MAKING MEDICAL EXPERTS FIT4NER: TRANSFORMING DOMAIN KNOWLEDGE THROUGH MACHINE LEARNING-BASED NAMED ENTITY RECOGNITION

International Journal on Natural Language Computing (IJNLC) Vol.14, No.2, April 2025
DOI: 10.5121/ijnlc.2025.14202 11
MAKING MEDICAL EXPERTS FIT4NER:
TRANSFORMING DOMAIN KNOWLEDGE THROUGH
MACHINE LEARNING-BASED NAMED ENTITY
RECOGNITION
Florian Freund, Philippe Tamla, Frederik Wilde and Matthias Hemmje
Faculty of Mathematics and Computer Science, University of Hagen, 58097 Hagen,
Germany
ABSTRACT
This study presents a comprehensive survey examining the criteria used by Machine Learning (ML)
experts in selecting and comparing Names Entity Recognition (NER) frameworks. The survey revealed that
while performance is a key criterion, expert opinions vary significantly, highlighting the need for a flexible
system that considers various criteria alongside performance. Based on the survey results, a system was
developed using the structured Nunamaker methodology to assist medical experts in both comparing NER
frameworks and training ML-based NER models. The prototype, including its user interfaces, was
qualitatively evaluated using the Cognitive Walkthrough method. The paper concludes with a summary
and an outlook on future research.
KEYWORDS
Natural Language Processing, Named Entity Recognition, Machine Learning, Cloud Computing, Medical
Expert Systems, Clinical Decision Support
1. INTRODUCTION AND MOTIVATION
Medical experts possess essential domain knowledge that plays a crucial role in the evidence
based development of Clinical Practice Guidelines (CPGs) [1]. CPGs serve as standardized
recommendations that assist physicians in making well-informed decisions for the optimal
treatment of their patients, ultimately minimizing patient risk [2]. For example, CPGs provide
specific protocols for managing chronic diseases like diabetes, outlining recommended blood
glucose targets, medication choices, and lifestyle modifications. The development of CPGs relies
heavily on extensive sources of information, often presented in large volumes and natural
language, such as clinical study reports, case studies, and scientific literature [1]. For instance, a
clinical study on a new cancer treatment might contain thousands of pages detailing patient
responses, adverse effects, and long-term survival rates. Medical experts must sift through these
massive datasets to extract relevant findings, making the process time-consuming and prone to
information overload [3]. Named Entity Recognition (NER), a subfield of Natural Language
Processing (NLP), helps convert unstructured text into structured data, making knowledge
extraction more efficient [4]. For example, an NER model can identify and categorize critical
entities such as drug names (e.g., "Metformin"), diseases (e.g., "Type 2 Diabetes"), and medical
procedures (e.g., "MRI scan") from clinical documents. Recent advancements in NER have
significantly improved accuracy by leveraging Artificial Intelligence (AI) techniques, including
Machine Learning (ML), Deep Learning, and Large Language Models (LLMs) [4]. However,
achieving high performance in specialized domains like medicine requires the development of

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domain-specific NER models tailored to recognize intricate medical terminology and
abbreviations (e.g., "CABG" for Coronary Artery Bypass Graft) [1], [4]. The creation of ML-
based NER models is complex, requiring expert guidance throughout the process to ensure
accuracy and reliability [1]. With the increasing adoption of ML-based NER, research activities
and the availability of both local and cloud-based NER tools and frameworks have expanded
significantly [5]. For example, platforms like spaCy, SciSpacy, and Google's AutoML offer pre-
trained and customizable NER models for biomedical text processing. As a result, domain
experts often struggle to keep up with rapid developments, compare various NER tools, and
determine the most suitable ones for their specific needs, such as extracting patient symptoms
from Electronic Health Records (EHRs) or analyzing drug interactions in pharmacovigilance
studies [6].
Building on the recognition that ML-based NER is a vital technology for medical experts, this
research is driven by several key projects. The RecomRatio project [7], initiated by the
University of Bielefeld in 2018, aims to assist medical professionals in therapy decision-making
by extracting arguments for or against specific medical treatments from the medical literature
using ML-based NER and the spaCy framework [8]. The extracted data is stored in a knowledge
database to support clinical decision-making. Following RecomRatio's outcomes, the Artificial
Intelligence for Hospitals, Healthcare & Humanity (AI4H3) project focuses on enhancing the
transparency and explainability of medical decisions through AI [9]. It proposes a layered
architecture with a central hub, the "KlinGard Smart Medical Knowledge Harvesting Hub",
which serves as a registration point for AI modules applicable in natural language text analysis.
This hub architecture facilitates the decentralized integration of heterogeneous data and AI
modules, enabling the efficient integration of information sources, including medical literature,
electronic health records, and healthcare social media data, all critical for Clinical Decision
Support (CDS). The Cloud-based Information Extraction (CIE) project, building on the
AI4H3 hub architecture, provides cloud-based resources such as computing power and storage
for the automated extraction of natural language texts using ML techniques [10]. These resources
support end-to-end NER pipelines in a cloud environment and optimize resource allocation.
Framework-Independent Toolkit for Named Entity Recognition (FIT4NER), another project
within the AI4H3 context, aims to empower medical experts to utilize various AI-based text
analysis techniques, including NER, for efficient Information Retrieval (IR) in developing
CPGs [6]. It employs the Content and Knowledge Management Ecosystem Portal (KM-EP)
[11], co-developed by the Faculty of Mathematics and Computer Science at FernUniversität
Hagen [12] and the FTK e.V. Research Institute for Telecommunications and Cooperation [13],
to facilitate knowledge management across multiple domains. KM-EP manages documents such
as medical research findings and clinical studies, serving as an evidence base for the
development of CPGs [6]. To enhance IR, KM-EP offers document classification features using
NER, along with a faceted search engine built on these classifications [14]. The necessary ML-
based NER models are integrated into KM-EP and should ideally be trained by medical experts.
The medical field relies on a wide array of domain-specific terms and abbreviations, which are
often ambiguous or have variations in spelling [15]. Therefore, involving medical experts who
consider specific terms, abbreviations, and potential spelling errors is crucial for training new
models and achieving optimal results [16]. However, the dynamic nature of NER research
presents several challenges for experts. First, they must compare various tools to identify NLP
features such as Named Entities (NEs) and entity relations and select the most suitable solution
for their tasks [6]. This comparison is demanding, as NLP practitioners often find it difficult to
clearly determine which software performs best and which tools efficiently extract, analyze, and
visualize NLP features [5]. Second, choosing the right tool is critical, as it significantly impacts
the accuracy of analytical tasks [17]. Third, users often lack the necessary computational and
storage resources to train high-quality NER models within their domain [10]. While cloud
computing could potentially address this issue, experts frequently lack the requisite knowledge

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and experience to effectively utilize this technology [10]. The primary research objective of this
work is to develop a flexible NER system that aids medical professionals in efficiently analyzing
domain-specific texts while addressing challenges such as selecting and comparing new NER
frameworks. To achieve this goal, the following research questions have been defined and will be
addressed in this study: (RQ1) What are effective methods for domain experts to experiment with
and compare NER frameworks? (RQ2) How can an integrated and distributed information
system be developed that enables domain experts to apply ML-based NER methods and supports
the continuous development of NER frameworks?
We employ the well-established Nunamaker methodology [18] to systematically answer our
research questions. This approach guides the development of information systems through
multiple Research Objectives (ROs) encompassing observation, theory building,
implementation, and evaluation phases. Section 2 address the observation objectives by
reviewing the current state of the art. Section 3 focuses on theory building objectives, developing
models to aid medical experts in training ML-based NER models. Section 4 sets out the system
development objectives, which include describing a prototype system for training ML-based
NER models. Section 5 describes the experimentation objectives and describes the execution and
analysis of expert tests using the prototype. Finally, Section 6 summarizes the results of the
study.
2. STATE OF THE ART IN SCIENCE AND TECHNOLOGY
This chapter explores the observation phase, providing the background of this work and relevant
research activities. It aims to review the state of the art and identify potential Remaining
Challenges (RCs) in the addressed domains. First, NER and the challenges of dealing with
various NER tools are examined. Second, a short overview of cloud technologies is provided.
Finally, a survey is presented to identify the criteria ML experts use to evaluate NER tools and
frameworks, highlighting the key challenges they face in selecting the most suitable solutions.
NER is an NLP technique that aims to extract NEs from unstructured text documents [19]. A NE
is a word or phrase that refers to a specific entity such as a person, place, or organization. NER is
a crucial technique used in various applications, including IR [20], question answering systems
[21], machine translation [22], and social media analysis [23]. In the medical domain, NER plays
a pivotal role in Clinical Decision Support Systems (CDSSs) and enables clinical information
mining from Electronic Health Records (EHRs) [24]. In recent years, NER has seen significant
progress due to the development of new techniques and models, including deep learning [25].
These advancements have led to substantial improvements in the performance of NER systems,
making NER one of the most extensively researched NLP tasks today [25]. In NER, there are
different techniques available, including traditional, ML-based, and hybrid approaches [26].
Traditional NER approaches rely on methods that use manually created rules or are dictionary-
based. Although these systems are often efficient and accurate, they are also limited by fixed
rules or dictionaries and do not generalize well across different domains and languages [26]. ML-
based approaches to NER have gained popularity in recent years, mainly due to the availability
of large annotated datasets and advancements in deep learning techniques [25]. These approaches
are capable of efficiently processing unstructured and large datasets and achieve superior results.
Instead of relying on fixed rules or dictionaries, ML-based NER uses statistical models that learn
to detect NEs from annotated data through a process of training and testing. ML techniques are
divided into supervised, unsupervised, and semi-supervised learning [27]. Supervised learning
[27] relies on manually annotated data to train a model, where the model learns to predict the
labels of unseen data. Unsupervised learning [27], on the other hand, relies only on statistical
algorithms to detect patterns from unlabeled data. Semi-supervised learning [27] combines these
two approaches by training a model with a small set of annotated data and using it to label a
larger set of unlabeled data, thus improving the accuracy of the model. In recent years, pre-

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training large language models such as BERT [28], GPT-2 [29], and RoBERTA [30] on large
corpora have shown remarkable improvements in NER performance. These models can achieve
state-of-the-art performance on NER tasks and can efficiently finetune on smaller datasets for
domain-specific tasks. Although further improvements can be made, AI advancements have
already made significant progress in addressing complex NER challenges. The research field of
NER continues to evolve rapidly, with new and innovative tools being developed to address
different challenges and use cases. Therefore, it is crucial for ML experts to compare and
evaluate the performance of available NER tools and to select the one that best fits their specific
task, such as training and fine-tuning ML models on custom datasets.
Amazon Web Service (AWS) launched in the early 2000s, pioneering the concept of cloud
computing by offering scalable computing resources on demand as a service [31]. This
groundbreaking technology has since evolved into a widely available solution that offers vast
amounts of computing resources at any given time. The availability of scalable and costeffective
cloud computing has revolutionized the field of AI by providing a scalable and costeffective
platform for creating, training, and deploying AI models. ML-based NER is one of the many AI
applications that have benefited from the cloud’s capabilities [10]. The unprecedented growth of
data has made it challenging to manage and analyze large amounts of information using local
compute resources [25]. To tackle this issue, leading providers such as AWS, Microsoft Azure,
and Google Cloud Platform offer cloud-based platforms at various levels of abstraction,
including Infrastructure as a Service (IaaS), Platform as a Service (PaaS), and Software as a
Service (SaaS) [31]. These platforms provide the necessary computing resources and tools to
store, process, and analyze massive amounts of data efficiently and cost-effectively. Cloud-based
ML platforms not only provide computing power (IaaS) but also offer a comprehensive suite of
tools and services for data processing, model training, and deployment (PaaS). These platforms
make it easy to scale performance up or down as needed, even for demanding applications with
real-time requirements. Cloud providers offer not only cloudbased ML platforms but also NLP
and NER services. These services include pre-built models and Application Programming
Interfaces (APIs) that enable users to easily incorporate AI functionality into their applications
without requiring extensive expertise in the AI domain [10]. To leverage cloud-based resources
effectively, ML experts must carefully evaluate which level of abstraction and which cloud-
based services from which provider to use. Furthermore, utilizing cloud-based resources requires
familiarity with the relevant technologies, including understanding their strengths, limitations,
and best practices [32]. Although cloud technology offers many benefits, including scalability
and cost effectiveness, there are legitimate concerns about privacy, security, and ethical
implications, particularly in the medical field [33]. As a result, ML experts must carefully
consider these factors and evaluate whether cloud-based resources can be used while still
meeting regulatory and ethical standards. In summary, cloud technology has rapidly evolved into
a powerful platform for creating, training, and deploying AI models. However, ML experts face
the challenge of determining whether and which cloudbased resources to deploy, requiring
careful evaluation of factors such as scalability, cost, security, privacy, and ethical
implications.In recent years, several scientific papers have compared and evaluated NER tools
for various application domains, such as formal and social media texts [34], software
documentation [35], historical texts [36], news sources [17], [37], and specific languages [38].
Pinto et al. [34] conducted a study to compare and analyze the performance of multiple NLP
tools, including their effectiveness on formal and social media texts in four commonly used NLP
tasks, which include NER. Their findings suggest that it is a challenge “to select which one to
use, out of the range of available tools”, and “this choice may depend on several aspects,
including the kind and source of text” [34]. Al Omran et al. [35] emphasized the importance of
choosing the right NLP library for tasks like tokenization and POS tagging, as these significantly
impact NER performance. Won et al. [36] demonstrated that NER performance is corpus-
dependent and can be enhanced by combining different tools, a finding also supported by

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Aldumaykhi et al. [38] for Arabic texts. Weiying et al. [17] conducted benchmarking for
enterprise applications, while Schmitt et al. [37] noted the challenges in NER tool comparability
and called for structured comparison methodologies. Jehangir et al. [19] analyzed various NER
approaches, recommending a combination of deep learning and rulebased methods for optimal
results. Overall, their findings suggest the need for contextdependent selection and comparison of
NER tools, considering corpus-specific performance and the potential for tool combination.
Figure 1 Priority Distribution per Selection Criteria
However, these studies did not address the challenges ML experts face when comparing NER
tools to find the most suitable solution for their projects. A new study was conducted in the fall
of 2024 [5] to fill this research gap. The Kasunic’s survey research methodology [39] was
employed to gather insights from nearly 90 NLP experts regarding their experiences in
comparing and selecting NER frameworks and tools. Responses were received from 23 experts,
most of whom had advanced degrees, such as a PhD or Master's. While most of the experts were
from the field of computer science, there were also participants with backgrounds in history or
economics. Figure 1 details the evaluations of participants of various selection criteria across all
NER tools and frameworks, revealing performance (average 4.57) as the most critical factor. The
consistently high prioritization of performance underscores the need for NER tools to deliver
accurate and reliable results in different operational contexts. Questions were also posed
regarding cloud-based tools, such as Microsoft Azure Cognitive Services. Especially, for these
cloud-based tools, licensing and cost (average 3.89), as well as user interface and ease of use
(average 3.59), also rank highly. This reflects the growing importance of affordability and
accessibility in encouraging adoption among diverse user groups, such as newbies and ML
experts. In contrast, factors such as integration (average 2.95) and customization (average 3.27)
were moderately important, suggesting that participants found these areas less critical when
evaluating NER tools. Privacy (average 3.31) received mixed scores, signaling varying levels of
concern depending on the application and deployment model. In general, it can be concluded that
all the criteria were considered relevant. This suggests that the importance of criteria is highly
dependent on the specific project and that there are no criteria that can be universally deemed
unimportant. This is also illustrated by the fact that there are different specific challenges for
NER, depending on which knowledge domain NER is to be applied [4]. Numerous studies
highlight the importance of performance in NER tools and frameworks by comparing their
effectiveness [17], [37], [40]. Therefore, a supportive system should be designed with flexibility
to accommodate diverse evaluation criteria, ensuring adaptability to project-specific needs while
maintaining high model training performance (RC1). When analyzing the results of cloud-based
and locally installable NER tools and frameworks, and calculating the average performance
values, notable insights emerge. Table 1 illustrates the average results for both types of tools,
highlighting the differences (Delta) between them. For locally installable systems, documentation
and support play a critical role, as evidenced by a Delta of -1.14. This observation aligns with
findings from related studies, where documentation is frequently emphasized as a key factor in
evaluating NER tools. For instance, Schmitt et al. argue that criteria such as documentation

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should be carefully assessed before selecting and deploying an NER solution [37]. However, for
cloud-based systems, the user interface and ease of use are particularly relevant (Delta 1.09).
Tamla et al. highlighted that managing cloud-based resources poses challenges for both
beginners and ML experts [10], emphasizing the importance of user interface design and
usability. Similarly, Kurdi et al. recognized that an intuitive interface significantly enhances the
usability of cloud-based services [41]. Therefore, users of cloud-based NER services would
greatly benefit from systems designed to simplify their use, making user-friendliness a crucial
requirement (RC2).
Table 1 Comparison of Average Priority per Selection Criteria
Criteria Cloud Local Delta
Accessibility 3.57 3.0 0.57
Customization 3.43 3.31 0.12
Documentation and support 2.57 3.71 -1.14
Integration 2.57 3.1 -0.53
Knowledge Domain Requirements 3.43 3.45 -0.02
Licensing and cost 3.71 3.9 -0.19
Performance 4.57 4.55 0.02
Privacy 3.14 3.29 -0.15
User interface and ease of use 4.43 3.34 1.09
The responses to the question “How hindering have the following challenges or limitations with
< selectedTool > been in the past?” for all NER tools and frameworks are presented in Fehler!
Verweisquelle konnte nicht gefunden werden.. The responses are surprising in that very few
challenges were classified by participants as very hindering. The most frequently cited issue was
“Time and effort to learn the new framework” (average 2.84). This was followed by
“Performance Issues” (average 2.57), which is consistent with the findings in Figure 1.
“Challenges with integration into existing applications” were mentioned the least as a hindrance
(average 2.05). Other challenges, such as “Cost” (average 2.36), “Lack of support” (average
2.32), and “Lack of documentation” (average 2.30), were ranked mid-range but low. Each
challenge was mentioned at least once as hindering or very hindering, supporting the assertion
that the requirements for NER tools and frameworks are project specific. In general, it can be
concluded that reducing the time and effort required to learn new frameworks is essential. Here,
also, the results of this question were grouped with respect to cloud-based and locally installable
NER tools and frameworks and the average value was calculated. As shown in Table 2, the time
and effort required to learn the new framework are particularly restrictive for locally installable
systems (Delta -0.57). There, a system designed to support the comparison and selection of NER
tools and frameworks must also enable users to work efficiently across different platforms. For
locally installed solutions, reducing the adoption effort through intuitive software and seamless
integration is crucial (RC3). In contrast, for cloud-based services, cost remains a major barrier to
adoption (Delta 1.79). Therefore, effective cost management and optimization strategies, such as
pay-as-you-go models and resource monitoring, are essential to ensure cost efficiency [42]
(RC4). The survey emphasized that performance is a key criterion, though expert opinions varied
significantly. Notably, every specified selection criterion was deemed important or very
important at least once, suggesting that their relevance depends on the specific project.
Therefore, a supportive system must be flexible enough to accommodate diverse criteria while
ensuring strong model training performance (RC1). A distinction is made between cloud-based

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services and locally installed tools. For cloud-based NER services, cost efficiency and
userfriendliness are particularly crucial, making them essential requirements for any system
utilizing cloud-based resources (RC2, RC4). In contrast, for locally installed solutions,
minimizing the adoption effort is critical, which can be achieved through well-designed software
integration (RC3). After reviewing the state of the art in science and technology and identifying
key research challenges (RCs) in NER and cloud computing, the next chapter presents the
modelling and design of a system tailored to address these challenges.
Figure 2 Priority Distribution per Hindrance Criteria
Table 2 Comparison of Average Priority per Hindrance Criteria
Hindrance Cloud Local Delta
Challenges with integration into existing applications 2.29 1.90 0.39
Cost 3.71 1.93 1.79
Lack of documentation 2.43 2.31 0.12
Lack of support 3.00 2.21 0.79
Performance issues 2.29 2.62 -0.33
Time and effort to learn the new framework 2.43 3.00 -0.57
3. MODELLING
This section focuses on the theory-building phase, aiming to develop essential models for a
system that supports medical experts in creating ML-based NER models. This is achieved by
integrating the Research Challenges (RCs) outlined in Chapter 2, grounded in the latest scientific
and technological advancements. User-Centered System Design (UCSD) [43] is employed for
design and conceptual modeling, while the Unified Modeling Language (UML) [44] serves as
the specification language. Within the FIT4NER project, Use Cases (UCs) were developed for
the roles of Model Definition User, Model End User, and Administrator, alongside a generic
architecture [6]. These components enable domain experts to experiment with various ML-based
NER frameworks, compare their results, and select the most suitable framework for their
application needs. As highlighted in Chapter 2, a survey of ML experts identified key aspects
FIT4NER should support for effective framework comparison. A Master's thesis based on
FIT4NER further refined the existing models to align with these requirements [45]. The
subsystem developed in this thesis, termed the Framework-Independent Layer for Training
and Applying Named Entity Recognition (FILTANER), enhances the flexibility and
adaptability of ML-based NER applications.

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3.1. Use Cases
The FIT4NER Use Cases (UCs) are first analyzed and further refined, with enhancements
introduced by FILTANER highlighted in magenta. As shown in Figure 3, UC1 "Extract Data"
facilitates the retrieval of necessary data for training. UC2 "Select NER Framework" helps
identify the most suitable framework for training NER models, ensuring a solid foundation for
the training process. Since each framework comes with distinct functionalities and requirements,
this selection is crucial. Building on this, UC2.1 "Support Model Training" assists the Model
Definition User in training NER models, regardless of the chosen framework, ensuring flexibility
and broad applicability.
Figure 3 Use Cases for Model Definition User and Model End User
This is achieved through a generic approachthat enables the consistent use of various
frameworks without requiring specific implementation details. A key emphasis is placed on
transformer-based models, given their central role in current research and practice. To address
their unique requirements, "UC2.2 Support Transformer-Based Model Training" provides
dedicated support for training these models. To standardize while maintaining flexibility in the
training process, "UC2.1.1 Select Training Config Profile" allows users to choose from
predefined configuration profiles. These profiles offer a structured way to explore different
training strategies without the need for manual parameter adjustments in every training run. After
a model is successfully trained, it is essential to ensure sustainable storage and versioning.
"UC2.1.2 "Store Model" guarantees that trained NER models are securely stored for application,
evaluation, or retraining, with a strong focus on version control and traceability. Additionally,
documenting the entire training process is crucial for maintaining transparency and
reproducibility. "UC2.1.3 Document Model Training" ensures that all relevant information is
recorded, facilitating the reconstruction of complex training pipelines across different
frameworks. To preserve training configurations for future reuse, "UC2.1.4 Store Training
Config" saves the applied settings, enabling rapid model adjustments and optimizations without
restarting from scratch. For comparing different NER frameworks, "UC3 Compare NER
Framework" allows the Model Definition User to systematically evaluate and contrast
framework performance based on the criteria outlined in Chapter 2. The sub-use case "UC3.1
Evaluate and Validate Models" ensures that trained models undergo consistent and comparable
assessments across frameworks. Expanding FIT4NER’s capabilities, "UC3.1.1 Compare
Models" (a FILTANER UC) enhances model comparison by enabling direct evaluations across
multiple frameworks. Using a standardized evaluation format, this feature allows detailed

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performance assessments between models trained on different frameworks. For efficient model
organization and management, "UC3.2 Manage Models" provides functionalities for saving,
loading, and reusing models for further training, re-evaluation, or deployment in various
applications. A key component, "UC3.2.1 Serve Models", supports the deployment of trained
models for real-world production use. Finally, "UC4 Analyze Document" utilizes the trained
models to analyze documents from KM-EP, with the results visually presented in "UC4.1
Visualize Document Features".
Figure 4 Use Cases for Administrator
The "UC5 Add NER Framework" in Figure 4 aims to integrate new frameworks. Within the
scope of FILTANER, this use case is expanded with four additional UCs. “UC5.1 Provide NER
Framework Service” which focuses on offering NER frameworks as a service, while providing
functionalities such as training, evaluation, and application of NER models as independent
services. The initial step, “UC5.1.1 Develop Framework”, involves developing the foundational
structure for utilizing NER frameworks, emphasizing the definition of standards that ensure
consistent integration and lay the groundwork for delivering NER framework services. “UC5.1.2
Configure NER Framework Service” allows for the customization and fine-tuning of the
provided services, enabling administrators to make framework-specific adjustments, such as
disabling transformer support. Finally, “UC5.1.3 Describe NER Framework” permits a detailed
description of the features and functionalities of each framework. These descriptions are
displayed to service consumers, providing a well-informed basis for selecting the appropriate
framework.
3.2. Components
Figure 5 FIT4NER Revised General Architecture

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Following the description of the UCs, this section provides a detailed overview of the FIT4NER
General Architecture [6]. The components expanded within the FILTANER project are
highlighted in magenta. The updated diagram (Figure 5) introduces a new component, the Model
Definition Registry. This central repository allows for the storage and retrieval of specific
configuration files for the NER training process. The configurations facilitate the
parameterization of the training process and can be tailored to meet specific requirements. Each
configuration may include metadata or tags that provide information on expected training
duration and accuracy. This feature enables domain experts with limited experience in NLP to
select appropriate predefined configurations for the training process. The Model Evaluator View
is another new component designed to assess NER models using test datasets and key
performance indicators, such as Precision, Recall, and F1. Additionally, the FILTANER project
defines three specific NER framework services that can be utilized in the service cloud for
training ML-based NER models. For this purpose, three NER frameworks were selected:
Stanford CoreNLP [46], a well-established Java-based NER framework previously used in
various projects; and spaCy [47] and Hugging Face Transformers [48], which were chosen due to
their prevalent use among experts, as indicated by the prior survey [5].
Next, the core components, including their interfaces, operations, and interactions with external
systems are specified. The goal is to create a modular and scalable structure that standardizes the
management and deployment of trained models and configurations, enabling dynamic use of
various NER frameworks. Figure 6 illustrates the detailed structures of the components,
including the interfaces and operations of the services and controllers that govern communication
between the components and the KM-EP. On the left side are the ModelRegistry and the
ModelDefinitionRegistry, which are used for storing and providing trained NER models as well
as reusable configuration files for model training. The ModelRegistry allows for the storage of
new models via the Upload Model operation and the retrieval of stored models using Download
Model and Get Models by Tag. Models can also be filtered by tags or searched by associated
frameworks. The ModelDefinitionRegistry manages configuration files required for the training
process and provides operations such as Upload Config, Download Config, Get Configs by Tag,
and Get Framework Configs. The NER Framework Service provides an abstract representation
of how various services for individual NER frameworks, such as Stanford CoreNLP, spaCy, and
Hugging Face Transformers, are internally structured.
This service includes three key components: ApplyNERService, EvaluateNERService, and
TrainNERModelService, which are responsible for applying trained models, evaluating models
with validation data, and training or fine-tuning models, respectively. Additionally, the
RegistrationController ensures the registration of the NER Framework Service with the NER
Framework Independent Service. On the right side is the NER Framework Independent Service,
which provides controllers for applying, training, and evaluating NER models centrally, thereby
functioning as a middleware unit within the overall system. External systems like the KM-EP can
access this service via REST interfaces to analyze documents, train models, or perform
evaluations. The UsageController in the NER Framework Independent Service consolidates
access to all NER Framework Services and provides a central interface for the KM-EP. It
coordinates requests such as Apply Model for document analysis using a selected model, Train
Model to initiate the training process, or Evaluate Model for model evaluation using validation
data. Additionally, the status of an ongoing process can be queried through Get Job Status. The
ServiceRegistry manages the registration and discoverability of available NER services and
offers operations such as Register NER Service, Get NER Service, and Delete NER Service. An
NERService entity stored in the ServiceRegistry describes a registered service through attributes
like framework_name, endpoint_url, description, and has_base_model_support. Training,
evaluation, and application processes are represented by the TrainJob, EvaluationJob, and
ApplyJob entities. A TrainJob instance contains information such as framework_name,

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config_path, model_name, optional base_model_path, and references to train_data and
eval_data. The EvaluationJob entity stores framework_name, model_path, and eval_data, while
the ApplyJob includes attributes like framework_name, model_path, and text_file. The status of
an ongoing or completed process is indicated by the JobStatus entity, which includes job_id,
framework_name, status, and result. This architecture facilitates a modular and scalable solution,
wherein NER Framework Services are centrally accessible via the NER Framework Independent
Service. The KM-EP can control all processes through well-defined interfaces. The
ModelRegistry and ModelDefinitionRegistry ensure structured management of trained models
and associated configurations, allowing for a dynamic application landscape and flexible
extensibility to accommodate additional NER frameworks.
Figure 6 FIT4NER Component Diagram
4. IMPLEMENTATION
This section covers the system development phase, focusing on the research objective of building
a prototype that enables medical experts to train ML-based NER models. The implementation of
FIT4NER is ongoing, and this chapter details the planned user interfaces, and the current
progress of system components as modelled in the previous chapter.
4.1. Graphical User Interfaces
The proposed user interfaces are designed to help domain experts make informed choices among
NER frameworks. The NER Framework Comparator View (Figure 7) provides a structured
and intuitive presentation of key frameworks, including SpaCy, Stanford CoreNLP, and
Hugging Face Transformers, each accompanied by concise descriptions highlighting their core
features and benefits. To streamline interaction, the interface features three primary action
buttons: "Train" initiates the training of new NER models, "Evaluate" assesses the
performance of existing models, and "Use" applies a trained model directly. A comprehensive
tabular view presents details of previously trained models, displaying critical performance
metrics such as Precision, Recall, and F1-Score for each model within its respective
framework. Interactive buttons enable domain experts to seamlessly engage with specific models

22
and navigate through the system with ease. To enhance usability and navigation, the user
interface employs a consistent color-coding scheme, where green is used for training, blue for
applying models, and gray for evaluation. This uniform design approach ensures an intuitive user
experience, allowing medical experts to efficiently compare, train, and deploy NER models
within the FIT4NER system.
Figure 7 KM-EP NER Framework Comparator View
Designing efficient user interfaces for complex processes like NER model training requires
reducing perceived complexity and ensuring intuitive usability. Blechschmitt [49] emphasizes
the need to decompose complex user interfaces into smaller, manageable components to enhance
user-friendliness. This approach, known as "tailoring," aims to guide domain experts step-by-step
through interactions. Adaptive user interfaces, such as the use of sliders, have proven particularly
effective in reducing complexity [50]. Building on this approach, model configuration is
simplified through prototypical training profiles that represent various parameter combinations.
Domain experts can use these profiles as starting points. The profiles are organized into
dimensions such as "Fast - Medium - Accurate," "Learning Rate (low, medium, high)", or
"Evaluation Strategy (none, medium, detailed)", as exemplified in the Model Definition Manager
View in Figure 8 (spacy/1-basic-config.cfg – spacy2-advanced-config.cfg). These dimensions
can be adjusted using sliders, allowing for gradual customization. Domain experts can select a
base model from a dropdown menu, upload separate files for training and evaluation data, and
adjust training parameters via sliders. The parameters are dynamically displayed and can be
manually edited if necessary. A collapsible configuration editor ensures a tidy interface, and a
prominent start button facilitates the initiation of the training process. The Model Evaluator View
(Figure 9) is designed to make the assessment process clear and straightforward for domain
experts. A dropdown menu allows experts to select the specific model to be evaluated, and the
evaluation file can be adjusted via an edit icon. The evaluation results focus on performance
metrics such as Precision, Recall, and F1-Score, as the survey described in Chapter 2 [5]
identified these as the most important criteria for selecting NER frameworks. Below this, a

23
detailed table breaks down the results for each entity type, providing targeted insights into the
model's strengths and weaknesses.
Figure 8 KM-EP Model Definition Manager View
Figure 9 KM-EP Model Evaluator View

24
Figure 10 KM-EP Document Analyzer View
Consistent color coding is maintained: the green "Start Evaluation" button indicates an actionable
step, while the "Change Framework" button allows switching to a different environment. This
clear color scheme ensures intuitive navigation, helping domain experts quickly orient
themselves within the interface. The Document Analyzer View intuitively allows trained models
to be applied to text documents (Figure 10). In the upper section, domain experts can select the
desired model, such as "spacy/GlucoseWaterEthanol-Model.zip", from a dropdown menu.
Additionally, a "Change Framework" button permits switching to a different framework if
needed. The central part of the interface contains a text field where domain experts can select the
documents to be analyzed. With a click on the prominently visible "Apply Model" button, the
model is applied to the entered text, and the results are displayed in the lower section.
Recognized NEs are highlighted with colors. Each entity category has a consistent color-coding,
described by legend buttons such as "Entity 1", "Entity 2", and "Entity 3". The results are directly
embedded in the analyzed text, visually highlighting the recognized entities. This design allows
users to quickly identify which parts of the text have been classified as specific entities. It
facilitates rapid interpretation of the model results and allows for adjustments to the text if
necessary.
4.2. Implementation Plan
Following the presentation of the user interfaces, the implementation plan is now detailed.
Various technologies have been selected for development. Integration into KM-EP will be
achieved using PHP, HTML, and JavaScript, ensuring seamless interaction with existing
components. The user interfaces will communicate with the NER Framework Independent
Service and the corresponding NER Framework Services via a REST API. These backend
services will be implemented in Python, as it is widely supported by NER frameworks. Even
Java-based frameworks like Stanford CoreNLP can be accessed via Python, ensuring broad
compatibility. FastAPI will be used to generate the required REST APIs, providing high
performance communication between components. A key aspect of the implementation is
defining the data models, which must accommodate both the requirements of the user interfaces
and the specifications of the NER services. JSON schemas will be employed to structure the data
and ensure validation, facilitating consistency across the system. To enable efficient metadata

25
management and cloud-based storage within the Model Registry and Model Definition Registry
components, an S3-compatible storage solution such as MinIO will be utilized. The
implementation will also incorporate model versioning, allowing previous versions to be restored
when necessary. All services will be containerized using Docker to ensure modularity and
portability. During development, Docker Compose will be used for orchestration, supporting
flexible local deployment and simplifying the transition to cloud-based environments. For cloud-
based container management, Kubernetes will be implemented to provide scalability and fault
tolerance. Comprehensive testing will be conducted throughout the development process,
including unit and integration tests to validate the functionality of individual components.
Automated testing will be integrated into Continuous Integration/Continuous Deployment
(CI/CD) pipelines, which will be managed using GitLab to ensure smooth deployment
workflows. As part of the system implementation, interfaces and data formats for internal
communication will be clearly defined. This will include the creation of detailed API
documentation to facilitate developer integration, leveraging OpenAPI specifications to provide
clear and structured documentation of the API endpoints.
5. EVALUATION
The previous chapter detailed the user interfaces, and the implementation plan of a prototype
aimed at assisting medical experts in training ML-based NER models. This chapter focuses on
the experimentation phase and addresses the research objective of conducting and describing
expert tests based on the developed prototype. It first introduces the evaluation methodologies
used, followed by an assessment of the prototype's effectiveness in supporting medical experts in
training ML-based NER models across various NER frameworks through expert evaluations.
Table 3 Tasks for the Cognitive Walkthrough
Task Description Stereotype Objective
Task 1
Comparison of NER Services:
Analyze available NER services
and select a local
(non-cloud-based) service.
Model
Definition
User
Identify a suitable local service and
initiate NER model training.
Task 2
Selection of an NER Framework:
Start training using an Advanced
Configuration training profile.
Model
Definition
User
Evaluate system flexibility and the
capability to implement specific training
configurations.
Task 3
Evaluation of an NER Model:
Select and assess an existing
NER model from the Model
Registry.
Model
Definition
User
Assess the performance of the selected
NER model and identify potential
optimization opportunities.
Task 4
Adjustment of the Training
Configuration: Initiate training
with a customized model
definition.
Model
Definition
User
Evaluate the integration of individual
training configurations and their impact.
Task 5
Document Analysis: Choose an
NER model for document
analysis.
Model End
User
Conduct and evaluate the document
analysis.
A Cognitive Walkthrough (CW)was selected as the qualitative evaluation approach, a method
for assessing user interfaces as described by Polsen et al. . A CW involves simulating and
analyzing the cognitive processes of a user interacting with the interface. During the preparation

26
phase, tasks with specific objectives and required action sequences are defined. Subsequently, a
panel of experts evaluates the anticipated user interaction with the interface, considering criteria
such as action availability and labeling, the likelihood of correct action selection, and action
complexity. For the initial CW evaluation of the user interfaces, a meeting was conducted with
one PhD, three doctoral candidates, and one master's student, all of whom are researching in the
fields of NLP and NER. Future CW sessions are planned with medical professionals to assess
usability outside the realm of computer science. For this meeting, five tasks were prepared (Table
3), covering UC2, UC3, and UC4 (Figure 3), including their respective sub-use cases. The tasks
were carried out in a development environment that provided the user interfaces, although not all
functionalities were fully implemented. The evaluation findings are presented in Table 4. In Task
1, the NER services available in the GUI (Figure 7) were initially compared. The locally
provisioned service spaCy was selected because no cloud-based services are integrated at the
current stage of development. The Model Definition Manager View (Figure 8) then opened for
training an NER model. Experts provided feedback that the interface texts and descriptions
should be expanded and improved to facilitate use by domain experts (Finding 1 and 3).
Additionally, implementing version control for trained models would be beneficial, allowing
models trained with the same data but different parameters to be compared (Finding 2).
Following the training, the model was evaluated in Task 2 within the Model Evaluator View
(Figure 9). It was noted that users were unclear about which data and formats should be used
when selecting a test dataset. A more detailed presentation of the data formats and datasets could
improve this (Finding 4). During the retraining of an NER model with a modified model
definition (Task 4), experts observed several points. It would be advantageous to upload custom
pre-trained models to the Model Registry, as currently only system-trained models are available
(Finding 5). The model training configuration should be automatically saved to document the
configuration used (Finding 6). Finally, it should be possible to reuse the configuration of
previous trainings as a basis for new ones (Finding 7). There were no additional comments
during the final document analysis (Task 5).
Table 4 Evaluation Results of the Cognitive Walkthrough
Finding Task Description
Finding 1 Task 2 Enhance information delivery by providing explanatory texts for terms such as
Model Name and Base Model, as well as explanations of the functions of
respective GUI elements.
Finding 2 Task 2 Implement version control in the model registry to prevent overwriting models and
to archive previous training states.
Finding 3 Task 2 Expand the configuration GUI with meaningful descriptions of slider step values
to make the impact of parameter changes through training profiles more
transparent.
Finding 4 Task 3 Provide a more detailed representation of the data formats and datasets used in the
evaluation of NER models.
Finding 5 Task 4 Implement a manual upload option for models into the model registry.
Finding 6 Task 4 Automatically save the model definition used in the Model Definition Registry to
document the training process.
Finding 7 Task 4 Integrate a copy button for reusing relevant parameters/model definition and base
model for model training.
This chapter explained how the developed user interfaces of FIT4NER were qualitatively
evaluated by NLP experts. Seven findings were identified, which will be addressed in further
research. The prototype was considered a suitable foundation during the session to support

27
domain experts in selecting and comparing NER frameworks and will therefore be further
developed in future work. Additionally, further quantitative evaluation experiments are planned,
along with an additional qualitative evaluation of the system with medical experts.
6. CONCLUSION
This article presented a survey that investigates how ML experts compare and select NER
frameworks. Based on the survey results, a system was designed and evaluated using the
structured Nunamaker methodology for developing information systems [18], [51]. This system
aims to assist medical experts in comparing and selecting NER frameworks, as well as in training
ML-based NER models.
Chapter 1 provides an overview of the topic and situates the research within its relevant context,
laying the groundwork for the subsequent analysis. Chapter 2 conducted a comprehensive review
of the current state of the art by planning and executing an expert survey. The survey highlighted
that performance is a particularly important criterion. Furthermore, expert opinions varied
significantly. All specified selection criteria were regarded important or very important at least
once. This indicates that the relevance of the criteria may vary depending on the project.
Therefore, a supportive system should be flexible enough to accommodate various criteria along
with performance. A distinction is made between cloud-based services and locally installed tools
and frameworks. For cloud-based services, cost and user-friendliness are particularly significant.
Both aspects represent important requirements for a system that uses cloud-based services for
NER. In the case of locally installed systems, the effort required for users to adopt a new system
should be minimized, which can be facilitated by an appropriate software solution. These
remaining challenges are addressed in Chapter 3, which lays the foundation for the design of an
information system aimed at assisting medical experts in the comparison and selection of ML-
based NER frameworks, as well as in training NER models using these frameworks. Chapter 3
presents the modeling of this system, named FIT4NER. In Chapter 4, the graphical user
interfaces of FIT4NER are developed and showcased, thereby achieving the objectives of the
system development. Chapter 5 discusses the experimental goals and evaluates, through expert-
supported evaluation experiments, the extent to which the developed user interfaces are suitable
for supporting domain experts. During these experiments, areas for future work were identified,
including addressing the findings from the expert evaluation of the FIT4NER interfaces. The
prototype will be further developed to better assist domain experts in selecting NER frameworks.
Additionally, further quantitative and qualitative evaluations are planned, including those with
medical experts.
In summary, this study successfully addressed the defined research questions and resolved the
challenges identified in Chapter 2. The results highlight the potential of the prototype to support
NER model training for medical professionals. Future experiments will involve additional
sessions with medical experts to assess the effectiveness of FIT4NER in developing ML-based
NER models. The contributions of this work provide a solid foundation for advancements in the
field of NER within medical informatics.
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