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研究生: 李慈航
Lee, Tzu-Hang
論文名稱: 利用半監督變分自編碼器用於配體優化及過渡金屬錯合物設計的轉移學習
Semi-Supervised Variational Autoencoders for Ligand Optimization and Transfer Learning for Transition Metal Complexes Design
指導教授: 楊自雄
Yang, Tzu-Hsiung
口試委員: 王育恒
Wang, Yu-Heng
李奕霈
Li, Yi-Pei
學位類別: 碩士
Master
系所名稱: 理學院 - 化學系
Department of Chemistry
論文出版年: 2024
畢業學年度: 112
語文別: 英文
論文頁數: 77
中文關鍵詞: 數據驅動探索深度生成式模型無機錯合物配體場強度機器學習
外文關鍵詞: Data-driven discovery, Deep generative model, Inorganic complexes, Ligand field strength, Machine learning
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  • 過渡金屬配合物展現多樣的結構和電子特性。這些特性可以通過調節配體施加的配
    體場強度來改變過渡金屬配合物的性質。目前評估配體場強度主要依賴於特定對稱
    過渡金屬配合物的實驗數據,這對其在各種配體上的廣泛應用存在限制。為了解決
    這個問題,我們提出了一種利用從劍橋晶體結構數據庫獲取的過渡金屬配合物的晶
    體結構來量化配體場強度的數據分析方法。通過應用此數據分析方法,我們利用一
    種半監督深度生成模型框架,聯合樹變分自編碼器 (junction tree variational
    autoencoder, JTVAE),用於預測其配體場強度。我們的模型在訓練集上實現了平均
    絕對誤差為0.047和均方根誤差為0.072。此外,該模型能夠生成具有所需配體場強
    度值的新配體。此外,我們已將這種方法擴展到不僅生成配體,還能設計整個錯合
    物,利用預先訓練的變分自編碼器 (variational autoencoder, VAE) 模型,我們實施了
    一個人工神經網絡artificial neural network, ANN) 分類器,利用半監督變分自編碼器
    (semi-supervised variational autoencoder, SSVAE) 的潛在分佈來預測錯合物的自旋狀
    態,我們概述了兩種設計策略:第一種涉及單一突變,而第二種則使用種子生成。
    這些策略可幫助我們在設計錯合物時,能朝特定自旋狀態進行生成,以及對特定錯
    合物進行局部修改以產生類似自旋狀態且結構相似的錯合物。


    Transition metal complexes display diverse structural and electronic characteristics.
    These properties of a TM complex can be altered by modulating the ligand field strength
    (LFS) inflicted by its ligands. Presently, assessing LFS relies heavily on experimental data
    from a limited set of symmetric transition metal complexes, which poses constraints on its
    broader applicability across various ligands. To address this, we propose a data-driven
    approach using crystal structures of transition metal complexes sourced from the
    Cambridge Structural Database (CSD) to quantify the ligand field strength. By employing
    this data-driven metric, we demonstrate the effectiveness of a semi-supervised deep
    generative model, specifically the junction tree variational autoencoder (JTVAE), in
    predicting ligand field strength values. Our model achieves a mean absolute error (MAE)
    of 0.047 and root mean squared error of 0.072 on the training set. Moreover, the model
    enables the generation of new ligands with desired ligand field strength values.
    Moreover, we've broadened this approach to not only generate ligands but also design
    entire complexes. Leveraging a pretrained VAE model, we've implemented an artificial
    neural network (ANN) classifier utilizing the latent distribution of the semi-supervised
    variational autoencoder (SSVAE) to predict the spin state of a complex. With these models,
    we're capable of generating new ligands possessing targeted properties and assembling
    them into complexes exhibiting our desired spin states. We've outlined two design strategies:
    the first involves single mutations, while the second employs seeded generation. These
    strategies facilitate the deliberate evolution of parent complexes towards specific spin states
    and localized modifications of seed complexes to produce similar spin states, respectively.

    Abstract i 摘要 ii Table of Contents iii List of Figures vi List of Schemes x List of Tables xi Chapter 1. 1 1.1. Cambridge Structural Database (CSD) 2 1.2. Transition metal complex and ligand field strength 3 1.3. Development of machine learning 4 1.4. Generative model 6 1.5. Junction tree variational autoencoder (JTVAE) 9 1.6. Density function theory 12 1.7. Thesis scope 13 Chapter 2 Inverse design of ligands using a deep generative model semi-supervised by a data-driven ligand field strength metric 14 2.1. Abstract 15 2.2. Results and Discussion 16 2.2.1. Data collection from Cambridge Structural Database 16 2.2.2. Fitting gaussian curves for bimodal bond length distribution 16 2.2.3. Quantifying ligand field strength (LFS) of a ligand through probablitiy ………………………………………………………………………18 2.2.4. Variational autoencoder for ligand generation and clustering 21 2.3. Conclusion 24 Chapter 3 A Joint Semi-Supervised Variational Autoencoder and Transfer Learning Model for Designing Molecular Transition Metal Complexes 25 3.1. Abstract 26 3.2. Results and Discussion 27 3.2.1 Gaussian fitting and LFS label assignments 27 3.2.2. Data preprocess for the ANN transfer learning model for SS prediction 27 3.3.3. A joint semi-supervised variational autoencoder and transfer learning model ………………………………………………………………………28 3.3.4. Three strategies for designing complex using a joint VAE and TL model ………………………………………………………………………33 3.4. Methods 40 3.4.1. Training detail of semi-supervised variational autoencoder 40 3.4.2. Artificial neural network (ANN) training for SS prediction 40 3.4.3. TM Complex building 40 3.4.4. DFT prescreening of the built complexes 41 3.4.5. DFT calculation for the built complexes 41 3.4.6. Estimate the accuracy of DFT on predicting the correct experiment SS ………………………………………………………………………42 3.4.7. Single mutation on crystal structures of octahedral TM complexes 42 3.4.8. Seeded generation based on crystal structures of octahedral TM complexes 43 3.5. Conclusion 44 Supporting Information 45 Reference 69

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