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選擇性強化資料擴增之生物醫學文獻疾病命名實體識別

為了解決Augment synonym的問題，作者丁怡婷 這樣論述：

在生醫研究領域中,疾病的命名實體識別於生醫領域的文獻探勘和自然語言處理,是一項基礎的任務,透過各種命名實體識別,可以延伸出更多進一步的研究,例如疾病與基因之間的關聯性。多數的疾病命名實體識別都會依賴於經過人工設計的特徵及專業的特定領域知識,同時,在收集訓練資料集時不但耗時而且也需要大量的人工標註者來進行訓練集標記工作。近期,大部分的命名實體識別系統都著重於利用預訓練的詞向量來解決人工的特徵工程問題,以及訓練類神經網路模型來減少以前命名實體識別系統的高運算複雜度。雖然在特徵工程部分獲得更有效率的設計,但是仍然無法解決在生醫領域中資料缺乏的問題,我們提出一個選擇性資料擴增的命名實體識別系統,名為

「SDA-LSTM-CRF」,利用訓練資料集來產生大量的擴增資料,並透過選擇性的機制來評估擴增資料的品質與對模型訓練的效益。透過結合不同面向之擴增資料來提升原本訓練集中的資料多樣性,同時利用選擇性評估機制來過濾出更有效能之擴增資料,藉以提升整體模型的學習效能及預測表現。我們利用兩個生醫領域的語料集來對我們的方法進行評估,分別是在 2015 年國際生物文獻自動探勘競賽中提供的 CDR Corpus―以及美國國家生物技術資訊中心提供的疾病資料集,而我們的系統在兩個語料集的實驗中獲得良好的表現。同時我們進行許多面向的分析,將我們系統的擴增方法與選擇機制,以交互對比的方式來評估方法中各部分的優勢與重要

性,使得 SDA-LSTM-CRF 能夠達到良好的表現。

格氏乳酸球菌在懸浮態和生物膜態之蛋白質表現分析及辨識生物膜形成相關的免疫原性蛋白

為了解決Augment synonym的問題，作者汪鼎傑 這樣論述：

Lactococcus garvieae is an aquatic pathogen that causes disease in a wide range of aquatic species all over the world. It is generally believed that latent bacterial infections and resulting antibiotic resistance are caused by the in vivo formation of biofilms. Moreover, previous studies have revea

led that biofilm formation causes a change in protein expression and the antigen profile available for host-recognition. In view of this, proteomic and immunoproteomic analysis were used to compare the proteomes of L. garvieae grown either as a biofilm or in the planktonic state. Proteomic analysis

using two-dimensional gel electrophoresis (2-DE) revealed varying amounts of protein in nine protein spots, among which seven were up-regulated and two were down-regulated in the biofilm form when compared to the planktonic controls. Among the up-regulated proteins, four of them (glmU, gtaB, rmlB,

and rfbC) participated in extracellular polymeric substances (EPS) synthesis, which is the main component of biofilm. In the immunoproteomic analysis, polyclonal rabbit antibodies raised against biofilm and planktonic bacteria reduced biofilm formation by L. garvieae, while the anti-biofilm serum sh

owed stronger inhibition of biofilm formation. The sera were later used to perform 2-DE Western blot assays on whole cell protein extracted from both biofilm and planktonic forms. Two immunoreactive proteins specifically recognized by anti-biofilm sera were selected, among which a moonlighting prote

in, arginine deiminase (AD), was considered to be associated with biofilm formation, and thus may be a potential vaccine candidate against biofilm infections.