Supervised Line Attention for Tumor Attribute Classification from Pathology Reports: Higher Performance with Less Data

2021 ◽  
pp. 103872
Author(s):  
Nicholas Altieri ◽  
Briton Park ◽  
Mara Olson ◽  
John DeNero ◽  
Anobel Y. Odisho ◽  
...  
1972 ◽  
Vol 11 (03) ◽  
pp. 152-162 ◽  
Author(s):  
P. GAYNON ◽  
R. L. WONG

With the objective of providing easier access to pathology specimens, slides and kodachromes with linkage to x-ray and the remainder of the patient’s medical records, an automated natural language parsing routine, based on dictionary look-up, was written for Surgical Pathology document-pairs, each consisting of a Request for Examination (authored by clinicians) and its corresponding report (authored by pathologists). These documents were input to the system in free-text English without manual editing or coding.Two types of indices were prepared. The first was an »inverted« file, available for on-line retrieval, for display of the content of the document-pairs, frequency counts of cases or listing of cases in table format. Retrievable items are patient’s and specimen’s identification data, date of operation, name of clinician and pathologist, etc. The English content of the operative procedure, clinical findings and pathologic diagnoses can be retrieved through logical combination of key words. The second type of index was a catalog. Three catalog files — »operation«, »clinical«, and »pathology« — were prepared by alphabetization of lines formed by the rotation of phrases, headed by keywords. These keywords were automatically selected and standardized by the parsing routine and the phrases were extracted from each sentence of each input document. Over 2,500 document-pairs have been entered and are currently being utilized for purpose of medical education.


2020 ◽  
Vol 4 (1) ◽  
pp. 26-33
Author(s):  
Galuh Ayu Treswari ◽  
Bambang Soeprijanto ◽  
Indrastuti Normahayu ◽  
Lenny Violetta

Wilms’ tumor is the most frequent renal malignancy in childhood with the highest incidence per year, approximately 7,8 cases per 1.000.000in children under 15 years-old and frequently occurred in 2-5 years of age (highest incidences in 3 years-old). There are many differential diagnosis of intra-abdominal tumors and the correct differential diagnosis are detrimental to the prescribed treatments for the patients.Medical imaging along with pathology reports is a precise way to determine the appropriate diagnosis and treatment. Imaging gives information about tumor extension and distant metastasis, especially useful for indicating pre-operative chemotherapy.


2017 ◽  
Author(s):  
James Peaker ◽  
Meleri Morgan ◽  
Aled Rees ◽  
Mohid Khan ◽  
Adam Christian

2019 ◽  
pp. 1-8 ◽  
Author(s):  
Tomasz Oliwa ◽  
Steven B. Maron ◽  
Leah M. Chase ◽  
Samantha Lomnicki ◽  
Daniel V.T. Catenacci ◽  
...  

PURPOSE Robust institutional tumor banks depend on continuous sample curation or else subsequent biopsy or resection specimens are overlooked after initial enrollment. Curation automation is hindered by semistructured free-text clinical pathology notes, which complicate data abstraction. Our motivation is to develop a natural language processing method that dynamically identifies existing pathology specimen elements necessary for locating specimens for future use in a manner that can be re-implemented by other institutions. PATIENTS AND METHODS Pathology reports from patients with gastroesophageal cancer enrolled in The University of Chicago GI oncology tumor bank were used to train and validate a novel composite natural language processing-based pipeline with a supervised machine learning classification step to separate notes into internal (primary review) and external (consultation) reports; a named-entity recognition step to obtain label (accession number), location, date, and sublabels (block identifiers); and a results proofreading step. RESULTS We analyzed 188 pathology reports, including 82 internal reports and 106 external consult reports, and successfully extracted named entities grouped as sample information (label, date, location). Our approach identified up to 24 additional unique samples in external consult notes that could have been overlooked. Our classification model obtained 100% accuracy on the basis of 10-fold cross-validation. Precision, recall, and F1 for class-specific named-entity recognition models show strong performance. CONCLUSION Through a combination of natural language processing and machine learning, we devised a re-implementable and automated approach that can accurately extract specimen attributes from semistructured pathology notes to dynamically populate a tumor registry.


2020 ◽  
pp. 019262332094671
Author(s):  
Brian Short

Ocular toxicity studies are the bedrock of nonclinical ocular drug and drug–device development, and there has been an evolution in experience, technologies, and challenges to address that ensures safe clinical trials and marketing authorization. The expectations of a well-designed ocular toxicity study and the generation of a coherent, integrative ocular toxicology report and subreports are high, and this article provides a pathology/toxicology consultant’s perspective on achieving that goal. The first objective is to cover selected aspects of study designs for ocular toxicity studies including considerations for contract research organization selection, minipig species selection, unilateral versus bilateral dosing, and in-life parameters based on fit-for-purpose study objectives. The main objective is a focus on a high-quality ocular pathology report that includes ocular histology procedures to meet regulatory expectations and a report narrative and tables that correlate microscopic findings with key ophthalmic findings and presents a clear interpretation of test article-, vehicle-, and procedure-related ocular and extraocular findings with identification of adversity and a pathology peer review. The last objective covers considerations for a high-quality ophthalmology report, which in concert with a high-quality pathology report, will pave the way for a best quality toxicology report for an ocular toxicity study.


2019 ◽  
Vol 152 (Supplement_1) ◽  
pp. S35-S36
Author(s):  
Hadrian Mendoza ◽  
Christopher Tormey ◽  
Alexa Siddon

Abstract In the evaluation of bone marrow (BM) and peripheral blood (PB) for hematologic malignancy, positive immunoglobulin heavy chain (IG) or T-cell receptor (TCR) gene rearrangement results may be detected despite unrevealing results from morphologic, flow cytometric, immunohistochemical (IHC), and/or cytogenetic studies. The significance of positive rearrangement studies in the context of otherwise normal ancillary findings is unknown, and as such, we hypothesized that gene rearrangement studies may be predictive of an emerging B- or T-cell clone in the absence of other abnormal laboratory tests. Data from all patients who underwent IG or TCR gene rearrangement testing at the authors’ affiliated VA hospital between January 1, 2013, and July 6, 2018, were extracted from the electronic medical record. Date of testing; specimen source; and morphologic, flow cytometric, IHC, and cytogenetic characterization of the tissue source were recorded from pathology reports. Gene rearrangement results were categorized as true positive, false positive, false negative, or true negative. Lastly, patient records were reviewed for subsequent diagnosis of hematologic malignancy in patients with positive gene rearrangement results with negative ancillary testing. A total of 136 patients, who had 203 gene rearrangement studies (50 PB and 153 BM), were analyzed. In TCR studies, there were 2 false positives and 1 false negative in 47 PB assays, as well as 7 false positives and 1 false negative in 54 BM assays. Regarding IG studies, 3 false positives and 12 false negatives in 99 BM studies were identified. Sensitivity and specificity, respectively, were calculated for PB TCR studies (94% and 93%), BM IG studies (71% and 95%), and BM TCR studies (92% and 83%). Analysis of PB IG gene rearrangement studies was not performed due to the small number of tests (3; all true negative). None of the 12 patients with false-positive IG/TCR gene rearrangement studies later developed a lymphoproliferative disorder, although 2 patients were later diagnosed with acute myeloid leukemia. Of the 14 false negatives, 10 (71%) were related to a diagnosis of plasma cell neoplasms. Results from the present study suggest that positive IG/TCR gene rearrangement studies are not predictive of lymphoproliferative disorders in the context of otherwise negative BM or PB findings. As such, when faced with equivocal pathology reports, clinicians can be practically advised that isolated positive IG/TCR gene rearrangement results may not indicate the need for closer surveillance.


2019 ◽  
Vol 85 (2) ◽  
pp. 219-222 ◽  
Author(s):  
Joshua Gazzetta ◽  
Betty Fan ◽  
Paul Bonner ◽  
John Galante

Patients with classic biliary colic symptoms and documented gallbladder ejection fractions on the higher end of the spectrum on hepatobiliary iminoacetic acid scans with cholecystokinin stimulation are presently understudied and the benefits of cholecystectomy are unclear. To determine whether patients with biliary-type pain and biliary hyperkinesia (defined as a gallbladder ejection fractions of 80% or greater) benefit from laparoscopic cholecystectomy, a retrospective chart review encompassing five community hospitals was performed. Patients 16 years and older with diagnosed biliary hyperkinesia who underwent laparoscopic cholecystectomy between January 1, 2010 and May 31, 2015 were included. Pathology reports were reviewed for histologic changes indicating cholecystitis. Resolution of biliary colic symptoms was reviewed one to three weeks after surgery in their postoperative follow-up documentation. Within our study cohort, we found 97 patients who underwent laparoscopic cholecystectomy for biliary hyperkinesia. Within this population, 84.5 per cent of patients undergoing laparoscopic cholecystectomy for biliary hyper-kinesia had positive findings for gallbladder disease on final pathology. Of the 77 patients with data available from their first postoperative visit, 70 (90.9%) reported improvement or resolution of symptoms. Our findings suggest that symptomatic biliary hyperkinesia may be treated successfully with surgery.


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