Presentation by S. Helgadottir at SAIS Workshop, 17 June 2020

Saga Helgadottir will give a presentation at the 32nd annual workshop of the Swedish Artificial Intelligence Society (SAIS), that will be held as an online conference on June 16 – 17, 2020.

The SAIS workshop is a forum for building the Swedish AI research community and nurture networks across academia and industry. Because of the concern for the COVID-19, the workshop this year is an online conference.

The contributions of Saga Helgadottir will be presented according to the following schedule:

Saga Helgadottir
Medical Diagnosis with Machine Learning
Date: 17 June 2020
Time: 15:00 CEST

Link: SAIS Workshop 2020 program

Hillevi Wachtmeister defended her Master Thesis on June 11, 2020. Congrats!

Hillevi Wachmeister defend her Master Thesis in Physics at Chalmers University of Technology on 11 June 2020. Congrats!

Screenshot of Hillevi Wachmeister’s Master Thesis defence.
Title: Tracking marine micro organisms using deep learning

The goal of this project is to develop a software that can be used to study swimming patterns of marine micro organisms. The software is based on a neural network, which is trained to recognize different types of plankton. The predictions from the network are then used to find the positions of the plankton, and then track their movements.

The project is divided into two parts. First, videos containing only one type of plankton, Lingulodinium polyedra and Alexandrium tamarense respectively, are analyzed. A type of neural network, called U-net, is trained to segment the input images into background and plankton sections. From the segmented images, positions can be obtained and then connected to form a trajectory for each plankton. The drift of the plankton movements is calculated and subtracted from the trajectories, and finally the speed and net displacement is calculated. The results from the single plankton experiments are compared to a previous analysis that was made using the algorithmic method TrackMate.

Secondly, videos containing two types of plankton are analyzed. Two experiments are conducted using Strombidium arenicola and Rhodomonas baltica in the first experiment, and Alexandrium tamarense and Rhodomonas baltica in the second. The segmented images, obtained from the U-net, consists of an additional plankton section for the second type of plankton present in the experiment.

The analysis of the single plankton experiments yields longer and fewer trajectories using the U-net method, compared to the previous TrackMate results. This shows that the TrackMate method is losing plankton at more positions, compared to the U-net method. The U-net method is therefore able to track each plankton for a longer time. The multi-plankton experiments proves the network’s ability to distinguish and track multiple plankton at the same time.

Master programme: MPPHYS – Physics
Supervisor: Daniel Midtvedt
Examiner: Giovanni Volpe
Opponent: Frida Eriksson

Date: 11 June 2020, 9:00
Place: Nexus + Online via Zoom

Anisotropic dynamics of a self-assembled colloidal chain in an active bath published on Soft Matter

Bright-field microscopy image of a magnetic chain trapped at the liquid-air interface in a bacterial bath

Anisotropic dynamics of a self-assembled colloidal chain in an active bath
Mehdi Shafiei Aporvari, Mustafa Utkur, Emine Ulku Saritas, Giovanni Volpe & Joakim Stenhammar
Soft Matter, 2020, 16, 5609-5614
arXiv: 2002.09961

Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid–air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient D features a non-monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of D parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.

Sofia Lundborg defended her Master Thesis on June 4, 2020. Congrats!

Sofia Lundborg defended her Master Thesis in Complex Adaptive Systems at Chalmers University of Technology on 4 June 2020. Congrats!

Screenshot of Sofia Lundborg’s Master Thesis defence.
Title: Training Binary Deep Neural Networks Using Knowledge Distillation

Binary networks can be used to speed up inference time and make image analysis possible on less powerful devices. When binarizing a network the accuracy drops.
The thesis aimed to investigate how the accuracy of a binary network can be improved by using knowledge distillation.
Three different knowledge distillation methods were tested for various network types. Additionally, different architectures of a residual block in ResNet were suggested and tested. Test on CIFAR10 showed an 1.5% increase in accuracy when using knowledge distillation and an increase of 1.1% when testing on ImageNet dataset. The results indicate that the suggested knowledge distillation method can improve the accuracy of a binary network. Further testing needs to be done to verify the results, especially longer training. However, there is great potential that knowledge distillation can be used to boost the accuracy of binary networks.

Master programme: MPCAS – Complex Adaptive Systems
Supervisor: Giovanni Volpe
Supervisors @ Bit Addict: Karl Svensson, Fredrik Ring and Niclas Wikström
Examiner: Giovanni Volpe
Opponent: Viktor Olsson, Wilhelm Tranheden

Time: June 4, 2020 at 15:00
Place: Online via Zoom