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• 10월 2주차 NMR-guided directed evolution | Nature Discovering faster matrix multiplication algorithms with reinforcement learning | Nature Discovering faster matrix multiplication algorithms with reinforcement learning - Nature A reinforcement learning approach based on AlphaZero is used to discover efficient and provably correct algorithms for matrix multiplication, finding faster algorithms for a variety.. 이번 주 논문들 2022. 10. 7.

• [Python] 모든 열, 모든 행 보기 쓸 때 마다 구글링하게 되는데, 왜 이리 안외워지는지. import pandas as pd pd.set_option('display.max_rows', 500) pd.set_option('display.max_columns', 500) pd.set_option('display.width', 1000) 개발 2022. 10. 7.

• Building simple app from python Streamlit🔥+ FastAPI ⚡️- The ingredients you need for your next Data Science Recipe | by Afaque Umer | Sep, 2022 | Medium 개발 2022. 9. 29.

• 9월 5주차 Biomolecules | Free Full-Text | MCN-CPI: Multiscale Convolutional Network for Compound–Protein Interaction Prediction (mdpi.com) MCN-CPI: Multiscale Convolutional Network for Compound–Protein Interaction Prediction In the process of drug discovery, identifying the interaction between the protein and the novel compound plays an important role. With the development of technology, deep learning met.. 이번 주 논문들 2022. 9. 28.

• [FASTA] Ways to split FASTA file GAAS/split_fasta.md at master · NBISweden/GAAS (github.com) 데이터/Bioinformatics tools 2022. 9. 28.

• [Tool invision] BBMap BBMap download | SourceForge.net 데이터/Bioinformatics tools 2022. 9. 28.

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  [UniProt Challenge] MMseqs2 : 10,000x faster BLAST & profile generator BLAST 보다 10,000x 빠른 searching algorithm. C 로 짜여졌고 마틴 슈타이네거 교수님 논문. 17' Nat. Biotech 에 나온 툴로, 상당히 빠르긴 하다. 근데 문제는 내가 Many-for-many algorithm 이 아니라, One-for-many algorithm 을 사용해 query 각각의 PSSM 을 구해야 한다는 것. 어제 두 개를 비교해 보니 비슷한 느낌이긴 한데, 아마 DB 가 너무 커서 그럴수도 있어서 오늘 좀 더 작은 것으로 바꿔 볼 예정이다. 이하 내가 사용했던 부분 발췌. MMseqs2 User Guide soedinglab/MMseqs2: MMseqs2: ultra fast and sensitive search and clustering suite .. Resources/Personal Projects 2022. 9. 27.

• [UniProt Challenge] Protein database download Protein database 다운로드에 대한 archiving. 1. Uniprot Downloads | UniProt help | UniProt UniProt www.uniprot.org Resources/Personal Projects 2022. 9. 27.

• [UniProt Challenge] PSI-BLAST & PSSM : Protein representation import subprocess import os # Local Psi Blast installation path path_to_psiblast = 'C:\\Program Files\\NCBI\\blast-2.7.1+\\bin\\psiblast.exe' # Path to Proteins in Fasta format fasta_path = 'processed_fastas/mouse_train/' from os import listdir from os.path import isfile, join onlyfiles = [f for f in listdir(fasta_path) if isfile(join(fasta_path, f))] # psiblast -query A0JNU3.fasta -db swissprot.. Resources/Personal Projects 2022. 9. 26.

• 9월 4주차 Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer’s disease drug repurposing | PLOS Computational Biology Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its applicati Author summary Conventional target-based compound screen.. 이번 주 논문들 2022. 9. 20.

• 9월 4주차 High-Throughput sequencing-based 3D chromatin architecture mapping 연구 동향 > BRIC (ibric.org) Resources/Weekly reading list 2022. 9. 20.

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  [UniProt Challenge] CNN + Attention Attention-augmented CNN [1904.09925] Attention Augmented Convolutional Networks (arxiv.org) Attention Augmented Convolutional Networks Convolutional networks have been the paradigm of choice in many computer vision applications. The convolution operation however has a significant weakness in that it only operates on a local neighborhood, thus missing global information. Self-attention, on arxiv... Resources/Personal Projects 2022. 9. 17.