arXiv subjects

Narsis A. Kiani

Publications and source records attributed to Narsis A. Kiani.

At least 19 recordsLinked to original sources

arXiv2026

Epigenetic feedback reshapes dynamical landscapes in gene regulatory networks

Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape. While experimental approaches such as single-cell transcriptomics reveal rich dynamical behaviour, a tractable theoretical framework that links gene expression, epigenetic control, and collective dynamics remains challenging. Here, we develop an extended Dynamical Mean Field Theory (DMFT) framework for GRNs that incorporates epigenetic modifications as slow, feedback-driven variables. Building on the analogy between Hopfield networks and spin glass systems, we derive effective stochastic equations that reduce high-dimensional dynamics to a tractable form across multiple timescales. This formulation enables quantitative characterization of both stable and oscillatory regimes and reveals how epigenetic feedback reshapes the effective potential landscape governing cell fate decisions. Our model shows how epigenetic feedback regulation dynamically reshapes the Waddington landscape. Our results and methodology provide a unified theoretical framework for understanding developmental dynamics and epigenetic reprogramming in complex biological systems.

q-bio.MN↗

arXiv2025

Assembly Theory Reduced to Shannon Entropy and Rendered Redundant by Naive Statistical Algorithms

Assembly Theory (AT) and its central measure, the assembly index (Ai), represent an invaluable opportunity to address some of the most persistent and widespread conflations and misconceptions about computability and complexity theory in science. The AT defence embodies several common concurrent misconceptions that pile on each other: the belief that Turing machines impose artefactual constraints, the mischaracterisation of Kolmogorov complexity as inapplicable, and the claims around Ai as different from Shannon entropy or compression algorithms. Here we show that the new arguments advanced by the AT group in their defence, are based on misleading and incomplete experiments that, when completed, show the extent of the correlations and overlapping with popular statistical compression algorithms, conforming with the mathematical equivalence to Shannon entropy previously mathematically proved and reported, which remains undisputed. Through theoretical and empirical analysis, we show that Ai does not offer a path towards fundamental novel causal or informational insights beyond what existing statistical frameworks already offer. Rather than offering a unifying theory of life as the AT authors suggest, we argue that AT obfuscates the field and provides a cautionary example of how the accumulation of conceptual mistakes can lead to a misleading theory. Finally, we show that Ai is a particular limited case of another complexity metric based on algorithmic (Kolmogorov) complexity, consisting of decomposing an object into its causal blocks that goes beyond, and outperforms, AT.

cs.IT↗

arXiv2025

Minimal Algorithmic Information Loss Methods for Dimension Reduction, Feature Selection and Network Sparsification

We present a novel, domain-agnostic, model-independent, unsupervised, and universally applicable Machine Learning approach for dimensionality reduction based on the principles of algorithmic complexity. Specifically, but without loss of generality, we focus on addressing the challenge of reducing certain dimensionality aspects, such as the number of edges in a network, while retaining essential features of interest. These features include preserving crucial network properties like degree distribution, clustering coefficient, edge betweenness, and degree and eigenvector centralities but can also go beyond edges to nodes and weights for network pruning and trimming. Our approach outperforms classical statistical Machine Learning techniques and state-of-the-art dimensionality reduction algorithms by preserving a greater number of data features that statistical algorithms would miss, particularly nonlinear patterns stemming from deterministic recursive processes that may look statistically random but are not. Moreover, previous approaches heavily rely on a priori feature selection, which requires constant supervision. Our findings demonstrate the effectiveness of the algorithms in overcoming some of these limitations while maintaining a time-efficient computational profile. Our approach not only matches, but also exceeds, the performance of established and state-of-the-art dimensionality reduction algorithms. We extend the applicability of our method to lossy compression tasks involving images and any multi-dimensional data. This highlights the versatility and broad utility of the approach in multiple domains.

cs.DS↗

arXiv2024

On the Salient Limitations of the Methods of Assembly Theory and their Classification of Molecular Biosignatures

We demonstrate that the assembly pathway method underlying assembly theory (AT) is an encoding scheme widely used by popular statistical compression algorithms. We show that in all cases (synthetic or natural) AT performs similarly to other simple coding schemes and underperforms compared to system-related indexes based upon algorithmic probability that take into account statistical repetitions but also the likelihood of other computable patterns. Our results imply that the assembly index does not offer substantial improvements over existing methods, including traditional statistical ones, and imply that the separation between living and non-living compounds following these methods has been reported before.

cs.IT↗

arXiv2024

Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution

We prove the full equivalence between Assembly Theory (AT) and Shannon Entropy via a method based upon the principles of statistical compression renamed `assembly index' that belongs to the LZ family of popular compression algorithms (ZIP, GZIP, JPEG). Such popular algorithms have been shown to empirically reproduce the results of AT, results that have also been reported before in successful applications to separating organic from non-organic molecules and in the context of the study of selection and evolution. We show that the assembly index value is equivalent to the size of a minimal context-free grammar. The statistical compressibility of such a method is bounded by Shannon Entropy and other equivalent traditional LZ compression schemes, such as LZ77, LZ78, or LZW. In addition, we demonstrate that AT, and the algorithms supporting its pathway complexity, assembly index, and assembly number, define compression schemes and methods that are subsumed into the theory of algorithmic (Kolmogorov-Solomonoff-Chaitin) complexity. Due to AT's current lack of logical consistency in defining causality for non-stochastic processes and the lack of empirical evidence that it outperforms other complexity measures found in the literature capable of explaining the same phenomena, we conclude that the assembly index and the assembly number do not lead to an explanation or quantification of biases in generative (physical or biological) processes, including those brought about by (abiotic or Darwinian) selection and evolution, that could not have been arrived at using Shannon Entropy or that have not been reported before using classical information theory or algorithmic complexity.

cs.IT↗

arXiv2023

Whispering LLaMA: A Cross-Modal Generative Error Correction Framework for Speech Recognition

We introduce a new cross-modal fusion technique designed for generative error correction in automatic speech recognition (ASR). Our methodology leverages both acoustic information and external linguistic representations to generate accurate speech transcription contexts. This marks a step towards a fresh paradigm in generative error correction within the realm of n-best hypotheses. Unlike the existing ranking-based rescoring methods, our approach adeptly uses distinct initialization techniques and parameter-efficient algorithms to boost ASR performance derived from pre-trained speech and text models. Through evaluation across diverse ASR datasets, we evaluate the stability and reproducibility of our fusion technique, demonstrating its improved word error rate relative (WERR) performance in comparison to n-best hypotheses by relatively 37.66%. To encourage future research, we have made our code and pre-trained models open source at https://github.com/Srijith-rkr/Whispering-LLaMA.

cs.CL↗

arXiv2023

A Parameter-Efficient Learning Approach to Arabic Dialect Identification with Pre-Trained General-Purpose Speech Model

In this work, we explore Parameter-Efficient-Learning (PEL) techniques to repurpose a General-Purpose-Speech (GSM) model for Arabic dialect identification (ADI). Specifically, we investigate different setups to incorporate trainable features into a multi-layer encoder-decoder GSM formulation under frozen pre-trained settings. Our architecture includes residual adapter and model reprogramming (input-prompting). We design a token-level label mapping to condition the GSM for Arabic Dialect Identification (ADI). This is challenging due to the high variation in vocabulary and pronunciation among the numerous regional dialects. We achieve new state-of-the-art accuracy on the ADI-17 dataset by vanilla fine-tuning. We further reduce the training budgets with the PEL method, which performs within 1.86% accuracy to fine-tuning using only 2.5% of (extra) network trainable parameters. Our study demonstrates how to identify Arabic dialects using a small dataset and limited computation with open source code and pre-trained models.

cs.CL↗

arXiv2023

IHCV: Discovery of Hidden Time-Dependent Control Variables in Non-Linear Dynamical Systems

Discovering non-linear dynamical models from data is at the core of science. Recent progress hinges upon sparse regression of observables using extensive libraries of candidate functions. However, it remains challenging to model hidden non-observable control variables governing switching between different dynamical regimes. Here we develop a data-efficient derivative-free method, IHCV, for the Identification of Hidden Control Variables. First, the performance and robustness of IHCV against noise are evaluated by benchmarking the IHCV method using well-known bifurcation models (saddle-node, transcritical, pitchfork, Hopf). Next, we demonstrate that IHCV discovers hidden driver variables in the Lorenz, van der Pol, Hodgkin-Huxley, and Fitzhugh-Nagumo models. Finally, IHCV generalizes to the case when only partial observational is given, as demonstrated using the toggle switch model, the genetic repressilator oscillator, and a Waddington landscape model. Our proof-of-principle illustrates that utilizing normal forms could facilitate the data-efficient and scalable discovery of hidden variables controlling transitions between different dynamical regimes and non-linear models.

q-bio.QM↗

arXiv2020

Evolving Neural Networks through a Reverse Encoding Tree

NeuroEvolution is one of the most competitive evolutionary learning frameworks for designing novel neural networks for use in specific tasks, such as logic circuit design and digital gaming. However, the application of benchmark methods such as the NeuroEvolution of Augmenting Topologies (NEAT) remains a challenge, in terms of their computational cost and search time inefficiency. This paper advances a method which incorporates a type of topological edge coding, named Reverse Encoding Tree (RET), for evolving scalable neural networks efficiently. Using RET, two types of approaches -- NEAT with Binary search encoding (Bi-NEAT) and NEAT with Golden-Section search encoding (GS-NEAT) -- have been designed to solve problems in benchmark continuous learning environments such as logic gates, Cartpole, and Lunar Lander, and tested against classical NEAT and FS-NEAT as baselines. Additionally, we conduct a robustness test to evaluate the resilience of the proposed NEAT algorithms. The results show that the two proposed strategies deliver improved performance, characterized by (1) a higher accumulated reward within a finite number of time steps; (2) using fewer episodes to solve problems in targeted environments, and (3) maintaining adaptive robustness under noisy perturbations, which outperform the baselines in all tested cases. Our analysis also demonstrates that RET expends potential future research directions in dynamic environments. Code is available from https://github.com/HaolingZHANG/ReverseEncodingTree.

cs.NE↗

arXiv2019

Algorithmic Probability-guided Supervised Machine Learning on Non-differentiable Spaces

We show how complexity theory can be introduced in machine learning to help bring together apparently disparate areas of current research. We show that this new approach requires less training data and is more generalizable as it shows greater resilience to random attacks. We investigate the shape of the discrete algorithmic space when performing regression or classification using a loss function parametrized by algorithmic complexity, demonstrating that the property of differentiation is not necessary to achieve results similar to those obtained using differentiable programming approaches such as deep learning. In doing so we use examples which enable the two approaches to be compared (small, given the computational power required for estimations of algorithmic complexity). We find and report that (i) machine learning can successfully be performed on a non-smooth surface using algorithmic complexity; (ii) that parameter solutions can be found using an algorithmic-probability classifier, establishing a bridge between a fundamentally discrete theory of computability and a fundamentally continuous mathematical theory of optimization methods; (iii) a formulation of an algorithmically directed search technique in non-smooth manifolds can be defined and conducted; (iv) exploitation techniques and numerical methods for algorithmic search to navigate these discrete non-differentiable spaces can be performed; in application of the (a) identification of generative rules from data observations; (b) solutions to image classification problems more resilient against pixel attacks compared to neural networks; (c) identification of equation parameters from a small data-set in the presence of noise in continuous ODE system problem, (d) classification of Boolean NK networks by (1) network topology, (2) underlying Boolean function, and (3) number of incoming edges.

cs.LG↗

arXiv2019

Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying

The concept of information has emerged as a language in its own right, bridging several disciplines that analyze natural phenomena and man-made systems. Integrated information has been introduced as a metric to quantify the amount of information generated by a system beyond the information generated by its elements. Yet, this intriguing notion comes with the price of being prohibitively expensive to calculate, since the calculations require an exponential number of sub-divisions of a system. Here we introduce a novel framework to connect algorithmic randomness and integrated information and a numerical method for estimating integrated information using a perturbation test rooted in algorithmic information dynamics. This method quantifies the change in program size of a system when subjected to a perturbation. The intuition behind is that if an object is random then random perturbations have little to no effect to what happens when a shorter program but when an object has the ability to move in both directions (towards or away from randomness) it will be shown to be better integrated as a measure of sophistication telling apart randomness and simplicity from structure. We show that an object with a high integrated information value is also more compressible, and is, therefore, more sensitive to perturbations. We find that such a perturbation test quantifying compression sensitivity provides a system with a means to extract explanations--causal accounts--of its own behaviour. Our technique can reduce the number of calculations to arrive at some bounds or estimations, as the algorithmic perturbation test guides an efficient search for estimating integrated information. Our work sets the stage for a systematic exploration of connections between algorithmic complexity and integrated information at the level of both theory and practice.

q-bio.NC↗

arXiv2019

The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

The principle of maximum entropy (Maxent) is often used to obtain prior probability distributions as a method to obtain a Gibbs measure under some restriction giving the probability that a system will be in a certain state compared to the rest of the elements in the distribution. Because classical entropy-based Maxent collapses cases confounding all distinct degrees of randomness and pseudo-randomness, here we take into consideration the generative mechanism of the systems considered in the ensemble to separate objects that may comply with the principle under some restriction and whose entropy is maximal but may be generated recursively from those that are actually algorithmically random offering a refinement to classical Maxent. We take advantage of a causal algorithmic calculus to derive a thermodynamic-like result based on how difficult it is to reprogram a computer code. Using the distinction between computable and algorithmic randomness we quantify the cost in information loss associated with reprogramming. To illustrate this we apply the algorithmic refinement to Maxent on graphs and introduce a Maximal Algorithmic Randomness Preferential Attachment (MARPA) Algorithm, a generalisation over previous approaches. We discuss practical implications of evaluation of network randomness. Our analysis provides insight in that the reprogrammability asymmetry appears to originate from a non-monotonic relationship to algorithmic probability. Our analysis motivates further analysis of the origin and consequences of the aforementioned asymmetries, reprogrammability, and computation.

cs.IT↗

arXiv2018

Algorithmic Causal Deconvolution of Intertwined Programs and Networks by Generative Mechanism

Complex data usually results from the interaction of objects produced by different generating mechanisms. Here we introduce a universal, unsupervised and parameter-free model-oriented approach, based upon the seminal concept of algorithmic probability, that decomposes an observation into its most likely algorithmic generative sources. Our approach uses a causal calculus to infer model representations. We demonstrate its ability to deconvolve interacting mechanisms regardless of whether the resultant objects are strings, space-time evolution diagrams, images or networks. While this is mostly a conceptual contribution and a novel framework, we provide numerical evidence evaluating the ability of our methods to separate data from observations produced by discrete dynamical systems such as cellular automata and complex networks. We think that these separating techniques can contribute to tackling the challenge of causation, thus complementing other statistically oriented approaches.

cs.AI↗

arXiv2018

Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, and modularity

Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations. Here we investigate the application of a simplicity bias based on a natural but algorithmic distribution of mutations (no recombination) in various examples, particularly binary matrices in order to compare evolutionary convergence rates. Results both on synthetic and on small biological examples indicate an accelerated rate when mutations are not statistical uniform but \textit{algorithmic uniform}. We show that algorithmic distributions can evolve modularity and genetic memory by preservation of structures when they first occur sometimes leading to an accelerated production of diversity but also population extinctions, possibly explaining naturally occurring phenomena such as diversity explosions (e.g. the Cambrian) and massive extinctions (e.g. the End Triassic) whose causes are currently a cause for debate. The natural approach introduced here appears to be a better approximation to biological evolution than models based exclusively upon random uniform mutations, and it also approaches a formal version of open-ended evolution based on previous formal results. These results validate some suggestions in the direction that computation may be an equally important driver of evolution. We also show that inducing the method on problems of optimization, such as genetic algorithms, has the potential to accelerate convergence of artificial evolutionary algorithms.

cs.NE↗

arXiv2018

A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

We investigate the properties of a Block Decomposition Method (BDM), which extends the power of a Coding Theorem Method (CTM) that approximates local estimations of algorithmic complexity based upon Solomonoff-Levin's theory of algorithmic probability providing a closer connection to algorithmic complexity than previous attempts based on statistical regularities e.g. as spotted by some popular lossless compression schemes. The strategy behind BDM is to find small computer programs that produce the components of a larger, decomposed object. The set of short computer programs can then be artfully arranged in sequence so as to produce the original object and to estimate an upper bound on the length of the shortest computer program that produces said original object. We show that the method provides efficient estimations of algorithmic complexity but that it performs like Shannon entropy when it loses accuracy. We estimate errors and study the behaviour of BDM for different boundary conditions, all of which are compared and assessed in detail. The measure may be adapted for use with more multi-dimensional objects than strings, objects such as arrays and tensors. To test the measure we demonstrate the power of CTM on low algorithmic-randomness objects that are assigned maximal entropy (e.g. $π$) but whose numerical approximations are closer to the theoretical low algorithmic-randomness expectation. We also test the measure on larger objects including dual, isomorphic and cospectral graphs for which we know that algorithmic randomness is low. We also release implementations of the methods in most major programming languages---Wolfram Language (Mathematica), Matlab, R, Perl, Python, Pascal, C++, and Haskell---and a free online algorithmic complexity calculator.

cs.IT↗

arXiv2018

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To this end we performed experiments and validated the results on (1) a very large set of small graphs, (2) a number of larger networks with different topologies, and (3) biological networks from a widely studied and validated genetic network (e.coli) as well as on a significant number of differentiating (Th17) and differentiated human cells from high quality databases (Harvard's CellNet) with results conforming to experimentally validated biological data. Based on these results we introduce a conceptual framework, a model-based interventional calculus and a reprogrammability measure with which to steer, manipulate, and reconstruct the dynamics of non- linear dynamical systems from partial and disordered observations. The method consists in finding and applying a series of controlled interventions to a dynamical system to estimate how its algorithmic information content is affected when every one of its elements are perturbed. The approach represents an alternative to numerical simulation and statistical approaches for inferring causal mechanistic/generative models and finding first principles. We demonstrate the framework's capabilities by reconstructing the phase space of some discrete dynamical systems (cellular automata) as case study and reconstructing their generating rules. We thus advance tools for reprogramming artificial and living systems without full knowledge or access to the system's actual kinetic equations or probability distributions yielding a suite of universal and parameter-free algorithms of wide applicability ranging from causation, dimension reduction, feature selection and model generation.

q-bio.OT↗

arXiv2018

Algorithmic Information Dynamics of Persistent Patterns and Colliding Particles in the Game of Life

Without loss of generalisation to other systems, including possibly non-deterministic ones, we demonstrate the application of methods drawn from algorithmic information dynamics to the characterisation and classification of emergent and persistent patterns, motifs and colliding particles in Conway's Game of Life (GoL), a cellular automaton serving as a case study illustrating the way in which such ideas can be applied to a typical discrete dynamical system. We explore the issue of local observations of closed systems whose orbits may appear open because of inaccessibility to the global rules governing the overall system. We also investigate aspects of symmetry related to complexity in the distribution of patterns that occur with high frequency in GoL (which we thus call motifs) and analyse the distribution of these motifs with a view to tracking the changes in their algorithmic probability over time. We demonstrate how the tools introduced are an alternative to other computable measures that are unable to capture changes in emergent structures in evolving complex systems that are often too small or too subtle to be properly characterised by methods such as lossless compression and Shannon entropy.

nlin.CG↗

arXiv2018

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

q-bio.MN↗