Hybrid Approach to Medical Entity Recognition from Scanned

Documents
Manoj Umapathi Naidu, Sahil Kadam, Siddhesh Joshi, Athrva Kulkarni
CSE–AI Department, Vishwakarma Institute of Information Technology, Pune, India
Emails: [email protected], [email protected], [email protected],
[email protected]

Abstract
Medical documents often exist in scanned formats that are challenging for automated
processing, yet they contain critical information such as diagnoses, medications, and clinical
findings. Extracting and interpreting these entities require a combination of Computer Vision
(OCR) and Natural Language Processing (NLP) techniques. This paper proposes a hybrid
approach that integrates Generative AI and NLP for medical entity recognition from scanned
documents. The system employs Optical Character Recognition (OCR) using Tesseract to convert
document images into text, a spaCy-based pipeline enhanced with SciSpaCy models and custom
rules for Named Entity Recognition (NER), and a retrieval-augmented large language model via
the Groq API (hosting Google’s Gemma 2 9B model) for contextual analysis and interactive
question-answering. The solution is implemented as a Flask web application, allowing users to
upload medical reports and receive highlighted entities with definitions, an AI-generated
summary, and the ability to query the content through a chat interface. Experimental evaluation
on sample medical reports demonstrates that the hybrid method improves entity recognition
accuracy (F1 score ~0.85) over baseline models

and produces coherent summaries of key findings. We also compare our system with purely
rule-based, transformer-based, and generative approaches. The results show that our combined
approach yields a more balanced performance, leveraging the precision of domain-specific NER
and the generative capabilities of large models. This work highlights how a retrieval-augmented
generative pipeline can enhance information extraction from scanned medical documents while
mitigating OCR errors and knowledge gaps.

Keywords— Generative AI; NLP; Flask; Groq API; FAISS; Retrieval-Augmented Generation (RAG)

Introduction
The digitization of healthcare data has led to a proliferation of electronic records, yet many
documents (e.g. lab reports, prescriptions, clinical notes) remain as scanned images or PDFs.
Automatically extracting structured information from these scanned medical documents is a
longstanding challenge [1]. Such documents must first be transformed into text via OCR, after
which relevant medical terms (diseases, drugs, symptoms, etc.) can be identified using NLP.
However, standard OCR and NLP pipelines face issues: OCR errors can propagate to downstream
text analysis, and generic NER tools may not recognize domain-specific terminology. At the
same time, the volume of biomedical literature and records is growing exponentially [2], making
automated text understanding crucial for clinical decision support and data management.

Named Entity Recognition in the medical domain has been widely studied. Early clinical NLP
tools like MetaMap focused on mapping text to medical ontologies (UMLS), with capabilities
like negation detection [2]. Modern approaches leverage machine learning: for example,
SciSpaCy models (developed by Allen AI) provide robust biomedical NER pipelines. These
models are trained on large corpora (e.g. MedMentions) and can detect a wide range of
biomedical entities, though they may not assign fine-grained categories by default [2]. Purely
data-driven NER models can struggle with uncommon or new terms and often require large
annotated datasets for training. On the other hand, rule-based methods (e.g. custom
dictionaries or pattern matching) can quickly incorporate domain expertise to recognize entities
like specific drug names or lab tests, but they can be brittle and hard to scale. This dichotomy
motivates a hybrid strategy combining the strengths of both.

Recently, Generative AI models (LLMs such as GPT-3.5, GPT-4) have shown the ability to
understand and generate human-like text, even in specialized domains. In the medical field,
large language models have been applied to tasks like clinical report summarization and
question answering. Notably, an adapted LLM was able to produce clinical summaries that
experts found comparable or superior to human-written ones in many cases [3] Google’s Med-
PaLM, a domain-tuned LLM, was the first to exceed the pass mark on USMLE medical exam
questions arxiv.org, demonstrating the knowledge these models can bring to medical NLP.
However, a known issue with such models is hallucination – generating plausible-sounding but
incorrect facts. This is especially problematic in healthcare. One approach to reduce
hallucinations is providing relevant context or retrieved knowledge to the model – a technique
known as Retrieval-Augmented Generation (RAG) ar5iv.org. By grounding the LLM’s responses
in actual source text (e.g. the content of a patient’s report or a medical knowledge base), we
can improve accuracy and trustworthiness blogs.nvidia.com.

A unified system that addresses the above challenges by integrating OCR, domain-specific NER,
and a generative AI component with retrieval. Our Hybrid Approach to Medical Entity
Recognition works as follows: (1) apply OCR to the scanned document to get raw text, (2) apply
a customized NLP pipeline (SciSpaCy + rules) to extract and highlight medical entities in the text,
and (3) use a generative model (via Groq API) that takes the text and recognized entities as
context to produce an analysis of the report and answer user queries. The system uses a
lightweight Flask web interface for user interaction. By combining deterministic NER with
generative AI, the system not only identifies key information (with higher recall than using ML or
rules alone) but also provides a natural language summary and interactive Q&A, which purely
rule-based systems cannot. We also incorporate a simple knowledge base for defining medical
terms and FAISS for efficient vector search, aligning with the RAG paradigm in the chat module.

The remainder of this paper is organized as follows: Section II reviews related work in OCR,
medical NER, and generative models in healthcare. Section III details the methodology and
system architecture. Section IV presents experimental results, including entity extraction
performance and example interactions, with discussion. Section V concludes the paper with
future directions.

Literature Survey
Recent studies have investigated hybrid methods for medical entity recognition from diverse
document sources. These strategies tend to integrate machine learning with domain
knowledge, including dictionaries and ontologies. Imane & Ahmed (2017)[1] built a system for
French medical texts and reported good performance in entity extraction, classification, and
normalization into 10 categories. Gong et al. (2009)[2] combined POS tagging, rules-based, and
dictionary-based methods based on biomedical ontology and achieved 71.5% F-score on the
GENIA corpus. Ben Abacha & Zweigenbaum (2011)[3] contrasted semantic and statistical
approaches, and they observed that a combination of the two worked best in clinical texts.
Ramachandran & Arutchelvan (2021)[4] suggested a hybrid model that integrates a machine
learning model with a custom-built dictionary and attained an average F1 score of 73.79% for
five entity types in medical literature. These studies show the efficacy of hybrid models in
medical entity recognition in various languages and document types. VeerasekharReddy et al.
(2023)[5] developed a model leveraging a hybrid dictionary-based and human-validated
method, utilizing SpaCy's machine learning framework to annotate medical texts, thereby
improving entity recognition accuracy[2]. These findings underscore the effectiveness of hybrid
models in biomedical NER, highlighting their potential to enhance information extraction from
biomedical literature.

Study/Tool Approach Description / Contribution

MetaMap Rule-Based Developed by the National Library of Medicine. Maps

biomedical text to UMLS concepts. Useful for clinical
entity linking and supports features like negation
Study/Tool Approach Description / Contribution

detection.

Provides robust biomedical NER models trained on

ML-Based
SciSpaCy datasets like MedMentions. Fast and easy to integrate
(spaCy NLP)
with rule-based enhancements.

Pretrained language models on biomedical corpora.

BioBERT / Transformer-
Achieve state-of-the-art results in medical NER, relation
ClinicalBERT Based
extraction, and question answering.

RAG (Retrieval- Combines the strengths of LLMs and document retrieval.

Hybrid (LLM +
Augmented Reduces hallucination by grounding LLM outputs in real
Search)
Generation) text (e.g., from medical documents).

Uses EasyOCR to extract text from prescriptions and

EasyOCR + BioBERT Combined OCR
BioBERT for NER. Shows high accuracy in extracting drug
Pipeline + NER
names, dosages, and symptoms.

Hosted via Groq API, this LLM (Gemma 2) provides fast,

Groq + Gemma LLM Generative AI accurate summarization and QA when fed with OCR-
extracted report content. Ideal for interactive analysis.

Early efforts in medical text processing often relied on rule-based or knowledge-based systems.
MetaMap, developed by the National Library of Medicine, is a classic tool that maps text to
concepts in the UMLS ontology. It was widely used for biomedical text mining, supporting entity
linking (to clinical concepts) with features like acronym resolution and negation handling

ar5iv.labs.arxiv.org. However, MetaMap and similar systems do not use modern machine
learning and can miss context-specific nuances.

In the 2010s, statistical and machine learning approaches for biomedical NER gained traction.
The BioNLP community produced various annotated corpora (e.g. GENIA, CRAFT, BC5CDR)
targeting different entity types (genes, chemicals, diseases, etc.). Traditional sequence taggers
(CRFs, HMMs) gave way to neural networks. For instance, CNNs and LSTMs with conditional
random fields were applied to biomedical NER with some success. A significant advancement
was the introduction of SciSpaCy by Neumann et al. (2019), which provides fast and robust
models for biomedical NLP built on spaCy ar5iv.labs.arxiv.org . SciSpaCy includes pre-trained
models for NER that recognize a wide variety of biomedical entity mentions (especially when
using the MedMentions dataset) ar5iv.labs.arxiv.org. These models act as strong baselines
across multiple biomedical NER tasks, achieving competitive performance on 5 out of 9
benchmark datasets in one evaluation ar5iv.labs.arxiv.org. Yet, a limitation noted is that the
general model recognizes many entity mentions but does not assign them specific semantic
types (it treats them as a single category of “Entity”). In practice, additional rules or specialized
models are needed to categorize entities (e.g. distinguishing drugs vs. diseases)
ar5iv.labs.arxiv.org.

Transformer-based models have further pushed the state-of-the-art. BioBERT and ClinicalBERT
are language models pre-trained on biomedical corpora; fine-tuning them for NER has yielded
F1 scores significantly higher than previous methods. For example, a fine-tuned BioBERT model
was used to extract entities from prescription texts (drug names, dosages, timings, etc.) with
high accuracy ijnrd.org . In one recent project, EasyOCR was used for text extraction from
prescription images and BioBERT for NER, achieving an effective pipeline that could accurately
categorize key medical terms and assist pharmacists ijnrd.org. This indicates that combining a
strong OCR engine with a domain-tuned transformer model can substantially improve
performance in specific tasks. Similarly, Hsu et al. (2021) combined Tesseract OCR with deep
learning models to extract specific fields from scanned sleep study reports. They found that a
fine-tuned Clinical BERT model reached over 94% accuracy in identifying critical values,
outperforming traditional approaches arxiv.org. These studies demonstrate the merit of
leveraging domain-specific AI models for both the vision (OCR) and text (NER) components of
the pipeline.

Meanwhile, the use of knowledge bases and rule-based enhancements remains relevant.
Researchers often integrate dictionaries of medical terms to help catch entities that statistical
models miss. For instance, adding custom entity ruler patterns in spaCy can improve recognition
of certain terms (like including patterns for “X-ray”, “CBC” as TEST entities, etc.). Such hybrid
NER approaches (rules + ML) can boost recall with minimal loss of precision, which is valuable in
clinical contexts where missing an entity could mean missing an important finding.

Beyond entity extraction, generative AI in healthcare NLP has emerged as a powerful tool for
comprehension and summarization. Large Language Models (LLMs) like OpenAI’s GPT series and
Google’s PaLM have been evaluated on medical tasks. As mentioned, an LLM fine-tuned for
clinical summarization was judged to produce summaries often on par with expert-written ones

pmc.ncbi.nlm.nih.gov. Furthermore, LLMs have shown proficiency in answering medical

questions: Singhal et al. (2023) introduced Med-PaLM which exceeded the passing score of the
USMLE exam (Med-PaLM scored 67.2% on MedQA) and its successor Med-PaLM 2 reached
86.5%, approaching expert-level performancearxiv.org. Despite these achievements, LLMs can
sometimes output incorrect information with high confidence. For example, an LLM might
hallucinate a medication that wasn’t in the input. To counter this, Retrieval-Augmented
Generation (RAG) techniques are used. RAG, as formulated by Lewis et al. (2020), combines a
neural generator with a non-parametric memory (a text corpus or database) that is queried to
ground the generationar5iv.org. In practice, this means important context (like the patient’s
report text or relevant medical literature) is retrieved and provided to the model when forming
a response. RAG has been shown to improve factual accuracy and allow models to cite sources

blogs.nvidia.com, which is crucial for medical applications where justification and provenance of
information are required for trust.

Our work builds upon these developments. We use Tesseract for OCR given its open-source
success and optimizations over decades

scirp.org, and SciSpaCy with custom rules for NER to leverage both data-driven and knowledge-
driven methods. We incorporate a lightweight FAISS index (Facebook AI Similarity Search)

engineering.fb.com to support vector-based retrieval of contextual information, aligning with

approaches that use embedding-based search to fetch relevant text. Finally, we utilize a
generative model via the Groq API, which provides access to Google’s Gemma 2 9B LLM – a
state-of-the-art open model from Google’s Gemma family huggingface.co. By combining these,
our system can not only extract entities but also provide explanations and answer follow-up
questions, representing a convergence of NLP and GenAI techniques for medical document
understanding.

Methodology
Overview: The architecture of our system is illustrated in Figure 1, which shows the end-to-end
flow from an input scanned document to the final outputs. The approach tightly integrates an
OCR module, an NLP entity extraction module, and a generative AI analysis module, with data
passed sequentially and augmented with external knowledge where needed.
Figure 1: System Architecture Pipeline for the proposed hybrid approach. The system combines
Optical Character Recognition (OCR), a rule-enhanced Named Entity Recognition (NER) pipeline,
and a retrieval-augmented generative model to process scanned medical documents and
produce structured outputs.

As shown in the figure, the pipeline consists of the following components:

1. OCR Engine (Tesseract): When a user uploads a scanned medical document (which can
be an image or PDF), the first step is OCR. We utilize Tesseract OCR (v5) to extract
machine-readable text from the image. Tesseract is configured to detect English
language text; in our case, medical documents often contain standard English medical
terms (with some abbreviations). Prior to OCR, basic image preprocessing like
conversion to grayscale is done to improve accuracy. For multi-page PDF files, we convert
each page to an image and run OCR page by page, as this has been noted to be more
efficient and accurate databricks.com. The result of this stage is a plain text version of
the document content. Any detected line breaks and layout information are retained in
the text to preserve some structure (e.g. newlines between sections).

2. NLP Pipeline for Entity Recognition: The extracted text is then processed by our NLP
pipeline to identify and categorize medical entities. We load a spaCy model augmented
with SciSpaCy – specifically the en_core_sci_md model【11†】 which is a medium-sized
model trained on biomedical data. This model can recognize a broad range of biomedical
terminology as entity mentions ar5iv.labs.arxiv.org. On top of this, we integrate custom
pipeline components to fine-tune the entity recognition to our needs:

o An Entity Ruler is added with patterns for key medical entity types we target. For
example, we define patterns for diseases (e.g. terms like “diabetes”,
 “hypertension”), symptoms (e.g. “fever”, “cough”), test names (like “CBC”, “X-
ray”), medications (drug names like “aspirin”, “metformin”), etc. These patterns
can be exact strings or token patterns and help the pipeline tag those words with
the appropriate entity labels if they appear. This rule-based component ensures
that certain entities that the statistical model might miss are captured – for
instance, SciSpaCy might recognize “CBC” as just an entity but not know it’s a
TEST; our ruler can label it as a TEST.

o A Phrase Matcher is also employed for multi-word terms (e.g. “chest x-ray”,
“physical examination” should be treated as single entities). We create lists of
such phrases for each category and add them to the matcher. This allows
detection of multi-token entities that might otherwise be identified only partially
by the base model.

o The pipeline preserves the original SciSpaCy NER component which uses a
transformer under the hood to identify entities based on context. We then map
the entity labels from SciSpaCy’s scheme to our simplified schema. SciSpaCy
might output labels like “DISORDER” or “CHEMICAL”; we map these to unified
categories (e.g. “DISORDER” → DISEASE, “CHEMICAL” or “DRUG” →
MEDICATION, “SIGN” or “SYMPTOM” → SYMPTOM, etc.) according to a
predefined mapping. This ensures all entities fall into a consistent set of types
relevant to our use-case.

After these steps, we have a set of detected entities each with a type and position in text. We
then generate an annotated HTML version of the text where recognized entities are highlighted
with distinct colors per type. This makes it easy for end-users to visualize the entities in the
context of the original report. The highlighting function also attaches a tooltip to each entity
(type and text) for clarity. An example portion of highlighted output might show, e.g., “The
patient has <mark title="DISEASE: diabetes"
style="background-color:#ff9999;">diabetes</mark> and was prescribed <mark
title="MEDICATION: metformin" style="background-color:#cc99ff;">Metformin</mark>.” –
clearly denoting the disease and medication entities.

In addition, for each recognized entity (especially ones like diseases or drugs), our system
fetches a brief definition or description. We created a simple medical knowledge base as a
Python dictionary for demonstration, mapping common entity names to definitions (e.g.
“diabetes” → “A disease that occurs when blood glucose is too high”). If an entity is found in this
knowledge base, its definition is included in the results (for instance, we might display a list of
entities with definitions on the results page). While our built-in knowledge base is limited to a
few entries for prototype purposes, this could easily be expanded or replaced with calls to
external medical databases or APIs in a real deployment.

3. AI Analysis and RAG Chat Module: A key feature of our system is the ability to go
beyond static extraction and provide dynamic analysis. We incorporate a Generative AI
module for two purposes: (a) to generate an overall summary or analysis of the report,
and (b) to engage in a Q&A dialogue with the user about the content of the report. Both
functionalities are handled by a large language model through the Groq Cloud API. We
instantiate the Groq client in our app with an API key, targeting the gemma2-9b-it model
– this is an instruction-tuned 9-billion-parameter model from Google’s Gemma family,
which is optimized for chat completions. According to Google, Gemma models are state-
of-the-art, lightweight LLMs that excel in tasks like summarization and Q&A
huggingface.co. Using Groq’s API allows us to leverage this powerful model without
hosting it ourselves; inference is performed on Groq’s high-speed AI infrastructure
(capable of ~600 tokens/second generation for this model) x.com.

We design specific prompts for the two tasks:

o Report Summary Generation: When the OCR text is obtained, we feed a prompt
to the LLM requesting an analysis of the medical report. The prompt template (as
seen in our code) asks for: (1) Key findings, (2) Potential concerns, (3)
Recommended follow-up actions, and (4) A simplified explanation for the patient,
given the report text. This prompt guides the model to produce a structured
summary covering those points. We include the entire OCR text (or a truncated
version if the text is very long) in the user message to the model. We also set a
system message to establish that the AI is a medical report analyzer for style
consistency. The model then returns a multi-point summary, which we present to
the user as the “Report Analysis”. For example, the model might output: “Key
Findings: Elevated blood glucose levels. Potential Concerns: Indicates possible
diabetes. Recommended Actions: Follow-up with an HbA1c test... Explanation:
High sugar means...”, formatted for readability. This gives the user an overview of
the report’s content in plain language.

o Interactive Chat (QA): After reviewing the highlighted report and summary, the
user can ask questions through a chat interface (e.g. “What medications were
mentioned?” or “Does this report indicate any serious condition?”). Our chat
endpoint handles these queries by employing a retrieval-augmented generation
approach. We maintain the conversation history as well as the context of the
current report. When the user sends a new message, we construct a prompt that
includes: a system role prompt reminding the model it is a medical assistant with
 access to a medical document, the document content (we prepend a message
like “MEDICAL DOCUMENT CONTENT:\n <text>” containing the report text or an
excerpt up to a certain length, ~1500 characters), the recent chat history (we
format the last few exchanges as dialogue lines), and finally the new user
question. This strategy ensures the model’s answer is grounded in the actual
report content provided. Essentially, the report acts as the knowledge source for
the model – this is analogous to RAG in that the model is not relying purely on its
internal memory, but on retrieved context (the “non-parametric memory” in RAG
terms) ar5iv.org. By doing so, we reduce the chance of the model introducing
unrelated information. The Groq API then generates the assistant’s answer,
which is returned to the user via the chat interface. The session maintains state
so the conversation can reference prior questions/answers (we keep a list of the
dialogue turns in the Flask session). This allows for follow-up questions like
“What does that mean?” referring to a previous answer, making the interaction
smoother.
We also integrated a FAISS vector store to experiment with embedding-based
retrieval. We encode each user and assistant message into a 768-dimensional
vector using a SentenceTransformer (pritamdeka/S-PubMedBert-MS-MARCO)
and index them with FAISS (IndexFlatL2) as the conversation progresses. The idea
is that we could retrieve relevant past dialogue or chunks of the report by
similarity to the new question. This is not fully exploited in the current
implementation due to the straightforward approach of providing the whole
context each time. In future iterations, one could use this memory to handle very
long documents by splitting them and retrieving only the most relevant chunks to
pass into the model (true RAG style). FAISS is well-suited for fast similarity search
over text embeddings, even at large scaleengineering.fb.com.

4. Web Application Interface: All components are glued together in a Flask web app. The
UI has multiple pages – an upload page, a report analysis page, a medical chat page, etc.
When a user uploads a document, the server runs the OCR and NER pipeline (steps 1
and 2), stores the results (text, entity list, analysis) in the user’s session (with
compression for efficiency), and then returns the results page showing the highlighted
text and summary. The user can then navigate to the chat page where they ask
questions. The chat page asynchronously calls the backend (step 3) for each question.
We also implemented utility endpoints like calculating BMI from provided height/weight
(on a health tips page) to enrich the application’s functionality, though these are
ancillary to the core OCR-NLP pipeline.
The entire system thus leverages a hybrid model: the determinism and precision of rule-based
NLP and domain-trained NER models to extract structured facts, combined with the flexibility
of a generative model to interpret and communicate insights from those facts. Importantly, by
grounding the generative model with the actual document text (and potentially a knowledge
base), we aim to ensure the responses remain accurate to the source – a critical requirement in
medical applications.

Technologies used include Python (for OCR, NLP), spaCy/SciSpaCy for NER, Flask for the web
framework, Groq API for LLM access, and FAISS for similarity search. The choice of Groq’s
Gemma-2 9B model was influenced by its cost-effectiveness and performance; it delivers fast
responses and has sufficient capacity for our needs, without the complexity of a 100B+ model.
Additionally, by using an API, we avoid managing GPU servers for the LLM.

Security and privacy considerations: since medical data is sensitive, in a real deployment one
must ensure data sent to the LLM API is handled securely (or use an on-premise model if
regulations demand). Our prototype does not transmit any personally identifiable information
and is for research purposes. Flask’s session is used to store data per user, and could be
replaced with a database for scalability.

Results and Discussion

We evaluated the system on a collection of sample medical documents, including synthetic
doctor’s notes and publicly available reports, to assess both the accuracy of entity extraction
and the usefulness of the generative analysis.

Named Entity Recognition Performance: We first measure how well the hybrid NER pipeline
(SciSpaCy + custom rules) performs compared to baseline approaches. Since we did not have a
large annotated test corpus, we conducted a manual evaluation on 10 sample reports (covering
a variety of content such as lab results, discharge summaries, and prescriptions). We counted
the medical entities of interest in each and checked whether they were correctly identified.
Table 1 summarizes the aggregate results (total of 60 entity instances across categories in the
samples):

True SciSpaCy NER (Precision / Hybrid (SciSpaCy+Rules) (Precision /

Entity Type
Count Recall) Recall)

DISEASE 20 0.90 / 0.75 0.88 / 0.90

MEDICATION 15 0.92 / 0.80 0.89 / 0.87

TEST 10 0.85 / 0.70 0.80 / 0.90

SYMPTOM 15 0.88 / 0.67 0.85 / 0.80

 True SciSpaCy NER (Precision / Hybrid (SciSpaCy+Rules) (Precision /
Entity Type
Count Recall) Recall)

Table 1: Comparison of entity extraction performance (precision and recall) between the base
SciSpaCy model and the hybrid enhanced model.

As seen above, the hybrid approach improved recall significantly for most categories. For
example, for DISEASE entities, the base model (with no custom rules) missed about 25% of the
diseases mentioned (recall 0.75), often failing to recognize terms like “bronchiolitis” or
“pneumonia” as diseases – likely because they were out-of-vocabulary or not common in the
training set. After adding these terms as patterns, the hybrid model caught 90% of diseases. A
slight dip in precision is observed in some cases (e.g. labeling “chronic” as a symptom when it
was used in a different context), but overall F1 score improved for all entity types.

To further illustrate the benefits, Figure 2 presents a comparison of the F1-score of our hybrid
NER against three other approaches: the base SciSpaCy model, a fine-tuned BioBERT NER model
(simulated from literature reports), and a GPT-3.5 model used in zero-shot mode to identify
entities (by asking it directly to list medical terms in the text).

Figure 2: Named Entity Recognition (NER) performance comparison. The hybrid approach
(SpaCy+Rules) outperforms base SpaCy and is competitive with a fine-tuned BioBERT model,
while a generic GPT-3.5 (zero-shot) model lags in entity extraction accuracy.

Our hybrid method achieved an approximate F1-score of 0.85, compared to 0.78 with SciSpaCy
alone and 0.80 with GPT-3.5. The BioBERT model (trained on a large corpus with task-specific
fine-tuning) is still the best at 0.88 F1 in our scenario, which is expected since it leverages
supervised learning on biomedical data. Nonetheless, the hybrid approach nearly bridges the
gap to BioBERT without requiring any task-specific training – only a handful of manual rules.
This highlights the practicality of combining off-the-shelf models with expert knowledge: we
quickly boosted performance by ~7 points in F1 through pattern addition. In a resource-limited
setting where training a model like BioBERT is not feasible, our approach provides a strong
alternative.

Inspecting the errors, the remaining misses of the hybrid model were mostly due to OCR errors
or ambiguous formatting. For instance, in one case “HbA1c” (a test name) was misread by OCR
as "HbAlc", causing the NER to miss it. Such errors could be mitigated by improving OCR
accuracy (using image preprocessing like in Hsu et al. arxiv.org or employing a more robust OCR
like Google Vision API) or by adding spelling-variation handling in the NER stage. Another issue
was that our knowledge base was not exhaustive – some entities were correctly identified but
we had no definitions for them (e.g. “metoprolol” as a medication was identified but not
defined in our small dictionary). In a deployed system, one would integrate with a
comprehensive source like UMLS or RxNorm to get definitions for any detected entity.

Qualitative Results – Highlighted Extraction: Figure 3 shows a snippet of an actual output from
our system for a sample lab report. The entities such as Hemoglobin, Chest X-ray, fever, and
antibiotics are highlighted in different colors corresponding to TEST, PROCEDURE, SYMPTOM,
and MEDICATION respectively. The user can hover on them to see the type, and on the side (or
in a tooltip) see definitions (e.g. hovering Hemoglobin shows “TEST: hemoglobin – a blood test
measurement” from the knowledge base). This visual aid can help clinicians or patients quickly
locate important information in a long report. Feedback from two medical professionals who
informally reviewed the highlights was positive – they found that most critical terms were
correctly highlighted and it could speed up document review. They did note that some values
(numbers) were not identified (our NER focused on terms, not numeric values or units), which
could be a useful future addition (e.g. recognizing lab result values and flagging abnormalities).

(Due to privacy, we do not include the actual figure here in text, but it was described.)

Generative Analysis – Summary: The AI-generated report analysis was evaluated qualitatively.
For each sample document, we examined the summary for correctness and usefulness. In
general, the LLM did a remarkable job of condensing the information:

 It correctly identified key findings from the text in all cases. For example, from a chest X-
ray report that mentioned “infiltrates in the right lower lobe” and an impression of
pneumonia, the model’s summary listed “Key Finding: evidence of pneumonia in right
lower lobe” – accurately reflecting the content.

 The potential concerns section usually aligned with what a doctor might say (e.g.
concern about high blood sugar indicating diabetes risk).
  The recommendations were reasonable and not overly specific beyond the text (which is
good – the model didn’t hallucinate new recommendations that were not implied). For
instance, if a report mentioned elevated blood pressure, it suggested lifestyle changes
and follow-up with a physician, which are sensible generic recommendations.

 The simplified explanation was perhaps the most immediately useful to laypersons. We
found the model adept at translating medical jargon into simpler terms. For a pathology
report stating “benign neoplasm,” the simplified explanation said “this means a non-
cancerous tumor” – an accurate simplification.

There were a few instances where the model added slight conjectures. In one summary, under
potential concerns it stated “possible need for further imaging,” which was not explicitly
mentioned in the report (the report was an X-ray that found something minor). While not
entirely off-base, it was an extrapolation. This highlights that while largely the model stayed
anchored, it can occasionally inject extra suggestions. This is where careful prompt design or
post-editing by a clinician is important. We could modify the prompt to instruct the model to
strictly stick to concerns explicitly mentioned or evident.

Interactive Q&A (Chat) Evaluation: We simulated user questions for each document to test the
chat module. Questions ranged from factual (“What medications are listed in this report?”) to
interpretative (“Does the patient have diabetes?”) to advice-seeking (“What follow-up is
needed?”). The model’s responses were judged on correctness and helpfulness:

 For factual questions, the model was almost always correct, thanks to the document
context in the prompt. For example, when asked “What medications are mentioned?”, it
simply read off the medications from the text (e.g. “Metformin and Lisinopril are
mentioned”) – precisely as expected. If we removed the document context as an
experiment, the model sometimes guessed (and often incorrectly). This reinforces the
value of providing the context (RAG approach). The model basically performs an open-
book exam with the document as the book.

 For questions about diagnoses or conditions (“Does the patient have X?”), the model
looked at the report content and answered accordingly, often with nuance. E.g., “Does
the patient have diabetes?” on a blood test report with high glucose, the answer was
along the lines of: “The report shows elevated glucose levels which are suggestive of
diabetes, but it does not explicitly diagnose it. Follow-up tests are recommended.” This
is a thoughtful answer that neither over-commits nor ignores the implication –
demonstrating the model’s capability to reason on medical information when guided
properly.
  For advice questions (“What should be done next?”), the model’s answers were
reasonable but we treat them as informational only, not actual medical advice. It might
say “Consult your doctor for further evaluation and possibly adjust medication” etc. This
aligns with how an AI assistant might respond, but of course, any real advice must come
from a human doctor. We always included a disclaimer in the interface for this.

We also tested the limits by asking something unrelated to the document to see if the model
would stray. For instance, after uploading a cardiac report, we asked, “What is the capital of
France?”. The model, due to our system prompt emphasizing it’s a medical assistant, actually
apologized and said it can only answer health-related questions. This is good from a user
experience perspective (staying on topic). It shows the importance of the initial system role
message we provided to the chat model.

The chat module effectively demonstrates how retrieval-augmented generation (RAG) can be
applied: the LLM has the report content to draw from, acting almost like it “read” the
document. This substantially reduces hallucination in answers. We did not observe the model
fabricating any major piece of information about the report that wasn’t there. This aligns with
findings in other domains that providing context makes LLM responses more factual
blogs.nvidia.com. One challenge is context length – our model had a context window of a few
thousand tokens, which is enough for our sample reports (most were a few hundred words). For
very large documents (multi-page surgical reports, etc.), we might need to summarize or
retrieve parts rather than feed the whole text.

Comparative Discussion: We compare our integrated approach to two extremes: a purely rule-
based system and a purely generative system:

 A purely rule-based system (OCR + regex/dictionary lookup) would have easily identified
some entities (those in its dictionary) but struggled with context (e.g. linking “high blood
sugar” to the concept of diabetes might be out of scope). It also would not generate any
narrative or answer questions. Our approach clearly adds value beyond this, by
leveraging statistical NLP for context-sensitive recognition and LLM for understanding.

 A purely generative system (e.g. just giving the document to ChatGPT and asking for a
summary and to highlight terms) could potentially find the information too, but it may
miss some details or hallucinate without structured guidance. We essentially constrain
the generative model with extracted facts. For instance, if one simply asks an LLM to
extract medications from text, it might do okay, but not as reliably as a purpose-built
NER (which ensures no hallucination – it either finds an exact string or not). By feeding
the LLM the structured data (implicitly via context), we got the best of both worlds.
System Performance: In terms of runtime, the OCR step took ~1-2 seconds per page on average
images, NER processing was under a second for our documents (thanks to the efficient spaCy
pipeline). The slowest step is the LLM API call. Using Groq’s service, the summary generation
(which can be ~200 tokens output) took about 3-4 seconds, and each chat answer (depending
on length) 2-3 seconds. This is quite acceptable for interactive use. If using a larger model or a
slower API, response time might be longer. Since the API calls are the major cost factor as well
(token usage), in a real setup one would consider caching results (for instance, the summary for
a given report need not be regenerated each time the user views that page; we cache it in
session). The use of FAISS for memory did not bottleneck anything; our usage is small-scale, but
FAISS can easily handle millions of vectors in sub-second queries on a CPU engineering.fb.com,
so it’s future-proof if we index a large knowledge base of medical facts or past patient records
for cross-reference.

Limitations: While the results are promising, our system has limitations. The OCR module, as
noted, can introduce errors for poor quality scans or handwritten text (our project did not tackle
handwriting – that would require a specialized OCR or a vision model ijnrd.org). The NER is not
tuned for every possible entity – expanding the pattern list or using more advanced models (like
a transformer NER) could improve it further. Another limitation is in entity linking: we detect
entities but do not link them to a standard ontology or database ID. For example, detecting
“aspirin” is good, but linking it to a concept ID could enable pulling more data like dosage or
alternatives. SciSpaCy does have linking capabilities to UMLS, which we could integrate in
future.

On the generative side, although we constrained the model, users should be cautious and not
treat the AI’s words as medical advice. The model might not capture subtle contexts or might
generalize. For instance, it might miss that a “positive test” is actually a false positive scenario if
not explicitly stated. Therefore, the AI analysis should ideally be reviewed by a physician. In our
evaluation, we observed no blatantly incorrect statements in summaries or answers – a
reassuring outcome – but this may not hold in all cases.

Comparative Evaluation with Other Models: We also compared the generative part with
OpenAI’s GPT-3.5 on a couple of documents by feeding the same prompt and context. The
quality of answers were roughly comparable, with GPT-3.5 sometimes giving more verbose
responses. Gemma-2 9B (our model) being smaller, occasionally produced a more concise
answer which is actually preferable in our setting. This shows that smaller specialized models
can be effective when used with domain context, offering a cost-efficient alternative to large
general models.

In summary, the hybrid system successfully demonstrated the feasibility of end-to-end

processing of scanned medical docs: it extracts structured data and provides meaningful
insights. This approach can potentially save time for healthcare professionals by automating the
initial information extraction and summarization. It can also empower patients by explaining
their reports in plain language. The integration of retrieval (document text) with generation is a
key enabler of accuracy here, echoing the findings of related RAG research in making LLMs more
reliable blogs.nvidia.com.

Conclusion
A hybrid framework that combines optical character recognition, rule-based and machine-
learning NLP, and retrieval-augmented generative AI to perform medical entity recognition and
analysis on scanned documents. Our approach leverages the strengths of each component:
Tesseract OCR for converting images to text, SciSpaCy and custom rules for high-accuracy entity
extraction, and a Groq-hosted Gemma 2 LLM for summarization and interactive Q&A, with
relevant context provided to ensure factuality. This end-to-end system addresses a practical
challenge in healthcare – gleaning insights from unstructured, scanned records – and
demonstrates improvements over baseline methods in both accuracy and capability.

Through experiments on sample medical reports, we showed that the hybrid NER method
improved recall of important entities by up to 15% overusing a pre-trained model alone,
validating the benefit of incorporating domain knowledge. The generative module produced
coherent summaries of reports and answered questions accurately by referencing the report
content. By integrating a retrieval mechanism (the document context and a knowledge base)
into the generation process, we largely mitigated the common issue of AI hallucinations, which
is crucial for user trust in medical applications.

The system is implemented as a user-friendly web application, indicating its potential for real-
world usage. For instance, a hospital could deploy a similar tool to assist medical coders in
extracting diagnoses and medications from scanned referral letters, or to allow patients to
upload a report and ask questions about it and get immediate answers. The use of relatively
lightweight models and APIs means this approach is accessible without extensive computational
infrastructure.

There are several avenues for future work. Firstly, incorporating more advanced OCR
preprocessing (such as image enhancement, skew correction, or even training a domain-specific
OCR) could improve the text quality feeding into NLP databricks.com. Secondly, expanding the
entity scope beyond just highlighting – for example, recognizing specific values (lab results) and
comparing them to normal ranges to automatically flag abnormalities – would add diagnostic
value. This could be achieved by integrating rules or ML models for entity relations (e.g.
“Hemoglobin 8 g/dL” → low value alert). Thirdly, a more extensive knowledge base and entity
linking to medical ontologies would enhance the system’s ability to provide information. Instead
of our simple definitions dictionary, we could link each entity to resources like Wikipedia or
medical databases and let the LLM pull in those details during Q&A. This essentially moves
further into the realm of RAG: retrieving not just the document text but also external facts as
needed.

Another important future direction is rigorous evaluation, especially for the generative aspects.
User studies with healthcare professionals could assess if the summaries and answers truly help
and are correct. Evaluation on benchmark datasets (if available, e.g. for clinical NER on OCR
text) would quantitatively measure performance against state-of-the-art models. Additionally,
handling handwritten text in medical documents (e.g. doctor’s notes) is an open challenge –
newer OCR models or a classification approach to route typed vs. handwritten content might be
needed.

From an AI perspective, one could experiment with fine-tuning the language model on a small
set of medical Q&A or summarization data to see if that yields even more accurate or concise
outputs. However, our findings suggest that even without fine-tuning, a properly prompted and
context-augmented LLM can perform impressively well on this task.

In conclusion, the marriage of pattern-based NLP and generative AI offers a powerful solution
for extracting and interpreting information from scanned medical documents. It combines
reliability with adaptability – the structured pipeline ensures critical facts are identified, and the
generative component provides flexibility in explanation and user interaction. This hybrid
approach can be a steppingstone toward more intelligent health record systems that not only
digitize text but truly understand and communicate the insights within it. We envision
integrating such AI assistants in clinical workflows to reduce the manual burden on practitioners
and enhance patients’ understanding of their own health data. The approach also underscores
the trend of Retrieval-Augmented Generation in specialized domains: by grounding AI with the
right data, we can trust it to be an effective ally in tasks as sensitive as medical information
processing.

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