Medical NER

Medical NER - Revolutionizing Medical Data Analysis

Charlotte Goetz

In modern medicine, the precise extraction of relevant information from the vast field of unstructured medical data is of paramount importance. The emergence of the Names Entity Recognition, or NER technology, shows a way to meet this challenge.

It is very likely that, as a result of recent developments in the Artificial intelligence (AI), medical professionals no longer struggle with deciphering mountains of medical data, but instead access important insights in real time at the touch of a button.

This blog post describes the critical role of precise Data extraction as well as the NER in healthcare. Imagine a scenario where a medical professional has a long patient history with a large number of intricate medical details in front of them. Every second spent deciphering this data could mean a delay in the delivery of critical care.

At these crucial moments, the importance of accurate data extraction in the medical field becomes clear. Konfuzio Medical NER provides medical professionals with the efficiency and precision they need to make fast, informed and potentially life-saving decisions.

Understanding the need for NER in healthcare

NER is essentially a technology that enables automatic identification and classification of entities - such as patient names, medical conditions, medications, procedures and more - in a sea of unstructured text data.

The importance of NER is particularly evident in the Public health, where the complexity of medical documentation presents significant challenges to accurate data extraction. A physician looking to quickly access a patient's medical history, or researchers sifting through mountains of clinical trials, could all benefit from the automatic extraction of important information.

Konfuzio Medical NER
Konfuzio Medical NER Application example for some automatically detected entities in a medical report.

Imagine another situation: A physician is confronted with a patient's medical history in the emergency room. NER seamlessly identifies allergies, medications and existing conditions, ensuring prompt and informed decision making that has a significant impact on the patient's health.

NER acts as a link between raw data and actionable insights in the medical field. NER technology streamlines workflows, increases precision, and allows medical staff to focus on core tasks: providing the best possible care and achieving medical advances.

Medical NER from Konfuzio - Your medical data assistant

Medical NER by Konfuzio is a state-of-the-art language model that revolutionizes the way medical professionals handle data. The specially developed medical NER model is based on a fine-tuned version of DistilBERT.

Konfuzio's medical data wizard is able to identify named Entities from the medical, clinical, biomedical and epidemiological fields. to identify. A total of 22 entities can be identified from a given medical text, in particular the following information:

Benefits of NER for different stakeholders

Entity (in English)DescriptionTypeExample
activityAn action performed by the patient.TextGive up smoking
administrationThe way a treatment was administered or the treatment itself.TextIntravenous, oxygen/air
ageThe age of the patient.Text34 years old
clinical_eventAn event related to a clinical procedure.TextRecorded, Dismissed
diagnostic_procedureWhat type of diagnostic procedure was performed.TextGenetic screening, magnetic resonance imaging
disease_disorderA disease or disorder.TextLiver cancer, respiratory diseases
dosageDosage of a drug.Text4 g/day, 2 tablets daily
durationThis usually refers to the duration of a treatment.Text2 days, Over 6 weeks, After that ten years
family_historyA recurrent illness in the patient's family or a phrase describing that there are no special circumstances related to family medical history.TextDiabetes mellitus, No family history of cancer
frequencyThe interval at which a drug or treatment should be taken or administered.TextOnce a week, Every 3 weeks, Daily
heigtThe vertical measurement of a person, expressed in centimeters.Number180
lab_valueA quantitative measurement from laboratory tests used to evaluate various aspects of a person's health.Text37 °C, 6.1 mg/dL, The value was less than 5
massA general measure, usually in kg.TextOne large liver (6.5 kg), 5 kg weight loss
medicationA substance or preparation prescribed for the treatment, control, or prevention of disease.TextPhenytoin, hormone replacement therapy
occupationThe patient's regular occupation, profession or occupation.TextFarmer, student, office worker
severityThe extent or intensity of a medical condition, symptom, or event.TextLarge, Light, High Risk
sexThe biological classification of a person as male or female based on physiological and genetic characteristics.TextMale, Female, Boy, Girl
sign_symptomA demonstrable manifestation of a medical condition or disease experienced by a patient.TextFatigue, rash, dizziness
subjectIn this model, it refers to a person related to the patient.TextMother, husband, sister
therapeutic_procedureA medical procedure or treatment.TextSurgery, intubation, injection
weightA person's body mass, usually measured in kilograms or grams.Number45

Konfuzio's Medical NER capabilities span a wide range of stakeholders with different needs and goals. Learn below how Konfuzio's Medical NER provides tailored benefits to a range of customer segments:

Medical Practitioners - Improved Workflow Efficiency

For frontline medical professionals, time is of the essence. Medical NER from Konfuzio increases efficiency by quickly extracting important patient information from complex medical records. This allows you to access patient records, treatment plans and medication details in moments. This newfound efficiency leads to more informed diagnoses, personalized care and improved patient outcomes.

Healthcare organizations and hospitals - Automate administrative tasks

The administrative burden in healthcare is overwhelming. Medical NER from Konfuzio steps in as an expert administrative assistant, completely automating data entry, coding and documentation tasks. With streamlined workflows, healthcare organizations and hospitals optimize resource allocation and focus on patient care and strategic initiatives.

Pharmaceutical companies and research institutes - Extract critical information

In the field of pharmaceutical research, Konfuzio's Medical NER is an invaluable asset. By accurately identifying drug names, dosages, adverse effects and patient demographics from literature and study reports, our Medical NER technology accelerates drug development, clinical trials and regulatory compliance.

Medical researchers and scientists - literature reviews illuminate

Medical NER serves as a guide for researchers in the medical literature. With the help of NER, the most important elements in research papers are quickly identified. Researchers thus gain insights and receive support in formulating hypotheses. In summary, Medical NER contributes to the expansion of medical knowledge.

IT company for healthcare industry - improve product capabilities

Medical NER extends the offerings of technology companies providing IT services and software to the healthcare sector. By integrating seamless data extraction capabilities, Medical NER extends the functionality and value proposition of healthcare management platforms, telemedicine applications and electronic health records (EHR).

Legal and law enforcement - support for court proceedings

In legal malpractice and law enforcement investigations, Konfuzio's Medical NER acts as an indispensable tool. By facilitating the extraction of relevant information from medical reports, Medical NER helps attorneys and agencies build resilient cases.

Medical NER from Konfuzio crosses boundaries and provides tailored benefits for all healthcare stakeholders. From physicians and researchers to organizations of all industries and sizes and insurers, Konfuzio's Medical NER empowers everyone to excel in their respective fields and drive efficiency, accuracy and innovation.

How does Medical NER work?

In the past, we at Konfuzio have been concerned with the natural language understanding of computers. Due to the rapid development in the field of NLP various new NLP models have been published, among others BERT. These so-called transformers provide a new level of access to natural as well as technical language. For efficiency reasons, a shallower and less resource-intensive implementation of BERT is often used: DistilBERT. This is a lightweight model with fewer layers and fewer parameters that retains a significant amount of the power of BERT.

The Medical NER is, at its core, a transformer-based model with self-observation blocks. Put simply, a transformer assigns meaning to words in a text relative to all other words in the text. This mechanism is called self-attention, and it allows for the detection of local (within-sentence) and global (across-sentence or across-paragraph) relationships within the text. In addition, the transformer consists of an "encoder" and a "decoder". The encoder prepares the input text into a mathematical representation, while the decoder generates the output text.

The authors of the original transformation model based on DistilBERT replaced the last layer of the network to perform classification for entity recognition of biomedical categories. This allows taking advantage of the pre-trained version of BERT without having to completely re-train a language model. The ability to reuse and adapt existing large language models (LLMs) is one of the reasons for the rapid growth of NLP applications in the area of the machine learning.

Konfuzio Medical NER leverages the flexibility of the Konfuzio framework, which, combined with the fine-tuned DistilBERT model, enables non-technical users to effortlessly extract relevant information from biomedical documents.

Step-by-step tutorial

Use of Konfuzio Medical NER for medical data extraction.

  • Step 1: If you are new to the Konfuzio platform, you must first create a Account register, which is free of charge.
  • Step 2: Access to the Konfuzio Marketplace, and click "Join Now" next to the medical NER entry. You can find detailed instructions here.
  • Step 3: You can now text the model by uploading a PDF document from your computer, or use the sample document.
An example of how to easily extract text from a medical document using Konfuzio Medical NER.

Medical NER - Integration and customization

Seamless integration and customization are at the heart of Konfuzio's Medical NER, enabling users to realize the solution's potential in their individual workflows to use. Learn below how you can easily integrate our solution into your existing healthcare systems, applications or platforms:

Integration with existing systems using REST API: Konfuzio Medical NER is designed to fit easily into your existing healthcare ecosystem. Our solution leverages the power of a dedicated REST API and connects effortlessly with your systems to extract and integrate data in real time. Whether you use electronic health records (EHR), research databases, or health management platforms, Konfuzio Medical NER is an integral layer that improves the efficiency of data-driven operations.

Customization to your needs: We know that every healthcare scenario is unique, with specific requirements and nuances. That's why our Medical NER offers unparalleled customization options. Customize the flexibility, the model for your field, your workflows, and your information extraction requirements. One of the best ways to achieve this is to manually annotate additional documents specific to your field. Through this fine-tuning process, the model adapts and excellently captures the subtleties of your data to ensure precision and relevance in extraction.

Future developments and support

At Konfuzio, we are committed not only to the present, but also to the future of the Document processing. This first version of Konfuzio Medical NER is just the beginning. Here is a small preview of what lies ahead:

Future functions and extensions

Our team works hard to develop advanced features that further refine accuracy, constantly expand the scope of recognized entities, and increase the speed of extraction. With each update, we aim to provide you with a constantly evolving tool that keeps pace with the dynamic landscape of medical data.

Our commitment to continuous progress

Innovation is a cornerstone of our philosophy. Our commitment to your success goes beyond the initial release. We are committed to releasing regular updates that bring you the latest advances in NER technology. In addition, we welcome your feedback. Your experiences and suggestions play a critical role in shaping the direction of our development efforts. This is how we ensure that Konfuzio Medical NER remains an innovative solution that truly addresses your needs.

Relentless customer support

We know that technology is most effective when backed by exceptional support. Our Customer Support Team is ready to support you every step of the way with Konfuzio Medical NER. Whether you have questions about integration, customization, or ongoing use, we are here to provide timely and comprehensive assistance.

Your success is our success. We are committed to helping you realize the full potential of our solution.

The future holds exciting possibilities. That's why we invite you to join us in this transformative endeavor. As we work together to harness the power of Konfuzio Medical NER, you can expect a service based on Innovation, continuous improvement and unwavering support.


In the field of medical data analytics, precision, efficiency, and insights are the pillars upon which exceptional care and breakthrough discoveries stand. Konfuzio Medical NER strengthens these pillars and enables medical professionals, researchers and healthcare organizations to unlock the true potential of their data.

Now it's in your hands. Experience the transformative potential of Konfuzio's Medical NER firsthand. Request a demo, try it yourself or make an appointment with our Sales Team. Our experts are ready to guide you on your project and answer all your questions.

The future of medical data analytics is here. It's time to seize it.

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