Using machine learning to parse breast pathology reports

Abstract

Our learning curve analysis shows that the model can achieve reasonable results even when trained on a few annotations. We developed a user-friendly interface to the database that allows physicians to easily identify patients with target characteristics and export the matching cohort. This model has the potential to reduce the effort required for analyzing large amounts of data from medical records, and to minimize the cost and time required to glean scientific insight from these data.

Gemcitabine and Vinorelbine Combination Chemotherapy in Taxane-Pretreated Patients with Metastatic Breast Cancer: A Phase II Study of the Kinki Multidisciplinary Breast Oncology Group (KMBOG) 1015

“…In addition, most of the patients experienced grade 1 or 2 nonhematologic adverse events, and no severe event was reported. The toxicological profiles and findings in our results were tolerable and similar to those reported previously [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]. …”

“…Grade 3 and 4 neutropenia was observed in 22 patients (52%), consistent with previous reports [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]. Although the incidence of neutropenia in the combination therapy was higher than in capecitabine or vinorelbine monotherapy [34,37], the incidence of febrile neutropenia was considerably low, ranging from 0 to 11% [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27], and it would not be associated with infective complications. The compliance with the protocol observed in our trial was favorable, due to the reasonable dose intensity and moderate toxicity.…”

“…These characteristics can make the combination regimen effective for MBC patients pretreated with taxanes or anthracyclines. Several phase II studies have investigated using the combination regimen for various lines of treatment of MBC patients [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]. The ORR in these studies ranged from 20 to 55%, PFS ranged from 3.5 to 10.8 months, and OS ranged from 9.2 to 20 months.…”

“…Phase II studies demonstrated that the combination chemotherapy has favorable activity, but most of these were nonrandomized, single-arm studies [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]. Several randomized phase II and III studies have been conducted for MBC patients evaluating the combination therapy versus monotherapy or sequential therapy, and they reported conflicting results [34,35,36,37].…”

A frame semantic overview of NLP-based information extraction for cancer-related EHR notes

“…0.6 mm in diameter) [52] TISSUE BANK: identifiers about location of tissue samples within an institution [52] STATUS: whether confirmed, suspected and there is no evidence of finding (e.g. probable, definite, without) [42], [57] RECURRENT STATUS: the value of recurrent status [42], [63], [57] TEMPORAL INFORMATION: refers to information about time (e.g., year, month, and date, 2007-08-04) [42], [57] SPECIMEN TYPE: the type of specimen involved in diagnosis [53] LATERALITY: describes the side of a paired organ associated with origin of the primary cancer [53], [54], [25], [48], [64], [27], [51] TUMOR SIZE: how large across the tumor is at its widest point (part of cancer staging) [52], [53], [54], [25], [48], [65], [59], [60], [62], [57] TNM STAGE: cancer staging system, can be a separate frame with further information (TNM CLASSIFICATION) [55], [53], [2], [3], [25], [66], [67], [60], [50], [40], [61] EXTENSION: direct extension of tumor [53] UNCERTAINTY: used to differentiate clinical suspicions from conclusive findings (e.g., possible, likely) [68],…”