Publications related to Reconstructing Evolving Tree Structures in Time Lapse Sequences by Enforcing Time-Consistency

Related publications (32)

Enabling Uncertainty Estimation in Iterative Neural Networks

Pascal Fua, Minh Hieu Lê, Doruk Oner, Nikita Durasov

Turning pass-through network architectures into iterative ones, which use their own output as input, is a well-known approach for boosting performance. In this paper, we argue that such architectures offer an additional benefit: The convergence rate of the ...

Curran Associates2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

swissALPS: a Dataset for Imbalanced Land Cover Mapping in Alpine Regions

Valérie Zermatten

Our dataset consists of very high-resolution aerial images (50cm) and a digital elevation model (50cm) that covers approx. 2300 km2 of land above 2000m altitude in the southwestern part of Switzerland. Our land cover labels focus on alpine land cover that ...

IEEE DataPort2023

3D reconstruction of curvilinear one-dimensional objects viewed in transmission electron microscopy

Gulnaz Ganeeva

To obtain a more complete understanding of material microstructure at the nanoscale and to gain profound insights into their properties, there is a growing need for more efficient and precise methods that can streamline the process of 3D imaging using a tr ...

EPFL2023

Time Series Analysis of Urban Liveability

Devis Tuia, Diego Marcos Gonzalez

In this paper we explore deep learning models to monitor longitudinal liveability changes in Dutch cities at the neighbourhood level. Our liveability reference data is defined by a country-wise yearly survey based on a set of indicators combined into a liv ...

IEEE2023

A new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Casper Alexander Goverde, Arne Schneuing, Hamed Khakzad, Ilia Igashov

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Cell Press2023

Stay close, but not too close: aerial image analysis reveals patterns of social distancing in seal colonies

Devis Tuia, Benjamin Alexander Kellenberger

Many species aggregate in dense colonies. Species-specific spatial patterns provide clues about how colonies are shaped by various (a)biotic factors, including predation, temperature regulation or disease transmission. Using aerial imagery, we examined the ...

2023

AutoSynth: Learning to Generate 3D Training Data for Object Point Cloud Registration

Mathieu Salzmann, Zheng Dang

In the current deep learning paradigm, the amount and quality of training data are as critical as the network architecture and its training details. However, collecting, processing, and annotating real data at scale is difficult, expensive, and time-consum ...

Ieee Computer Soc2023

Deep Learning for 3D Surface Modelling and Reconstruction

Benoît Alain René Guillard

In recent years, there has been a significant revolution in the field of deep learning, which has demonstrated its effectiveness in automatically capturing intricate patterns from large datasets. However, the majority of these successes in Computer Vision ...

EPFL2023

Learnable latent embeddings for joint behavioural and neural analysis

Mackenzie Mathis, Steffen Schneider

Mapping behavioural actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioural data increases, there is growing interest in modelling neural dynamics during adaptive behaviours to probe neural re ...

NATURE PORTFOLIO2023

De novo protein design by inversion of the AlphaFold structure prediction network

Benedict Dieter Gregor Wolf, Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Hamed Khakzad

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

Topologically Better Delineation of Curvilinear Structures

Doruk Oner

Curvilinear structures are frequently observed in a variety of domains and are essential for comprehending neural circuits, detecting fractures in materials, and determining road and irrigation canal networks. It can be costly and time-consuming to manuall ...

EPFL2023

Semantic Segmentation of Remote Sensing Images With Sparse Annotations

Devis Tuia

Training convolutional neural networks (CNNs) for very high-resolution images requires a large quantity of high-quality pixel-level annotations, which is extremely labor-intensive and time-consuming to produce. Moreover, professional photograph interpreter ...

2022

Advanced Techniques in Optical Diffraction Tomography

Ahmed Bassam Sayed Ayoub Mohamed Emam

In this thesis, we study the 3 challenges described above. First, we study different reconstruction techniques and assess the fidelity of each reconstruction results by means of structured illumination and phase conjugation. By reconstructing the 3D refrac ...

EPFL2022

Event-driven acquisition for content-enriched microscopy

Suliana Manley, Dora Mahecic, Martin Weigert, Juliette Griffie, Chen Zhang, Willi Leopold Stepp

Event-driven acquisition uses neural-network-based recognition of specific biological events to trigger switching between slow and fast super-resolution imaging, enriching the capture of interesting events with high spatiotemporal resolution. A common goal ...

Nature Publishing Group2022

UAV in the advent of the twenties: Where we stand and what is next

Jan Skaloud, Davide Antonio Cucci

The use of Unmanned Aerial Vehicles (UAVs) has surged in the last two decades, making them popular instruments for a wide range of applications, and leading to a remarkable number of scientific contributions in geoscience, remote sensing and engineering. H ...

2022

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...

EPFL2022

Synthesis and Analysis of 3D shapes with Geometric Deep Learning in Computer-Aided Engineering

Edoardo Remelli

In this thesis, we advocate that Computer-Aided Engineering could benefit from a Geometric Deep Learning revolution, similarly to the way that Deep Learning revolutionized Computer Vision. To do so, we consider a variety of Computer-Aided Engineering pr ...

EPFL2022

Controllability and Interpretability in Affective Speech Synthesis

Bastian Schnell

Thanks to Deep Learning Text-To-Speech (TTS) has achieved high audio quality with large databases. But at the same time the complex models lost any ability to control or interpret the generation process. For the big challenge of affective TTS it is infeasi ...

EPFL2022

Local Kernel Regression and Neural Network Approaches to the Conformational Landscapes of Oligopeptides

Michele Ceriotti, Anne-Clémence Corminboeuf, Alberto Fabrizio, Benjamin André René Meyer, Raimon Fabregat I De Aguilar-Amat, Edgar Albert Engel, Veronika Juraskova

The application of machine learning to theoretical chemistry has made it possible to combine the accuracy of quantum chemical energetics with the thorough sampling of finite-temperature fluctuations. To reach this goal, a diverse set of methods has been pr ...

2022