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2024

Jun 14Sequence aligners can guarantee accuracy in almost $O(mlog n)$ time： a rigorous average-case analysis of the seed-chain-extend heuristic
May 09Near-Linear Time Edit Distance for Indel Channels
May 02The Backpack Quotient Filter： a dynamic and space-efficient data structure for querying k-mers with abundance
Feb 07Lecture 5:Suffix Array and Skew Algorithm
Jan 29Ba_lec_4
Jan 24Ba_ext_2
Jan 22Lecture 3:Suffix Trie and Suffix Tree
Jan 15Lecture 2:Trie and Aho-Corasick Algorithm
Jan 10Extra topic 1:Palindrome and Manacher algorithm
Jan 08Lecture 1:Knuth-Morris-Pratt (KMP) algorithm
Jan 06Prerequisite:Logic and Number Theory

2023

Dec 09Expectation of absolute distance in Random walk
Nov 23Virtual Memory
Nov 22Randomized Algs:Permutation Routing Problem
Nov 20Randomized Algs:Chernoff Bound
Nov 15Randomized Algs:Randomized Selection
Nov 13Randomized Algs:Occupancy Problems & Markov's and Chebyshev's inequalities
Nov 08Randomized Algs:Randomized Min-Cut
Nov 08Lecture 21:Farkas' Lemma
Nov 06Randomized Algs:Randomized QuickSort
Nov 06Lecture 20:Duality--Duality Theory
Nov 03Lecture 19:Duality--Dual Problem
Nov 01Rounding and Dynamic Programming:Parallel Machines Job Scheduling
Nov 01Lecture 18:Initial basic feasible solution
Oct 30Rounding and Dynamic Programming:Parallel Macines Job Scheduling
Oct 30Lecture 17:Anticycling
Oct 27Lecture 16:Implementations of the simplex method
Oct 25Gready Alg and Local Search:Minimum-Degree Spanning Tree
Oct 23Gready Alg and Local Search:Parallel Macines Job Scheduling
Oct 20Lecture 15:Develop of the simplex method
Oct 18Gready Alg and Local Search:The k-center problem
Oct 16Gready Alg and Local Search:Single Macine Job Scheduling
Oct 13Lecture 14:Optimality of a basic feasible solution
Oct 11Intro Appro Alg:Randomized Rounding Algorithm
Oct 09Intro Appro Alg:Gready Algorithm
Oct 09Lecture 13:Optimality and extreme points
Oct 05Out-of-Order (OoO) Superscalar
Oct 04Intro Appro Alg:Primal-Dual Method
Oct 02Intro Appro Alg:Rounding and Dual rounding algorithm
Oct 02Lecture 12:Existence of extreme points
Sep 28Review of Midterm 1
Sep 27Intro Appro Alg:Definition and LP techniques
Sep 25Linear Programming and Its Dual Problem
Sep 25Lecture 11:Degeneracy
Sep 20NP, NP-Complete Problems
Sep 18Polynimial Reduction
Sep 18Lecture 10:Polyhedra in Standard form
Sep 13Applications of Max flow
Sep 11Polynomial time Algorithm to Max flow problem
Sep 11Lecture 9:Corners of a polyhedron
Sep 08Lecture 8:Polyhedra and Convex Set
Sep 06Ford-Fulkerson Algorithm
Sep 06Lecture 7:Solving Linear Optimization Graphically
Sep 01Lecture 6:Objective function involving absolute values
Aug 30Max flow and Min Cut
Aug 30Lecture 5:Piecewise linear convex objective funvctions (2)
Aug 28Dynamic Programming:RNA secondary strucure problem, Sequence alignment, Multiple sequence alignment
Aug 28Lecture 4:Piecewise linear convex objective functions (1)
Aug 25Lecture 3:Convex, Concave, and Affine functions
Aug 23Dynamic Programming:Knapsack Problem, Fibonacci number
Aug 23Lecture 2:General form, Standard form
Aug 21Dynamic Programming:Weighted interval Scheduling
Aug 21Lecture 1:Introduction to Linear Optimization
Jul 08Linear-time Sorting:Lower Bounds, Counting Sort, Radix Sort
Jun 09Bits, Bytes, and Integers I
Jun 08Course Overview
Jun 02Exercises in Lecture 4
May 11Quicksort, Randomized Algorithms
Apr 15How C++ Compiler Works
Apr 04Exercises in Lecture 3
Apr 03Divide-and-Conquer:Strassen, Fibonacci, Polynomial Multiplication
Mar 26How C++ Works
Mar 26Elimination with Matrices
Mar 06Exercises in Lecture 2
Mar 05Asymptotic Notation; Recurrences; Substitution, Master Method
Mar 01Exercises in Lecture 1
Feb 25Analysis of Algorithms, Insertion Sort, Megre Sort
Feb 25The Geometry of Linear Equations

2022

Dec 02Statistical and machine learning methods for spatially resolved transcriptomics data analysis
Apr 04文献分享：Haplotype-resolved assembly of diploid genomes without parental data
Jan 10自编码网络
Jan 10GCN实践
Jan 10GCN简介
Jan 10How
Jan 10MLP和CNN实践
Jan 10MLP与CNN简介
Jan 10VGAE实践
Jan 10Why and what
Jan 10Let's try

2021

Sep 06文献分享：Jumper Enables Discontinuous Transcript Assembly in Coronaviruses
Aug 30Pytorch深度学习——网络搭建、模型训练
Jul 21文献分享：MECAT：fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
Jul 14文献分享：Assembly of long, error-prone reads using repeat graphs Assembly
Jul 10文献分享：De Novo Repeat Classification and Fragment Assembly
May 267.1.1 无约束问题的并行变量分配算法
May 267.1.2 同步运算的并行变量转换算法
May 26优化问题的并行算法
May 06文献分享：Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
May 01文献分享：Fast and accurate long-read assembly with wtdbg2
Apr 27Readme

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