004 Datenverarbeitung; Informatik
Refine
Year of publication
Document Type
- Article (29)
- Preprint (15)
- Doctoral Thesis (4)
- Part of a Book (2)
- Contribution to a Periodical (1)
Has Fulltext
- yes (51)
Is part of the Bibliography
- no (51)
Keywords
- computer vision (2)
- deep learning (2)
- intrinsic plasticity (2)
- sparse coding (2)
- 3D image analysis (1)
- Amblyopia (1)
- Autonomous Learning (1)
- Bilderkennung (1)
- Binocular Rivalry (1)
- CBM detector (1)
Institute
- Frankfurt Institute for Advanced Studies (FIAS) (51) (remove)
Multi-view microscopy techniques are used to increase the resolution along the optical axis for 3D imaging. Without this, the resolution is insufficient to resolve subcellular events. In addition, parts of the images of opaque specimens are often highly degraded or masked. Both problems motivate scientists to record the same specimen from multiple directions. The images, then have to be digitally fused into a single high-quality image. Selective-plane illumination microscopy has proven to be a powerful imaging technique due to its unsurpassed acquisition speed and gentle optical sectioning. However, even in the case of multi view imaging techniques that illuminate and image the sample from multiple directions, light scattering inside tissues often severely impairs image contrast.
Here we show that for c-elegans embryos multi view registration can be achieved based on segmented nuclei. However, segmentation of nuclei in high density distribution like c-elegans embryo is challenging. We propose a method which uses 3D Mexican hat filter for preprocessing and 3D Gaussian curvature for the post-processing step to separate nuclei. We used this method successfully on 3 data sets of c-elegans embryos in 3 different views. The result of segmentation outperforms previous methods. Moreover, we provide a simple GUI for manual correction and adjusting the parameters for different data.
We then proposed a method that combines point and voxel registration for an accurate multi view reg- istration of c-elegans embryo, which does not need any special experimental preparation. We demonstrate the performance of our approach on data acquired from fixed embryos of c-elegans worms. This multi step approach is successfully evaluated by comparison to different methods and also by using synthetic data. The proposed method could overcome the typically low resolution along the optical axis and enable stitching to- gether the different parts of the embryo available through the different views. A tool for running the code and analyzing the results is developed.
"Prognosen sind schwierig, besonders, wenn sie die Zukunft betreffen", sagt ein geflügeltes Wort. Die letzte Finanzkrise ist dafür ein gutes Beispiel, denn die wenigsten Analysten und Wirtschaftsweisen haben sie kommen sehen. Da Finanzkrisen glücklicherweise selten sind, ist es allerdings schwierig, Modelle zu entwickeln, die rechtzeitig vor einem Crash warnen.
During the last decade, Bayesian probability theory has emerged as a framework in cognitive science and neuroscience for describing perception, reasoning and learning of mammals. However, our understanding of how probabilistic computations could be organized in the brain, and how the observed connectivity structure of cortical microcircuits supports these calculations, is rudimentary at best. In this study, we investigate statistical inference and self-organized learning in a spatially extended spiking network model, that accommodates both local competitive and large-scale associative aspects of neural information processing, under a unified Bayesian account. Specifically, we show how the spiking dynamics of a recurrent network with lateral excitation and local inhibition in response to distributed spiking input, can be understood as sampling from a variational posterior distribution of a well-defined implicit probabilistic model. This interpretation further permits a rigorous analytical treatment of experience-dependent plasticity on the network level. Using machine learning theory, we derive update rules for neuron and synapse parameters which equate with Hebbian synaptic and homeostatic intrinsic plasticity rules in a neural implementation. In computer simulations, we demonstrate that the interplay of these plasticity rules leads to the emergence of probabilistic local experts that form distributed assemblies of similarly tuned cells communicating through lateral excitatory connections. The resulting sparse distributed spike code of a well-adapted network carries compressed information on salient input features combined with prior experience on correlations among them. Our theory predicts that the emergence of such efficient representations benefits from network architectures in which the range of local inhibition matches the spatial extent of pyramidal cells that share common afferent input.
Artificial neural networks, taking inspiration from biological neurons, have become an invaluable tool for machine learning applications. Recent studies have developed techniques to effectively tune the connectivity of sparsely-connected artificial neural networks, which have the potential to be more computationally efficient than their fully-connected counterparts and more closely resemble the architectures of biological systems. We here present a normalisation, based on the biophysical behaviour of neuronal dendrites receiving distributed synaptic inputs, that divides the weight of an artificial neuron’s afferent contacts by their number. We apply this dendritic normalisation to various sparsely-connected feedforward network architectures, as well as simple recurrent and self-organised networks with spatially extended units. The learning performance is significantly increased, providing an improvement over other widely-used normalisations in sparse networks. The results are two-fold, being both a practical advance in machine learning and an insight into how the structure of neuronal dendritic arbours may contribute to computation.
Inspired by the physiology of neuronal systems in the brain, artificial neural networks have become an invaluable tool for machine learning applications. However, their biological realism and theoretical tractability are limited, resulting in poorly understood parameters. We have recently shown that biological neuronal firing rates in response to distributed inputs are largely independent of size, meaning that neurons are typically responsive to the proportion, not the absolute number, of their inputs that are active. Here we introduce such a normalisation, where the strength of a neuron’s afferents is divided by their number, to various sparsely-connected artificial networks. The learning performance is dramatically increased, providing an improvement over other widely-used normalisations in sparse networks. The resulting machine learning tools are universally applicable and biologically inspired, rendering them better understood and more stable in our tests.
Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable renewable generation, storage units, coupling to other energy sectors, and mixed alternating and direct current networks. It is designed to be easily extensible and to scale well with large networks and long time series. In this paper the basic functionality of PyPSA is described, including the formulation of the full power flow equations and the multi-period optimisation of operation and investment with linear power flow equations. PyPSA is positioned in the existing free software landscape as a bridge between traditional power flow analysis tools for steady-state analysis and full multi-period energy system models. The functionality is demonstrated on two open datasets of the transmission system in Germany (based on SciGRID) and Europe (based on GridKit).
PolarCAP – A deep learning approach for first motion polarity classification of earthquake waveforms
(2022)
Highlights
• We present PolarCAP, a deep learning model that can classify the polarity of a waveform with a 98% accuracy.
• The first-motion polarity of seismograms is a useful parameter, but its manual determination can be laborious and imprecise.
• We demonstrate that in several cases the model can assign trace polar-ity more accurately than a human analyst.
Abstract
The polarity of first P-wave arrivals plays a significant role in the effective determination of focal mechanisms specially for smaller earthquakes. Manual estimation of polarities is not only time-consuming but also prone to human errors. This warrants a need for an automated algorithm for first motion polarity determination. We present a deep learning model - PolarCAP that uses an autoencoder architecture to identify first-motion polarities of earth-quake waveforms. PolarCAP is trained in a supervised fashion using more than 130,000 labelled traces from the Italian seismic dataset (INSTANCE) and is cross-validated on 22,000 traces to choose the most optimal set of hyperparameters. We obtain an accuracy of 0.98 on a completely unseen test dataset of almost 33,000 traces. Furthermore, we check the model generalizability by testing it on the datasets provided by previous works and show that our model achieves a higher recall on both positive and negative polarities.
In this proceeding, we review our recent work using deep convolutional neural network (CNN) to identify the nature of the QCD transition in a hybrid modeling of heavy-ion collisions. Within this hybrid model, a viscous hydrodynamic model is coupled with a hadronic cascade “after-burner”. As a binary classification setup, we employ two different types of equations of state (EoS) of the hot medium in the hydrodynamic evolution. The resulting final-state pion spectra in the transverse momentum and azimuthal angle plane are fed to the neural network as the input data in order to distinguish different EoS. To probe the effects of the fluctuations in the event-by-event spectra, we explore different scenarios for the input data and make a comparison in a systematic way. We observe a clear hierarchy in the predictive power when the network is fed with the event-by-event, cascade-coarse-grained and event-fine-averaged spectra. The carefully-trained neural network can extract high-level features from pion spectra to identify the nature of the QCD transition in a realistic simulation scenario.
Residual connections have been proposed as an architecture-based inductive bias to mitigate the problem of exploding and vanishing gradients and increased task performance in both feed-forward and recurrent networks (RNNs) when trained with the backpropagation algorithm. Yet, little is known about how residual connections in RNNs influence their dynamics and fading memory properties. Here, we introduce weakly coupled residual recurrent networks (WCRNNs) in which residual connections result in well-defined Lyapunov exponents and allow for studying properties of fading memory. We investigate how the residual connections of WCRNNs influence their performance, network dynamics, and memory properties on a set of benchmark tasks. We show that several distinct forms of residual connections yield effective inductive biases that result in increased network expressivity. In particular, those are residual connections that (i) result in network dynamics at the proximity of the edge of chaos, (ii) allow networks to capitalize on characteristic spectral properties of the data, and (iii) result in heterogeneous memory properties. In addition, we demonstrate how our results can be extended to non-linear residuals and introduce a weakly coupled residual initialization scheme that can be used for Elman RNNs.
Active efficient coding explains the development of binocular vision and its failure in amblyopia
(2020)
The development of vision during the first months of life is an active process that comprises the learning of appropriate neural representations and the learning of accurate eye movements. While it has long been suspected that the two learning processes are coupled, there is still no widely accepted theoretical framework describing this joint development. Here, we propose a computational model of the development of active binocular vision to fill this gap. The model is based on a formulation of the active efficient coding theory, which proposes that eye movements as well as stimulus encoding are jointly adapted to maximize the overall coding efficiency. Under healthy conditions, the model self-calibrates to perform accurate vergence and accommodation eye movements. It exploits disparity cues to deduce the direction of defocus, which leads to coordinated vergence and accommodation responses. In a simulated anisometropic case, where the refraction power of the two eyes differs, an amblyopia-like state develops in which the foveal region of one eye is suppressed due to inputs from the other eye. After correcting for refractive errors, the model can only reach healthy performance levels if receptive fields are still plastic, in line with findings on a critical period for binocular vision development. Overall, our model offers a unifying conceptual framework for understanding the development of binocular vision.