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Duccio Fanelli

Publications and source records attributed to Duccio Fanelli.

At least 37 records · Page 2Linked to original sources

A short introduction to Neural Networks and their application to Earth and Materials Science Science

Neural networks are gaining widespread relevance for their versatility, holding the promise to yield a significant methodological shift in different domain of applied research. Here, we provide a simple pedagogical account of the basic functioning of a feedforward neural network. Then we move forward to reviewing two recent applications of machine learning to Earth and Materials Science. We will in particular begin by discussing a neural network based geothermobarometer, which returns reliable predictions of the pressure/temperature conditions of magma storage. Further, we will turn to illustrate how machine learning tools, tested on the list of minerals from the International Mineralogical Association, can help in the search for novel superconducting materials.

physics.data-an↗

Resolving the kinetics of an ensemble of muscle myosin motors via a temperature-dependent fitting procedure

A data fitting procedure is devised and thoroughly tested to provide self-consistent estimates of the relevant mechanokinetic parameters involved in a plausible scheme underpinning the output of an ensemble of myosin II molecular motors mimicking the muscle contraction. The method builds on a stochastic model accounting for the force exerted by the motor ensemble operated both in the low and high force-generating regimes corresponding to different temperature ranges. The proposed interpretative framework is successfully challenged against simulated data, meant to mimic the experimental output of a unidimensional synthetic nanomachine powered by pure muscle myosin isoforms.

cond-mat.stat-mech↗

Force and kinetics of fast and slow muscle myosin determined with a synthetic sarcomere-like nanomachine

Myosin II is the muscle molecular motor that works in two bipolar arrays in each thick filament of the striated (skeletal and cardiac) muscle, converting the chemical energy into steady force and shortening by cyclic ATP--driven interactions with the nearby actin filaments. Different isoforms of the myosin motor in the skeletal muscles account for the different functional requirements of the slow muscles (primarily responsible for the posture) and fast muscles (responsible for voluntary movements). To clarify the molecular basis of the differences, here the isoform--dependent mechanokinetic parameters underpinning the force of slow and fast muscles are defined with a unidimensional synthetic nanomachine powered by pure myosin isoforms from either slow or fast rabbit skeletal muscle. Data fitting with a stochastic model provides a self--consistent estimate of all the mechanokinetic properties of the motor ensemble including the motor force, the fraction of actin--attached motors and the rate of transition through the attachment--detachment cycle. The achievements in this paper set the stage for any future study on the emergent mechanokinetic properties of an ensemble of myosin molecules either engineered or purified from mutant animal models or human biopsies.

cond-mat.stat-mech↗

Turing patterns on discrete topologies: from networks to higher-order structures

Nature is a blossoming of regular structures, signature of self-organization of the underlying microscopic interacting agents. Turing theory of pattern formation is one of the most studied mechanisms to address such phenomena and has been applied to a widespread gallery of disciplines. Turing himself used a spatial discretization of the hosting support to eventually deal with a set of ODEs. Such an idea contained the seeds of the theory on discrete support, which has been fully acknowledged with the birth of network science in the early 2000s. This approach allows us to tackle several settings not displaying a trivial continuous embedding, such as multiplex, temporal networks, and, recently, higher-order structures. This line of research has been mostly confined within the network science community, despite its inherent potential to transcend the conventional boundaries of the PDE-based approach to Turing patterns. Moreover, network topology allows for novel dynamics to be generated via a universal formalism that can be readily extended to account for higher-order structures. The interplay between continuous and discrete settings can pave the way for further developments in the field.

nlin.PS↗

Stable Attractors for Neural networks classification via Ordinary Differential Equations (SA-nODE)

A novel approach for supervised classification is presented which sits at the intersection of machine learning and dynamical systems theory. At variance with other methodologies that employ ordinary differential equations for classification purposes, the untrained model is a priori constructed to accommodate for a set of pre-assigned stationary stable attractors. Classifying amounts to steer the dynamics towards one of the planted attractors, depending on the specificity of the processed item supplied as an input. Asymptotically the system will hence converge on a specific point of the explored multi-dimensional space, flagging the category of the object to be eventually classified. Working in this context, the inherent ability to perform classification, as acquired ex post by the trained model, is ultimately reflected in the shaped basin of attractions associated to each of the target stable attractors. The performance of the proposed method is here challenged against simple toy models crafted for the purpose, as well as by resorting to well established reference standards. Although this method does not reach the performance of state-of-the-art deep learning algorithms, it illustrates that continuous dynamical systems with closed analytical interaction terms can serve as high-performance classifiers.

cond-mat.dis-nn↗

Engineered Ordinary Differential Equations as Classification Algorithm (EODECA): thorough characterization and testing

EODECA (Engineered Ordinary Differential Equations as Classification Algorithm) is a novel approach at the intersection of machine learning and dynamical systems theory, presenting a unique framework for classification tasks [1]. This method stands out with its dynamical system structure, utilizing ordinary differential equations (ODEs) to efficiently handle complex classification challenges. The paper delves into EODECA's dynamical properties, emphasizing its resilience against random perturbations and robust performance across various classification scenarios. Notably, EODECA's design incorporates the ability to embed stable attractors in the phase space, enhancing reliability and allowing for reversible dynamics. In this paper, we carry out a comprehensive analysis by expanding on the work [1], and employing a Euler discretization scheme. In particular, we evaluate EODECA's performance across five distinct classification problems, examining its adaptability and efficiency. Significantly, we demonstrate EODECA's effectiveness on the MNIST and Fashion MNIST datasets, achieving impressive accuracies of $98.06\%$ and $88.21\%$, respectively. These results are comparable to those of a multi-layer perceptron (MLP), underscoring EODECA's potential in complex data processing tasks. We further explore the model's learning journey, assessing its evolution in both pre and post training environments and highlighting its ability to navigate towards stable attractors. The study also investigates the invertibility of EODECA, shedding light on its decision-making processes and internal workings. This paper presents a significant step towards a more transparent and robust machine learning paradigm, bridging the gap between machine learning algorithms and dynamical systems methodologies.

cs.LG↗

Complex Recurrent Spectral Network

This paper presents a novel approach to advancing artificial intelligence (AI) through the development of the Complex Recurrent Spectral Network ($\mathbb{C}$-RSN), an innovative variant of the Recurrent Spectral Network (RSN) model. The $\mathbb{C}$-RSN is designed to address a critical limitation in existing neural network models: their inability to emulate the complex processes of biological neural networks dynamically and accurately. By integrating key concepts from dynamical systems theory and leveraging principles from statistical mechanics, the $\mathbb{C}$-RSN model introduces localized non-linearity, complex fixed eigenvalues, and a distinct separation of memory and input processing functionalities. These features collectively enable the $\mathbb{C}$-RSN evolving towards a dynamic, oscillating final state that more closely mirrors biological cognition. Central to this work is the exploration of how the $\mathbb{C}$-RSN manages to capture the rhythmic, oscillatory dynamics intrinsic to biological systems, thanks to its complex eigenvalue structure and the innovative segregation of its linear and non-linear components. The model's ability to classify data through a time-dependent function, and the localization of information processing, is demonstrated with an empirical evaluation using the MNIST dataset. Remarkably, distinct items supplied as a sequential input yield patterns in time which bear the indirect imprint of the insertion order (and of the time of separation between contiguous insertions).

cs.LG↗

How a student becomes a teacher: learning and forgetting through Spectral methods

In theoretical ML, the teacher-student paradigm is often employed as an effective metaphor for real-life tuition. The above scheme proves particularly relevant when the student network is overparameterized as compared to the teacher network. Under these operating conditions, it is tempting to speculate that the student ability to handle the given task could be eventually stored in a sub-portion of the whole network. This latter should be to some extent reminiscent of the frozen teacher structure, according to suitable metrics, while being approximately invariant across different architectures of the student candidate network. Unfortunately, state-of-the-art conventional learning techniques could not help in identifying the existence of such an invariant subnetwork, due to the inherent degree of non-convexity that characterizes the examined problem. In this work, we take a leap forward by proposing a radically different optimization scheme which builds on a spectral representation of the linear transfer of information between layers. The gradient is hence calculated with respect to both eigenvalues and eigenvectors with negligible increase in terms of computational and complexity load, as compared to standard training algorithms. Working in this framework, we could isolate a stable student substructure, that mirrors the true complexity of the teacher in terms of computing neurons, path distribution and topological attributes. When pruning unimportant nodes of the trained student, as follows a ranking that reflects the optimized eigenvalues, no degradation in the recorded performance is seen above a threshold that corresponds to the effective teacher size. The observed behavior can be pictured as a genuine second-order phase transition that bears universality traits.

cs.LG↗

Multiplicative noise induced bistability and stochastic resonance

Stochastic resonance is a well established phenomenon, which proves relevant for a wide range of applications, of broad trans-disciplinary breath. Consider a one dimensional bistable stochastic system, characterized by a deterministic double well potential and shaken by an additive noise source. When subject to an external periodic drive, and for a proper choice of the noise strength, the system swings regularly between the two existing deterministic fixed points, with just one switch for each oscillation of the imposed forcing term. This resonant condition can be exploited to unravel weak periodic signals, otherwise inaccessible to conventional detectors. Here, we will set to revisit the stochastic resonance concept by operating in a modified framework where bistability is induced by the nonlinear nature of the multiplicative noise. A candidate model is in particular introduced which fulfils the above requirements while allowing for analytical progress to be made. Working with reference to this case study, we elaborate on the conditions for the onset of the generalized stochastic resonance mechanism. As a byproduct of the analysis, a novel resonant regime is also identified which displays no lower bound for the frequencies that can be resolved, at variance with the traditional setting.

cond-mat.stat-mech↗

Brain-wide functional imaging to highlight differences between the diurnal and nocturnal neuronal activity in zebrafish larvae

Most living organisms show highly conserved physiological changes following a 24-hour cycle which goes by the name of circadian rhythm. Among experimental models, the effects of light-dark cycle have been recently investigated in the larval zebrafish. Owing to its small size and transparency, this vertebrate enables optical access to the entire brain. Indeed, the combination of this organism with light-sheet imaging grants high spatio-temporal resolution volumetric recording of neuronal activity. This imaging technique, in its multiphoton variant, allows functional investigations without unwanted visual stimulation. Here, we employed a custom two-photon light-sheet microscope to study brain-wide differences in neuronal activity between diurnal and nocturnal periods in larval zebrafish assessed at the transition between day and night. We describe for the first time an activity increase in the low frequency domain of the pretectum and a frequency-localized activity decrease of the anterior rhombencephalic turning region during the nocturnal period. Moreover, our data confirm a nocturnal reduction in habenular activity. Furthermore, brain-wide detrended fluctuation analysis revealed a nocturnal decrease in the self-affinity of the neuronal signals in parts of the dorsal thalamus and the medulla oblongata and an increase in the pretectum. Our data show that brain-wide nonlinear light-sheet imaging represents a useful tool to investigate circadian rhythm effects on neuronal activity.

q-bio.NC↗

Non-parametric analysis of the Hubble Diagram with Neural Networks

The recent extension of the Hubble diagram of Supernovae and quasars to redshifts much higher than 1 prompted a revived interest in non-parametric approaches to test cosmological models and to measure the expansion rate of the Universe. In particular, it is of great interest to infer model-independent constraints on the possible evolution of the dark energy component. Here we present a new method, based on a Neural Network Regression, to analyze the Hubble Diagram in a completely non-parametric, model-independent fashion. We first validate the method through simulated samples with the same redshift distribution as the real ones, and discuss the limitations related to the "inversion problem" for the distance-redshift relation. We then apply this new technique to the analysis of the Hubble diagram of Supernovae and quasars. We confirm that the data up to $z \sim 1-1.5$ are in agreement with a flat $ΛCDM$ model with $Ω_M \sim 0.3$, while $\sim 5$-sigma deviations emerge at higher redshifts. A flat $ΛCDM$ model would still be compatible with the data with $Ω_M > 0.4$. Allowing for a generic evolution of the dark energy component, we find solutions suggesting an increasing value of $Ω_M$ with the redshift, as predicted by interacting dark sector models.

astro-ph.CO↗

Theory of synchronisation and pattern formation on time varying networks

Synchronisation and pattern formation have been intensely addressed for systems evolving on static networks. Extending the study to include the inherent ability of the network to adjust over time proved cumbersome and led to conclusions which lack of generality, as relying on peculiar assumptions. Here, the master stability formalism is extended to account, in a thoroughly general prospect, for the additional contributions as stemming from the time evolution of the underlying network. The theory is successfully challenged against two illustrative testbeds, which can be respectively ascribed to synchronisation and Turing settings.

cond-mat.stat-mech↗

Recurrent Spectral Network (RSN): shaping the basin of attraction of a discrete map to reach automated classification

A novel strategy to automated classification is introduced which exploits a fully trained dynamical system to steer items belonging to different categories toward distinct asymptotic attractors. These latter are incorporated into the model by taking advantage of the spectral decomposition of the operator that rules the linear evolution across the processing network. Non-linear terms act for a transient and allow to disentangle the data supplied as initial condition to the discrete dynamical system, shaping the boundaries of different attractors. The network can be equipped with several memory kernels which can be sequentially activated for serial datasets handling. Our novel approach to classification, that we here term Recurrent Spectral Network (RSN), is successfully challenged against a simple test-bed model, created for illustrative purposes, as well as a standard dataset for image processing training.

cond-mat.dis-nn↗

Spectral pruning of fully connected layers: ranking the nodes based on the eigenvalues

Training of neural networks can be reformulated in spectral space, by allowing eigenvalues and eigenvectors of the network to act as target of the optimization instead of the individual weights. Working in this setting, we show that the eigenvalues can be used to rank the nodes' importance within the ensemble. Indeed, we will prove that sorting the nodes based on their associated eigenvalues, enables effective pre- and post-processing pruning strategies to yield massively compacted networks (in terms of the number of composing neurons) with virtually unchanged performance. The proposed methods are tested for different architectures, with just a single or multiple hidden layers, and against distinct classification tasks of general interest.

cond-mat.dis-nn↗

Fast whole-brain imaging of seizures in zebrafish larvae by two-photon light-sheet microscopy

Light-sheet fluorescence microscopy (LSFM) enables real-time whole-brain functional imaging in zebrafish larvae. Conventional one photon LSFM can however induce undesirable visual stimulation due to the use of visible excitation light. The use of two-photon (2P) excitation, employing near-infrared invisible light, provides unbiased investigation of neuronal circuit dynamics. However, due to the low efficiency of the 2P absorption process, the imaging speed of this technique is typically limited by the signal-to-noise-ratio. Here, we describe a 2P LSFM setup designed for non-invasive imaging that enables quintuplicating state-of-the-art volumetric acquisition rate of the larval zebrafish brain (5 Hz) while keeping low the laser intensity on the specimen. We applied our system to the study of pharmacologically-induced acute seizures, characterizing the spatial-temporal dynamics of pathological activity and describing for the first time the appearance of caudo-rostral ictal waves (CRIWs).

q-bio.QM↗

Prestrain-induced contraction in 1D random elastic chains

Prestrained elastic networks arise in a number of biological and technological systems ranging from the cytoskeleton of cells to tensegrity structures. To understand the response of such a network as a function of the prestrain, we consider a minimal model in one dimension. We do this by considering a chain (1D network) of elastic springs upon which a random, zero mean, finite variance prestrain is imposed. Numerical simulations and analytical predictions quantify the magnitude of the contraction as a function of the variance of the prestrain, and show that the chain always shrinks. To test these predictions, we vary the topology of the chain and consider more complex connectivity and show that our results are relatively robust to these changes.

cond-mat.stat-mech↗

On the training of sparse and dense deep neural networks: less parameters, same performance

Deep neural networks can be trained in reciprocal space, by acting on the eigenvalues and eigenvectors of suitable transfer operators in direct space. Adjusting the eigenvalues, while freezing the eigenvectors, yields a substantial compression of the parameter space. This latter scales by definition with the number of computing neurons. The classification scores, as measured by the displayed accuracy, are however inferior to those attained when the learning is carried in direct space, for an identical architecture and by employing the full set of trainable parameters (with a quadratic dependence on the size of neighbor layers). In this Letter, we propose a variant of the spectral learning method as appeared in Giambagli et al {Nat. Comm.} 2021, which leverages on two sets of eigenvalues, for each mapping between adjacent layers. The eigenvalues act as veritable knobs which can be freely tuned so as to (i) enhance, or alternatively silence, the contribution of the input nodes, (ii) modulate the excitability of the receiving nodes with a mechanism which we interpret as the artificial analogue of the homeostatic plasticity. The number of trainable parameters is still a linear function of the network size, but the performances of the trained device gets much closer to those obtained via conventional algorithms, these latter requiring however a considerably heavier computational cost. The residual gap between conventional and spectral trainings can be eventually filled by employing a suitable decomposition for the non trivial block of the eigenvectors matrix. Each spectral parameter reflects back on the whole set of inter-nodes weights, an attribute which we shall effectively exploit to yield sparse networks with stunning classification abilities, as compared to their homologues trained with conventional means.

cs.LG↗

Dynamical systems on hypergraphs

We present a general framework that enables one to model high-order interaction among entangled dynamical systems, via hypergraphs. Several relevant processes can be ideally traced back to the proposed scheme. We shall here solely elaborate on the conditions that seed the spontaneous emergence of patterns, spatially heterogeneous solutions resulting from the many-body interaction between fundamental units. In particular we will focus, on two relevant settings. First, we will assume long-ranged mean field interactions between populations, and then turn to considering diffusive-like couplings. Two applications are presented, respectively to a generalised Volterra system and the Brusselator model.

cond-mat.stat-mech↗