# Uyenle - Machine Learning (Level 3) Pathway

**URL:** <http://staging.stemaway.com/t/uyenle-machine-learning-level-3-pathway/8706>\
**Category:** Drug Discovery Using ML (CA) 2021\
**Created:** [July 5, 2021, 5:38pm UTC](http://staging.stemaway.com/t/uyenle-machine-learning-level-3-pathway/8706 "2021-07-05T17:38:32Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![uyenle](https://d3rzmptxz7fqzy.cloudfront.net/user_avatar/staging.stemaway.com/uyenle/32/3941_2.png) [@uyenle](http://staging.stemaway.com/u/uyenle)\
**Post date:** [July 5, 2021, 5:38pm UTC](http://staging.stemaway.com/t/uyenle-machine-learning-level-3-pathway/8706/1 "2021-07-05T17:38:32Z")

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**Module 1 and 2:**

**1. Overview of things learned:**

- Technical Area:
  - Deeper understanding on bioinformatic and the process of research paper for later replication.
  - Getting use to the concept of dependency parsing and dependency matrix
  - Learning to retrieve data for replication

- Tools:
  - Git for team coding collaboration
  - vscode as ILE
  - pubmed parser for reading .xml file from Pubmed
  - spacy for tokenization drug-gene name and relationships
  - Stanford parser for dependency parsing

- Soft Skills:
  - Team work and communication
  - Task management and assignment
  - Sprint work scheme
  - Journal club

**2. Three achievement highlight**

- Implementing pubmed parser, spacy and Stanford parser correctly
- Getting familiar with new environment vscode and Github
- Planning and assigning tasks effectively among team to achieve desired results

**3. Goals for upcoming week**

- Understanding and applying EBC algorithm
- Learning Docker and AWS

**4. Detailed statement of tasks done**

- Understanding and retrieving required databases for replication (except Drugbank due to account verification)

- Setting up the working pipeline for the team to keep in track and in the same page

- Hurdles:

**Different timezone** : difficult for the whole team to set up group meeting =\> recording meeting and documenting for later review; dividing sub-team with closely timezone

**Understanding new concepts in bioinformatic and NLP** : all members have no prior knowledge on bioinformatic, also each member have own level in technical area, so that sometimes we’re not in the same page =\> learning new knowledge in Journal club style is more efficient and consuming; dividing tasks based on required skills so each member can choose what he/she want to take responsible for; reaching out for the mentors when unsure or need help

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<div class="post-metadata">

**Author:** ![uyenle](https://d3rzmptxz7fqzy.cloudfront.net/user_avatar/staging.stemaway.com/uyenle/32/3941_2.png) [@uyenle](http://staging.stemaway.com/u/uyenle)\
**Post date:** [July 28, 2021, 4:57am UTC](http://staging.stemaway.com/t/uyenle-machine-learning-level-3-pathway/8706/2 "2021-07-28T04:57:35Z")

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**Module 3:**

**1. Overview of things learned:**

- Technical Area:

- Tools:

- Soft Skills:

**2. Three achievement highlight**

- Being able to run stanford-parser woth jython
- Trying Dask to understand how it works
- Running EBC to get the co-occurence matrix

**3. Goals for upcoming week**

- Working on supervised step of EBC

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<div class="post-metadata">

**Author:** ![uyenle](https://d3rzmptxz7fqzy.cloudfront.net/user_avatar/staging.stemaway.com/uyenle/32/3941_2.png) [@uyenle](http://staging.stemaway.com/u/uyenle)\
**Post date:** [August 10, 2021, 5:37am UTC](http://staging.stemaway.com/t/uyenle-machine-learning-level-3-pathway/8706/3 "2021-08-10T05:37:19Z")

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**Module 4:**

**1. Overview of things learned:**

- Technical Area:

- Tools:

- Soft Skills:

**2. Three achievement highlight**

- Being able plot dendrogram ![cluster_dendrogram](https://d1xykt6w2ydx2s.cloudfront.net/original/2X/e/ebf28e910f86a8ee0140a695883328e9e4047d55.jpeg) ![dendrogram](https://d1xykt6w2ydx2s.cloudfront.net/original/2X/6/6241494e895af2936bc9d2e31901b6cf2cc2958d.jpeg)

\*\*3. Upcoming Goals \*\*

- Interpreting the dendrogram as landscape of drug-gene dataset