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Advanced Courses in Life Sciences

2nd Edition

Python Machine Learning in Biology

October 7th-11th, 2019, Crete (Greece)

System Biology

Systems Biology Logo

Python Machine Learning in Biology

The field of biological sciences is becoming increasingly information-intensive and data-rich. For example, the growing availability of DNA sequence data or clinical measurements from humans promises a better understanding of the important questions in biology. However, the complexity and high-dimensionality of these biological data make it difficult to pull out mechanisms from the data. Machine Learning techniques promise to be useful tools for resolving such questions in biology because they provide a mathematical framework to analyze complex and vast biological data. In turn, the unique computational and mathematical challenges posed by biological data may ultimately advance the field of machine learning as well.

This course will cover basics of the Python programming language as well as the pandas and sklearn Python libraries for data wrangling and machine learning.

By the end of this course, participants will understand:

  • How to input and clean data in Python using the pandas library
  • How to perform exploratory data analysis in Python
  • How to use the sklearn library in Python for machine learning workflows
  • How to choose an appropriate machine learning model for the task
  • How to use supervised machine learning models (SVM, Decision Trees, Neural Networks, etc.) for classification tasks
  • How to use unsupervised machine learning models for clustering tasks
  • How to evaluate machine learning models and interpret their results

This course is intended to give participants a conceptual overview of machine learning algorithms and an intuition for the mathematics underlying them, equipping participants to be able to choose and implement appropriate models for biological datasets.

LOCATION

Alexander Hotel

Gerakári, Municipality of Amari, 74 061
Rethymno
Crete, Greece

DATE

October 7th-11th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

35 hours on-site.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 25 participants and will be occupied by strict registration order. If the course fills up there will be an assistant instructor to help during the practise time.

Participants who have completed the course will receive a certificate at the end of it.

Instructor

Nichole Bennett instructor fro Transmitting Science

Nichole Bennett
The University of Texas at Austin
United States of America

Coordinator

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Requirements

Graduate or postgraduate degree in Life Sciences and basic knowledge of Statistics. While some Python knowledge is useful, the course will cover basic Python skills necessary to input, clean, and explore data as well as build and evaluate machine learning models.

All participants must bring their own personal laptop (Windows, Macintosh, Linux).

Program

Monday, October 7th, 2019.

Python Foundations

  • Morning: Python Basics, Handling Data in Pandas, Basic Pandas Data Cleaning
  • Afternoon: Exploratory Data Analysis in Pandas, Data Visualization in Python.

Tuesday, October 8th, 2019.

Supervised Machine Learning: Classification

  • Morning: KNN, Introduction to sklearn workflow.
  • Afternoon: Train/Test Split, and Bias-Variance Tradeoff, Model Evaluation.

Wednesday, October 9th, 2019.

Supervised Machine Learning: Classification

  • Morning: Decision Trees and Random Forest
  • Afternoon: Support Vector Machines

Thursday, October 10th, 2019.

Unsupervised Machine Learning

  • Morning: Clustering Methods (K Means Clustering)
  • Afternoon: Advanced Clustering Methods Hierarchical Clustering, DBSCAN

Friday, October 11th, 2019.

  • Special Topics
  • Participants will have the option to learn a particular model or receive an introduction to Neural Networks theory and applications.

Fees

  • Course Fee
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  • Early bird (until June 30th, 2019):
  • 590 *
  • Regular (after June 30th, 2019):
  • 737 *
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • {{content-1}}
  • Early bird (until June 30th, 2019):
  • 590 * + 350 = 940
  • Regular (after June 30th, 2019):
  • 737 * + 350 = 1087
  • This includes course material, coffee breaks, transportation between the Venue and Heraklion or Chania city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

20 % discount will be applied to your fee If you belong to any of the Institutions listed HERE. Discounts (see Funding below) are not cumulative and apply only on the fee.

We offer the possibility of paying in two instalments (contact the course coordinator).

Accommodation

If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village (take a look at the venue), in shared en-suite twin rooms, although you will only share rooms with other course participants. There is a possibility that the rooms will be mixed. If this is an inconvenience for you, and you would prefer to stay in an all-female or all-male room, please indicate so in the “Comments” field of the Registration form (below).

If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.

The Accommodation Package includes transportation from the centre of both Heraklion and Chania (the two main cities of Crete with airports) to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. Once you have booked your flights, please let the course coordinator know which airport you are flying in and out of, in order to arrange your transportation.

If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.

Alexander Hotel, Gerakári

Alexander Hotel 1

Alexander Hotel twin room

Alexander Hotel, Gerakári

Alexander Hotel 2

Alexander Hotel, Gerakári

Alexander Hotel 3

Schedule

Course Schedule

Monday to Friday:

  • 9:30 to 13:30 Lessons.
  • 13:30 to 15:00 Lunch (included).
  • 15:00 to 18:00 Lessons.

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Accommodation Package Schedule

Sunday:

  • 17:00 Registration at the hotel in central Heraklion.
  • 20:30 Dinner in Heraklion.

Monday:

  •  7:30 to 8:30 Breakfast and check-out.
  • 8:30 Transfer from central Heraklion to Arolithos, where the group will stay the rest of the week, and check-in.
  • 20:30 Dinner.

Tuesday to Thursday:

  • 8:30 to 9:00 Breakfast.
  • 20:30 Dinner.

Friday:

  • 8:30 to 9:00 Breakfast.
  • 19:00 Transfer from Arolithos to central Heraklion.
  • 19:45 Arrival in central Heraklion (Archaeological Museum).

Funding

Discounts

Former participants will have a 5 % discount on the Course Fee.

Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Greece, as well as PhD students based in Greece without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Organizers

Transmitting Science Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Registration