Learning RFdiffusion: build protein backbones with diffusion ML model
Published:
Learning notes of the RFdiffusion software developed by the Baker group.
Posts by Tags
Baker Lab
ML
Learning RFdiffusion: build protein backbones with diffusion ML model
Published:
Learning notes of the RFdiffusion software developed by the Baker group.
algorithms
Smith-Waterman dynamics programming for calculating edit distance.
Published:
The recursive method runs slow as it calls the same function many times. Dynamics programming address that by recording the answer for later calling.
Edit distance calculation: recursive edit distance of prefixes
Published:
The edit distance of X and Y can be solved by looking at prefixes that are 1 character shorter, and solve the smaller edit distance problem recursively.
Coding example: Boyer-Moore Matching Algorithm
Published:
Writing Boyer-Moore machtching from scratch in Python, implementing the bad character rule and the good suffix rule.
Coding example: index assited approximate matching: kmer, sorted list, pigeonhole principle and subsequence
Published:
Here we implement the index assisted mathcing algorithm by recording substrings/subsequences of text T into a sorted list, and implement the approximate matching according to pigeonhole principle.
Approximate matching, hamming and edit distance, pigeonhole principle
Published:
Exact matching algorithms like the naive, Boyer-Moore and index assisted matching can align a pattern P (sequence read) to a text T (genome).
Indexing the genome - index assisted pattern matching, sorted list & hash table, subsequences vs substrings
Published:
The Boyer-Moore matching algorithm uses the bad character and the good suffix rules to skip futile alignments and speed up the search. It preprocesses the pattern P to build up look up tables for the two rules.
Boyer-Moore Matching Algorithm: The Art of Giving Up
Published:
For searches that won’t yield a match, givng up faster saves us time, the same principle applies to life too :)
Naive Exact Matching Algorithm
Published:
Naive exact match is a simple algorithm to solve alignment problems in genomics.
barbara mcclintock
Barbara McClintock: A Geneticist, A Lonely Pioneer, A Warrior That Defied Her Time
Published:
“There’s got to be a musical somewhere in the future of this.” — Robert Sapolsky
diffusion model
Learning RFdiffusion: build protein backbones with diffusion ML model
Published:
Learning notes of the RFdiffusion software developed by the Baker group.
genomics
Barbara McClintock: A Geneticist, A Lonely Pioneer, A Warrior That Defied Her Time
Published:
“There’s got to be a musical somewhere in the future of this.” — Robert Sapolsky
huberman
Huberman Podcast Notes: Dr. Elissa Epel - Control Stress for Healthy Eating, Metabolism & Aging
Published:
Stress response can offer just what we need in a crisis, but it comes with a great cost.
life
My First Marathon
Published:
Life is good, and we often forget about that.
Huberman Podcast Notes: Dr. Elissa Epel - Control Stress for Healthy Eating, Metabolism & Aging
Published:
Stress response can offer just what we need in a crisis, but it comes with a great cost.
The Sunscreen Song/Wear Sunscreen
Published:
“Wear Sunscreen” was an essay written by Mary Schmich, published on Chicago Tribune in June 1997, in which the Pulitzer winning wise lady offered advice that I have benefitted greatly from.
ngs
Smith-Waterman dynamics programming for calculating edit distance.
Published:
The recursive method runs slow as it calls the same function many times. Dynamics programming address that by recording the answer for later calling.
Edit distance calculation: recursive edit distance of prefixes
Published:
The edit distance of X and Y can be solved by looking at prefixes that are 1 character shorter, and solve the smaller edit distance problem recursively.
Coding example: Boyer-Moore Matching Algorithm
Published:
Writing Boyer-Moore machtching from scratch in Python, implementing the bad character rule and the good suffix rule.
Coding example: index assited approximate matching: kmer, sorted list, pigeonhole principle and subsequence
Published:
Here we implement the index assisted mathcing algorithm by recording substrings/subsequences of text T into a sorted list, and implement the approximate matching according to pigeonhole principle.
Approximate matching, hamming and edit distance, pigeonhole principle
Published:
Exact matching algorithms like the naive, Boyer-Moore and index assisted matching can align a pattern P (sequence read) to a text T (genome).
Indexing the genome - index assisted pattern matching, sorted list & hash table, subsequences vs substrings
Published:
The Boyer-Moore matching algorithm uses the bad character and the good suffix rules to skip futile alignments and speed up the search. It preprocesses the pattern P to build up look up tables for the two rules.
Boyer-Moore Matching Algorithm: The Art of Giving Up
Published:
For searches that won’t yield a match, givng up faster saves us time, the same principle applies to life too :)
Naive Exact Matching Algorithm
Published:
Naive exact match is a simple algorithm to solve alignment problems in genomics.
okay so series
Okay… so, what is protein design?
Published:
In plain English: it’s “2dloFahplA” - AlphaFold2 reversed.
podcast
Huberman Podcast Notes: Dr. Elissa Epel - Control Stress for Healthy Eating, Metabolism & Aging
Published:
Stress response can offer just what we need in a crisis, but it comes with a great cost.
programming
Smith-Waterman dynamics programming for calculating edit distance.
Published:
The recursive method runs slow as it calls the same function many times. Dynamics programming address that by recording the answer for later calling.
Edit distance calculation: recursive edit distance of prefixes
Published:
The edit distance of X and Y can be solved by looking at prefixes that are 1 character shorter, and solve the smaller edit distance problem recursively.
Coding example: Boyer-Moore Matching Algorithm
Published:
Writing Boyer-Moore machtching from scratch in Python, implementing the bad character rule and the good suffix rule.
Coding example: index assited approximate matching: kmer, sorted list, pigeonhole principle and subsequence
Published:
Here we implement the index assisted mathcing algorithm by recording substrings/subsequences of text T into a sorted list, and implement the approximate matching according to pigeonhole principle.
Approximate matching, hamming and edit distance, pigeonhole principle
Published:
Exact matching algorithms like the naive, Boyer-Moore and index assisted matching can align a pattern P (sequence read) to a text T (genome).
Indexing the genome - index assisted pattern matching, sorted list & hash table, subsequences vs substrings
Published:
The Boyer-Moore matching algorithm uses the bad character and the good suffix rules to skip futile alignments and speed up the search. It preprocesses the pattern P to build up look up tables for the two rules.
Boyer-Moore Matching Algorithm: The Art of Giving Up
Published:
For searches that won’t yield a match, givng up faster saves us time, the same principle applies to life too :)
Naive Exact Matching Algorithm
Published:
Naive exact match is a simple algorithm to solve alignment problems in genomics.
protein design
Okay… so, what is protein design?
Published:
In plain English: it’s “2dloFahplA” - AlphaFold2 reversed.
Learning RFdiffusion: build protein backbones with diffusion ML model
Published:
Learning notes of the RFdiffusion software developed by the Baker group.
python
Learning RFdiffusion: build protein backbones with diffusion ML model
Published:
Learning notes of the RFdiffusion software developed by the Baker group.
Smith-Waterman dynamics programming for calculating edit distance.
Published:
The recursive method runs slow as it calls the same function many times. Dynamics programming address that by recording the answer for later calling.
Edit distance calculation: recursive edit distance of prefixes
Published:
The edit distance of X and Y can be solved by looking at prefixes that are 1 character shorter, and solve the smaller edit distance problem recursively.
Coding example: Boyer-Moore Matching Algorithm
Published:
Writing Boyer-Moore machtching from scratch in Python, implementing the bad character rule and the good suffix rule.
Coding example: index assited approximate matching: kmer, sorted list, pigeonhole principle and subsequence
Published:
Here we implement the index assisted mathcing algorithm by recording substrings/subsequences of text T into a sorted list, and implement the approximate matching according to pigeonhole principle.
Boyer-Moore Matching Algorithm: The Art of Giving Up
Published:
For searches that won’t yield a match, givng up faster saves us time, the same principle applies to life too :)
Naive Exact Matching Algorithm
Published:
Naive exact match is a simple algorithm to solve alignment problems in genomics.
running
My First Marathon
Published:
Life is good, and we often forget about that.