arXiv subjects

Serafim Rodrigues

Publications and source records attributed to Serafim Rodrigues.

At least 19 recordsLinked to original sources

arXiv2025

Topological Data Analysis in Finsler Spaces

We introduce a new approach to Topological Data Analysis (TDA) based on Finsler metrics and we also generalize the classical concepts of Vietoris-Rips and Cech complexes within this framework. In particular, we propose a class of directionally dependent Finsler metrics and establish key results demonstrating their relevance to TDA. Moreover, we show that several Information Theoretic perspectives on TDA can often be recovered through the lens of Finsler geometry.

math.DG↗

arXiv2025

Depolarization block induction via slow NaV1.1 inactivation in Dravet syndrome

Dravet syndrome is a developmental and epileptic encephalopathy, characterized by the early onset of drug-resistant seizures and various comorbidities. Most cases of this severe and complex pathology are due to mutations of NaV1.1, a sodium channel mainly expressed in fast-spiking inhibitory neurons. Layer et al. (Front. Cell. Neurosci. 15, 2021) showed that one of these mutations alters the voltage dependence of channel activation, as well as the voltage dependence and kinetics of slow inactivation. Implementing the three effects into a computational model, they predict that altered activation has the largest impact on channel function, as it causes the most severe firing rate reduction. Using a conductance-based model tailored to the dynamics of fast-spiking inhibitory neurons, we look deeper into slow inactivation. We exploit the timescale difference between this very slow process and the rest of the system to conduct a multiple-timescale analysis. We find that, upon prolonged stimulation, the onset of slow inactivation at lower voltage in mutant channels promotes depolarization block, another possible firing deficit aside from frequency reduction. The accelerated kinetics of slow inactivation in mutant channels hastens this transition. This suggests that slow inactivation alterations might for some Dravet variant contribute to the pathological mechanism.

q-bio.NC↗

arXiv2025

Efficient Decomposition of Forman-Ricci Curvature on Vietoris-Rips Complexes and Data Applications

Discrete Forman-Ricci curvature (FRC) is an efficient tool that characterizes essential geometrical features and associated transitions of real-world networks, extending seamlessly to higher-dimensional computations in simplicial complexes. In this article, we provide two major advancements: First, we give a decomposition for FRC that inhently allows a local computations of FRC. Second, we construct a set-theoretical proof enabling an efficient algorithms for the local computation of FRC in Vietoris-Rips (VR) complexes. Our findings open new avenues for geometric computations in VR complexes and highlight an essential yet under-explored aspect of data analysis and visualisation: the geometry underpinning statistical patterns.

math.GT↗

arXiv2025

Alternative set-theoretical algorithms for efficient computations of cliques in Vietoris-Rips complexes

Identifying cliques in dense networks remains a formidable challenge, even with significant advances in computational power and methodologies. To tackle this, numerous algorithms have been developed to optimize time and memory usage, implemented across diverse programming languages. Yet, the inherent NP-completeness of the problem continues to hinder performance on large-scale networks, often resulting in memory leaks and slow computations. In the present study, we critically evaluate classic algorithms to pinpoint computational bottlenecks and introduce novel set-theoretical approaches tailored for network clique computation. Our proposed algorithms are rigorously implemented and benchmarked against existing Python-based solutions, demonstrating superior performance. These findings underscore the potential of set-theoretical techniques to drive substantial performance gains in network analysis.

math.CO↗

arXiv2023

Observing hidden neuronal states in experiments

In this article we demonstrate a general protocol for constructing systematically experimental steady-state bifurcation diagrams for electrophysiologically active cells. We perform our experiments on entorhinal cortex neurons, both excitatory (pyramidal neurons) and inhibitiory (interneurons). A slowly ramped voltage-clamp electrophysiology protocol serves as closed-loop feedback controlled experiment for the subsequent current-clamp open-loop protocol on the same cell. In this way, the voltage-clamped experiment determines dynamically stable and unstable (hidden) steady states of the current-clamp experiment. The transitions between observable steady states and observable spiking states in the current-clamp experiment provide partial evidence for stability and bifurcations of the steady states. This technique for completing steady-state bifurcation diagrams in a model-independent way expands support for model validation to otherwise inaccessible regions of the phase space. Overlaying the voltage-clamp and current-clamp protocols leads to an experimental validation of the classical slow-fast dissection method introduced by J. Rinzel in the 1980s and routinely applied ever since in order to analyse slow-fast neuronal models. Our approach opens doors to observing further complex hidden states with more advanced control strategies, allowing to control real cells beyond pharmacological manipulations.

q-bio.NC↗

arXiv2023

Efficient set-theoretic algorithms for computing high-order Forman-Ricci curvature on abstract simplicial complexes

Forman-Ricci curvature (FRC) is a potent and powerful tool for analysing empirical networks, as the distribution of the curvature values can identify structural information that is not readily detected by other geometrical methods. Crucially, FRC captures higher-order structural information of clique complexes of a graph or Vietoris-Rips complexes, which is not readily accessible to alternative methods. However, existing FRC platforms are prohibitively computationally expensive. Therefore, herein we develop an efficient set-theoretic formulation for computing such high-order FRC in simplicial complexes. Significantly, our set theory representation reveals previous computational bottlenecks and also accelerates the computation of FRC. Finally, We provide a pseudo-code, a software implementation coined FastForman, as well as a benchmark comparison with alternative implementations. We envisage that FastForman will be used in Topological and Geometrical Data analysis for high-dimensional complex data sets. Moreover, our development paves the way for future generalisations towards efficient computations of FRC on cell complexes.

physics.data-an↗

arXiv2023

Synchronization in STDP-driven memristive neural networks with time-varying topology

Synchronization is a widespread phenomenon in the brain. Despite numerous studies, the specific parameter configurations of the synaptic network structure and learning rules needed to achieve robust and enduring synchronization in neurons driven by spike-timing-dependent plasticity (STDP) and temporal networks subject to homeostatic structural plasticity (HSP) rules remain unclear. Here, we bridge this gap by determining the configurations required to achieve high and stable degrees of complete synchronization (CS) and phase synchronization (PS) in time-varying small-world and random neural networks driven by STDP and HSP. In particular, we found that decreasing $P$ (which enhances the strengthening effect of STDP on the average synaptic weight) and increasing $F$ (which speeds up the swapping rate of synapses between neurons) always lead to higher and more stable degrees of CS and PS in small-world and random networks, provided that the network parameters such as the synaptic time delay $\tau_c$, the average degree $\langle k \rangle$, and the rewiring probability $\beta$ have some appropriate values. When $\tau_c$, $\langle k \rangle$, and $\beta$ are not fixed at these appropriate values, the degree and stability of CS and PS may increase or decrease when $F$ increases, depending on the network topology. It is also found that the time delay $\tau_c$ can induce intermittent CS and PS whose occurrence is independent $F$. Our results could have applications in designing neuromorphic circuits for optimal information processing and transmission via synchronization phenomena.

q-bio.NC↗

arXiv2023

Slow-fast dynamics in a neurotransmitter release model: delayed response to a time-dependent input signal

We propose a generalization of the neurotransmitter release model proposed in \emph{Rodrigues et al. (PNAS, 2016)}. We increase the complexity of the underlying slow-fast system by considering a degree-four polynomial as parametrization of the critical manifold. We focus on the possible transient and asymptotic dynamics, exploiting the so-called entry-exit function to describe slow parts of the dynamics. We provide extensive numerical simulations, complemented by numerical bifurcation analysis.

math.DS↗

arXiv2023

Invariants for neural automata

Computational modeling of neurodynamical systems often deploys neural networks and symbolic dynamics. A particular way for combining these approaches within a framework called vector symbolic architectures leads to neural automata. An interesting research direction we have pursued under this framework has been to consider mapping symbolic dynamics onto neurodynamics, represented as neural automata. This representation theory, enables us to ask questions, such as, how does the brain implement Turing computations. Specifically, in this representation theory, neural automata result from the assignment of symbols and symbol strings to numbers, known as Gödel encoding. Under this assignment symbolic computation becomes represented by trajectories of state vectors in a real phase space, that allows for statistical correlation analyses with real-world measurements and experimental data. However, these assignments are usually completely arbitrary. Hence, it makes sense to address the problem question of, which aspects of the dynamics observed under such a representation is intrinsic to the dynamics and which are not. In this study, we develop a formally rigorous mathematical framework for the investigation of symmetries and invariants of neural automata under different encodings. As a central concept we define patterns of equality for such systems. We consider different macroscopic observables, such as the mean activation level of the neural network, and ask for their invariance properties. Our main result shows that only step functions that are defined over those patterns of equality are invariant under recodings, while the mean activation is not. Our work could be of substantial importance for related regression studies of real-world measurements with neurosymbolic processors for avoiding confounding results that are dependant on a particular encoding and not intrinsic to the dynamics.

cs.NE↗

arXiv2023

Charge Transport at Atomic Scales in 1D-Semiconductors: A Quantum Statistical Model Allowing Rigorous Numerical Studies

There has been a recent surge of interest in understanding charge transport at atomic scales. The motivations are myriad, including understanding the conductance properties of peptides measured experimentally. In this study, we propose a model of quantum statistical mechanics which aims to investigate the transport properties of 1D-semiconductor at nanoscales. The model is a two-band Hamiltonian in which electrons are assumed to be quasi-free. It allows us to investigate the behaviour of current and quantum fluctuations under the influence of numerous parameters, showing the response with respect to varying voltage, temperature and length. We compute the current observable at each site and demonstrate the local behaviour generating the current.

physics.bio-ph↗

arXiv2021

Are Brain-Computer Interfaces Feasible with Integrated Photonic Chips?

The present paper examines the viability of a radically novel idea for brain-computer interface (BCI), which could lead to novel technological, experimental and clinical applications. BCIs are computer-based systems that enable either one-way or two-way communication between a living brain and an external machine. BCIs read-out brain signals and transduce them into task commands, which are performed by a machine. In closed-loop, the machine can stimulate the brain with appropriate signals. In recent years, it has been shown that there is some ultraweak light emission from neurons within or close to the visible and near-infrared parts of the optical spectrum. Such ultraweak photon emission (UPE) reflects the cellular (and body) oxidative status, and compelling pieces of evidence are beginning to emerge that UPE may well play an informational role in neuronal functions. In fact, several experiments point to a direct correlation between UPE intensity and neural activity, oxidative reactions, EEG activity, cerebral blood flow, cerebral energy metabolism, and release of glutamate. Here, we propose a novel skull implant BCI that uses UPE. We suggest that a photonic integrated chip installed on the interior surface of the skull may enable a new form of extraction of the relevant features from the UPE signals. In the current technology landscape, photonic technologies advance rapidly and poised to overtake many electrical technologies, due to their unique advantages, such as miniaturization, high speed, low thermal effects, and large integration capacity that allow for high yield, volume manufacturing, and lower cost. For our proposed BCI, we make some major conjectures, which need to be experimentally verified, and hence we discuss the controversial parts, feasibility of technology and limitations, and potential impact of this envisaged technology if successfully implemented in the future.

q-bio.NC↗

arXiv2021

Stochastic facilitation in heteroclinic communication channels

Biological neural systems encode and transmit information as patterns of activity tracing complex trajectories in high-dimensional state-spaces, inspiring alternative paradigms of information processing. Heteroclinic networks, naturally emerging in artificial neural systems, are networks of saddles in state-space that provide a transparent approach to generate complex trajectories via controlled switches among interconnected saddles. External signals induce specific switching sequences, thus dynamically encoding inputs as trajectories. Recent works have focused either on computational aspects of heteroclinic networks, i.e. Heteroclinic Computing, or their stochastic properties under noise. Yet, how well such systems may transmit information remains an open question. Here we investigate the information transmission properties of heteroclinic networks, studying them as communication channels. Choosing a tractable but representative system exhibiting a heteroclinic network, we investigate the mutual information rate (MIR) between input signals and the resulting sequences of states as the level of noise varies. Intriguingly, MIR does not decrease monotonically with increasing noise. Intermediate noise levels indeed maximize the information transmission capacity by promoting an increased yet controlled exploration of the underlying network of states. Complementing standard stochastic resonance, these results highlight the constructive effect of stochastic facilitation (i.e. noise-enhanced information transfer) on heteroclinic communication channels and possibly on more general dynamical systems exhibiting complex trajectories in state-space.

q-bio.NC↗

arXiv2021

Spike-adding and reset-induced canard cycles in adaptive integrate and fire models

We study a class of planar integrate and fire (IF) models called adaptive integrate and fire (AIF) models, which possesses an adaptation variable on top of membrane potential, and whose subthreshold dynamics is piecewise linear (PWL). These AIF models therefore have two reset conditions, which enable bursting dynamics to emerge for suitable parameter values. Such models can be thought of as hybrid dynamical systems. We consider a particular slow dynamics within AIF models and prove the existence of bursting cycles with $N$ resets, for any integer $N$. Furthermore, we study the transition between $N$- and $(N+1)$-reset cycles upon vanishingly small parameter variations and prove (for $N=2$) that such transitions are organised by canard cycles. Finally, using numerical continuation we compute branches of bursting cycles, including canard-explosive branches, in these AIF models, by suitably recasting the periodic problem as a two-point boundary-value problem.

math.DS↗

arXiv2020

Why we should use Topological Data Analysis in Ageing: towards defining the "Topological shape of ageing"

Living systems are subject to the arrow of time; from birth, they undergo complex transformations (self-organization) in a constant battle for survival, but inevitably ageing and disease trap them to death. Can ageing be understood and eventually reversed? What tools can be employed to further our understanding of ageing? The present article is an invitation for biologists and clinicians to consider key conceptual ideas and computational tools (known to mathematicians and physicists), which potentially may help dissect some of the underlying processes of ageing and disease. Specifically, we first discuss how to classify and analyze complex systems, as well as highlight critical theoretical difficulties that make complex systems hard to study. Subsequently, we introduce Topological Data Analysis - a novel Big Data tool - which may help in the study of complex systems since it extracts knowledge from data in a holistic approach via topological considerations. These conceptual ideas and tools are discussed in a rather informal way to pave future discussions and collaborations between mathematicians and biologists studying ageing.

q-bio.OT↗

arXiv2020

Towards a new classification of bursting patterns: review & extensions

The mathematical classification of complex bursting oscillations in multiscale excitable systems, seen for example in physics and neuroscience, has been the subject of active enquiry since the early 1980s. This classification problem is fundamental as it also establishes analytical and numerical foundations for studying complex temporal behaviours in multiple timescale models. This manuscript begins by reviewing the seminal works of Rinzel and Izhikevich in classifying bursting patterns of excitable cell models. Moreover, we recall an alternative, yet complementary, mathematical classification approach by Golubitsky, which together with the Rinzel-Izhikevich proposals provide the state-of-the-art foundations to the classification problem. Unexpectedly, while keeping within the Rinzel-Izhikevich framework, we find novel cases of bursting mechanisms not considered before. Moving beyond the state-of-the-art, we identify novel bursting mechanisms that fall outside the current classifications. This leads us towards a new classification, which requires the analysis of both the fast and the slow subsystems of an underlying slow-fast model. This new classification allows the dynamical dissection of a larger class of bursters. To substantiate this, we add a new class of bursters with at least two slow variables, which we denote folded-node bursters, to convey the idea that the bursts are initiated or annihilated via a folded-node singularity. In fact, there are two main families of folded-node bursters, depending upon the phase of the bursting cycle during which folded-node dynamics occurs. If it occurs during the silent phase, we obtain the classical folded-node bursting (or simply folded-node bursting). If it occurs during the active phase, we have cyclic folded-node bursting. We classify both families and give examples of minimal systems displaying these novel types of bursting behaviour.

math.DS↗

arXiv2016

A modular architecture for transparent computation in Recurrent Neural Networks

Computation is classically studied in terms of automata, formal languages and algorithms; yet, the relation between neural dynamics and symbolic representations and operations is still unclear in traditional eliminative connectionism. Therefore, we suggest a unique perspective on this central issue, to which we would like to refer as to transparent connectionism, by proposing accounts of how symbolic computation can be implemented in neural substrates. In this study we first introduce a new model of dynamics on a symbolic space, the versatile shift, showing that it supports the real-time simulation of a range of automata. We then show that the Goedelization of versatile shifts defines nonlinear dynamical automata, dynamical systems evolving on a vectorial space. Finally, we present a mapping between nonlinear dynamical automata and recurrent artificial neural networks. The mapping defines an architecture characterized by its granular modularity, where data, symbolic operations and their control are not only distinguishable in activation space, but also spatially localizable in the network itself, while maintaining a distributed encoding of symbolic representations. The resulting networks simulate automata in real-time and are programmed directly, in absence of network training. To discuss the unique characteristics of the architecture and their consequences, we present two examples: i) the design of a Central Pattern Generator from a finite-state locomotive controller, and ii) the creation of a network simulating a system of interactive automata that supports the parsing of garden-path sentences as investigated in psycholinguistics experiments.

cs.NE↗

arXiv2016

Canards, folded nodes and mixed-mode oscillations in piecewise-linear slow-fast systems

Canard-induced phenomena have been extensively studied in the last three decades, both from the mathematical and from the application viewpoints. Canards in slow-fast systems with (at least) two slow variables, especially near folded-node singularities, give an essential generating mechanism for Mixed-Mode oscillations (MMOs) in the framework of smooth multiple timescale systems. There is a wealth of literature on such slow-fast dynamical systems and many models displaying canard-induced MMOs, in particular in neuroscience. In parallel, since the late 1990s several papers have shown that the canard phenomenon can be faithfully reproduced with piecewise-linear (PWL) systems in two dimensions although very few results are available in the three-dimensional case. The present paper aims to bridge this gap by analysing canonical PWL systems that display folded singularities, primary and secondary canards, with a similar control of the maximal winding number as in the smooth case. We also show that the singular phase portraits are compatible in both frameworks. Finally, we show on an example how to construct a (linear) global return and obtain robust PWL MMOs.

math.DS↗

arXiv2015

Turing Computation with Recurrent Artificial Neural Networks

We improve the results by Siegelmann & Sontag (1995) by providing a novel and parsimonious constructive mapping between Turing Machines and Recurrent Artificial Neural Networks, based on recent developments of Nonlinear Dynamical Automata. The architecture of the resulting R-ANNs is simple and elegant, stemming from its transparent relation with the underlying NDAs. These characteristics yield promise for developments in machine learning methods and symbolic computation with continuous time dynamical systems. A framework is provided to directly program the R-ANNs from Turing Machine descriptions, in absence of network training. At the same time, the network can potentially be trained to perform algorithmic tasks, with exciting possibilities in the integration of approaches akin to Google DeepMind's Neural Turing Machines.

cs.NE↗