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data/ring12_20/README.md
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data/ring12_20/README.md
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Your Filtered Macrolactone Database
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11036 compounds have been filtered from MacrolactoneDB based on your specified inputs.
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```bash
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uv run embedding-atlas data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet --text ecfp4_binary
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uv run embedding-atlas data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet --text tanimoto_top_neighbors
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uv run embedding-atlas data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet --text smiles
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```
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## 嵌入和投影优化
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### projection_x 和 projection_y 的生成过程
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UMAP 降维计算
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这两个坐标是通过 _run_umap() 函数生成的，该函数使用 UMAP 算法将高维嵌入向量降维到 2D 空间 projection.py:64-88 。
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具体流程如下：
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计算最近邻 - 首先使用 nearest_neighbors() 计算每个点的 k 个最近邻 projection.py:76-83
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UMAP 投影 - 然后使用预计算的邻居信息进行 UMAP 降维 projection.py:85-86
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坐标分配 - 结果的第一列成为 projection_x，第二列成为 projection_y projection.py:259-260
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默认参数设置
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UMAP 算法使用以下默认参数：
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邻居数量: 15 个最近邻 projection.py:74
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距离度量: cosine 距离 projection.py:73
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在不同数据类型中的应用
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文本数据处理
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对于您的 SMILES 分子数据，系统首先使用 SentenceTransformers 生成文本嵌入，然后通过 UMAP 降维 projection.py:251-260 。
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预计算向量处理
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如果您有预计算的 ECFP4 向量，系统会直接对这些向量进行 UMAP 降维 projection.py:311-318 。
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可视化中的作用
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在前端可视化界面中，这些坐标用作：
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散点图的 X/Y 轴 - 每个数据点在 2D 空间中的位置
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颜色编码的基础 - 可以根据坐标值进行颜色映射 embedding-atlas.md:68-70
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演示数据示例
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在项目的演示数据生成中，可以看到相同的处理流程：使用 SentenceTransformers 计算嵌入，然后通过 UMAP 生成 projection_x 和 projection_y 坐标 generate_demo_data.py:42-43 。
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Notes
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这些投影坐标的质量很大程度上取决于原始嵌入的质量和 UMAP 参数的选择。对于化学分子数据，使用专门的分子嵌入模型通常会产生更有意义的 2D 投影，其中化学结构相似的分子会在投影空间中聚集在一起。
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### UMAP 参数调优
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您可以通过调整 UMAP 参数来获得更好的可视化效果：
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```bash
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# 调整邻居数量和距离参数
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uv run embedding-atlas data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet --text smiles \
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--umap-n-neighbors 30 \
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--umap-min-dist 0.1 \
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--umap-metric cosine \
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--umap-random-state 42
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```
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## 自定义嵌入模型
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对于化学分子数据，您可能想使用专门的模型：
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并且符合：
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模型支持范围
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embedding-atlas 支持两种类型的自定义模型：
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文本嵌入模型
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对于文本数据（如您的 SMILES 分子数据），系统使用 SentenceTransformers 库 projection.py:118-126 。这意味着您可以使用任何与 SentenceTransformers 兼容的 Hugging Face 模型。
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图像嵌入模型
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对于图像数据，系统使用 transformers 库的 pipeline 功能 projection.py:168-180 。
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模型格式要求
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SentenceTransformers 兼容性
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文本模型必须与 SentenceTransformers 库兼容 projection.py:98-99 。这包括：
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专门训练用于句子嵌入的模型
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支持 .encode() 方法的模型
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能够输出固定维度向量的模型
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```bash
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uv run embedding-atlas data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet --text smiles \
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--umap-n-neighbors 30 \
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--umap-min-dist 0.1 \
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--umap-metric cosine \
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--umap-random-state 42
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```
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data/ring12_20/counts.txt
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data/ring12_20/counts.txt
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Target Organisms
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Homo sapiens 815
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Homo sapiens, None 180
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Plasmodium falciparum 161
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Hepatitis C virus, None 112
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Homo sapiens, Plasmodium falciparum 63
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Oryctolagus cuniculus 62
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Mus musculus 60
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Toxoplasma gondii 39
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Homo sapiens, Rattus norvegicus 27
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Mus musculus, Homo sapiens 24
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None, Rattus norvegicus 23
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Human immunodeficiency virus 1 20
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Hepatitis C virus 18
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Rattus norvegicus 17
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Homo sapiens, Sus scrofa 11
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Homo sapiens, Chlorocebus aethiops 10
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Serratia marcescens 9
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Escherichia coli 8
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Oryctolagus cuniculus, Homo sapiens 7
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Streptococcus pneumoniae 6
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Oryctolagus cuniculus, Staphylococcus aureus, Raoultella planticola, Bacillus subtilis, Mus musculus, Micrococcus luteus, None, Escherichia coli, Plasmodium falciparum, Streptococcus pneumoniae, Homo sapiens, Escherichia coli K-12, Toxoplasma gondii 6
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Plasmodium falciparum K1 5
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Bacillus anthracis 5
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Mus musculus, Homo sapiens, None 5
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Bacillus anthracis, Homo sapiens 4
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Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus 4
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Mus musculus, None 4
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Plasmodium falciparum, Homo sapiens, None 4
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None, Homo sapiens, Plasmodium falciparum 3
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Bacillus subtilis, Homo sapiens 3
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Oryctolagus cuniculus, Homo sapiens, None 3
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Sus scrofa, Mus musculus, None, Plasmodium falciparum, Homo sapiens, Rattus norvegicus 2
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Homo sapiens, None, Rattus norvegicus 2
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Cryptococcus neoformans 2
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Homo sapiens, None, Chlorocebus aethiops 2
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Staphylococcus aureus 2
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Candida albicans, Cryptococcus neoformans, Mycobacterium intracellulare, Aspergillus fumigatus 2
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Mus musculus, None, Human immunodeficiency virus 1 2
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Escherichia coli (strain K12) 2
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Plasmodium falciparum 3D7, Homo sapiens 2
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Aspergillus fumigatus 1
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Sus scrofa 1
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Saccharomyces cerevisiae S288c, Human immunodeficiency virus 1, Human herpesvirus 1, Plasmodium falciparum, None, Homo sapiens, Rattus norvegicus 1
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Hepatitis C virus, Homo sapiens, None 1
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Plasmodium falciparum 3D7 1
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Bacillus subtilis 1
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Mus musculus, Homo sapiens, None, Saccharomyces cerevisiae 1
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Chlorocebus aethiops 1
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Homo sapiens, Escherichia coli K-12, None 1
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Hepatitis C virus, Homo sapiens, None, Rattus norvegicus 1
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None, Homo sapiens, Human herpesvirus 1 1
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Homo sapiens, None, Trypanosoma brucei brucei 1
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Homo sapiens, None, Cryptococcus neoformans 1
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Homo sapiens, Rattus norvegicus, Human immunodeficiency virus 1 1
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None, Plasmodium falciparum, Escherichia coli, Streptococcus pneumoniae, Naegleria fowleri, Homo sapiens, Streptococcus, Toxoplasma gondii 1
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Giardia intestinalis, Trypanosoma cruzi, Equus caballus, Bos taurus, Mus musculus, None, Plasmodium falciparum, Chlorocebus aethiops, Homo sapiens 1
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Plasmodium falciparum NF54, Trypanosoma cruzi, Trypanosoma brucei rhodesiense, Rattus norvegicus 1
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None, Homo sapiens, Plasmodium falciparum K1, Plasmodium falciparum 1
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Saccharomyces cerevisiae S288c, Homo sapiens, None, Saccharomyces cerevisiae, Phytophthora sojae 1
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Bacillus subtilis, Homo sapiens, Schistosoma mansoni, Saccharomyces cerevisiae, Giardia intestinalis 1
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Streptococcus, Homo sapiens, None 1
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Mus musculus, Homo sapiens, Rattus norvegicus 1
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Homo sapiens, Spinacia oleracea 1
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Human immunodeficiency virus 1, Mus musculus, None, Hepatitis C virus, Homo sapiens, Rattus norvegicus 1
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None, Plasmodium falciparum, Trypanosoma brucei rhodesiense 1
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Hepatitis C virus, None, Rattus norvegicus 1
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Homo sapiens, Equus caballus 1
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Plasmodium falciparum NF54, Trypanosoma cruzi, Trypanosoma brucei rhodesiense 1
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Schistosoma mansoni, Influenza A virus 1
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Leishmania chagasi, Trypanosoma cruzi 1
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Candida albicans, Cryptococcus neoformans 1
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None, Plasmodium falciparum 1
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Caenorhabditis elegans 1
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Bos taurus, Sus scrofa 1
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Plasmodium falciparum, Enterococcus faecium 1
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Homo sapiens, Gallus gallus 1
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Homo sapiens, Escherichia coli 1
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Plasmodium falciparum, Homo sapiens, None, Rattus norvegicus, Schistosoma mansoni 1
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Homo sapiens, None, Influenza A virus 1
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Mycobacterium tuberculosis, None 1
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Escherichia coli, Homo sapiens, Toxoplasma gondii, None, Streptococcus pneumoniae 1
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Bacillus subtilis, Oryctolagus cuniculus, Homo sapiens, Schistosoma mansoni, Giardia intestinalis 1
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Homo sapiens, None, Rattus norvegicus, Escherichia coli O157:H7 1
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Giardia intestinalis, Schistosoma mansoni, Mus musculus, None, Homo sapiens, Saccharomyces cerevisiae 1
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Trypanosoma cruzi 1
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Influenza A virus 1
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Escherichia coli K-12 1
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Human herpesvirus 4 (strain B95-8) 1
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11037
data/ring12_20/temp.csv
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11037
data/ring12_20/temp.csv
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File diff suppressed because one or more lines are too long
11037
data/ring12_20/temp_with_macrocycles.csv
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11037
data/ring12_20/temp_with_macrocycles.csv
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File diff suppressed because one or more lines are too long
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data/ring12_20/temp_with_macrocycles_with_ecfp4.csv
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data/ring12_20/temp_with_macrocycles_with_ecfp4.csv
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File diff suppressed because one or more lines are too long
BIN
data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet
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BIN
data/ring12_20/temp_with_macrocycles_with_ecfp4.parquet
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Binary file not shown.
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