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Old ideas in a mental kaleidoscope.
AOP
4
ARM7
1
Algorithm
8
Ant
4
Biology
16
C
5
C++
87
CXF
1
Compiler
1
Continuous-Integration
1
Database
1
Docker
2
Hardware
1
Hibernate
1
Information-Retrieval
2
Interview
1
JSP
4
Java
61
JavaScript
10
Jekyll
3
Lab
3
Latex
1
LeetCode
3
Linux
1
Machine-Learning
40
Math
62
Memcached
1
MySQL
6
Network
7
Numpy
2
OS
6
Octave
1
Pandas
4
PyTorch
1
Python
51
R
30
SICP
1
SQL
3
SSH
1
Shell
1
Spring
8
SpringMVC
3
Struts
1
TDD
2
Tensorflow
1
Thought
9
Tomcat
1
UML
1
Windows
2
asyncio
1
iBatis
2
jBPM-4.3
5
log4j
1
scipy
1
sklearn
3
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
Comparing Time Complexity
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
Computational Complexity Review
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
Variable / Bound Variable / Free Variable / Scope / Closure
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
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
Interview
Algorithm Quizzes
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
Single Dispatch in Java and Python
Install Oracle JDK 8 and switch between JDKs in Ubuntu 18.04
Learn Design Patterns: Resources
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
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
SimpleDateFormat 不是线程安全的
primitive type 可以为 null
ScheduledExecutorService.scheduleAtFixedRate() 注意事项两则
Digest of
Test Driven Development
visibility symbol in UML
shallow copy v.s. deep clone
url-patttern
有关 Java 的 main 方法
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
多线程示意和 thread.join() 用法示意
Java 的值传递
当接口方法有声明 throws Exception 时，实现方法可以选择不 throws
a simple delegation example
class loading: further discussion involving steps of instance creation
the proxy parameter of the invoke() method
throw 的屏蔽作用
涉及继承的异常声明及捕捉
finally 总是会被执行
first catch
foreach 与 iterable
Arrays.asList()
proxy
关于继承的新认识：导出类调用基类方法其实是向上转型
对内部类的继承
static inner class
局部内部类 (local inner class)
内部类：对外部类的访问及 .this 和 .new
匿名内部类 (anonymous inner class)：简化形式及自动向上转型
entends interface
interface
关于覆写方法的访问权限
abstract
warning: 在构造器中请谨慎使用被覆写方法
关于覆写方法的 return type
多态
有关向下转型的必要性和动态绑定的细节
final
class loading: an example
private、package 权限字段不可继承 + 向上转型的新理解
overload and override: 重载与覆写
initializer
关于 class 和 class member 的访问权限
static
array reference and initialization
Java Identifier
JavaScript
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
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, R
2
and Adjusted R
2
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
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
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: 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
Velocity Config in Spring
static 属性的注入必须使用非 static 的 setter
"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
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
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