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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
PhD Defense Success at Champalimaud Centre for the Unknown
Published:
I’m thrilled to share that I successfully defended my PhD in Lisbon at the Champalimaud Foundation!
Diffilqrax: Differentiable optimal control package published on github
Published:
Jax-based python package implementing fully differentiable iLQR algorithm, used for optimal control and neural networks.
Balanced Model Order Reduction Tutorial
Published:
Application of model reduction to interpret high dimensional data. Provide a brief overview of the theory and pyhton implementation.
Breaking down barriers: Science on the Walls outreach project
Published:
An science outreach project created by group of PhD students at the Champalimaud working with children at Cova da Moura, Amadora.
Larval Zebrafish: A biological model in neuroscience
Published:
Illustrate the benefits of using the zebrafish in studying behaviour and importantly to probe their brains
Student Imbizo Summer School 2022
Published:
Group photo on day trip at Kirstenbosch National Botanical Garden
Probabilistic Spiking Model
Published:
Simulate different neural spiking behaviour via generalised linear model
Understanding Dynamic Mode Decomposition: From Theory to Swimming
Published:
Outline dynamic mode decomposition as an alternative for PCA which factors in temporal structure of the data.
projects
publications
Effects of Contouring Variation on Cancer Treatment Planning
Published in Medical Physics, 2021
This paper proposes a novel methodology to quantify how target contour variations in radiotherapy affect treatment outcomes, demonstrated through a study of prostate cancer biochemical recurrence
Recommended citation: Soares Mullen, T., Jenkins, A., Johnson-Hart, C., Green, A., McWilliam, A., Aznar, M., van Herk, M., Vasquez Osorio, E. (2021). "Novel methodology to assess the effect of contouring variation on treatment outcome." Medical Physics. 48(6).
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Inferring the Control Signal Driving Zebrafish Locomotion
Published in Computational and Systems Neuroscience (Cosyne), 2024
This paper proposes a model of zebrafish locomotion using a controlled dynamical system.
Recommended citation: Soares Mullen*, T., Schimel*, M., Hennequin, G., Machens, C., Orger, M., Jouary, A.. (2024). "Inferring the Control Signal Driving Zebrafish Locomotion." COSYNE.
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Learning Interpretable Control Inputs and Dynamics Underlying Animal Locomotion
Published in The Twelfth International Conference on Learning Representations, 2024
This paper is about learning a latent input-driven dynamics to animal behaviour and interpretting the underlying mechanisms of movement.
Recommended citation: Soares Mullen*, T., Schimel*, M., Hennequin, G., Machens, C., Orger, M., Jouary, A.. (2024). "Learning Interpretable Control Inputs and Dynamics Underlying Animal Locomotion." The Twelfth International Conference on Learning Representations.
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talks
The effect of contouring variation on biochemical recurrence following prostate radiotherapy
Published:
Contouring variation is one of the largest systematic uncertainties in modern radiotherapy. Many studies have evaluated inter-observer variation in small patient cohorts, yet its effect on clinical outcomes has never been analysed quantitatively. We propose a novel framework to analyse the effect of contouring variation on clinical outcome for a large cohort of patients.
Head-restrained behavioural assay to capture multi-timescale switches of fear induced states
Published:
Presented a poster at Federation of European Neuroscience Society (FENS) on a novel behaviour assay that induces zebrafish larvae to undergo a cascade of behavioural states. Using optovin, a UV light flash triggers a cycle through different graded levels of fear that are reflected in different behavioural outputs, including various locomotor patterns and suppressed movement. Preliminary neural recordings show temporal similarities to the behavioural sequence, with the goal of identifying neural populations that modulate fear-related internal states.
Head-restrained behavioural assay to capture multi-timescale switches of fear induced states
Published:
Presented a poster at Federation of European Neuroscience Society (FENS) on a novel behaviour assay that induces zebrafish larvae to undergo a cascade of behavioural states. Using optovin, a UV light flash triggers a cycle through different graded levels of fear that are reflected in different behavioural outputs, including various locomotor patterns and suppressed movement. Preliminary neural recordings show temporal similarities to the behavioural sequence, with the goal of identifying neural populations that modulate fear-related internal states.
Inferring control signals that drive locomotion in the larval zebrafish
Published:
Gave a talk at a Workshop on Computational & Theoretical Zebrafish Neuroscience, Janelia Farm Research Center, on System Identification to learn the underlying dynamics of zebrafish larvae behaviour.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.