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<span class="blog-description">A nook to hoard my manuscripts.</span>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-10-18-rdkit-import-export-file.html" rel="bookmark" title="Permalink to RDKit 入门：文件的导入与导出">RDKit 入门：文件的导入与导出</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 10月18日">2022年 10月18日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
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<p class="post-excerpt">
介绍一些 RDKit 的基本操作，包括简单地创建分子、从外部文件中导入分子以及导出分子为外部文件。
</p>
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<aside class="post-tags">
<a href="https://leonis.cc/tag/rdkit.html"># RDKit</a><a href="https://leonis.cc/tag/python.html"># Python</a> </aside>
</div>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-10-15-summary-doi.org/10.1021/acs.jcim.0c00915.html" rel="bookmark" title="Permalink to 文献总结｜REINVENT 2.0：用于从头药物设计的 AI 工具">文献总结｜REINVENT 2.0：用于从头药物设计的 AI 工具</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 10月15日">2022年 10月15日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
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<p class="post-excerpt">
本文介绍于 2020 年发表在 Journal of Chemical Information and Modeling 上的一篇 Application Note，文章原标题为 REINVENT 2.0: An AI Tool for De Novo Drug Design。文章主要介绍了一种开源、便于使用的分子生成工具的原理及其使用案例。
</p>
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<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/rnn.html"># RNN</a><a href="https://leonis.cc/tag/rl.html"># RL</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-10-08-summary-doi.org/10.1038/s42256-021-00403-1.html" rel="bookmark" title="Permalink to 文献总结｜基于 Conditional Transformer、知识蒸馏与强化学习的多约束分子生成">文献总结｜基于 Conditional Transformer、知识蒸馏与强化学习的多约束分子生成</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 10月08日">2022年 10月08日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文介绍了来自浙江大学侯廷军老师的工作，文章原标题为 Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning，于 2021 年发表在 Nature Machine Intelligence 上。文章基于 transformer 建立了分子生成模型，并借助知识蒸馏与强化学习算法，提出了一种新的分子生成模型。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/transformer.html"># Transformer</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-30-summary-doi.org/10.1021/acscentsci.7b00512.html" rel="bookmark" title="Permalink to 文献总结｜使用循环神经网络为药物发现生成指定的分子库">文献总结｜使用循环神经网络为药物发现生成指定的分子库</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月30日">2022年 9月30日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文介绍 2018 年发表在 ACS Central Science 上的一篇文献，文章原题目为 Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks。文章利用基于 LSTM 的循环神经网络构建了分子生成模型，在输入具有特定活性化合物训练集后，该模型能够产生新分子库，新分子库中的许多分子具有与训练集相似的活性。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/rnn.html"># RNN</a> </aside>
</div>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-27-generate-ppt-by-marp.html" rel="bookmark" title="Permalink to 用 Markdown 创作 pptx 的尝试">用 Markdown 创作 pptx 的尝试</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月27日">2022年 9月27日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
总是遇到一些时候，一个又一个的 presentation 接踵而来，制作幻灯片就变成了令人头疼的事情。Marp 是一款支持使用 Markdown 语法生成 pptx 的工具，使用它或许可以解放双手。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/marp.html"># Marp</a><a href="https://leonis.cc/tag/markdown.html"># Markdown</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-21-summary-doi.org/10.1016/j.sbi.2021.10.001.html" rel="bookmark" title="Permalink to 文献总结｜从头药物设计中的深度学习方法">文献总结｜从头药物设计中的深度学习方法</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月21日">2022年 9月21日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文主要介绍来自浙江大学的 Mingyang Wang 等人的综述，综述名称为 Deep learning approaches for de novo drug design: An overview，发表在 Current Opinion in Structural Biology 上。文章主要介绍了深度学习技术在从头药物设计领域的应用与分子生成方法，同时还指出了深度学习技术在药物设计方面目前所面临的问题。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/review.html"># Review</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-16-statistical-learning-chapter7.html" rel="bookmark" title="Permalink to 《统计学习方法》第七章：支持向量机">《统计学习方法》第七章：支持向量机</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月16日">2022年 9月16日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
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《统计学习方法》第五章介绍了支持向量机模型以及支持向量机模型在处理线性可分、线性近似可分、线性不可分数据时的应用。支持向量机的学习过程同样采用对偶算法，此外还有 SMO 算法，大大提高了运算速度。
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<a href="https://leonis.cc/tag/tong-ji-xue-xi-fang-fa.html"># 统计学习方法</a><a href="https://leonis.cc/tag/machine-learning.html"># Machine learning</a><a href="https://leonis.cc/tag/algorithm.html"># Algorithm</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-09-statistical-learning-chapter6.html" rel="bookmark" title="Permalink to 《统计学习方法》第六章：逻辑斯谛回归与最大熵模型">《统计学习方法》第六章：逻辑斯谛回归与最大熵模型</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月09日">2022年 9月09日</time>
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《统计学习方法》第五章主要介绍逻辑斯谛回归模型与最大熵模型，这两种模型具有类似的对数结构，都利用了极大似然估计原理。本章还介绍了广义拉格朗日函数和拟牛顿法。
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<a href="https://leonis.cc/tag/tong-ji-xue-xi-fang-fa.html"># 统计学习方法</a><a href="https://leonis.cc/tag/machine-learning.html"># Machine learning</a><a href="https://leonis.cc/tag/algorithm.html"># Algorithm</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-06-dns-forbidden-of-github-pages.html" rel="bookmark" title="Permalink to 国内部分网络无法访问 githui.io 的解决方案">国内部分网络无法访问 githui.io 的解决方案</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月06日">2022年 9月06日</time>
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和往常一样，在浏览器中键入我的 GitHub Pages 地址，Firefox 却提示「找不到服务器」。发现运营商自动提供的 DNS 服务不解析 github.io，需要通过更改 DNS 服务来解决。
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<a href="https://leonis.cc/tag/blog.html"># Blog</a><a href="https://leonis.cc/tag/githhub.html"># GithHub</a><a href="https://leonis.cc/tag/dns.html"># DNS</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2022-09-05-function-drawer.html" rel="bookmark" title="Permalink to 函数绘图工具的选择">函数绘图工具的选择</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2022年 9月05日">2022年 9月05日</time>
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不管是论文、博客文章还是 PPT，凡是有数学公式的地方，常常都需要伴有函数图象。绘制插图的工具多到难以计数，找到称心顺手的工具更是难上加难，以下就尝试过的工具给出我的评价，或许能提供一些参考。
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