Categories

• AOP 4
• ARM7 1
• Algorithm 7
• Ant 4
• Biology 16
• C 5
• C++ 87
• CXF 1
• Compiler 4
• Continuous-Integration 1
• Database 1
• Docker 2
• Git 1
• Hardware 1
• Hibernate 1
• Information-Retrieval 2
• JSP 4
• Java 61
• JavaScript 11
• Jekyll 3
• Lab 3
• Latex 1
• LeetCode 4
• Linux 1
• Machine-Learning 40
• Math 62
• Memcached 1
• MySQL 6
• Network 10
• Numpy 2
• OS 8
• Octave 1
• Pandas 4
• PyTorch 1
• Python 54
• R 30
• SICP 1
• SQL 3
• SSH 1
• Shell 1
• Spring 8
• SpringMVC 3
• Struts 1
• TDD 2
• Tensorflow 1
• Thought 10
• Tomcat 1
• UML 1
• Windows 2
• asyncio 1
• iBatis 2
• jBPM-4.3 5
• log4j 1
• scipy 1
• sklearn 3
• vs-code 2

AOP

• Spring AOP 学习（四）：简单 XML 配置
• Spring AOP 学习（三）：例子与基本概念
• Spring AOP 学习（二）：动态代理
• Spring AOP 学习（一）：组合对比继承的优势

ARM7

• ARM7 学习笔记

Algorithm

• Algorithm Quizzes
• Python: Quick Sort Revisited / Relation To BST / Lomuto Partition Scheme / Hoare Partition Scheme
• Python: Heap Select / Quick Select
• Laplacian Matrix
• Big-O vs Little-O notation
• Advanced Algorithms
• Basic Graph Algorithms

Ant

• Ant target 的 unless 含义
• Ant 中的 fork="true"
• Ant 路径之 **
• Ant 中 javac 假死的解决办法

Biology

• What does effect size mean in GWAS?
• Terminology Recap: DNase / DHS / Dnase-seq
• Terminology Recap: ChIP / ChIP-on-chip (ChIP-chip) / ChIP-seq
• Terminology Recap: SNP / SNV / LD / GWAS / eQTL / DNA Microarray (DNA chip)
• Terminology Recap: Pre-transcriptional Gene Regulation / Transcription / Translation / mRNA / TF / TFBS / Promoter / Enhancer / Silencer / Insulator / Exon / Intron / Codon / Alternative Splicing / Gene Isoform / Protein Isoform / ORF
• Terminology Recap: Genome / Chromosome / Nucleosome / Chromatin / Chromatid / DNA / Double Strands / Coordinates System / Upstream & Downstream / TSS Distance
• Terminology Recap: Gene / Allele & Dominance & Zygosity / Haplotype / Genotype / Phenotype / Trait
• Promoter-Enhancer Interactions: Resources
• PWM (PSSM) / Sequence Logo
• Homology, Conserved Sequence and Conservation Scores
• What is the epigenome?
• Eukaryotic Cell Structure
• Cell Cycle
• Taxonomic Ranks
• Digest of Molecular Biology for Computer Scientists
• Signal Peptide & Protein Targeting

C

• C: Pointer Arithmetic
• C: function pointers
• C: Advanced Preprocessor Features
• C: struct
• C: sizeof is an operator

C++

• Digest of Effective C++
• C++11: inline namespace
• C++: Standard Type Transformation Templates
• C++: noexcept
• C++: type conversion operator
• C++: override
• C++: final
• C++: The Rule of Three/Five
• C++: move constructor & move assignment operator / lvalue & rvalue / reference qualifier
• C++11 Smart Pointer: auto_ptr is deprecated. Use unique_ptr instead. Here also come shared_ptr and weak_ptr.
• C++11: bind1st() and bind2nd() are deprecated. Use bind() instead.
• C++ Lambda Expression
• C++ Primitive Built-in Types
• C++: 6 things you must know about functions
• C++: =default & =delete
• C++ range for: To get item by value or by reference?
• C++: initializer_list
• C++: typedef & alias declaration (using)
• C++ Type Specifiers: auto / decltype
• C++: constexpr
• C++: Specifiers / Literal Prefix & Suffix
• C++: Null Pointer
• C++: static inside functions
• C++ double dispatch: 函数参数并不支持多态
• C++: A quick view of design pattern
• C++: Virtual Inheritance
• C++: typeid
• C++: Interface Class
• C++: Generic Containers
• C++: Iterator Types
• C++: A quick view of STL algorithms
• C++: Generic Algorithm Examples
• C++: function object
• C++: Template Trait
• C++: typename & template
• C++: template specialization
• C++: operator void*
• C++: Introduction to iostream
• C++ String
• C++: Turning off asserts
• C++ Exception Handling / auto_ptr
• C++: local scope
• C++: Introduction to Templates
• C++: Inheritance / virtual
• C++: 在子类中 override 或 overload 父类方法会屏蔽对 overloaded 方法的访问. This is different from Java!
• C++: overloading new & delete
• C++: new T and new T() are different!
• C++: Automatic type conversion / explicit
• C++ overloading `operator=`: shallow copy vs. deep copy / reference counting / copy on write
• C++: Operator Overloading
• C++: Simple object assignment means copying. This is different from Java!
• C++: pointer to class members
• C++: Complex copy-construction & How to prevent copy-construction (thus preventing pass-by-value)
• C++: static member funcion
• C++: Rules of static member initialization
• C++: pointer reference
• C++: Copy-constructor & the return value on the stack
• C++: Namespace
• C++: inline function
• C++: const object / const member & const member function / mutable
• C++: Const Reference
• C++: Temporary Objects, are you Rvalues?
• C++: More on const
• C++: Const Pointer
• C++: union 也有春天
• C++: Overloading on return values is NOT allowed (neither in java)
• C++: new & delete
• C++: Default function arguments & Placeholder arguments
• C++: constructors and destructors
• C++: Aggregate initialization
• C++: friend
• C++: Using struct like a class / Nested struct / Global scope resolution inside struct
• C++: The multiple-declaration problem / Never put using in headers
• C++: Setting the debugging flags / assert
• C++: array in argument list
• C++: typedef sees int* and int& as new types
• C++: enum
• C++ Explicit Operators
• C++ explicit cast operator: static_cast / const_cast / reinterpret_cast / dynamic_cast
• C++: auto / register / static / const / volatile / linkage / scope
• C++: dereference
• C++: There are void pointers but no void references
• C++: pass-by-value / pass-by-pointer / pass-by-reference
• C++: A syntax constraint when defining variables in the statements of if, while and switch
• C++: declarations vs. definitions / extern
• C++: Including headers
• The compilation process

CXF

• org.apache.cxf.interceptor.Fault: Could not send Message

Compiler

• What does context-free mean in CFLs?
• Escape Character / Control Character / Python Raw Strings / Python Bytes Literals
• Variable / Bound Variable / Free Variable / Scope / Closure
• Computational Complexity Review

Continuous-Integration

• clover 测试 servlet，提示找不到类 com_cenqua_clover/CoverageRecorder 的解决方法

Database

• Isolation

Docker

• Docker: volume
• Docker: generate a Dockerfile from an image

Git

• Git: How to sync a fork

Hardware

• Disk Drive（磁盘驱动器）

Hibernate

• hibernate 延迟加载的错误

Information-Retrieval

• IR 经典模型之向量模型
• IR 经典模型之布尔模型

JSP

• Unified EL implicit objects are vulnerable to XSS attack
• <%@ page contentType%> 注意事项两则
• a weird problem caused by encoding
• JSP: use ${fn:escapeXml()} to escape double quotes

Java

• Middleman Patterns: Adapter / Proxy / Decorator
• Visitor Pattern Revisited
• Single Dispatch in Java and Python
• Install Oracle JDK 8 and switch between JDKs in Ubuntu 18.04
• Digest of Agile Software Development: Principles, Patterns, and Practices
• Digest of Effective Java
• 《分布式 Java 应用：基础与实践》第四章总结其二：并发工具类
• 《分布式 Java 应用：基础与实践》第四章总结其一：集合类
• 《分布式 Java 应用：基础与实践》第三章总结其一：理解 JVM（未完待续）
• 《分布式 Java 应用：基础与实践》第二章总结：SOA 扫盲
• 《分布式 Java 应用：基础与实践》第一章总结：分布式 Java 应用的系统间通信的种类
• Java: 局部内部类、匿名内部类对外部变量的访问权限 + 闭包
• Service Locator Pattern
• How to use @link, @see and @code in JavaDoc
• 自定义 ServletContextListener 的写法举例
• Java: SimpleDateFormat 不是线程安全的
• Java: primitive type 可以为 null
• Java: ScheduledExecutorService 的 scheduleAtFixedRate() 方法注意事项两则
• Digest of Test Driven Development
• visibility symbol in UML
• Java: shallow copy v.s. deep clone
• JSP: url-patttern
• Java: main 方法细则若干
• Java 多线程：synchronized
• Java 多线程：Runnable 接口 v.s. Thread 类
• Java 多线程：终止线程的方法
• Java: 多线程示意和 thread.join() 用法示意
• Java 的值传递
• Java: 当接口方法有声明 throws Exception 时，实现方法可以选择不 throws
• Java: a simple delegation example
• Java Class Loading: further discussion involving steps of instance creation
• Java: the proxy parameter of the invoke() method
• Java: throw 的屏蔽作用
• Java: 涉及继承的异常声明及捕捉
• Java: finally 总是会被执行
• Java: first catch
• Java: foreach 与 iterable
• Java: Arrays.asList()
• Java: proxy 式组合关系
• 关于 Java 继承的新认识：导出类调用基类方法其实是向上转型
• Java: 对内部类的继承
• Java: static inner class
• Java: 局部内部类 (local inner class)
• Java 内部类：对外部类的访问及 .this 和 .new
• Java: 匿名内部类 (anonymous inner class)：简化形式及自动向上转型
• Java: entends & interface
• Java: interface
• Java: 关于覆写方法的访问权限
• Java: abstract
• Java: 在构造器中请谨慎使用被覆写方法
• Java: 关于覆写方法的 return type
• Java: 多态
• Java: 有关向下转型的必要性和动态绑定的细节
• Java: final
• Java Class Loading: an example
• Java: private、package 权限字段不可继承 + 向上转型的新理解
• Java: overload and override / 重载与覆写
• Java: initializer
• Java: 关于 class 和 class member 的访问权限
• Java: static
• Java: array reference and initialization

JavaScript

• Is JSON a string?
• JSON conversion
• JavaScript: window 注意事项
• JavaScript: sleep
• JavaScript: onclick 注意事项
• JavaScript: enable & disable
• JavaScript: ajax 注意事项
• IE 下的奇葩注意事项
• never fake a <input type=file>
• 阻止 form submit 的方法
• <form><input name=?>

Jekyll

• Jekyll: Liquid cannot handle numeric tags
• MathJax 血泪史
• 调教 GitHub Pages 与 jekyll bootstrap 时遇到的一些问题

Lab

• G. Polya’s generalized problem solving approach
• Building GWAVA environment on Ubuntu 16.04
• Lab Memo: Use Cases for Pipeline Refactoring

Latex

• Equation Numbering and Referencing in MathJax

LeetCode

• Closest Pair of Points
• Subarray / Substring / Subsequence
• LeetCode: Stock Problems
• LeetCode: Min Sub and Max Sub Problems

Linux

• Scripting Experience

Machine-Learning

• Terminology Recap: Method of Least Squares (and its relationship with MLE)
• Terminology Recap: Generative Models / Discriminative Models / Frequentist Machine Learning / Bayesian Machine Learning / Supervised Learning / Unsupervised Learning / Linear Regression / Naive Bayes Classifier
• Quick facts on SNAP / Node2vec cannot handle multi-graphs
• Hypothesis Space / Underfitting / Overfitting / Bias / Variance
• Expectation Maximization Algorithm Intuition
• Generative Models
• PR Curve
• ROC Curve: my interpretation
• SemiBoost
• ML Terminology
• Introduction to Linear Discriminant Analysis
• The MEME algorithm
• EM method for identifying motifs in unaligned biopolymer sequences
• Expectation-Maximization Algorithm
• Naive Bayes classifier
• Ensemble Methods in Machine Learning
• Structured Output Support Vector Machines
• Soft Margin Intuition
• WD kernel with shifts
• Support Vector Machines and Kernels
• Lagrange duality
• Hidden Markov Models
• A Little on Topic Model
• ISL: Unsupervised Learning
• ISL: Support Vector Machines
• ISL: Tree Based Methods
• ISL: Moving Beyond Linearity
• ISL: Linear Model Selection and Regularization - Part 2
• Bayesian Interpretation for Ridge Regression and the Lasso + Exercise 7
• RSS, MSE, RMSE, RSE, TSS, R² and Adjusted R²
• ISL: Linear Model Selection and Regularization - Part 1
• ISL: Resampling Methods
• ISL: Classification
• ISL: Classification - Conceptual Exercises
• ISL: Linear Regression - Part 2
• ISL: Linear Regression - Part 1
• ISL: Statistical Learning
• R PCA Example
• Machine Learning: Dimensionality Reduction
• Types of Data Science Questions

Math

• Modulo / Congruence
• Permutation Groups / Permutation Notations / Order of A Permutation / Transpositions
• Cross Entropy vs Cross Entropy Loss
• Convolution is convolution; it's NOT dot product
• Terminology Recap: Sampling / Sample / Sample Space / Experiment / Statistical Model / Statistic / Estimator / Empirical Distribution / Resampling / CV / Jackknife / Bootstrap / Bagging / Likelihood / Estimation and Machine Learning
• Ring / Ring of sets
• Terminology Recap: Random Variable / Distribution / PMF / PDF / Independence / Marginal Distribution / Joint Distribution / Conditional Random Variable
• PCA: my interpretation
• Matrix Rank / Row Linear Dependence / λ = 0 / |A| = 0 / Size of Nullspace (Kernel)
• Alias Sampling
• Scaling / Normalization / Standardization
• Isometry
• Homeomorphism / Open Map / Close Map / Embedding
• Terminology Recap: Functions
• SVD: Singular Value Decomposition
• Eigenbasis / Eigenspace
• Eigen-decomposition
• Hadamard Product / Diagonal Matrix / Orthogonal Matrix
• Tensor
• Minimum vs Minimal w.r.t. generalized inequality
• Linear Independence / Affine Independence / Non-singular Square Matrix / Definite Square Symmetric Matrix
• Digest of Terence Tao Analysis
• Infinite Cartesian Products
• Topology Induced by Metric / Equivalence of Metrics
• Topology / Topological Space / Redefine Neighborhood, Limit Point, Interior Point and Exterior Point
• Neighborhood / Open Set / Continuity / Limit Points / Closure / Interior / Exterior / Boundary
• Divergence / Gradient / Laplace Operator
• Gradient Field
• Scalar Field / Vector Field
• Is vector space a field? And what are: Groups / Rings / Fields / Vector Spaces?
• Harmonic Function / Laplace's equation
• Closed-Form Solution
• RBF (Radial Basis Function) Kernel
• Radial Function / Radial Basis Function / Base / Exponent / Power
• Kernel in Linear Algebra / Inner Product Space / Hyperplane / SVM / Kernel Function / Normed vector space / Metric Space
• Convex Functions / Jensen's Inequality / Jensen's Inequality on Expectations / Gibbs' Inequality / Entropy
• Gradient and Directional Derivative
• Digest of Information Theory, Inference, and Learning Algorithms
• Digest of Essence of Linear Algebra
• Applied Nonparametric and Modern Statistics
• Smoothing
• Statistical Data Types
• Parametric vs. non-parametric tests
• Parametric vs. non-parametric models
• t-tests introduction
• McNemar Test
• Shapiro-Wilk Test for Normality
• Fisher's Exact Test for Independence
• Chi-Square Test for Independence
• Simplex
• Statistic, Statistical Hypothesis Test(ing), Test Statistic, t-test and p-value
• Expectation Operator Rules, Covariance and Standard Error of the Mean
• Asymptotics: The Law of Large Numbers and The Central Limit Theorem
• Bernoulli vs Multinoulli (Categorical) vs Binomial vs Multinomial / Gaussian / Poisson Distributions
• Conditional Probability
• Probability
• Covariance and Correlation
• Moment, Expectation, Variance, Skewness and Kurtosis
• What are Confounding Factors and How do they Affect Studies?
• What are the differences among different study designs, and what are the relative advantages of each?
• Derivative and Partial Derivative
• Slope, Intercept and Distance

Memcached

• slab, page and chunk in memcached

MySQL

• How to rename MySQL databases or tables?
• How to import data to MySQL? / How to change MySQL data directory?
• MySQL dump, replace and insert-on-duplicate-update
• MySQL 使用和优化基础
• MySQL 5.5 版本下 my.ini 内 [mysqld] 项中不能再写 default-character-set=utf8
• MySQL REGEXP

Network

• URL Parameters / URL Query / Tornado get_argument()
• Python: Socket Programming 101
• A socket is like an endpoint... or a line segment
• SO_TIMEOUT and CONNECTION_TIMEOUT
• 常见 HTTP Status Code 及场景
• Three-way Handshake
• Subnet Mask
• GET 与 POST 的区别
• Network Protocols
• 一个 http 请求的详细过程

Numpy

• Python: Ellipsis (...) / Numpy: axis=-1 / np.newaxis
• Huber loss / np.where

OS

• OS: SELECT(2), POLL(2), and their variants
• heap memory / Buddy Memory Allocation
• Terminology Recap: Preemptive / Cooperative / Multitasking / Multithreading / Race Condition
• CPU bound vs IO bound
• Linking, Loading and Library
• callback 释义
• Pointer Swizzling
• page（页面）

Octave

• Octave: fmincg and Anonymous Functions

Pandas

• Pandas: one-column Boolean DataFrame vs Boolean Series
• Pandas: How to check if two DataFrames are equal
• Pandas: split a DataFrame into chunks
• Pandas: Accessing the index of a row in an apply function

PyTorch

• PyTorch: Computational Graphs

Python

• Python: sharing states between processes
• Python: play with backslashes
• Python: chained comparisons / short-circuit operations
• Python: super()
• 《Python黑魔法手册》摘抄
• Python: enumerate()
• Python: Be cautious when using generators/iterators in nested loops
• Python: It's safe to slice a list with index out of range
• Python: calling static methods within the same class / recursive static methods
• Python: sorted() vs list.sort()
• Python: set / dict / Counter / OrderedDict / defaultdict
• Python: Heaps
• Python: itertools.groupby() and pd.DataFrame.groupby() are different!
• Python: Vanilla $k$-way Merge Implementation & Lexical Order
• Python: and/or Operators on Objects
• Python: Bitwise Inverse Operator vs Complements vs Nagatives
• Python: pass-by-reference
• Python: global declaration not needed in main
• Python: Yes, you can unpack a generator!
• Python: Generator Expressions / joblib.Parallel
• Python: How to pip-install packages in virtualenv
• Python: pprint.pformat can be a good friend of __str__
• Digest of Essential SQLAlchemy
• Python: Use datatime instead of time for local clocks
• Python: Binary Search / Bisection / Binary Search Tree (BST)
• Python: __all__
• pdb: Your interactive python debugger
• Python: 3 ways to use metaclasses
• Python: Referencing and assignment in inner functions
• Python: for-else with break
• Python: Diamond Inheritance and super
• Python 3: Keyword-Only Arguments
• Python GIL: Global Interpreter Lock
• Python: Put simply, generators are special coroutines
• Python: Yes, coroutines are complicated, but they can be used as simply as generators
• Python: IDLE won't display anything for an expression evaluated to None
• Python: raise / 3 key elements of an exception
• Python: except
• Python: with-statement / variable scope in with-statement
• Python: try-except-else-finally
• Python: Variable scope in if-statement
• Python: Query reference sequences using rpy2 and BSgenome
• Python: List multiplication is actually repetition
• Python: Iterating a file by every 2 lines
• Handy Python Profiler: line_profiler + kernprof
• Python: Zip
• Python: Signature
• Python: *expression
• Digest of Fluent Python
• Python: Mixin
• Python: MySQLdb
• Python: sequences of booleans
• Install Scientific Environment in Ubuntu 14.04 With Python 3.4
• Digest of Dive into Python 3

R

• R: Quasiquotation
• R: dive into types
• Digest of R for Data Science
• R: implicit return values / return value of an assignment
• ggplot2: use geom_line() carefully when your x-axis data are descending
• R: Graphics Tricks
• Digest of ggplot2
• Rcpp: inline 生成的临时文件举例以及 exception 相关的宏
• Rcpp Hierarchy
• Digest of Advanced R (亟待更新)
• Digest of Seamless R and C++ Integration with Rcpp (待修改)
• Digest of R in Action
• R Dates
• R: Generating All Pairwise Combinations of Strings
• R %any% operator
• R: commandArgs(trailingOnly) and --args
• R Exploratory Data Analysis: Air Pollution Case Study
• R: Saving, Loading and Removing in-memory Data
• R: Getting and Cleaning Data
• An Example of Experimental Design
• R console theme
• R Generating Random Numbers and Random Sampling
• R Debugging
• R profiling
• R <<- operator
• R apply family
• R Scoping Rules
• R Data Types - Part 3: Missing Values, Data Frames & Names
• R Data Types - Part 2: Factors
• R Data Types - Part 1: Basis, Vectors, Matrices & Lists

SICP

• SICP: Recursion vs Iteration

SQL

• SQL: Autocommit does not guarantee immediate committing
• Join
• 简单 SQL 语句的逻辑顺序

SSH

• DSA setting at SSH client end

Shell

• Syntax Highlighting less

Spring

• Spring 小技巧
• @Transactional throws "no matching editors or conversion strategy found"
• @Autowired not working 的问题
• Spring: Velocity config
• Spring: static 属性的注入必须使用非 static 的 setter
• Spring: "Could not resolve placeholder" 解决方案
• Spring TestContext 测试框架中 @BeforeClass 方法无法使用 @ContextConfiguration 初始化的 bean
• Java: 依赖、依赖注入（DI）以及控制反转（IoC）

SpringMVC

• Every servlet, controller, service, DAO, etc is Singleton in a SpringMVC application context
• Simple Form Handling Example
• Spring MVC example anatomy

Struts

• struts2: interceptor config

TDD

• Digest of Working Effectively with Legacy Code
• Digest of Mocks Aren't Stubs

Tensorflow

• Tensorflow 2.0 Autograph and Tracing: an example

Thought

• What is REST?
• Locate Bugs by Replaying
• 直接访问测试机 ip 地址是无法获取 cookie 的
• 有关设计的一些事后诸葛亮
• 关于表字段数量与对象字段数量的思考
• 设计 Service 的一些经验
• 设计 PO 的一些经验
• 设计 Controller 的一些经验
• Deploy carefully!
• 2 most important questions when an old project is assigned to you

Tomcat

• Tomcat 6.0 环境变量和 Tomcat Manager Account

UML

• UML 类图之关联、聚合、组合、依赖

Windows

• goagent/server/uploader.bat 失败的解决办法
• windows 下查看端口是否被占用的方法

asyncio

• Python: asyncio

iBatis

• Sqlmap Namespace
• ibatis 小问题集合

jBPM-4.3

• jBPM-4.3 流程定义 zip 包中的所有文件都是资源
• jBPM-4.3 <process> 标签 name 属性中的短横线会变成下划线赋给 key 属性
• jBPM-4.3 中 deploymentId 和definitionId 应该是一对一的关系
• jbpm 4.3: variable 的 name 和 mapped-name
• jBPM 4.3 自动保存 TaskInstance 至数据库的机制

log4j

• Digest of Short introduction to log4j

scipy

• scipy: pdist indexing

sklearn

• scikit-learn: init your estimator lightly and fit heavily
• scikit-learn: A walk through of GroupKFold.split()
• scikit-learn: Pipeline

vs-code

• VS Code Docker: cannot build from local images
• VS Code: change the default path of integrated terminal to current file's directory