臺灣博碩士論文加值系統

在蛋白質交互作用網路中，通常包含有數以千計的蛋白質，甚至是更多。目前雖然有不少用來觀察分析的工具，例如InterViewer、Cytoscape、…等，但多數都只適用於複雜度較小的網路圖。因此當遇到複雜度較高的資料時，這些工具便無法將整個網路圖清楚地表現出來。
由於上述的問題，我們提出一套方法來降低網路圖顯示的複雜度，包括有將網路圖收縮、將網路圖切割成數個連通的網路子圖，並依此來建立成階層式架構，並以階層式表示方式來顯示整個網路圖。所謂的網路圖收縮是指將網路圖中的樹狀圖及團塊圖收縮到一個代表節點上；而網路圖分割主要是利用解決點連通問題的演算法來找出切點集，藉此將網路圖分割開來，如此遞迴分解下去，直到遇到適當的停止條件。透過上述兩種方式，可降低原來網路圖的複雜度。當建立出階層式架構，我們必須把網路圖清楚地繪製出來。在這裡處理網路圖的配置分兩部分：一是收縮的網路圖配置方法，讓每個收縮的網路圖在有限的空間內伸展出來；二是整體網路圖的配置，我們利用彈簧嵌入演算法，並適當加入不同性質的彈簧來配置階層式表示的網路圖。
因為研究上的需要，我們實作出一套系統，除了基本網路圖操作功能之外，我們利用上述方法將網路圖收縮及分割，藉此降低複雜度並建立階層式架構來表示整個網路圖；收縮配置法及彈簧嵌入演算法讓系統自動為使用者調整顯示的網路圖，讓最後的網路配置圖能清楚表示每個節點之間的關係。透過自動的網路圖配置，使網路圖不至於太凌亂，再以互動方式輔助使用者，讓使用者能方便檢視與分析整個網路圖，以利於發現在生物界中未知的事實。

Protein-protein interaction network usually have thousand of proteins. Today there have several visualization tools, for example, Interviewer、Cytoscape、...etc., but they are only suitable for simple graphs.
Because of this problem, we bring up some methods to reduce graph's complexity, including of sub-graph contraction、graph partition, and to establish hierarchial structure. About of graph's layout, We use two methods to handle it, including of special layout algorithm (contracted graph) and Spring-Embedder Method(general graph).
We use these methods to establish hierarchical structure, and use some automatic layout methods to layout graph, and let user easy to analyse graph, and discover new unknown fact.

目錄...........................................I
圖目錄........................................II
表目錄........................................IV
第一章 緒論................................... 1
第二章 網路圖配置之背景知識及相關研究......... 5
2.1 現有方法.......................... 5
2.1.1 一般網路圖的演算法......... 6
2.1.2 特殊條件的網路圖的演算法...10
2.2 現有視覺化工具....................13
第三章 系統描述...............................16
3.1 網路圖收縮........................18
3.2 網路圖分割........................19
3.3 收縮子圖的配置方法................25
3.4 整體網路圖的配置方法..............30
第四章 系統實作...............................34
4.1 輸入與輸出........................34
4.2 縮圖模組..........................36
4.3 分析模組..........................38
4.4 配置模組..........................39
4.5 功能操作介面......................40
第五章 系統測試...............................46
5.1 網路圖分割........................46
5.2 以階層式表示顯示網路圖............52
第六章 結論與未來工作.........................57
參考文獻......................................60
附錄一........................................62

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