arXiv subjects

Habib Benali

Publications and source records attributed to Habib Benali.

16 recordsLinked to original sources

arXiv2026

Weight geometry governs functional memory in complex systems

Complex systems, from gene regulatory networks to neural circuits and ecological food webs, exhibit rich functional behaviour that topology alone does not capture. Yet functional complexity remains difficult to quantify independently of structural organisation. Here we introduce a thermodynamic framework in which functional complexity is characterised through the hierarchical organisation of functional memory, quantifying how the influence of past interactions is distributed and progressively compressed across scales. Across thirty-four empirical networks spanning biological, ecological, social, technological, and biophysical systems and several orders of magnitude in size and density, real interaction strengths organise functional memory at greater hierarchical depth than random weight assignment on the same topology in every domain studied. The framework further reveals that functional memory occupies a remarkably low-dimensional space, collapsing onto four recurrent dynamical organisations. Comparisons with null models that selectively perturb weighted transport geometry, mesoscale wiring, and directionality show that these structural ingredients play distinct roles: weighted transport geometry systematically governs memory depth, whereas mesoscale wiring organises memory across scales and directionality modulates the response of the cascade to structural perturbation. The same comparisons provide an operational criterion for determining whether network weights encode functionally meaningful structure beyond topology. These results establish weighted transport geometry as a primary organiser of functional memory and provide a quantitative framework for studying functional complexity in directed weighted networks.

cond-mat.dis-nn↗

arXiv2026

Thermodynamic connectivity reveals functional specialization and multiplex organization of extrasynaptic signaling

Neural communication operates on both fast synaptic transmission and slower, diffusive extrasynaptic signaling, yet how these two modes jointly organize brain function remains unclear. Here, using the complete synaptic and neuropeptidergic connectomes of \emph{Caenorhabditis elegans}, we develop a unified multiplex framework linking anatomical wiring to functional communication. We infer structure-derived functional connectivity from the synaptic connectome using equilibrium principles from statistical physics, yielding a probabilistic map of information flow across all synaptic pathways, and compare this functional layer directly with the extrasynaptic connectome. This reveals a principled functional specialization across four communication regimes: (i) a topology-dependent layer that reinforces and stabilizes synaptic motor circuits, (ii) a topology-resilient modulatory layer supporting global regulation and behavioral state control, (iii) a purely extrasynaptic network sustaining survival and homeostasis, and (iv) a purely synaptic regime mediating rapid, low-latency sensorimotor processing. Together, these findings reveal that synaptic and extrasynaptic signaling form complementary architectures optimized for speed, modulation, robustness, and survival, and provide a general strategy for integrating structural and modulatory connectomes to understand how distinct communication modes cooperate to sustain coherent brain function.

q-bio.NC↗

arXiv2024

Kubo-Martin-Schwinger states of Path-structured Flow in Directed Brain Synaptic Networks

The brain's synaptic network, characterized by parallel connections and feedback loops, drives interaction pathways between neurons through a large system with infinitely many degrees of freedom. This system is best modeled by the graph C*-algebra of the underlying directed graph, the Toeplitz-Cuntz-Krieger (TCK) algebra, which captures the diversity of path-structured flow connectivity. Equipped with the gauge action, the TCK algebra defines an {\em algebraic quantum system}, and here we demonstrate that its thermodynamic properties provide a natural framework for describing the dynamic mappings of potential flow pathways within the network. Specifically, the KMS states of this system represent the stationary distributions of a non-Markovian stochastic process with memory decay, capturing how influence propagates along exponentially weighted paths, and yield global statistical measures of neuronal interactions. Applied to the {\em C. elegans} synaptic network, our framework reveals that neurolocomotor neurons emerge as the primary hubs of incoming path-structured flow at inverse temperatures where the entropy of KMS states peaks. This finding aligns with experimental evidence of the foundational role of locomotion in {\em C. elegans} behavior, suggesting that functional centrality may arise from the topological embedding of neurons rather than solely from local physiological properties. Our results highlight the potential of algebraic quantum methods and graph algebras to uncover patterns of functional organization in complex systems and neuroscience.

q-bio.NC↗

arXiv2024

Brain functions emerge as thermal equilibrium states of the connectome

A fundamental idea in neuroscience is that cognitive functions -- such as perception, learning, memory, and locomotion -- are shaped and constrained by the brain's structural organization. Despite significant progress in mapping and analyzing structural connectomes, the principles linking the brain's physical architecture to its functional capabilities remain elusive. Here, we introduce an algebraic quantum model to bridge this theoretical gap, offering new insights into the relationship between the connectome and emergent brain functions, while connecting structural data to functional predictions. Using the well-mapped C. elegans anatomical and extrasynaptic connectomes, we demonstrate that brain functions, defined as functional networks of a neural system, emerge as thermal equilibrium states of an algebraic quantum system derived from the graph algebra of the underlying directed multigraph. Specifically, these equilibrium states, characterized by the Kubo-Martin-Schwinger (KMS) formalism, reveal how individual neurons contribute to functional network formation. Our model illuminates the structure-function relationship in neural circuits through two key features: (1) a functional connectome that delineates topologically driven neuronal interactions and (2) an Integration Capacity (IC) index that quantifies how effectively neurons coordinate and modulate diverse information flows. Together, these features provide a statistical and mechanistic account of information flow and reveal how the network topology of the connectome predicts cognition and complex behaviors.

q-bio.NC↗

arXiv2024

Mitigating Aberration-Induced Noise: A Deep Learning-Based Aberration-to-Aberration Approach

One of the primary sources of suboptimal image quality in ultrasound imaging is phase aberration. It is caused by spatial changes in sound speed over a heterogeneous medium, which disturbs the transmitted waves and prevents coherent summation of echo signals. Obtaining non-aberrated ground truths in real-world scenarios can be extremely challenging, if not impossible. This challenge hinders the performance of deep learning-based techniques due to the domain shift between simulated and experimental data. Here, for the first time, we propose a deep learning-based method that does not require ground truth to correct the phase aberration problem and, as such, can be directly trained on real data. We train a network wherein both the input and target output are randomly aberrated radio frequency (RF) data. Moreover, we demonstrate that a conventional loss function such as mean square error is inadequate for training such a network to achieve optimal performance. Instead, we propose an adaptive mixed loss function that employs both B-mode and RF data, resulting in more efficient convergence and enhanced performance. Finally, we publicly release our dataset, comprising over 180,000 aberrated single plane-wave images (RF data), wherein phase aberrations are modeled as near-field phase screens. Although not utilized in the proposed method, each aberrated image is paired with its corresponding aberration profile and the non-aberrated version, aiming to mitigate the data scarcity problem in developing deep learning-based techniques for phase aberration correction.

eess.IV↗

arXiv2023

Frequency-Space Prediction Filtering for Phase Aberration Correction in Plane-Wave Ultrasound

Ultrasound imaging often suffers from image degradation stemming from phase aberration, which represents a significant contributing factor to the overall image degradation in ultrasound imaging. Frequency-space prediction filtering or FXPF is a technique that has been applied within focused ultrasound imaging to alleviate the phase aberration effect. It presupposes the existence of an autoregressive (AR) model across the signals received at the transducer elements and removes any components that do not conform to the established model. In this study, we illustrate the challenge of applying this technique to plane-wave imaging, where, at shallower depths, signals from more distant elements lose relevance, and a fewer number of elements contribute to image reconstruction. While the number of contributing signals varies, adopting a fixed-order AR model across all depths, results in suboptimal performance. To address this challenge, we propose an AR model with an adaptive order and quantify its effectiveness using contrast and generalized contrast-to-noise ratio metrics.

eess.IV↗

arXiv2023

Robust RF Data Normalization for Deep Learning

Radio frequency (RF) data contain richer information compared to other data types, such as envelope or B-mode, and employing RF data for training deep neural networks has attracted growing interest in ultrasound image processing. However, RF data is highly fluctuating and additionally has a high dynamic range. Most previous studies in the literature have relied on conventional data normalization, which has been adopted within the computer vision community. We demonstrate the inadequacy of those techniques for normalizing RF data and propose that individual standardization of each image substantially enhances the performance of deep neural networks by utilizing the data more efficiently. We compare conventional and proposed normalizations in a phase aberration correction task and illustrate how the former enhances the generality of trained models.

eess.IV↗

arXiv2023

Topology and spectral interconnectivities of higher-order multilayer networks

Multilayer networks have permeated all the sciences as a powerful mathematical abstraction for interdependent heterogenous complex systems such as multimodal brain connectomes, transportation, ecological systems, and scientific collaboration. But describing such systems through a purely graph-theoretic formalism presupposes that the interactions that define the underlying infrastructures and support their functions are only pairwise-based; a strong assumption likely leading to oversimplifications. Indeed, most interdependent systems intrinsically involve higher-order intra- and inter-layer interactions. For instance, ecological systems involve interactions among groups within and in-between species, collaborations and citations link teams of coauthors to articles and vice versa, interactions might exist among groups of friends from different social networks, etc. While higher-order interactions have been studied for monolayer systems through the language of simplicial complexes and hypergraphs, a broad and systematic formalism incorporating them into the realm of multilayer systems is still lacking. Here, we introduce the concept of crossimplicial multicomplexes as a general formalism for modelling interdependent systems involving higher-order intra- and inter-layer connections. Subsequently, we introduce cross-homology and its spectral counterpart, the cross-Laplacian operators, to establish a rigorous mathematical framework for quantifying global and local intra- and inter-layer topological structures in such systems. When applied to multilayer networks, these cross-Laplacians provide powerful methods for detecting clusters in one layer that are controlled by hubs in another layer. We call such hubs spectral cross-hubs and define spectral persistence as a way to rank them according to their emergence along the cross-Laplacian spectra.

math.AT↗

arXiv2023

Phase Aberration Correction without Reference Data: An Adaptive Mixed Loss Deep Learning Approach

Phase aberration is one of the primary sources of image quality degradation in ultrasound, which is induced by spatial variations in sound speed across the heterogeneous medium. This effect disrupts transmitted waves and prevents coherent summation of echo signals, resulting in suboptimal image quality. In real experiments, obtaining non-aberrated ground truths can be extremely challenging, if not infeasible. It hinders the performance of deep learning-based phase aberration correction techniques due to sole reliance on simulated data and the presence of domain shift between simulated and experimental data. Here, for the first time, we propose a deep learning-based method that does not require reference data to compensate for the phase aberration effect. We train a network wherein both input and target output are randomly aberrated radio frequency (RF) data. Moreover, we demonstrate that a conventional loss function such as mean square error is inadequate for training the network to achieve optimal performance. Instead, we propose an adaptive mixed loss function that employs both B-mode and RF data, resulting in more efficient convergence and enhanced performance. Source code is available at \url{http://code.sonography.ai}.

eess.IV↗

arXiv2022

Investigating Shift-Variance of Convolutional Neural Networks in Ultrasound Image Segmentation

While accuracy is an evident criterion for ultrasound image segmentation, output consistency across different tests is equally crucial for tracking changes in regions of interest in applications such as monitoring the patients' response to treatment, measuring the progression or regression of the disease, reaching a diagnosis, or treatment planning. Convolutional neural networks (CNNs) have attracted rapidly growing interest in automatic ultrasound image segmentation recently. However, CNNs are not shift-equivariant, meaning that if the input translates, e.g., in the lateral direction by one pixel, the output segmentation may drastically change. To the best of our knowledge, this problem has not been studied in ultrasound image segmentation or even more broadly in ultrasound images. Herein, we investigate and quantify the shift-variance problem of CNNs in this application and further evaluate the performance of a recently published technique, called BlurPooling, for addressing the problem. In addition, we propose the Pyramidal BlurPooling method that outperforms BlurPooling in both output consistency and segmentation accuracy. Finally, we demonstrate that data augmentation is not a replacement for the proposed method. Source code is available at https://git.io/pbpunet and http://code.sonography.ai.

eess.IV↗

arXiv2022

DF-SSmVEP: Dual Frequency Aggregated Steady-State Motion Visual Evoked Potential Design with Bifold Canonical Correlation Analysis

Recent advancements in Electroencephalography (EEG) sensor technologies and signal processing algorithms have paved the way for further evolution of Brain Computer Interfaces (BCI). When it comes to Signal Processing (SP) for BCI, there has been a surge of interest on Steady-State motion-Visual Evoked Potentials (SSmVEP), where motion stimulation is utilized to address key issues associated with conventional light-flashing/flickering. Such benefits, however, come with the price of having less accuracy and less Information Transfer Rate (ITR). In this regard, the paper focuses on the design of a novel SSmVEP paradigm without using resources such as trial time, phase, and/or number of targets to enhance the ITR. The proposed design is based on the intuitively pleasing idea of integrating more than one motion within a single SSmVEP target stimuli, simultaneously. To elicit SSmVEP, we designed a novel and innovative dual frequency aggregated modulation paradigm, referred to as the Dual Frequency Aggregated steady-state motion Visual Evoked Potential (DF-SSmVEP), by concurrently integrating "Radial Zoom" and "Rotation" motions in a single target without increasing the trial length. Compared to conventional SSmVEPs, the proposed DF-SSmVEP framework consists of two motion modes integrated and shown simultaneously each modulated by a specific target frequency. The paper also develops a specific unsupervised classification model, referred to as the Bifold Canonical Correlation Analysis (BCCA), based on two motion frequencies per target. The proposed DF-SSmVEP is evaluated based on a real EEG dataset and the results corroborate its superiority. The proposed DF-SSmVEP outperforms its counterparts and achieved an average ITR of 30.7 +/- 1.97 and an average accuracy of 92.5 +/- 2.04.

eess.SP↗

arXiv2021

Ultrasound Domain Adaptation Using Frequency Domain Analysis

A common issue in exploiting simulated ultrasound data for training neural networks is the domain shift problem, where the trained models on synthetic data are not generalizable to clinical data. Recently, Fourier Domain Adaptation (FDA) has been proposed in the field of computer vision to tackle the domain shift problem by replacing the magnitude of the low-frequency spectrum of a synthetic sample (source) with a real sample (target). This method is attractive in ultrasound imaging given that two important differences between synthetic and real ultrasound data are caused by unknown values of attenuation and speed of sound (SOS) in real tissues. Attenuation leads to slow variations in the amplitude of the B-mode image, and SOS mismatch creates aberration and subsequent blurring. As such, both domain shifts cause differences in the low-frequency components of the envelope data, which are replaced in the proposed method. We demonstrate that applying the FDA method to the synthetic data, simulated by Field II, obtains an 3.5\% higher Dice similarity coefficient for a breast lesion segmentation task.

eess.IV↗

arXiv2021

An Ultra-Fast Method for Simulation of Realistic Ultrasound Images

Convolutional neural networks (CNNs) have attracted a rapidly growing interest in a variety of different processing tasks in the medical ultrasound community. However, the performance of CNNs is highly reliant on both the amount and fidelity of the training data. Therefore, scarce data is almost always a concern, particularly in the medical field, where clinical data is not easily accessible. The utilization of synthetic data is a popular approach to address this challenge. However, but simulating a large number of images using packages such as Field II is time-consuming, and the distribution of simulated images is far from that of the real images. Herein, we introduce a novel ultra-fast ultrasound image simulation method based on the Fourier transform and evaluate its performance in a lesion segmentation task. We demonstrate that data augmentation using the images generated by the proposed method substantially outperforms Field II in terms of Dice similarity coefficient, while the simulation is almost 36000 times faster (both on CPU).

eess.IV↗

arXiv2020

X-vectors: New Quantitative Biomarkers for Early Parkinson's Disease Detection from Speech

Many articles have used voice analysis to detect Parkinson's disease (PD), but few have focused on the early stages of the disease and the gender effect. In this article, we have adapted the latest speaker recognition system, called x-vectors, in order to detect an early stage of PD from voice analysis. X-vectors are embeddings extracted from a deep neural network, which provide robust speaker representations and improve speaker recognition when large amounts of training data are used. Our goal was to assess whether, in the context of early PD detection, this technique would outperform the more standard classifier MFCC-GMM (Mel-Frequency Cepstral Coefficients - Gaussian Mixture Model) and, if so, under which conditions. We recorded 221 French speakers (including recently diagnosed PD subjects and healthy controls) with a high-quality microphone and with their own telephone. Men and women were analyzed separately in order to have more precise models and to assess a possible gender effect. Several experimental and methodological aspects were tested in order to analyze their impacts on classification performance. We assessed the impact of audio segment duration, data augmentation, type of dataset used for the neural network training, kind of speech tasks, and back-end analyses. X-vectors technique provided better classification performances than MFCC-GMM for text-independent tasks, and seemed to be particularly suited for the early detection of PD in women (7 to 15% improvement). This result was observed for both recording types (high-quality microphone and telephone).

eess.AS↗

arXiv2019

From Hand-Crafted to Deep Learning-based Cancer Radiomics: Challenges and Opportunities

Recent advancements in signal processing and machine learning coupled with developments of electronic medical record keeping in hospitals and the availability of extensive set of medical images through internal/external communication systems, have resulted in a recent surge of significant interest in "Radiomics". Radiomics is an emerging and relatively new research field, which refers to extracting semi-quantitative and/or quantitative features from medical images with the goal of developing predictive and/or prognostic models, and is expected to become a critical component for integration of image-derived information for personalized treatment in the near future. The conventional Radiomics workflow is typically based on extracting pre-designed features (also referred to as hand-crafted or engineered features) from a segmented region of interest. Nevertheless, recent advancements in deep learning have caused trends towards deep learning-based Radiomics (also referred to as discovery Radiomics). Considering the advantages of these two approaches, there are also hybrid solutions developed to exploit the potentials of multiple data sources. Considering the variety of approaches to Radiomics, further improvements require a comprehensive and integrated sketch, which is the goal of this article. This manuscript provides a unique interdisciplinary perspective on Radiomics by discussing state-of-the-art signal processing solutions in the context of Radiomics.

cs.CV↗

arXiv2015

A theoretical study of the role of astrocyte activity in neuronal hyperexcitability using a new neuro-glial mass model

The investigation of the neuronal environment allows us to better understand the activity of a cerebral region as a whole. The recent experimental evidences of the presence of transporters for glutamate and GABA in both neuronal and astrocyte compartments raise the question of the functional importance of the astrocytes in the regulation of the neuronal activity. We propose a new computational model at the mesoscopic scale embedding the recent knowledge on the physiology of neuron and astrocyte coupled activities. The neural compartment is a neural mass model with double excitatory feedback, and the glial compartment focus on the dynamics of glutamate and GABA concentrations. Using the proposed model, we first study the impact of a deficiency in the reuptake of GABA by astrocytes, which implies an increase in GABA concentration in the extracellular space. A decrease in the frequency of neural activity is observed and explained from the dynamics analysis. Second, we investigate the neuronal response to a deficiency in the reuptake of Glutamate by the astrocytes. In this case, we identify three behaviors : the neural activity may either be reduced, or enhanced or, alternatively, may experience a transient of high activity before stabilizing around a new activity regime with a frequency close to the nominal one. After translating theoretically the neuronal excitability modulation using the bifurcation structure of the neural mass model, we state the conditions on the glial feedback parameters corresponding to each behavior.

q-bio.NC↗