Time Log - GeorgeIniatis/Blood_Brain_Barrier_Drug_Prediction GitHub Wiki

Project Details

  • Project Name: Predicting drugs that can cross the blood-brain-barrier
  • Student Name: George Iniatis
  • Student ID: 2329642
  • Supervisor: Dr. Jake Lever

Week 2

30 Sep 2021

  • 2 hours Reading the project guidance notes
  • 2 hours Brain-storming and looking at ML
  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action

3 Oct 2021

  • 2.5 hours Literature review

Week 3

4 Oct 2021

  • 2 hours Literature review

7 Oct 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action

8 Oct 2021

  • 2.5 hours Restructuring of Research Journal

9 Oct 2021

  • 3 hours Literature review

10 Oct 2021

  • 3.5 hours Literature review

Week 4

11 Oct 2021

  • 2 hours Literature review

12 Oct 2021

  • 2 hours Literature review
  • 1.5 hours Dataset exploration. Noticed some abnormalities when comparing data with PubChem database

14 Oct 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action

15 Oct 2021

  • 2 hours Setting up PyCharm and fixing errors
  • 3.5 hours Writing some code and getting familiar with PubChem API

16 Oct 2021

  • 2.5 hours Some debugging and refactoring of the code
  • 0.5 hour Manually searching some compounds that couldn't be searched by the code. Led to me figuring out the special characters problem

17 Oct 2021

  • 0.5 hour Writing some code to use POST requests for SMILES with special characters
  • 0.5 hour Code refactoring
  • 1 hour Getting familiar with RDKit and setting up Anaconda Environment
  • 0.5 hour Looking at SIDER database

Week 5

18 Oct 2021

  • 0.5 hour Writing some code to use GET requests to populate chemical descriptors
  • 1 hour Code refactoring and some brainstorming on how to use SIDER database

19 Oct 2021

  • 2 hours Writing some code to integrate SIDER datasets and get side effects
  • 0.5 hour Had a look at Google Searches
  • 2 hours Dataset work
  • 0.5 hour Updating wiki
  • 2 hours Debugging a json related bug

20 Oct 2021

  • 2.5 hours Dataset work
  • 0.5 hour Updating wiki

21 Oct 2021

  • 0.5 hour Making Side_Effects json compatible
  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action
  • 0.5 hour Updating wiki
  • 2 hours One hot encoding for side effects
  • 1 hour Integrating Indications dataset and creating a one hot encoding

22 Oct 2021

  • 2.5 hours Automated Google Searches. Led me to discovering a really important bug
  • 2.5 hours Debugging and repopulating dataset

23 Oct 2021

  • 2 hours Trying to get some results from Google Searches. Google seems to only allow a certain number of results to be retrieved

24 Oct 2021

  • 1 hour Automated google searches coding

Week 6

26 Oct 2021

  • 5 hours Automated google searches coding
  • 0.5 hour Updating wiki

27 Oct 2021

  • 3 hours Automated google searches coding
  • 1.5 hours Manual verification of results

28 Oct 2021

  • 0.5 hour Updating wiki
  • 2 hours Site targeted google searches
  • 1 hour Manual verification of results

29 Oct 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action
  • 0.5 hour Working on presentation
  • 1.5 hours Manually verifying google searches
  • 1.5 hours PubMed API

30 Oct 2021

  • 3 hours PubMed API

31 Oct 2021

  • 0.5 hour Working on presentation
  • 0.5 hour Regular expression calibration
  • 0.5 hour Manually verifying results from PubMed searches

Week 7

1 Nov 2021

  • 0.5 hour PubMed API calls coding
  • 1 hour Manually verifying results from PubMed Central searches
  • 0.5 hour Updating the Wiki

2 Nov 2021

  • 0.5 hour Group meeting with supervisor and other students
  • 2.5 hours Trying to use Elsevier API. Unable to do so

3 Nov 2021

  • 1.5 hours Looking at Springer APIs

4 Nov 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Fixing Multiple SMILES issue
  • 6 hours Springer API work and PubMed API refactoring

5 Nov 2021

  • 0.5 hour Writing meeting minutes and plan of action
  • 0.5 hour Fixing bug in PubMed API calls. Need to rerun PMC searches
  • 1 hour Springer API work
  • 2 hours Manually verifying searches

6 Nov 2021

  • 1 hour Manually verifying searches

Week 8

11 Nov 2021

  • 0.5 hour Meeting with supervisor
  • 1 hour SK-Learn tutorial video. Wasn't really helpful
  • 3 hours Datalore exploration

12 Nov 2021

  • 0.5 hour Writing meeting minutes and plan of action
  • 2 hours SK-Learn tutorial video. Extremely helpful

Week 9

18 Nov 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action
  • 2 hours Working on visualisations

19 Nov 2021

  • 3 hours Datalore work

Week 10

23 Nov 2021

  • 1.5 hours Datalore work and UMAP implementation
  • 1 hour Model work
  • 1 hour Looking at metrics

24 Nov 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action

25 Nov 2021

  • 2 hours Brainstorming about the model categories and splitting data into test sets
  • 2 hours Brainstorming and writing the Machine Learning Journal

Week 11

2 Dec 2021

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action

Week 12

7 Dec 2021

  • 2 hours Project information session

Week 13

15 Dec 2021

  • 2 hours End of Semester 1 Status Report

19 Dec 2021

  • 1 hour Datalore work

Week 14

20 Dec 2021

  • 1 hour Brainstorming about models

21 Dec 2021

  • 2 hours Model work

22 Dec 2021

  • 1.5 hours Model work and RFECV

23 Dec 2021

  • 1.5 hours Model work

Week 15

27 Dec 2021

  • 2 hours Model work

28 Dec 2021

  • 0.5 hour Read ML columns

29 Dec 2021

  • 0.5 hour Went through the research journal

30 Dec 2021

  • 2 hours Model work

31 Dec 2021

  • 2 hours Model work

02 Jan 2022

  • 0.5 hour Plotly

Week 16

06 Jan 2022

  • 2 hours Model work and reading articles

07 Jan 2022

  • 1.5 hours Y-Scrambling

08 Jan 2022

  • 4 hours Y-Scrambling and Code Refactoring
  • 1 hour Creating tables

09 Jan 2022

  • 2.5 hours Permutation Testing and Code Refactoring

Week 17

10 Jan 2022

  • 2 hours Permutation Testing and Creating Tables

11 Jan 2022

  • 1 hour Updating ML journal

12 Jan 2022

  • 0.5 hour Meeting with supervisor
  • 0.5 hour Writing meeting minutes and plan of action

14 Jan 2022

  • 1 hour Streamlit application basics setup

15 Jan 2022

  • 2 hours Streamlit app progress

16 Jan 2022

  • 4 hours Streamlit app work

Week 18

17 Jan 2022

  • 4.5 hours Streamlit app work

18 Jan 2022

  • 4.5 hours Streamlit app work

19 Jan 2022

  • 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action

Week 19

24 Jan 2022

  • 2 hours Streamlit app work

25 Jan 2022

  • 3 hours Looking at error analysis

26 Jan 2022

  • 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action

Week 20

31 Jan 2022

  • 3 hours Error analysis work

01 Feb 2022

  • 5 hours Error analysis work

02 Feb 2022

  • 1 hour Meeting with supervisor & Writing meeting minutes and plan of action

05 Feb 2022

  • 3 hours LIME
  • 2.5 hours Updating Streamlit App

06 Feb 2022

  • 3.5 hours Updating Streamlit App
  • 1 hour Making python files csv friendly

Week 21

08 Feb 2022

  • 3 hours Dissertation work - Introduction

09 Feb 2022

  • 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action
  • 2.5 hours Dissertation work - Background

13 Feb 2022

  • 3 hours Dissertation work - Background

Week 22

14 Feb 2022

  • 3.5 hours Dissertation work - Background

15 Feb 2022

  • 4 hours Dissertation work - Background

16 Feb 2022

  • 3 hours Dissertation work - Requirements Analysis

19 Feb 2022

  • 4.5 hours Dissertation work - Requirements Analysis

20 Feb 2022

  • 4 hours Dissertation work - Requirements Analysis

Week 23

21 Feb 2022

  • 3 hours Dissertation work - Requirements Analysis

23 Feb 2022

  • 3 hours Dissertation work - Design & Implementation

25 Feb 2022

  • 2.5 hours Dissertation work - Design & Implementation

26 Feb 2022

  • 3 hours Dissertation work - Design & Implementation

27 Feb 2022

  • 3 hours Dissertation work - Design & Implementation

Week 24

28 Feb 2022

  • 2.5 hours Dissertation work - Results & Evaluation

01 Mar 2022

  • 3 hours Dissertation work - Results & Evaluation

02 Mar 2022

  • 1.5 hours Organising repo

03 Mar 2022

  • 2 hours Organising repo

05 Mar 2022

  • 3 hours Dissertation work - Results & Evaluation

06 Mar 2022

  • 3 hours Dissertation work - Results & Evaluation

Week 25

07 Mar 2022

  • 3 hours Dissertation work - Conclusion

08 Mar 2022

  • 4 hours Dissertation work - Checking

10 Mar 2022

  • 1 hour Dissertation work - Checking

11 Mar 2022

  • 1 hour Dissertation work - Checking

Week 26

16 Mar 2022

  • 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action

Week 27

27 Mar 2022

  • 2 hours Dissertation work - Abstract & Final adjustments

28 Mar 2022

  • 2 hours Dissertation work - Final adjustments

29 Mar 2022

  • 5 hours Dissertation & Presentation Work

30 Mar 2022

  • 4.5 hours Presentation Work & Submission