Retrieval-Augmented Generation Assistant for Anatomical Pathology Laboratories
Accurate and efficient access to laboratory protocols is essential in Anatomical Pathology (AP), where up to 70% of medical decisions depend on laboratory diagnoses. However, static documentation such as printed manuals or PDFs is often outdated, fragmented, and difficult to search, creating risks of workflow errors and diagnostic delays. This study proposes and evaluates a Retrieval-Augmented Generation (RAG) assistant tailored to AP laboratories, designed to provide technicians with context-grounded answers to protocol-related queries. We curated a novel corpus of 99 AP protocols from a Portuguese healthcare institution and constructed 323 question-answer pairs for systematic evaluation. Ten experiments were conducted, varying chunking strategies, retrieval methods, and embedding models. Performance was assessed using the RAGAS framework (faithfulness, answer relevance, context recall) alongside top-k retrieval metrics. Results show that recursive chunking and hybrid retrieval delivered the strongest baseline performance. Incorporating a biomedical-specific embedding model (MedEmbed) further improved answer relevance (0.74), faithfulness (0.70), and context recall (0.77), showing the importance of domain-specialized embeddings. Top-k analysis revealed that retrieving a single top-ranked chunk (k=1) maximized efficiency and accuracy, reflecting the modular structure of AP protocols. These findings highlight critical design considerations for deploying RAG systems in healthcare and demonstrate their potential to transform static documentation into dynamic, reliable knowledge assistants, thus improving laboratory workflow efficiency and supporting patient safety.
- Research Article
1
- 10.1097/pcr.0b013e3181a05a58
- Mar 1, 2009
- Pathology Case Reviews
Occasional diagnoses in surgical pathology and cytology require immediate notification of the physician to potentially initiate rapid treatment or change management of the patient, similar to critical values (CVs) in clinical pathology. However, while CVs in clinical pathology are well established, the concept of CVs in anatomic pathology has not been presented until recently. Based on our recent studies determining the prevalence of CVs in surgical pathology and cytology, and the perceptions of pathologists and clinicians concerning the concept of CVs in anatomic pathology, the Association of Directors of Anatomic and Surgical Pathology conducted a survey of its membership. Based on the response, an Association of Directors of Anatomic and Surgical Pathology Committee developed national guidelines for critical diagnoses (CVs) in anatomic pathology that included diagnoses that can have immediate clinical consequences, unexpected or discrepant findings, and a variety of infections in immunocompromised and immunocompetent patients. These guidelines are meant to serve as a template, which can be customized at individual hospitals. It is now apparent that the concept of critical diagnoses in anatomic pathology is becoming established in the pathology community and is in fact included in the College of American Pathologists laboratory accreditation checklist. Following the Institute of Medicine’s report on medical errors, there have been an increasing number of initiatives to improve patient safety. We believe that similar to CVs in clinical pathology, having guidelines for anatomic pathology CVs will enhance patient safety and represent a practice improvement in anatomic pathology.
- Research Article
1
- 10.5858/2013-0666-ed
- Mar 1, 2014
- Archives of Pathology & Laboratory Medicine
The special section entitled “The Future of Pathology Training and Training Programs” will appear in 2 parts: part 1 in this issue of the Archives and part 2 in the April 2014 issue. The special section is comprised of 9 articles written by many distinguished individuals around the United States who are leaders in pathology education, including members of the Accreditation Council for Graduate Medical Education (ACGME) Milestones Working Group, who authored the cornerstone article entitled “The Pathology Milestones and the Next Accreditation System.”In addition to “The Pathology Milestones and the Next Accreditation System,” this issue contains articles that focus on the transition from medical school to residency—a national curriculum for pathology undergraduate medical education, “boot camps” in anatomic and clinical pathology, and an example rotation in autopsy pathology that integrates clinical and anatomic pathology results.The Pathology Milestones are an extension and outgrowth of the Outcomes Project at ACGME. The phase I group of programs began the Milestones implementation on July 1, 2013; pathology residency programs are included in phase II, and will implement the changes on July 1, 2014. The authors of “The Pathology Milestones and the Next Accreditation System” include all members of the Milestones Working Group, assembled for the first time in November of 2011, but with groundwork done initially at the July 2011 Association of Pathology Chairs (APC)/Program Directors (PRODS) annual meeting. The Milestones product owes a substantial amount of credit to all of the pathology educators around the country who provided comment, input and suggestions during these past 3 years, but especially to Steven P. Nestler, PhD, executive director of the Pathology Residency Review Committee for 25 years. Of course, many others at ACGME have been part of this process and are collectively recognized for their dedication to graduate medical education. This lead article elucidates the Milestones for Pathology and includes ideas to facilitate implementation effective July 2014.Also in this issue, there are 3 articles that focus on improvement in the continuum of undergraduate to graduate medical education. “Anatomic and Clinical Pathology Boot Camps: Filling Pathology-Specific Gaps in Undergraduate Medical Education” focuses on possible ways to assist in the transition from medical school to pathology residency. An article entitled “A Team-Based Approach to Autopsy Education: Integrating Anatomic and Clinical Pathology at the Rotation Level” illustrates possible ways to integrate the laboratory and anatomic pathology findings from the premortem status and the postmortem status to enhance clinical care. The article “National Standards in Pathology Education: Developing Competencies for Integrated Medical School Curricula” expounds on developing national standards for competencies in pathology education in the integrated medical school curriculum.In the April 2014 issue of the Archives, we will present 5 additional articles.“Progress Toward Improved Leadership and Management Training in Pathology” provides an update on resident education in management stemming from the Laboratory Management PRODS working group, and “Progress and Potential: Training in Genomic Pathology” covers resident education in genomics stemming from the PRODS Training Residents in Genomics Working Group. The article “Pathology Training in Informatics—Evolving to Meet a Growing Need” reviews the current state of informatics education, the upcoming American Board of Pathology certification examination, and the beginning of the development of program requirements for accredited training in informatics by the ACGME.This special section is rounded out by “The American Board of Pathology's Maintenance of Certification Program Update,” and a review of those subspecialty programs that do not currently require board certification—the so-called selective pathology programs—that includes data on funding support and placement of graduates, entitled “Selective Pathology Fellowships: Diverse, Innovative, and Valuable Subspecialty Training.”I thank Mark Sobel, MD, PhD, and Priscilla Markwood, who have not only managed the annual APC/PRODS meetings for many years, but also managed and monitored the APC and APC Council and PRODS and PRODS Council e-mail listserves. Finally, I thank Philip Cagle, MD, Editor in Chief, and the staff of the Archives of Pathology & Laboratory Medicine for their support.
- Research Article
3
- 10.5858/2007-131-1334-mochwi
- Sep 1, 2007
- Archives of Pathology & Laboratory Medicine
Maintenance of Certification: How Will It Affect Pathology Practice?
- Research Article
2
- 10.1093/ajcp/aqad113
- Sep 29, 2023
- American Journal of Clinical Pathology
Pathology services are limited across most of sub-Saharan Africa. We sought to ascertain the availability of anatomic and clinical pathology services and diagnostic resources in Zambia. Two individual surveys-one for anatomic pathology and one for clinical pathology/laboratory medicine-were developed by subject matter experts. These surveys were administered to individuals involved in pathology and laboratory medicine diagnostic services at hospitals and laboratories across Zambia from May to October 2022 using the American Society for Clinical Pathology email listserv. A total of 20 responses were received from 17 unique laboratories-8 sites provide anatomic pathology (AP) services, 12 provide clinical pathology (CP) services, and 3 perform both AP and CP services. Anatomic pathology services are variable and generally limited to a few of the responding laboratories, as only 1 laboratory performs immunohistochemical staining on surgical pathology specimens, and only 2 perform general histochemical stains. Conversely, certain microbiology testing (eg, for HIV) is more widely available. This study of 17 unique laboratories represents the most complete analysis of pathology capabilities in Zambia. Despite initiatives to improve pathology services, both personnel and infrastructure challenges remain. Given a population of approximately 20 million, expansion of anatomic pathology in Zambia must be prioritized.
- Research Article
24
- 10.1093/ajcp/102.5.567
- Nov 1, 1994
- American Journal of Clinical Pathology
Participants of the College of American Pathologists Q-Probes program described their quality improvement practices for clinical and anatomic pathology. In 580 institutions, the median time required for a median of 12 indicators of quality was 40 hours/month, with the number of indicators and the time spent directly dependent on bed size (P = .0001). The overwhelming majority of participants reported benefit from their quality improvement programs in terms of patient outcomes, as a management tool, and for risk management. Six indicators in clinical pathology and four indicators in anatomic pathology were used in more than 75% of laboratories, whereas an additional seven indicators in clinical pathology and five in anatomic pathology were used in more than 50% of laboratories. The authors conclude that quality improvement practices are similar among laboratories, and irrespective of increasing regulatory requirements, pathologists and senior laboratory personnel spend large amounts of time for activities that they believe improve the quality of services rendered.
- Research Article
- 10.35381/s.v.v3i6.331
- Jul 1, 2019
- Revista Arbitrada Interdisciplinaria de Ciencias de la Salud. Salud y Vida
...
- Research Article
30
- 10.1016/j.humpath.2006.03.001
- Jun 2, 2006
- Human Pathology
Critical diagnoses (critical values) in anatomic pathology
- Research Article
2
- 10.1002/cncy.22418
- Mar 19, 2021
- Cancer cytopathology
Levering adult learning principles into a residency core curriculum.
- Research Article
- 10.2105/ajph.40.4.375
- Apr 1, 1950
- American Journal of Public Health and the Nations Health
The Laboratory Bookshelf
- Research Article
15
- 10.1309/rjd0-my82-9ke8-r9k2
- Jun 1, 2005
- American Journal of Clinical Pathology
Similar to critical values in clinical pathology, occasional diagnoses in surgical pathology and cytology may require urgent contact of the physician to facilitate rapid intervention or treatment. However, there are no established critical value (critical diagnosis) guidelines in anatomic pathology. As discussed herein, the Association of Directors of Anatomic and Surgical Pathology (ADASP) believes that establishing anatomic pathology critical diagnosis guidelines represents a practice improvement and patient safety initiative. ADASP also recognizes that a generic anatomic pathology critical diagnosis guideline such as this should be used only as a template because the list needs to be customized at each individual hospital following consultation with relevant clinical services. Based on surveys of the membership of the ADASP, this document provides examples of possible critical diagnoses in anatomic pathology.
- Front Matter
40
- 10.5858/arpa.2011-0400-sa
- Oct 13, 2011
- Archives of Pathology & Laboratory Medicine
Recognizing the difficulty in applying the concept of critical values to anatomic pathology diagnoses, the College of American Pathologists and the Association of Directors of Anatomic and Surgical Pathology have chosen to reevaluate the concept of critical diagnoses. To promote effective communication of urgent and significant, unexpected diagnoses in surgical pathology and cytology. A comprehensive literature search was conducted and reviewed by an expert panel. A policy of effective communication of important results in surgical pathology and cytology is desirable to enhance patient safety and to address multiple regulatory requirements. Each institution should create its own policy regarding urgent diagnoses and significant, unexpected diagnoses in anatomic pathology. This policy should be separate from critical results or panic-value policies in clinical pathology, with the expectation of a different time frame for communication. Urgent diagnosis is defined as a medical condition that, in most cases, should be addressed as soon as possible. Significant, unexpected diagnosis is defined as a medical condition that is clinically unusual or unforeseen and should be addressed at some point in the patient's course. Further details of this statement are provided.
- Research Article
24
- 10.1097/01.pas.0000213287.73530.0a
- Jul 1, 2006
- American Journal of Surgical Pathology
Similar to critical values in clinical pathology, occasional diagnoses in surgical pathology and cytology may require urgent contact of the physician to facilitate rapid intervention or treatment. However, there are no established critical value (critical diagnosis) guidelines in anatomic pathology. As discussed herein, the Association of Directors of Anatomic and Surgical Pathology (ADASP) believes that establishing anatomic pathology critical diagnosis guidelines represents a practice improvement and patient safety initiative. ADASP also recognizes that a generic anatomic pathology critical diagnosis guideline such as this should only be used as a template, because the list needs to be customized at each individual hospital after consultation with relevant clinical services. Based on surveys of the membership of the ADASP, this document provides examples of possible critical diagnoses in anatomic pathology.
- Research Article
29
- 10.1309/ajcpehgnfgbejz7h
- Nov 1, 2008
- American Journal of Clinical Pathology
Critical values (CVs) are well established in clinical pathology, and an analogous concept has recently been suggested in anatomic pathology, with the terminology of critical values, or, alternatively, critical diagnoses (CDs). To better identify anatomic pathology CVs, a survey was sent to 225 members of the Association of Directors of Anatomic and Surgical Pathology (ADASP) for grading 17 possible surgical pathology and 18 possible cytology CVs. There were 73 responses for surgical pathology and 57 for cytology. The majority of the respondents believed in the concept of CVs in anatomic pathology. There was good agreement concerning most of the possible CVs, although there were differences of opinion for some diagnoses. Several additional CVs were suggested, and there was discussion of the best terminology for CVs, degree of urgency, and appropriate notification documentation. A few respondents expressed concern about medicolegal implications. Based on the results of this survey, an ADASP committee has developed national guidelines for CDs (CVs) in surgical pathology and cytology.
- Research Article
- 10.1093/ajcp/aqaf021
- Jul 30, 2025
- American Journal of Clinical Pathology
ObjectiveThere is a paucity of data regarding the anatomic and clinical pathology capabilities at hospitals and laboratories across much of Africa, including in Kenya. We aimed to sample institutions in Kenya to identify the available pathology and laboratory diagnostic services.MethodsSubject matter experts developed 2 individual surveys assessing anatomic pathology (AP) and clinical pathology (CP), respectively. The surveys were administered to individuals involved in pathology services at hospitals and laboratories across Kenya between June and August 2022 using the American Society for Clinical Pathology email listserv.ResultsResponses from 18 unique laboratories in Kenya were analyzed. Five sites provided AP services, while 17 provided CP services; 4 sites provided both AP and CP services. Cytopathology, autopsy services, and hematopathology services were available at all 5 sites that performed AP; 4 provided surgical pathology services for large resections with margins (80%); and 2 provided services for small biopsies (40%). No location had molecular testing capabilities. Among the 17 sites that provided CP services, most had the capability to perform rapid diagnostic and/or point-of-care testing (n = 14, 82%), chemistry (n = 13, 76%), microbiology (n = 13, 76%), and hematology and/or coagulation (n = 13, 76%). However, cytogenetics and flow cytometry were generally not available (n = 4, 24%).ConclusionsThese findings demonstrate that, among this sample of institutions in Kenya, basic AP and CP services were frequently available. Conversely, advanced diagnostic modalities were the exception. Strategic investment to improve this capacity could contribute to optimization of the health care system in Kenya.
- Research Article
- 10.1016/j.acpath.2024.100116
- Mar 22, 2024
- Academic Pathology
Most Pathology residents take the Anatomic Pathology and/or Clinical Pathology primary pathology certification examination(s) near the end of their final year of training (i.e., Spring), whereas some postpone the examination(s) to the Fall administration of that year or even later. We compared the Spring and Fall administration pass rates of initial primary certification candidates for those who graduated in the same year they took the examination. We also compared the pass rates of same-year graduates with individuals who postponed the examination for a year or more. We also surveyed the candidates regarding the reasons they chose the Spring or Fall administration. Candidates who chose the earlier (i.e., Spring) administration were more likely to pass compared with those who took the later Fall administration (p = 0.0026 for Anatomic Pathology; p = 0.0004 for Clinical Pathology). Delaying the certifying exams beyond the calendar year of residency graduation was associated with a higher failure rate (p < 0.0001 for both Anatomic and Clinical Pathology). The survey results suggest that residents often take their certification examinations earlier to not interfere with fellowship training, because it coincides with the completion of residency training, or it is expected by their program. Pathology residents are more likely to pass the primary certification examinations when they are taken closer to the end of training, rather than postponing it to a later administration. Pathology residency program directors should encourage residents, who are deemed ready, to take their certification examinations at the earliest possible administration.
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