling https://github.com/dondinulos/patient-matching-service : Python with FastAPI, Streamlit, and the Azure AI SDKs Azure Cosmos DB (Gremlin API) for graph storage Azure OpenAI for embeddings and LLM analysis Azure AI Foundry for the conversational agent Azure Container Apps for deployment Synthea for FHIR test data generation The matching algorithms (Jaro-Winkler, Soundex, Metaphone, Levenshtein) use pure Python implementations — no proprietary matching engines required. Whether you're building a new EMPI from scratch or augmenting an existing one with AI capabilities, the three-layer approach gives you the best of all worlds: the certainty of deterministic matching, the flexibility of probabilistic scoring, and the intelligence of AI-enhanced analysis. Final Thoughts Can you use AI to implement an EMPI? Yes. And the answer isn't "replace everything with an LLM." It's "use AI where it adds the most value — semantic understanding, natural language reasoning, and augmenting human reviewers — while keeping deterministic and probabilistic matching as the foundation." The combination is more accurate than any single approach. The graph database makes relationships queryable. The conversational agent makes the system accessible. And the whole thing runs on Azure with FHIR-native data ingestion. Patient matching isn't a solved problem. But with AI in the stack, it's a much more manageable one. Tags: Healthcare, Azure, AI, EMPI, FHIR, Patient Matching, Azure Cosmos DB, Azure OpenAI, Graph Database, InteroperabilityHealthcare agent service in Microsoft Copilot Studio is now Generally Available
Healthcare organizations continue to face immense challenges: workforce shortages, rising costs, and growing demands for patient care. The clinical staff is overburdened, leading to stress, burnout, and staff shortages. Generative AI presents a powerful opportunity when it can automate administrative workflows, surface relevant insights, and assist the clinical staff with contextual, credible and up-to-date information. With that opportunity, we are excited to announce General Availability (GA) of healthcare agent service in Microsoft Copilot Studio. Building responsible, AI-powered healthcare agents With healthcare agent service, organizations can create healthcare-specialized AI applications that use generative AI within a framework that promotes trust, compliance, and real-world clinical scenarios. Agents combine built-in credible medical sources, such as FDA, CDC, MedlinePlus, MSD Manuals, DailyMed and more, with the organization’s own knowledge sources and plugins, while leveraging healthcare-specific actions. Customers can define the intended healthcare roles, such as healthcare professionals or patients, so the behavior is relevant and appropriate for the audience and use case. Pre-built use cases include clinical documentation assistance, patient self-service, helping healthcare professionals triage by organizing information, finding medication information, accessing recent clinical guidelines information, and more. Because responsible AI in healthcare is a top priority, healthcare agent service is infused with safeguards that are reinforced by a healthcare-adapted orchestrator optimized for safety. Clinical, chat, and compliance safeguards help keep interactions evidence-based and trustworthy, increasing the reliability and accuracy of generated responses and adherence to the highest standards of safety, privacy, and regulatory compliance. Healthcare agent service underscores our ongoing commitment to responsible AI in healthcare, by offering customers a reliable, production-ready foundation for healthcare solutions that can be used to help support patients and medical professionals. Extending Dragon Copilot with conversational solutions Healthcare agent service provides a framework for building conversational AI applications that can be integrated directly into Dragon Copilot, giving partners and healthcare organizations the ability to extend its functionality in a scalable, compliant way. Today, Information Assist in Dragon Copilot, built on healthcare agent service, delivers safeguarded generative AI answers grounded in trusted sources and enriched with patient history and context, ensuring clinicians receive accurate, timely, and context-aware insights. Clinicians can effortlessly access a broad range of clinical topics directly within their workflow using natural language, surfacing insights from leading, trusted healthcare content partners that promote more informed clinical decisions with less administrative work. Partners and healthcare organizations can use healthcare agent service to create tailored solutions with built-in safeguards that help ensure output meets healthcare standards and supports safe decision-making at the point of care. These solutions can be integrated directly into Dragon Copilot to enhance both clinical and financial performance. Real-world impact with customers Healthcare organizations are already adopting healthcare agent service to bring generative AI into real-world care settings. Early adopters are seeing meaningful impact in reducing administrative burden, improving patient experience, and empowering clinicians with trusted information. Bayer Pharmaceuticals has recently worked with Microsoft to enable new agentic AI workflows for drug submission using healthcare agent service in Copilot Studio: “We have collaborated with Microsoft to build an AI-powered multi-agent decision board using the healthcare agent service in Copilot Studio. This multi-agent decision board revolutionizes how we strategize drug submissions, pricing, and patient targeting for global market access. By simulating expert board discussions and synthesizing diverse data—from regulatory approvals to health economics and real-world evidence—the system streamlines the complex process of securing drug reimbursement. Healthcare agent service helped us get results quicker, empowering teams to make smarter, data-driven decisions without replacing human expertise, which would enable better access to life-changing therapies for patients worldwide. Importantly, this tool is not limited to pharmaceutical companies. It also supports decision-making for health authorities, NGOs, and other stakeholders across the healthcare ecosystem—enabling more informed, collaborative, and impactful choices that benefit public health at large.” — Shay Zohar, local Market Access Director and member of Bayer Pharmaceutical’s global Early Access team Allgemeines Krankenhaus (AKH) Wien, the largest hospital in Vienna, Austria and the Medical University of Vienna collaborated with Microsoft to extend Dragon Copilot with healthcare agent service, to automate pre-anesthesia intake. “Transforming pre-anesthesia assessments with AI agents for greater efficiency has a great potential to decrease the administrative burden on anesthesiologists. In this project we used healthcare agent service to extend Dragon Copilot with AI-powered agents that automate pre-anesthesia intake to enhance clinical documentation, significantly reducing the administrative workload for anesthesiologists. By orchestrating conversational and workflow agents, the solution interacts with patients, completes assessments, checks for data conflicts, and generates clinical notes, all consolidated for physician review in Dragon Copilot.” — Dr. Oliver Kimberger, Professor for Perioperative Information Management at the Department of General Anesthesia and Intensive Care Medicine, AKH Wien. Empowering healthcare innovation Healthcare agent service offers a low-code interface for building and deploying custom AI solutions with chat, compliance and clinical safeguards that support safety and accuracy in generative AI. With seamless integration and the ability to extend the capabilities of Dragon Copilot, you gain the flexibility to tailor solutions to your organization’s evolving needs. Learn more in healthcare agent service in Copilot Studio documentation Explore the possibilities with Microsoft Copilot Studio Expand your knowledge about Microsoft for Healthcare Discover how we are shaping the future of health with cutting-edge solutions and collaborative efforts here Medical Device Disclaimer: Microsoft products and services (1) are not designed, intended or made available as a medical device, and (2) are not designed or intended to be a substitute for professional medical advice, diagnosis, treatment, or judgment and should not be used to replace or as a substitute for professional medical advice, diagnosis, treatment, or judgment. Customers/partners are responsible for ensuring solutions comply with applicable laws and regulations. Generative AI Disclaimer: Generative AI does not always provide accurate or complete information. AI outputs do not reflect the opinions of Microsoft. Customers/partners will need to thoroughly test and evaluate whether an AI tool is fit for the intended use and identify and mitigate
Seamlessly manage Dragon Copilot with the new Microsoft Dragon admin center
Today, we are thrilled to announce the Microsoft Dragon admin center – a new way to manage your Microsoft Cloud for Healthcare clinical applications including Microsoft Dragon Copilot. This user-friendly platform, built upon Microsoft 365 and Microsoft’s e-commerce framework, enables healthcare administrators to control and manage their licensing, billing and organizational lifecycle with ease and efficiency. The Microsoft Dragon admin center streamlines the implementation and management of clinical applications in the health provider ecosystem, reducing time from weeks or months to days. Microsoft Dragon Copilot can be purchased and provisioned quickly with a few clicks. We are excited to have Microsoft partners and customers try it out! Benefits The Microsoft Dragon admin center provides numerous benefits to healthcare organizations and partners: Efficiency: Streamlines administration of clinical applications through a centralized and unified interface that provides consistency across all administrative functions. Partner Integration: Offers flexibility to embed Dragon Copilot in the Electronic Health Record (EHR) system of choice or resell the application out of the box. Customization: Enables high degrees of customization for administrators managing wide ranges of users. Scalability: Allows healthcare providers to scale clinical applications within a few hours. Compliance: Adheres to Microsoft standards of privacy, compliance, and security. Key Features The Microsoft Dragon admin center offers several key features that make it an indispensable tool for healthcare administrators: Simplified license management, user role assignment, and billing allows customers to easily purchase more or upgrade licenses depending on business needs. Seamless and automated provisioning of the Dragon Copilot application limits deployment delays. Customizable organization hierarchy empowers healthcare administrators to manage their organization in a few clicks. One stop shop for managing Electronic Health Record (EHR) partners and users operating in the embedded Dragon Copilot application reduces the complexity and time required to manage multiple systems and partners separately. Extensive configuration of settings and library objects of Dragon Copilot increases time-to-value. How to Get Started Getting started with the Microsoft Dragon admin center is straightforward: Purchase licenses: Identify the type of billing account you have in M365 and contact your Microsoft representative to purchase licenses. If you are a Microsoft Partner you can purchase through Partner Center. Assign licenses and conduct user role management: Assign licenses and provide different individuals the right roles to administer the Dragon admin center. Once the license and user role management is complete, navigate to the Microsoft Dragon admin center where you will be able to: Provision your Dragon Copilot application. Set up your organization hierarchy and healthcare groups, and manage your Electronic Health Record partners (EHRs). Manage and configure your Dragon Copilot application settings, features, and library objects in the context of your organization hierarchy. For a detailed step by step set-up guide for Microsoft Dragon admin center, please visit: End-to-end workflow overview | Microsoft Learn Conclusion The Microsoft Dragon admin center is a valuable tool that empowers healthcare administrators and streamlines clinical application management. By leveraging its advanced functionalities and user-friendly interface, healthcare organizations can enhance efficiency, accuracy, and customization in their workflows. Learn more about the Microsoft Dragon admin center here: Dragon admin center documentation | Microsoft LearnAzure OpenAI GPT model to review Pull Requests for Azure DevOps
In recent months, the use of Generative Pre-trained Transformer (GPT) models for natural language processing (NLP) has gained significant traction. GPT models, which are based on the Transformer architecture, can generate text from arbitrary sources of input data and can be trained to identify errors and detect anomalies in text. As such, GPT models are increasingly being used for a variety of applications, ranging from natural language understanding to text summarization and question-answering. In the software development world, developers use pull requests to submit proposed changes to a codebase. However, reviews by other developers can sometimes take a long time and not accurate, and in some cases, these reviews can introduce new bugs and issues. In order to reduce this risk, During my research I found the integration of GPT models is possible and we can add Azure OpenAI service as pull request reviewers for Azure Pipelines service. The GPT models are trained on developer codebases and are able to detect potential coding issues such as typos, syntax errors, style inconsistencies and code smells. In addition, they can also assess code structure and suggest improvements to the overall code quality. Once the GPT models have been trained, they can be integrated into the Azure Pipelines service so that they can automatically review pull requests and provide feedback. This helps to reduce the time taken for code reviews, as well as reduce the likelihood of introducing bugs and issues.
Microsoft Azure continues to expand scalability for Healthcare EHR Workloads
Microsoft Azure has reached a new milestone for Epic Chronicles Operational Database (ODB) scalability with the Standard_M416bs_v3 (Mbv3) VM. It can now scale up to 110 million GRefs/s (Global References per second) in the ECP configuration and up to 39 million GRefs/s in the SMP configuration, improving upon the previous Azure benchmarks of 65 million GRefs/s and 20 million GRefs/s respectively. Microsoft Azure now can host 96% of the Epic customer base, enabling healthcare organizations to run their EHR systems on Azure. New VM Size Purpose-Built for Epic’s Chronicles ODB The Standard_M416bs_v3 VM, newly added to Azure’s Mbv3 series, is purpose-built to meet the growing performance and scalability demands of large healthcare EHR environments. With higher CPU capacity, expanded memory and improved remote storage throughput, it delivers the reliability needed for mission-critical workloads at scale. Key specifications include: Mbv3 Processor Performance: Built on 4th Gen Intel® Xeon® Scalable processors, the Mbv3 series is optimized for high memory and storage performance, supporting workloads up to 4 TB of RAM with an NVMe interface for faster remote disk access. Compute Capacity: The Standard_M416bs_v3 delivers 416 vCPUs - more than twice the capacity of previous Mbv3 sizes, delivering stronger performance. Storage Performance: Achieves up to 550,000 IOPS and 10 GBps remote disk bandwidth using Azure Ultra Disk. Performance Optimization: Enhanced by Azure Boost, the M416bs_v3 provides low-latency, high remote storage performance, making it ideal for storage throughput-intensive applications such as Epic ODB, relational databases and analytics workloads. Available Regions: M416bs_v3 is available in 4 regions - East US, East US 2, Central US, and West US 2. Explore Epic on Azure to learn more. Epic and Chronicles are trademarks of Epic Systems Corporation.
Copilot Chat: Prompting
To start a new prompt, head over to Copilot Chat and hit the blue chat button in the upper right corner. 🔄 When should I start a new chat? A good rule of thumb: hit that button whenever you're switching contexts or subject areas. This helps keep Copilot focused and prevents information from getting muddled.🍸 🧪 How do I improve my prompts? To get the best results, use the GCSE Formula—that’s: Goal: What do you want Copilot to do? Context: What background info will help? Source: Where should Copilot pull from? Expectations: What kind of output do you want? 🧩 Example Here’s a basic prompt: Give me a concise summary of recent news about Pfizer. Now let’s expand it using the GCSE Formula: Summarize the latest news about Pfizer from reputable sources like Reuters or Bloomberg. Focus on developments in their vaccine pipeline and financial performance. Keep it concise—under 150 words. Let's see how this might look like in practice. This is my prompt: Give me a concise summary of recent news about Pfizer. Let's try expanding this to include our other key ingredients: 🎯 Challenge Try using the GCSE Formula in your next prompt and compare it to using just the goal. See how your results stack up!
