시간적 맥락을 활용한 임상 기록에서 폐암의 뇌 전이상태 분류

학위논문(석사) -- 서울대학교대학원 : 데이터사이언스대학원 데이터사이언스학과, 2023. 8. 이승근.폐암은 뇌로 자주 전이되는 가장 흔한 암 유형 중 하나로, 최적의 환자 치료와 정보 기반 의사 결정을 위해서는 암세포의 뇌 전이 상태를 정확히 분류하는 것이 중요하다. 본 연구에서는 폐암 환자의 MRI 판독소견서의 시간적 정보와 맥락적 정보를 함꼐 활용하여 폐암의 뇌전이 상태를 분류할 수 있는 두 가지 접근법을 제안한다. 첫번쨰 방법으로는 BERT기반의 사전된 모델을 fine-tuning하여 Conditional Random Field (CRF) 레이어와 결합하였으며, 두번째 방법으로는 사전학습된 모델에서 문장 수준의 임베딩 시퀀스를 추출하여 Bidirectional Long-Short Term Memory (BiLSTM)모델을 구축하였다. 데이터셋은 총 13,684개의 임상기록으로 구성되어있으며, 이 중 606개의 데이터만이 주석처리 되었다. 주석처리된 데이터의 수가 부족한 문제는 준지도학습 방법론을 동원하여 해결을 시도하였다. 450개의 주석이 달린 데이터를 활용하여 ClinicalBERT를 fine-tuning하였으며, 이를 통해 73.9%의 정확도를 달성하였다. 모델의 성능을 향상시키기 위해, 미세조정된 ClinicalBERT위에 CRF 레이어를 통합하였고, 이는 89.1%의 정확도를 달성하였다. 마지막으로, ClinicalBERT의 문장 수준의 임베딩을 사용하여 BiLSTM을 학습시켜 93.4%의 정확도를 달성하였다. 우리의 연구 결과는 임상기록을 사용한 폐암의 뇌 전이 상태 분류를 위해 시간 정보 준지도 학습 기법을 활용하는 것의 중요성을 확인하였고, 보다 신뢰할 수 있는 모델을 제공함으로써 의료진의 의사 결정을 도울수 있음을 시사한다.Lung cancer is one of the most common types of cancer that frequently metastasizes to the brain. For optimal patient care and informed decision-making, accurate metastatic status classification is crucial. In this study, we propose two approaches that can leverage temporal information with contextual information in clinical notes to categorize cancer status into four distinct classes. First, we combined a BERT-based model with a Conditional Random Field (CRF) layer. Second, we built a Bidirectional Long Short-Term Memory (BiLSTM) model with sequences of word embedding from the pre-trained model. The dataset comprises 13,684 clinical notes, of which only 606 are annotated. We first fine-tune ClincalBERT with 450 annotated data, achieving an accuracy of 73.9 %. To augment the model's performance, a CRF layer is integrated on top of fine-tuned ClincalBERT, exploiting the temporal information provided by each note's date. The CRF layer is trained using 4,237 pseudo-labeled notes with a confidence threshold of 0.95, resulting in a model with 89.1 % accuracy. Additionally, we employ a semi-supervised approach while training a BiLSTM model with Clinical BERT's word embeddings, resulting in a model with 93.4 % accuracy. Our findings underscore the significance of leveraging longitudinal information and semi-supervised learning techniques for cancer status classification using clinical notes, with implications for personalized medicine and clinical support systems.Chapter 1. Introduction 3 1.1. Study Background 3 1.2. Purpose of Research 4 1.3. Objectives 5 Chapter 2. Preliminary Literature Review 6 2.1. Deep learning for text classification 6 2.2. Improving BERTs performance with CRF layer 7 2.3. Integrating BERT and LSTM 8 Chapter 2. Methodlogy 11 3.1. Data Preparation 11 3.2. Fine-tuning ClinicalBERT 12 3.3. ClinicalBERT with CRF layer 13 3.3.1. Data preparation with pseudo-labeling 13 3.3.2. Condtional Random Field (CRF) layer 14 3.4. BiLSTM approach 16 3.4.1. Semi-supervised learning with self-training method 16 3.4.2. BiLSTM 19 Chapter 4. Result and Discussion 21 4.1. Result 22 4.2. Discussion 22석

보의 소성 곡가공에 관한 연구

학위논문(석사)--서울대학교 대학원 :조선해양공학과,1996.Maste

Prospective evaluation of the efficacy of peroral endoscopic myotomy in patients with achalasia

Peroral endoscopic myotomy (POEM) is an endoscopic alternative to surgical myotomy in patients with achalasia. This study aimed to evaluate the efficacy and clinical outcomes of POEM. A total of 20 patients with achalasia who underwent POEM between October 2016 and November 2017 were prospectively recruited. The intraoperative esophagogastric junction distensibility index (mm(2)/mm Hg) was measured pre- and post-myotomy using an endoluminal functional lumen imaging probe. Clinical response was defined as Eckardt score <= 3. Health-related quality of life was measured by the 36-item short-form health survey score. POEM was successfully completed in all cases. The median procedure time was 68.5 minutes (range 50.0-120.0), and the median myotomy length was 13 cm (range 11-18). Major adverse events were encountered in 2 cases. Overall, clinical responses were observed in all patients during a median follow-up of 11.9 months (range 1.2-26.2). Postoperative esophagogastric junction distensibility index was significantly higher than baseline (from 1.3 [range 0.8-6.9] to 6.3 [range 25-19.2], P < .001). The median Eckardt scores were decreased after POEM (5 [range 2-11] to 1 [range 0-3], P < .001), and the 36-item short-form health survey score was also improved significantly after POEM (67.5 [range 34.5-93.9] to 85.7 [range 53.4-93.3], P = .004). POEM is an effective treatment for achalasia, based on the improvement of both symptoms and objective measures. Clinicaltrial.gov NCT 0298988

Clinical Outcomes of Enteral Feeding Protocol Via Percutaneous Endoscopic Gastrostomy: A Single-Center, Retrospective Study

Background: The development of the endoscopic technique has resulted in an increasing number of patients undergoing percutaneous endoscopic gastrostomy (PEG) insertion; however, the protocols for increasing the volume of feeding formula after PEG insertion have not been established. Therefore, we compared the clinical outcomes of patients receiving low- and high-volume increase in enteral feeding formula. Methods: A total of 215 patients who underwent PEG insertion between January 2016 and March 2019 were included. They were divided into 2 groups according to the increase in volume of feeding formula: the low-volume group (n = 135) received ≤150 mL/d, and the high-volume group (n = 80) received ≥300 mL/d. Patient characteristics, procedure, and feeding-related clinical outcomes were retrospectively reviewed using medical records. Results: The adverse events of the feeding protocol did not significantly differ between the 2 groups. The number of days needed to attain the calorie targets was significantly lower in the high-volume group than in the low-volume group (5.4 ± 3.0 vs 2.4 ± 1.5; P <.001). The duration of supplemental parenteral nutrition and the length of hospitalization were also significantly lower in the high-volume group (3.9 ± 3.3 vs 1.2 ± 2.2; P <.001 and 5.8 ± 2.7 vs 4.6 ± 2.6; P =.007, respectively). Conclusion: To rapidly attain the calorie targets in appropriately selected patients with PEG insertion, a high-volume increase in daily feeding can safely be recommended given the favorable outcomes

Clinical outcomes of tumor bleeding in duodenal gastrointestinal stromal tumors: a 20-year single-center experience

Background: Duodenal gastrointestinal stromal tumors (GISTs) are rare, and reports on duodenal GIST bleeding are few. We analyzed the risk factors and clinical outcomes of hemorrhagic duodenal GISTs and compared them with those of gastric GISTs. Methods: Primary duodenal GISTs surgically diagnosed between January 1998 and December 2017 were retrospectively reviewed. Furthermore, patients with duodenal GIST were compared with those with primary gastric GIST histopathologically diagnosed between January 1998 and May 2015 using previously published data. Results: Of the 170 total patients with duodenal GISTs, 48 (28.2%) exhibited tumor bleeding. Endoscopic intervention, embolization, and non-interventional conservative treatment were performed for initial hemostasis in 17, 1, and 30 patients, respectively. The 5-year survival rate was 81.9% in the bleeding group and 89.4% in the non-bleeding group (P = 0.495). Multivariate analysis showed that p53 positivity was a significant risk factor for duodenal GIST bleeding (hazard ratio [HR] 2.781, P = 0.012), and age ≥ 60?years (HR 3.163, P = 0.027), a large maximum diameter (comparing four groups: < 2, 2?5, 5?10, and ≥ 10?cm), and mitotic count ≥ 5/high-power field (HPF) (HR 3.265, P = 0.032) were risk factors for overall survival. The incidence of bleeding was significantly higher in duodenal GISTs than in gastric GISTs (28.2% vs. 6.6%, P < 0.001), and the re-bleeding rate after endoscopic hemostasis was also higher in duodenal GISTs than in gastric GISTs (41.2% vs. 13.3%, P = 0.118). Conclusion: In patients with duodenal GIST with old age, large tumor diameter, and mitotic count ≥ 5/HPF, a treatment plan should be established in consideration of the poor prognosis, although tumor bleeding does not adversely affect the prognosis. Duodenal GISTs have a higher incidence of tumor bleeding and re-bleeding rate after endoscopic hemostasis than gastric GISTs

Mitochondrial DNA Haplogroup Related to the Prevalence of Helicobacter pylori

Mitochondria are essential organelles that are not only responsible for energy production but are also involved in cell metabolism, calcium homeostasis, and apoptosis. Targeting mitochondria is a key strategy for bacteria to subvert host cells’ physiology and promote infection. Helicobacter (H.) pylori targets mitochondria directly. However, mitochondrial genome (mtDNA) polymorphism (haplogroup) is not yet considered an important factor for H. pylori infection. Here, we clarified the association of mitochondrial haplogroups with H. pylori prevalence and the ability to perform damage. Seven mtDNA haplogroups were identified among 28 H. pylori-positive subjects. Haplogroup B was present at a higher frequency and haplotype D at a lower one in the H. pylori population than in that of the H. pylori-negative one. The fibroblasts carrying high-frequency haplogroup displayed a higher apoptotic rate and diminished mitochondrial respiration following H. pylori infection. mtDNA mutations were accumulated more in the H. pylori-positive population than in that of the H. pylorinegative one in old age. Among the mutations, 57% were located in RNA genes or nonsynonymous protein-coding regions in the H. pylori-positive population, while 35% were in the H. pylori-negative one. We concluded that gastric disease caused by Helicobacter virulence could be associated with haplogroups and mtDNA mutatio