Effective AI Prompting Strategies for Healthcare Applications

LLMs are now widespread and offer a plethora of benefits—this much we already know. We see dynamic adoption across many industries and use cases, including information aggregation, smart searches, user interactions, and more.

But there is one field that, despite its massive potential gains, is still slower to adopt such new tools—healthtech.

The Challenge Ahead

The specific realities of healthtech and healthcare pose a unique challenge for GenAI in general, and especially for the use of LLMs. Here, the margin for error is slim, data is highly sensitive, and the potential cost of mistakes can be severe.

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LLM M.D.: Why Accuracy and Trust Are Critical

At first glance, LLMs appear to be highly effective in the medical domain. Researchers have even shown that fine-tuned LLMs can outperform first-contact physicians—not just in diagnostic accuracy, but surprisingly, in empathy as well.

You might think examples like these would make LLMs a clear fit for healthcare, but there’s much more nuance.

Understanding Model Hallucinations and Trust Gaps

The first concern is the reliability of the model’s knowledge and answers. LLMs are trained on vast datasets that often contain conflicting data points. Crucially, we have no way of knowing which parts of this internal knowledge the model uses in its responses. This can result in seemingly coherent, but completely fabricated, answers—hallucinations.

These risks are not confined to diagnostic use cases. Even simpler tasks, such as document summarization, can lead to dangerous misinterpretations or incorrect outputs.

Responsibility and the Opacity Problem

When a human makes a decision, they take responsibility for it. We accept a margin of error because we trust their expertise. With AI models, the expectation is different. We demand higher accuracy and do not tolerate the idea that a model can "misjudge" something.

The opacity of LLMs—their black-box nature—only deepens this trust gap, eroding confidence instead of building it.

Data Privacy and Safety

A key concern in healthtech is data privacy. We often work with personally identifiable information (PII), which is strictly regulated under frameworks like HIPAA and GDPR. This data requires exceptional care.

For LLMs, this creates a significant obstacle. Models need to process data—whether patient inputs, internal documents, or other sensitive sources. Ideally, we could deploy LLMs on private servers with fully controlled security environments. Unfortunately, the computing power required to run high-performing LLMs makes this nearly impossible in most cases.

To complicate matters further, many advanced models are closed-source, meaning that even with the proper hardware, you cannot run a private instance.

This often leaves healthcare companies in an uncomfortable position: using third-party LLMs that may process sensitive data in different legal jurisdictions. In the context of healthtech, this is highly questionable.

How to Build Safe, Reliable LLM Systems for HealthTech

Despite these barriers, LLMs can be safely and effectively used in healthcare. It’s not about avoiding them entirely—it’s about building the right systems, using the right techniques.

The Art of AI Prompting for Healthcare Apps

Some issues with model outputs and response quality can be addressed—just as with any LLM—through prompt engineering. This is the most basic, yet most essential, part of building safe LLM systems.

While many general best practices apply (be precise, avoid verbosity, eliminate ambiguity), healthtech demands additional rigor.

Focus on Precision and Hard Data in Healthcare AI Prompts

In healthcare, precision is non-negotiable. You need to include the most relevant, hard data in your prompts—either as direct instructions or dynamic context.

You can dynamically format the prompt, depending on the state of the system, always passing hard data relevant to the query or operations. The more accurate context you provide, the more on-topic the answer will be.

Try, for example, parsing and introducing patient info into the context when building any solutions reasoning over patient documentation. Or define specifics of work and context of use for LLMs operated by specialist medical practitioners—defining that we navigate in terms commonly used by, let’s say, radiologists removes a level of ambiguity and double meaning, setting a hard context for the LLM.

The more accurate the context, the more relevant and reliable the response.

Addressing Model Certainty in Healthcare AI Responses

LLMs tend to respond with absolute certainty—even when unsupported by facts. In medical systems, this is not only misleading but may also be unethical or illegal, especially in regions where AI-generated diagnoses are not permitted.

Techniques like using structured prompts, markdown formatting, or the ReAct prompt pattern (which enables reasoning loops) can help manage this. These methods standardize model outputs and make the system safer.

Delegating Complex Tasks: Multi-Agent Systems in Healthcare AI

Aspects of prompting lead us straight into another point—thinking more towards multi-agent systems, utilizing query engines, specialized tools, and delegate agents.

Splitting Work Across Specialized AI Agents in HealthTech

When performing a complex and long task, LLMs tend to lose focus—this is where most of the information is lost, and most hallucinations are introduced. Moreover, as discussed earlier, successful prompts are precise and exact—this often clashes with complex tasks that require performing many different operations, following different sets of rules. When mixed like that, some spillover is inevitable.

The best approach is to split such tasks into specialized tools, for example:

• A main agent interacts with the clinician.
  
• An image interpreter processes scan data.
  
• An analytical engine handles tabular data.
  
• Sub-agents retrieve data from EHR systems.
  

Only after receiving all the data perspectives do they go over the results of the AI tools.

This multi-agent flow mirrors the architecture of advanced systems like modern ChatGPT or Perplexity but is fine-tuned for specific healthcare tasks. It allows you to control each step and ensure thorough analysis.

Model Guardrails: Keeping Healthcare AI Safe

On the topic of specialized LLM engines working on smaller parts of the system, a special case would be the use of so-called guardrail models—essentially input and output filters powered by LLMs. Here, our goal is to ensure that nothing conflicting with our instructions exits the model and nothing potentially harmful enters the model.

Input Filters: Moderators for Safer Inputs

Starting with input filters—moderators. These engines aim to filter user inputs and block obviously harmful messages: explicit content, attempts to bypass the system, and so on. They also filter out joke inputs or off-topic questions and instructions.

The first part is obvious, but the second might not be. Consider a patient-facing LLM asked about a controversial topic—you’ll quickly see why this matters. Any answer would not only be unrelated to the use case but also potentially damaging.

In LLM systems, conversation history is usually still held in context, meaning that any such answers might pollute future generations, leading to harmful consequences.

Output Filters: Guardrails for Safer Responses

While moderators might be intuitive enough, guardrails—or output filters—might not be. After all, why parse what we’ve just generated?

This ties directly to the principle of work splitting. While the main agent might be optimized for reasoning, trying to steer it towards a specific tone of voice can result in directionless prompting. It is often better to focus the core system on the task at hand and leave response refinement to these guardrails.

For example, we can ensure that a therapeutic chatbot maintains the right tone of voice and never slips up by reformatting the answer, cutting out unwanted parts, or forcing a new generation in extreme cases. This design pattern results in not only more accurate but also more natural-sounding LLMs.

Cite Your Sources: Increasing Transparency

We’ve talked about query engines, document interpretation, and tools for summarization, but those elements do not solve the issue of opacity that LLMs introduce. What’s more, the introduction of multiple tools and agents might obscure the decision process even further. It seems that by solving one issue, we’ve created a new one.

Here, the answer might be easier than you think.

The Power of Retrieval-Augmented Generation (RAG) in Healthcare

The solution is RAG—retrieval augmented generation—a simple yet elegant method for providing exact context matching current queries. This approach assumes building a vector database populated with hand-compiled documents, acting as a verified and coherent knowledge base for the LLM.

RAG systems connect the base AI agent with this knowledge base, allowing it to query over the database and retrieve the most relevant parts in response to the input. By combining such a tool with strict prompting—explicitly instructing the model to answer only in the context of retrieved information—we reduce hallucination or misinterpretation possibilities to a minimum.

RAG and semantic searches deserve an article of their own, but for now, it’s enough to understand that we have a wide range of tools and algorithms not only for retrieving this data but also for matching and processing it before it even reaches the main agent.

We can search by:

• Cosine similarity: providing high adaptability and flexibility.
  
• Keywords or matching/ranking functions like BM25: gaining accuracy and hard matches.
  
• Hybrid approaches: combining elements of both methods.

Closing the Opacity Gap: Using Citations

The final point here is citation itself—a simple mechanism that directly addresses the opacity problem we started with.

With RAG systems, we can easily show what sources were used to generate the final response. Simply append the retrieved chunks—along with the information on where they were originally sourced—at the end of the response, just like in an academic paper.

This way, the end user can easily verify whether the source really supports what the LLM claims.

Similarly, when parsing input documents, you can point to specific parts used to generate corresponding parts of the summary—resolving the issue of interacting with a black box.

Safe Data is Anonymous Data

So far, we’ve covered ways to manage LLMs to reduce hallucination, ground answers in reality, and use other safety techniques. But as we laid out in the beginning, all this is often constrained by a significant barrier—data safety.

The first thing to say here is that, more often than not, a solid legal framework will guarantee enough safety for your use cases, even in healthcare settings.

Many successful healthtech solutions are based on IaaS (Infrastructure as a Service) environments—private instances like AWS or Azure. With the proper setup, you are operating in a safe and compliant environment because you can define what data policies apply and where the instance is located.

Understanding Model-as-a-Service (MaaS) Solutions

Similar principles apply when it comes to MaaS (Model as a Service) solutions, where you access LLMs through the provided API—albeit with some crucial distinctions.

Most large providers like OpenAI offer BAA agreements for HIPAA or zero data retention and data residency options aimed more at GDPR regulations. This is a solid start.

The concern about models being trained on your inputs, using and storing your data, is also addressed in most cases. MaaS providers clearly define in their terms what will be used and how—usually guaranteeing that API-processed data will only be used for processing, not for training.

Options for Handling Delicate Data

For the most delicate use cases, there are still options.

The most straightforward is to host your own instance of an LLM model, but as noted earlier, this limits the model selection and is often prohibitively costly.

This brings us to the core of this section—data anonymization. This approach is flexible enough to offer both the benefits of MaaS solutions and the safety level provided by fully controlled infrastructure.

After all, if you do not send any personally identifiable information (PII), then no data can be leaked. But how do we achieve this?

Simply removing PII elements like names or addresses will often hurt accuracy, as we are removing a layer of information.

How Anonymization Works in Healthcare AI Systems

To solve this, we can add an additional processing step between our system and the target LLM—the anonymization service.

Every outgoing data point—documents, user inputs, or anything else—is parsed using dedicated ML models and NLP techniques to identify potential entities defined as private information. These entities are replaced with labels; for example, “John Doe” might become “PERSON_1.” This mapping is safely stored on our end, and sanitized data is sent to the LLM.

Once we receive the results back, we can simply replace each label with the matching name.

It sounds simple and elegant, but there’s a small catch.

This approach, depending on the method used, might not be absolutely accurate—we rely on models and algorithmic analysis to find all the PII. While this might be acceptable in some cases, in others we need an absolute guarantee of no data leakage.

One way to achieve this is to pass the responsibility for redacting the information to the personnel interacting with the system—either by defining a set list of entities to be anonymized or by manually replacing the names. It might be tedious and less elegant, but it reduces the risk of accidental PII slipping past the automated measures.

Safe LLMs in HealthTech: How Rather Than If

When we review all the aspects discussed, a clear picture emerges: LLMs can be safely used even in highly sensitive areas like healthtech.

The problem is not with the technology itself but with the lack of expertise and proper approaches. Many of the apparent barriers can be eliminated with the right strategies.

That’s exactly why we created the AI Implementation in Healthcare Masterclass—to help healthtech teams apply these strategies in the real world, safely and effectively.

If you’re building with AI in healthcare, this is where you’ll find the practical guidance to do it right.

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