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A working notebook of reproducible bioinformatics — genomes, structures, and data visualization.

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Is Evolution a Search Algorithm? How Life Explores Nearly Infinite Possibilities

把进化写成一个搜索问题：搜索空间有多大、适应度景观为什么崎岖、漂变与选择如何分工、中性网络怎样让生命穿越低谷，最后把自然选择、贝叶斯推断、梯度下降与强化学习放进同一个更新规则里比较。

Machine Learning in R: Algorithms, Mathematics and Packages

从最小二乘到随机森林、从 PCA 到 UMAP、从 glmnet 到 torch：用统一的损失-正则-优化视角讲清十种常用算法的数学，全部配 R 代码与可复现的图，并对照 tidymodels、mlr3、caret 三种工作流。

Encoding Single-Cell RNA Expression Data for Transformer Models

逐段中英对照的技术综述：以 Geneformer、scGPT、scFoundation、scPRINT 与 UCE 为例，还原从 raw counts 到 token 与 embedding 的完整计算过程，比较信息保留、计算成本与适用场景，并给出可验证的实验设计。

From One Multiplication to a Whole Network: Operators in AI

算子到底是什么：从 2 × 3 开始，经过矩阵乘法、激活函数、卷积与注意力，一直讲到 GPU kernel、FlashAttention 与虚拟细胞；同时区分数学定义、框架实现与硬件实现这三层，并给出判断“新算子”是否真的新的问题清单。

From Non-Life to Life: Philosophy, Self-Organization, Information, and the Emergence of Living Systems

一篇关于生命起源的深度综述：从亚里士多德与康德，到耗散结构、自催化闭合、RNA 复制、原始细胞与人工生命，梳理 2020–2026 年的实验与理论进展，并给出可检验的生命性评价框架。

Proteomics by mass spectrometry: what is inside a raw file

A technical walkthrough of bottom-up proteomics: sample preparation, LC-MS/MS acquisition, the anatomy of vendor and open raw formats (mzML, mzMLb, imzML), reading data with…

Single-cell sequencing: from a cell to a cell state

A technical walkthrough of single-cell RNA-seq: molecular chemistry, platforms, raw file formats, barcode and UMI processing, count matrices, QC, clustering, annotation and…