Dr. Beatriz Costa Gomes

Biomedical Engineer · Research Fellow in AI · Science Communicator · Wannabe Stand-up Comedian · Portugal & UK ·
beatriz costa-gomes.com

My passion is to understand how brains work, and what happens for them to become unhealthy. I am a skilled programmer, with a strong research expertise in both developing and applying algorithms: from a full-stack software to improve the analysis pipeline for neurobiologists, to currently prototyping a computer vision method to analyse low SNR images. Besides the interests in computer vision, deep learning and biology, I am an avid science communicator with a podcast and occasional stand-up comedy.

Experience

The Alan Turing Institute Logo JOSS Logo University of Manchester Logo Universidade de Coimbra Logo Google Logo IBM Logo

Turing Research Fellow

The Alan Turing Institute, London, UK

Development of Python packages for the downloading and handling of cryoEM data into machine-learning formats. (profet, EMPIARreader, CAKED)

Development of a graph analysis computer vision pipeline in Python for cryoEM images, analysing images of proteins and filaments in vitro. (GRACE)

April 2023 - Present

Editor

Journal of Open Source Software

Editing articles for JOSS. Including searching for reviewers, checking the article at all stages of the process.

January 2024 - Present

Student Project Co-Supervisor

Universidade de Coimbra, Portugal

Co-supervision of project working on the analysis of microscopy movies of red blood cells colliding.

January 2023 - September 2023

Post Doctoral Research Associate

The Alan Turing Institute, London, UK

Building and maintenance of the pipeline in Python for analysis of CryoEM images.
Deep Learning with PyTorch to perform Computer Vision analysis on cryo-EM images (segmentation models, graph neural networks and others).
GitHub repositories: profet (scrape and retrieve information from protein-structure databases), EMPIARreader (access and download any dataset in EMPIAR, via Python), odin (detection model developed using FasterRCNN as a backbone).
Model training using HPC (Baskerville)
Co-development of scivision, a package to build bridges between data owners and model developers.

April 2021 - March 2023

Data Study Group Co-Principal Investigator

The Alan Turing Institute

Challenge: Rapid plankton identification
Co-leading a group of 10 team members while they developed classification methods in computer vision to apply to the plankton dataset.

December 2021

COVID19 Response Team Leader

The Alan Turing Institute

Leading a hackathon to use Natural Language Processing of news and social media.
Building and maintenance of the pipeline in Python, with storage in Azure.

April 2020 - June 2020

Data Study Group Participant

The Alan Turing Institute

Challenge: DSTL - Bright-field Image Segmentation
Developed a data augmentation pipeline in Python, as well as data clean up and post-processing for a Generative Adversarial Network.

December 2019

Google CodeU Participant

Google HQ, London, UK

Using Java to complete assignments and challenges submitted by Google engineers. Attended meetings with a mentor to further improve the development of the solutions.
Attended seminars on the different stages of software engineering.

May 2019 - July 2019

Graduate Teaching Assistant

University of Manchester, UK

Faculty of Science and Engineering
Preparing and teaching Mathematics tutorial classes for over 20 students, for first year and foundation year.
Assisting computer labs in R and tutorials for a third year Multivariable Statistics and Machine Learning class.
Faculty of Biology, Medicine and Health
Organising and preparing experiments for courses of >50 students.
Assisting on practical courses supporting students through practical demonstrations and individual discussions.

September 2017 - March 2019

Intern

IBM Lab, Manchester, UK

Professional Internship for PhD Students (PIPs)
Joined the testing team in order to assess the software to be released in the first quarter of 2018.
Writing internal blog entries documenting the experience.

September 2017 - December 2017

Education

University of Manchester Logo The Alan Turing Institute Logo Universidade de Coimbra Logo

University of Manchester, UK

PhD
Image Analysis and Software development in Neurobiology
September 2016 - September 2021

The Alan Turing Institute, UK

Enrichment Student and Student Representative
Six-month enrichment placement working in Deep Learning methods in Python to analyse the biological data relevant to my PhD project. Student representative for the cohort.
September 2019 - March 2020

Universidade de Coimbra, Portugal

MSc
Biomedical Engineering
September 2011 - July 2016

Skills

Top skills

  • Neuroscience

  • Python/MATLAB/Java/C

  • R&D

  • AI/ML

  • Management

  • Data science

  • Public speaking

  • Biomedical Engineering

To be more precise
  • Python: deep learning frameworks + computer vision + graph neural networks + package development and deployment
  • MATLAB data science + software development
  • C: mathematical modelling
  • Neuroscience: research in neurodegenerative diseases
  • Deployment to clusters and HPC
  • Driving license category B (cars)

Talks, Conferences and Seminars

    DYI Guide to Comedy

    Lunch and Learn Series, The Alan Turing Institute, London, UK

    Workshop


    7 February 2024

    Neurons, Neural Networks and everything in between

    Research Week Postdocs Assemble!, York, UK

    Talk


    10 November 2023

    Bridging into AI: open source tools for computer vision

    Neuroinformatics Assembly, Online

    Talk + Poster with Alden Conner


    18-22 September 2023

    From micrograph to graph: Deconstructing cryoEM micrographs with a graph-based analysis for effective structure detection

    CCP-EM Symposium, Nottingham, UK

    Talk


    26 April 2023

    Research Stage Host

    AIUK 2023, London, UK

    MC


    21-22 March 2023

    Using deep learning to determine biomolecular structures in cryoEM images and simulated cryoET

    Department of Physics, University of Coimbra, Portugal

    Invited Seminar Speaker


    12 October 2022

    Parakeet's Turing Complete

    TEM Workshop, Rosalind Franklin Institute, UK

    Talk with Marjan Famili and Joel Greer


    September 2022

    Using deep learning to determine biomolecular structures in cryoEM images

    UK/Tunisia Bilateral Meeting, Online

    Talk


    17 January 2022

    ALFRED: user-friendly approach to obtain length and curvature and its application to microtubule networks in nerve cells

    Quantitative BioImaging Conference, University of Oxford, Oxford, United Kingdom

    Poster


    6-9 Jan 2020

    Upgrade biology with software: Building bridges between neuro and computer sciences

    IEEE Women in Engineering International Leadership Summit, Porto, Portugal

    Invited Talk


    26-27 July 2019

    ALFRED: a novel image analysis application to inform mathematical modelling of microtubule networks in nerve cells

    Department of Physics, University of Coimbra, Portugal

    Invited Seminar Speaker


    25 March 2019

    ALFRED: automated image analysis application to inform mathematical modelling of microtubule networks in nerve cells

    Network of European BioImage Analysts Conference, Luxembourg

    Flash Talk + Poster


    6-8 Feb 2019

    ALFRED: Automated image analysis of microtubule networks in nerve cells

    European Conference on Mathematical and Theoretical Biology, Lisbon, Portugal

    Talk


    23-27 July 2018

    ALFRED: Automated image analysis of microtubule networks in nerve cells

    EMBO|EMBL Symposium Microtubules: From Atoms to Complex Systems, Heidelberg, Germany

    Poster


    27-30 May 2018

    Automated approaches for the qualitative and quantitative analysis of microtubule networks

    Microscience Microscopy Congress, Manchester, UK

    Poster


    4-6 July 2017

    Mathematical Modelling and Image Analysis of Microtubule Behaviours

    British Microtubule Meeting, Edinburgh, UK

    Talk


    24 April 2017

Organised Events - Talks, Conferences and Seminars

Turing's Pint of Science

London, UK

Co-organised one night in 2023, two nights in 2024.
Curating talks, liasing with speakers, locations and the Pint of Science organisation. Development of curated sessions such as Imagined Futures and The Big Fat Quiz of AI.


2023, 2024

Living Systems Webinar

Online + London, UK

Co-organised the Living Systems online monthly webinar: curated the talks, liasing with speakers and moderating sessions.


January 2024 - Present

Writing Tomorrow, Imagined Futures, Presentation Karaoke, The Long Table

AIUK 2024, London, UK

Co-organised 11 sessions for a conference with over 2000 participants.
Writing Tomorrow: Fireside chat with an award winning science-fiction and fantasy author. Preparation: arranging the speaker, preparing the questions.
Imagined Futures: Three speakers had a prompt for a year and a mood in the future and presented what their idea of AI and the world will look like then, followed by discussion. Preparation: arranging speakers, curating the prompts, preparing the questions.
Presentation Karaoke: Speakers had to present a slide deck they had never seen before. Preparation: organising 11 slide decks, arranging speakers, presenting on stage.
The Long Table: 8 different sessions (on 8 different topics) of a conversation happening without formality. Preparation: arranging approximately 2 hosts per session, curating the session topics, briefing the hosts, preparing the logistics of a different "stage".


19-20 March 2024

Living Systems Symposium

London, UK

Co-organised the Living Systems hybrid symposium: curated the talks, liasing with speakers and location.


14 September 2023

Artificial Intelligence Workshop

Canopy Markets, Kings Cross, London, UK

Using different techniques (GANs, NLP and MuseNet), AI was explained to the general audience via the creation of a Christmas jingle, lyrics and the album cover.


21 December 2019

Postgraduate Summer Research Showcase Committee

University of Manchester, UK

Co-organiser of the conferences for over 500 students, across the three faculties of The University of Manchester. Responsible webadmin of the event websiteand database admin.


Jan 2017 - Jan 2020

Science Communication and Comedy

Interests

I am usually nose-deep in a (hopefully good) book. I love reading so much, and actually do so much of it, that I have a spreadsheet where I keep track of the books I own and my opinions on them.

The best way to deal with stress, for me, is to bake - which is a characteristic that usually the people around me LOVE. That, or endless hours of rage in video games.

When I'm not reading, baking or playing, I am going on hikes with my husband, or exploring new cities, new places to eat and, most importantly, new places to have coffee. I would substitute my blood for coffee but alas, not ideal.

After all of this, I still enjoy a good punching and kicking, so currently I've been back to boxing classes. I have done, however, two years of Muay Thai.

Awards

  • Runner-up - FameLab Competition, London Regional Heat, 2020
  • Highly Commended for Contribution to PGR Environment, University of Manchester, 2019
  • Enrichment Student, The Alan Turing Institute, Cohort of 2019
  • President's Doctoral Scholar Award, University of Manchester, Cohort of 2016 to 2020