Olle Fager defended his Master thesis in MPCAS at the Chalmers University of Technology on 15 June 2021. Congrats!
Title: Real-Time Multi-Object Tracking and Segmentation with Generated Data using 3D-modelling
Multi-Object Tracking and Segmentation (MOTS) is an important branch of computer vision that has applications in many different areas. In recent developments these methods have been able to reach favorable speed-accuracy trade-offs, making them interesting for real-time applications. In this work different deep learning based MOTS methods have been investigated with the purpose of extending the DeepTrack framework with real-time MOTS capabilities. Deep learning methods rely heavily on the data on which they are trained. The collection and annotation of the data can however be very time-consuming. Therefor, a pipeline is developed and investigated that automatically produces synthetic data by utilizing 3D-modelling. The most accurate tracker achieves a MOTSA score of 94 and the tracker with the best speed-accuracy trade-off achieves a MOTSA score of 88. It is also observed that satisfactory results can be achieved in most situations with a quite general data generation pipeline, indicating that the developed pipeline could be used in different scenarios.
Name of the master programme: MPCAS – Complex Adaptive Systems Supervisor: Giovanni Volpe Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg Opponent: Arianit Zeqiri and Morad Mahmoudyan
(Photo by A. Argun.)Santhosh Shivan Gurumurthy joined the Soft Matter Lab on 15 June 2021.
Santhosh is a master student in Complex Adaptive Systems at Chalmers University of Technology.
During his time at the Soft Matter Lab, he will focus on using Deeptrack tools to simulate microscopic particles, track them using various object detection algorithms, and predict their trajectory with time using graph neural networks (GNN).
(Image by Aykut Argun)Aykut Argun defended his Ph.D. thesis on June 14, 2021, at 2 pm CEST. Congrats!
The details of the presentation can be found below. The link to the webinar is announced on the faculty website.
Title: Thermodynamics of microscopic environments: From anomalous diffusion to heat engines.
Abstract:
Unlike their macroscopic counterparts, microscopic systems do not evolve deterministically due to the thermal noise becoming prominent. Such systems are subject to fluctuations that can only be studied within the framework of stochastic thermodynamics. Within the last few decades, the development of stochastic thermodynamics has lead to microscopic heat engines, nonequilibrium relations and the study of anomalous diffusion and active Brownian motion. In this thesis, I experimentally show that the non-Boltzmann statistics emerge in systems that are coupled to an active bath. These non-Boltzmann statistics that result from correlated active noise also disturb the nonequilibrium relations. Nevertheless, I show that these relations can be recovered using an effective potential approach. Next, I demonstrate an experimental realization of a microscopic heat engine. This engine is referred to as the Brownian gyrator, which is coupled to two different heat baths along perpendicular directions. I show that when confined into an elliptical trap that is not aligned with the temperature anisotropy, the Brownian particle is subject to a torque due to the symmetry breaking. This torque creates an autonomous engine whose direction and amplitude can be controlled by tuning the alignment of the elliptical trap. Then, I show that the force fields acting on Brownian particles can be calibrated using a data-driven method that outperforms the existing calibration methods. More importantly, I show that this method, named DeepCalib, can calibrate non-conservative and time-varying force fields that no standard calibration methods exist. Finally, I show that a similar machine-learning-based approach can be used to characterize anomalous diffusion from single trajectories. This method, named RANDI, is very versatile and performs very well in various tasks including classification, inference and segmentation of anomalous diffusion. The work presented in this thesis presents novel experiments that advance microscopic thermodynamics as well as newly developed methods that open up new possibilities in analyzing stochastic trajectories. These findings increased the scientific knowledge at the nexus between microscopic thermodynamics, anomalous diffusion, active matter and machine learning.
Supervisor: Giovanni Volpe Co-supervisors: Joakim Stenhammar, Mattias Goksör Examiner: Bernhard Mehlig Opponent: Juan M. R. Parrondo Committee: Monika Ritsch-Marte, Sabine H. L. Klapp, Édgar Roldán
Screenshots from Aykut Argun’s PhD Thesis defense.
PhD Thesis Committee, Supervisor, Co-Supervisor, Opponent, and GU Physics Department Chair.PhD Thesis Committee, Supervisor, Opponent, and GU Physics Department Chair.PhD Opponent presentation.PhD Thesis presentation starts.PhD Thesis front slide.PhD Thesis content slide.PhD Thesis final acknowledgment slide.PhD Thesis final acknowledgment slide.
Combined confocal microscopy picture showing a neuron with a soma free of PHF-tau.Dendritic spines are lost in clusters in patients with Alzheimer’s disease
Mite Mijalkov, Giovanni Volpe, Isabel Fernaud-Espinosa, Javier DeFelipe, Joana B. Pereira, Paula Merino-Serrais
Sci. Rep. 11, 12350 (2021)
doi: 10.1038/s41598-021-91726-x
biorXiv: 10.1101/2020.10.20.346718
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by a deterioration of neuronal connectivity. The pathological accumulation of tau protein in neurons is one of the hallmarks of AD and has been connected to the loss of dendritic spines of pyramidal cells, which are the major targets of cortical excitatory synapses and key elements in memory storage. However, the detailed mechanisms underlying the loss of dendritic spines in patients with AD are still unclear. Here, comparing dendrites with and without tau pathology of AD patients, we show that the presence of tau pathology determines the loss of dendritic spines in blocks, ruling out alternative models where spine loss occurs randomly. Since memory storage has been associated with synaptic clusters, the present results provide a new insight into the mechanisms by which tau drives synaptic damage in AD, paving the way to memory deficits by altering spine organization.
Job assignments: Possibility 1: Work at the development of DeepTrack 2.0 (https://aip.scitation.org/doi/10.1063/5.0034891 and https://github.com/softmatterlab/DeepTrack-2.0) in close cooperation with the existing developers’ team at Soft Matter Lab. DeepTrack 2.0 is a software framework we are developing to perform quantitative digital video microscopy using deep learning. The PhD student will actively contribute to the technical design and implementation of the components of DeepTrack. Precisely, the task involves the development, testing and application of optical simulation pipelines for training deep learning networks, as well as the development of collaborative projects with other groups interested in using DeepTrack. Possibility 2: Build and operate small robots to study swarm robotics with embedded intelligence. The task involves all stages of design, fabrication, testing and programming the robots for different experiments. The robot models (inspired by the Kilobots https://ssr.seas.harvard.edu/kilobots) are small programmable units capable of motion, short-range communications, neighbor detection and more.
Appointment procedure Please apply online
The application shall include:
– Cover letter with an explanation of why you apply for the position
– CV including scientific publications
– Copy of exam certificate
– Two referees (name, telephone number, relation)
For the required Qualifications, Eligibility, Assessment criteria, Employment, see the link to the announcement below.
Agaton Fransson defended his Master thesis in MPCAS at the Chalmers University of Technology on 4 June 2021. Congrats!
Big plankton tracked by network-based software in a sample of big (Strombidium arenicola) and small plankton (Rhodomonas baltica). (Image by Agaton Fransson)Title: Tracking plankton using neural networks trained on simulated images
Softwares to track particles often use algorithmic approaches to detect particles and to create tracks using the found positions, requiring human fine-tuning of parameters to achieve sought-for results. This can be time consuming and difficult, while also creating opportunities for human error and bias. With the developments of computational power and machine learning techniques such as deep learning, data driven approaches have made their way into many fields of science. Barriers preventing advances of such methods are the lack of available training data within a field and the level of proficiency required to create custom machine learning solutions. DeepTrack 2.0 is a software providing us with means to simulate digital microscopy images, build and train neural networks such as U-nets. In this paper DeepTrack 2.0 is utilized and built on to fit the needs of marine biologists when tracking plankton. Here I show that DeepTrack 2.0 provides us with the tools necessary to detect and track different types of plankton filmed in a variety of conditions with performance on par with and with the potential to outperform conventional tracking softwares. I also show that for plankton in a messy environment moving uniformly a network trained to detect motion rather than a shape proves more successful. These results demonstrate the versatility of deep learning methods and the potential of training networks on simulations for applications on real data, as is the case for marine biologists studying plankton. They also show the impact the structure of the training data has on the nature of the network.
Name of the master programme: MPCAS – Complex Adaptive Systems Supervisor: Giovanni Volpe, Daniel Midtvedt Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg Opponent: Kevin Rylander
Comparison of different evolution regimes of disease spreading: free evolution (bottom left half) vs network strategy (top right half). (Image by Laura Natali.)Improving epidemic testing and containment strategies using machine learning. Laura Natali, Saga Helgadottir, Onofrio M. Maragò, Giovanni Volpe. Submitted to SDS2020 Date: 11 June Time: 16:15 (CEST)
Abstract:
Containment of epidemic outbreaks entails great societal and economic costs. Cost-effective containment strategies rely on efficiently identifying infected individuals, making the best possible use of the available testing resources. Therefore, quickly identifying the optimal testing strategy is of critical importance. Here, we demonstrate that machine learning can be used to identify which individuals are most beneficial to test, automatically and dynamically adapting the testing strategy to the characteristics of the disease outbreak. Specifically, we simulate an outbreak using the archetypal susceptible-infectious-recovered (SIR) model and we use data about the first confirmed cases to train a neural network that learns to make predictions about the rest of the population. Using these prediction, we manage to contain the outbreak more effectively and more quickly than with standard approaches. Furthermore, we demonstrate how this method can be used also when there is a possibility of reinfection (SIRS model) to efficiently eradicate an endemic disease.
Kevin Andersson and Eric Lindgren defended their Master thesis on 2 June 2021. Congrats!
Title: Saliency mapping of RS-fMRI data in GCNs for sex and brain age prediction
Subtitle: Identifying important functional brain networks using explainability in Graph Convolutional Networks
Insights into how biological sex and healthy ageing affects the human brain are important for an increased understanding of the brain. Healthy ageing insights are also useful for clinical applications, for instance in identifying unhealthy ageing due to neurodegenerative disease. To this end, several studies in the last few years have used machine learning methods on neuroscientific data to predict subject sex and brain age. One particularly interesting approach has been to represent functionally connected networks in the brain as graphs, and apply Graph Convolutional Networks (GCNs). To investigate which functional brain networks are connected with sex and age, we develop and analyse GCN-based models that predicts sex and age from resting-state fMRI data. The analysis of the models is done using saliency mapping techniques which gives insight into what functional brain networks in the data are relevant for the predictions. With this approach, we obtain a sex prediction accuracy of up to 79% and an age prediction MAE of 5.9 years. Furthermore, we find indications that the Sensory Motor Network and the cerebellum are among the more important functional brain networks for predicting sex and brain age.
Master programme: Physics Supervisor: Alice Neimante Diemante (Syntronic AB) Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg Opponent: Rasmus Svensson
Pernilla Huynh, Hannes Johansson, Olof Lind Stefansson, Oskar More Arvidsson, William Olsson, Filip Sterner defended their Bachelor Thesis at Chalmers University of Technology on 27 May 2021. Congrats!
Title: Kollektiva beteenden hos aktiva agenter i komplexa system Topologiska interaktioner och skillnader med tidsfördröjning
Sammandrag:
Studierna av aktiva agenters beteende i komplexa system har rönt stort intresse den senaste tiden. Dels då det är en passande modell för att beskriva många biologiska system, men också för deras för potentiella tillämpningar. Syftet med studien är att undersöka skillnader mellan beteendet för agenter som interagerar genom metriska interaktioner (det vill säga beroende av det metriska avståndet mellan agenter) och agenter som interagerar genom topologiska interaktioner (beroende på ett bestämt antal närliggande agenter). Framförallt studeras hur de båda modellerna förändras då en tidsfördröjning mellan agenternas uppfattning och reaktion introduceras. Undersökningen utförs genom analys av tre olika komplexa system: (1) agenter som rör sig bland periodiska hinder; (2) agenter som följer en ledare genom en labyrint; och (3) aktiva agenters interaktioner med passiva agenter. Utifrån de resultat som erhålls kan det framgångsrikt observeras skillnader i interaktionerna hos den topologiska modellen gentemot den metriska modellen: de aktiva agenterna kan i den topologiska modellen interagera mer med varandra trots periodiska hinder, en större andel agenter tar sig genom labyrinten och klusterbildningen är oftast lägre i systemet med ett lågt antal passiva agenter. Resultaten tyder också på att den topologiska interaktionen i många fall är mindre känslig för tidsfördröjning.
Abstract:
Studies of the behavior of active agents in complex systems have received a lot of interest recently. This interest derives from the fact that active agents provide an ideal model to describe many biological systems and also because of their potential applications. The purpose of this study is to explore which differences there are between the behaviour of agents that interact through metric interactions (i.e. depending on the metric distance between agents) and those of agents that interact through topological interactions (i.e. depending on a certain number of surrounding agents). This report also discusses how the interaction models for active agents change when a time delay between sensing and acting is introduced. These investigations were made by analyzing three different complex environments: (1) agents moving in the presence of periodic obstacles; (2) agents following a leader in a maze; and (3) active agents interacting with passive agents. Based on the results obtained from this study, we could successfully observe differences in the topological interaction compared to the metric model: the active agents interacted more frequently with each other when using the topological model despite periodic obstacles, a larger proportion of agents managed to pass through the maze and the cluster formation was usually smaller in the system with a low number of passive agents. The result also shows that the topological interaction is less sensitive to time delay.
Supervisor: Giovanni Volpe, Department of Physics, University of Gothenburg Examiner: Lena Falk, Department of Physics, Chalmers University of Technology Time: 27 May, 2021
Gustaf Sjösten defended his Master thesis in MPCAS at the Chalmers University of Technology on 17 May 2021. Congrats!
Artistic rendering of a light source illumination a single biomolecule and scattered photons. (Image by Gustaf Sjösten, inspired by an image created by Barbora Spackova)Title: Deep Learning for Nanofluidic Scattering Microscopy
A novel technique for label-free, real-time characterization of single biomolecules called Nanofluidic Scatter Microscopy (NSM) has recently been developed by the Langhammer research group at Chalmers. We have created a machine learning (ML) framework consisting of deep convolutional neural networks such as U-nets, ResNets and YOLO in order to characterize single biomolecules through kymographs collected through NSM, as an alternative approach to a standard data analysis method (SA). As a laser irradiates visible light onto single biomolecules freely diffusing in solution inside nanofluidic channels, the biomolecule and the nanochannel scatter light coherently into the collection optics, such that the nanochannels improve the optical contrast of the imaged biomolecules by several orders of magnitude. A video of the total scattering intensity is then recorded with a high frame rate camera (capturing 200 fps) in order to capture the movement of the molecules as well as the optical contrast of the biomolecules with respect to the nanochannel. From the movement of one single biomolecule, it is possible to predict its diffusion constant, which can then be used to infer the hydrodynamic radius of the biomolecule. Additionally, the predicted optical contrast of one single biomolecule can in turn be used to infer its molecular weight. From the combination of hydrodynamic radius and molecular weight, information about the conformal state of single biomolecules can be inferred. In this thesis, we show that the ML approach yields results comparable to the SA which was developed independently of the ML technique for biomolecules in the weight span 66-669 kDa, and we also show that the ML technique is superior to the SA in other regards, such as computational speed and potential to characterize smaller molecules. The results of the data analysis performed with the ML framework will also make an appearance in the first paper on the NSM technique which has been submitted for publication and is currently under review.
Name of the master programme: MPCAS – Complex Adaptive Systems Supervisor: Giovanni Volpe, Daniel Midtvedt Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg Opponent: Anton Jansson
