arXiv subjects

Hector Zenil

Publications and source records attributed to Hector Zenil.

At least 37 records · Page 2Linked to original sources

arXiv2025

Complexity-Informed Causal Modeling of Neurodevelopmental Trajectories in Pediatric High-Grade Gliomas: Divergences from Neural Stem Cell Signatures

Pediatric high grade gliomas are lethal evolutionary disorders with stalled developmental trajectories and disrupted differentiation hierarchies. We integrate transcriptional and algorithmic network complexity based perturbation analysis to elucidate gene expression patterns and molecular divergence between Diffuse Midline Gliomas and glioblastoma, revealing shared developmental programs steering cell fate decision making. Our complex systems approach supports the emerging paradigm that pediatric high grade gliomas are neurodevelopmental disorders with hybrid lineage identities and disrupted patterning. We identify dysregulated neurodevelopmental and morphogenetic signatures, alongside bioelectric and neurotransmitter signaling programs that alter synaptic organization, neuronal fate commitment, and phenotypic plasticity, regulating glioma phenotypic switching. Causal drivers and regulators of plasticity were predicted as both biomarkers and therapeutic targets, reinforcing the view that pediatric gliomas are disorders of cell fate decisions and collective cellular identity. Decoded plasticity signatures indicate a teleonomic bias toward neural progenitor or neuron like identities, while synaptic transmission gene enrichment supports neuron glioma interactions shaping fate trajectories. These findings advance differentiation therapy as a systems medicine strategy, discovering plasticity regulators to reprogram malignant fates toward stable lineages, offering complex systems based targets for cancer reversion and predictive, preventive, precision oncology.

q-bio.QM↗

arXiv2025

Binarized Neural Networks Converge Toward Algorithmic Simplicity: Empirical Support for the Learning-as-Compression Hypothesis

Understanding and controlling the informational complexity of neural networks is a central challenge in machine learning, with implications for generalization, optimization, and model capacity. While most approaches rely on entropy-based loss functions and statistical metrics, these measures often fail to capture deeper, causally relevant algorithmic regularities embedded in network structure. We propose a shift toward algorithmic information theory, using Binarized Neural Networks (BNNs) as a first proxy. Grounded in algorithmic probability (AP) and the universal distribution it defines, our approach characterizes learning dynamics through a formal, causally grounded lens. We apply the Block Decomposition Method (BDM) -- a scalable approximation of algorithmic complexity based on AP -- and demonstrate that it more closely tracks structural changes during training than entropy, consistently exhibiting stronger correlations with training loss across varying model sizes and randomized training runs. These results support the view of training as a process of algorithmic compression, where learning corresponds to the progressive internalization of structured regularities. In doing so, our work offers a principled estimate of learning progression and suggests a framework for complexity-aware learning and regularization, grounded in first principles from information theory, complexity, and computability.

cs.LG↗

arXiv2025

Neurosymbolic Learning for Predicting Cell Fate Decisions from Longitudinal Single Cell Transcriptomics in Paediatric Acute Myeloid Leukemia

Paediatric Acute Myeloid Leukemia is a complex adaptive ecosystem with high morbidity. Current trajectory inference algorithms struggle to predict causal dynamics in AML progression, including relapse and recurrence risk. We propose a symbolic AI and deep learning framework grounded in complexity science, integrating Recurrent Neural Networks, Transformers, and Algorithmic Information Dynamics to model longitudinal single cell transcriptomics and infer complex state transitions in paediatric AML. We identify key plasticity markers as predictive signatures regulating developmental trajectories. These were derived by integrating deep learning with complex systems based network perturbation analysis and dynamical systems theory to infer high dimensional state space attractors steering AML evolution. Findings reveal dysregulated epigenetic and developmental patterning, with AML cells in maladaptive, reprogrammable plastic states, i.e., developmental arrest blocking terminal differentiation. Predictions forecast neurodevelopmental and morphogenetic signatures guiding AML cell fate bifurcations, suggesting ectoderm mesoderm crosstalk during disrupted differentiation. Neuroplasticity and neurotransmission related transcriptional signals implicate a brain immune hematopoietic axis in AML cell fate cybernetics. This is the first study combining RNNs and AID to predict and decipher longitudinal patterns of cell fate transition trajectories in AML. Our complex systems approach enables causal discovery of predictive biomarkers and therapeutic targets for ecosystem engineering, cancer reversion, precision gene editing, and differentiation therapy, with strong translational potential for precision oncology and patient centered care.

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arXiv2025

Neurodivergent Influenceability as a Contingent Solution to the AI Alignment Problem

The AI alignment problem, which focusses on ensuring that artificial intelligence (AI), including AGI and ASI, systems act according to human values, presents profound challenges. With the progression from narrow AI to Artificial General Intelligence (AGI) and Superintelligence, fears about control and existential risk have escalated. Here, we investigate whether embracing inevitable AI misalignment can be a contingent strategy to foster a dynamic ecosystem of competing agents as a viable path to steer them in more human-aligned trends and mitigate risks. We explore how misalignment may serve and should be promoted as a counterbalancing mechanism to team up with whichever agents are most aligned to human interests, ensuring that no single system dominates destructively. The main premise of our contribution is that misalignment is inevitable because full AI-human alignment is a mathematical impossibility from Turing-complete systems, which we also offer as a proof in this contribution, a feature then inherited to AGI and ASI systems. We introduce a change-of-opinion attack test based on perturbation and intervention analysis to study how humans and agents may change or neutralise friendly and unfriendly AIs through cooperation and competition. We show that open models are more diverse and that most likely guardrails implemented in proprietary models are successful at controlling some of the agents' range of behaviour with positive and negative consequences while closed systems are more steerable and can also be used against proprietary AI systems. We also show that human and AI intervention has different effects hence suggesting multiple strategies.

cs.AI↗

arXiv2025

Advancing the Scientific Method with Large Language Models: From Hypothesis to Discovery

With recent Nobel Prizes recognising AI contributions to science, Large Language Models (LLMs) are transforming scientific research by enhancing productivity and reshaping the scientific method. LLMs are now involved in experimental design, data analysis, and workflows, particularly in chemistry and biology. However, challenges such as hallucinations and reliability persist. In this contribution, we review how Large Language Models (LLMs) are redefining the scientific method and explore their potential applications across different stages of the scientific cycle, from hypothesis testing to discovery. We conclude that, for LLMs to serve as relevant and effective creative engines and productivity enhancers, their deep integration into all steps of the scientific process should be pursued in collaboration and alignment with human scientific goals, with clear evaluation metrics. The transition to AI-driven science raises ethical questions about creativity, oversight, and responsibility. With careful guidance, LLMs could evolve into creative engines, driving transformative breakthroughs across scientific disciplines responsibly and effectively. However, the scientific community must also decide how much it leaves to LLMs to drive science, even when associations with 'reasoning', mostly currently undeserved, are made in exchange for the potential to explore hypothesis and solution regions that might otherwise remain unexplored by human exploration alone.

cs.AI↗

arXiv2025

Scientific Hypothesis Generation by a Large Language Model: Laboratory Validation in Breast Cancer Treatment

Large language models LLMs have transformed AI and achieved breakthrough performance on a wide range of tasks In science the most interesting application of LLMs is for hypothesis formation A feature of LLMs which results from their probabilistic structure is that the output text is not necessarily a valid inference from the training text These are termed hallucinations and are harmful in many applications In science some hallucinations may be useful novel hypotheses whose validity may be tested by laboratory experiments Here we experimentally test the application of LLMs as a source of scientific hypotheses using the domain of breast cancer treatment We applied the LLM GPT4 to hypothesize novel synergistic pairs of FDA-approved noncancer drugs that target the MCF7 breast cancer cell line relative to the nontumorigenic breast cell line MCF10A In the first round of laboratory experiments GPT4 succeeded in discovering three drug combinations out of twelve tested with synergy scores above the positive controls GPT4 then generated new combinations based on its initial results this generated three more combinations with positive synergy scores out of four tested We conclude that LLMs are a valuable source of scientific hypotheses.

q-bio.QM↗

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↗

arXiv2025

An Optimal, Universal and Agnostic Decoding Method for Message Reconstruction, Bio and Technosignature Detection

We present an agnostic signal reconstruction method for zero-knowledge one-way communication channels in which a receiver aims to interpret a message sent by an unknown source about which no prior knowledge is available and to which no return message can be sent. Our reconstruction method is agnostic vis-à-vis the arbitrarily chosen encoding-decoding scheme and other observer-dependent characteristics, such as the arbitrarily chosen computational model, probability distributions, or underlying mathematical theory. We investigate how non-random messages encode information about their intended physical properties, such as dimension and length scales of the space in which a signal or message may have been originally encoded, embedded, or generated. We focus on image data as a first illustration of the capabilities of the new method. We argue that our results have applications to life and technosignature detection, and to coding theory in general.

cs.IT↗

arXiv2024

Non-Random Data Encodes its Geometric and Topological Dimensions

Based on the principles of information theory, measure theory, and theoretical computer science, we introduce a signal deconvolution method with a wide range of applications to coding theory, particularly in zero-knowledge one-way communication channels, such as in deciphering messages (i.e., objects embedded into multidimensional spaces) from unknown generating sources about which no prior knowledge is available and to which no return message can be sent. Our multidimensional space reconstruction method from an arbitrary received signal is proven to be agnostic vis-à-vis the encoding-decoding scheme, computation model, programming language, formal theory, the computable (or semi-computable) method of approximation to algorithmic complexity, and any arbitrarily chosen (computable) probability measure. The method derives from the principles of an approach to Artificial General Intelligence (AGI) capable of building a general-purpose model of models independent of any arbitrarily assumed prior probability distribution. We argue that this optimal and universal method of decoding non-random data has applications to signal processing, causal deconvolution, topological and geometric properties encoding, cryptography, and bio- and technosignature detection.

cs.IT↗

arXiv2024

Leveraging Pre-Trained Neural Networks to Enhance Machine Learning with Variational Quantum Circuits

Quantum Machine Learning (QML) offers tremendous potential but is currently limited by the availability of qubits. We introduce an innovative approach that utilizes pre-trained neural networks to enhance Variational Quantum Circuits (VQC). This technique effectively separates approximation error from qubit count and removes the need for restrictive conditions, making QML more viable for real-world applications. Our method significantly improves parameter optimization for VQC while delivering notable gains in representation and generalization capabilities, as evidenced by rigorous theoretical analysis and extensive empirical testing on quantum dot classification tasks. Moreover, our results extend to applications such as human genome analysis, demonstrating the broad applicability of our approach. By addressing the constraints of current quantum hardware, our work paves the way for a new era of advanced QML applications, unlocking the full potential of quantum computing in fields such as machine learning, materials science, medicine, mimetics, and various interdisciplinary areas.

cs.LG↗

arXiv2024

On sequential structures in incompressible multidimensional networks

In order to deal with multidimensional structure representations of real-world networks, as well as with their worst-case irreducible information content analysis, the demand for new graph abstractions increases. This article investigates incompressible multidimensional networks defined by generalized graph representations. In particular, we mathematically study the lossless incompressibility of snapshot-dynamic networks and multiplex networks in comparison to the lossless incompressibility of more general forms of dynamic networks and multilayer networks, from which snapshot-dynamic networks or multiplex networks are particular cases. Our theoretical investigation first explores fundamental and basic conditions for connecting the sequential growth of information with sequential interdimensional structures such as time in dynamic networks, and secondly it presents open problems demanding future investigation. Although there may be a dissonance between sequential information dynamics and sequential topology in the general case, we demonstrate that incompressibility dissolves it, preventing both the algorithmic dynamics and the interdimensional structure of multidimensional networks from displaying a snapshot-like behavior (as characterized by any arbitrary mathematical theory). Thus, beyond methods based on statistics or probability as traditionally seen in random graphs and complex networks models, representational incompressibility implies a necessary underlying constraint in the multidimensional network topology. We argue that the study of how isomorphic transformations and their respective algorithmic information distortions can characterize sequential interdimensional structures in (multidimensional) networks helps the analysis of network topological properties while being agnostic to the chosen theory, algorithm, computation model, and programming language.

cs.IT↗

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↗

arXiv2024

Fractal spatio-temporal scale-free messaging: amplitude modulation of self-executable carriers given by the Weierstrass function's components

In many communication contexts, the capabilities of the involved actors cannot be known beforehand, whether it is a cell, a plant, an insect, or even a life form unknown to Earth. Regardless of the recipient, the message space and time scale could be too fast, too slow, too large, or too small and may never be decoded. Therefore, it pays to devise a way to encode messages agnostic of space and time scales. We propose the use of fractal functions as self-executable infinite-frequency carriers for sending messages, given their properties of structural self-similarity and scale invariance. We call it `fractal messaging'. Starting from a spatial embedding, we introduce a framework for a space-time scale-free messaging approach to this challenge. When considering a space and time-agnostic framework for message transmission, it would be interesting to encode a message such that it could be decoded at several spatio-temporal scales. Hence, the core idea of the framework proposed herein is to encode a binary message as waves along infinitely many frequencies (in power-like distributions) and amplitudes, transmit such a message, and then decode and reproduce it. To do so, the components of the Weierstrass function, a known fractal, are used as carriers of the message. Each component will have its amplitude modulated to embed the binary stream, allowing for a space-time-agnostic approach to messaging.

cs.IT↗

arXiv2023

The Future of Fundamental Science Led by Generative Closed-Loop Artificial Intelligence

Recent advances in machine learning and AI, including Generative AI and LLMs, are disrupting technological innovation, product development, and society as a whole. AI's contribution to technology can come from multiple approaches that require access to large training data sets and clear performance evaluation criteria, ranging from pattern recognition and classification to generative models. Yet, AI has contributed less to fundamental science in part because large data sets of high-quality data for scientific practice and model discovery are more difficult to access. Generative AI, in general, and Large Language Models in particular, may represent an opportunity to augment and accelerate the scientific discovery of fundamental deep science with quantitative models. Here we explore and investigate aspects of an AI-driven, automated, closed-loop approach to scientific discovery, including self-driven hypothesis generation and open-ended autonomous exploration of the hypothesis space. Integrating AI-driven automation into the practice of science would mitigate current problems, including the replication of findings, systematic production of data, and ultimately democratisation of the scientific process. Realising these possibilities requires a vision for augmented AI coupled with a diversity of AI approaches able to deal with fundamental aspects of causality analysis and model discovery while enabling unbiased search across the space of putative explanations. These advances hold the promise to unleash AI's potential for searching and discovering the fundamental structure of our world beyond what human scientists have been able to achieve. Such a vision would push the boundaries of new fundamental science rather than automatize current workflows and instead open doors for technological innovation to tackle some of the greatest challenges facing humanity today.

cs.AI↗

arXiv2023

A Simplicity Bubble Problem in Formal-Theoretic Learning Systems

When mining large datasets in order to predict new data, limitations of the principles behind statistical machine learning pose a serious challenge not only to the Big Data deluge, but also to the traditional assumptions that data generating processes are biased toward low algorithmic complexity. Even when one assumes an underlying algorithmic-informational bias toward simplicity in finite dataset generators, we show that current approaches to machine learning (including deep learning, or any formal-theoretic hybrid mix of top-down AI and statistical machine learning approaches), can always be deceived, naturally or artificially, by sufficiently large datasets. In particular, we demonstrate that, for every learning algorithm (with or without access to a formal theory), there is a sufficiently large dataset size above which the algorithmic probability of an unpredictable deceiver is an upper bound (up to a multiplicative constant that only depends on the learning algorithm) for the algorithmic probability of any other larger dataset. In other words, very large and complex datasets can deceive learning algorithms into a ``simplicity bubble'' as likely as any other particular non-deceiving dataset. These deceiving datasets guarantee that any prediction effected by the learning algorithm will unpredictably diverge from the high-algorithmic-complexity globally optimal solution while converging toward the low-algorithmic-complexity locally optimal solution, although the latter is deemed a global one by the learning algorithm. We discuss the framework and additional empirical conditions to be met in order to circumvent this deceptive phenomenon, moving away from statistical machine learning towards a stronger type of machine learning based on, and motivated by, the intrinsic power of algorithmic information theory and computability theory.

cs.IT↗

arXiv2023

Algorithmic information distortions and incompressibility in uniform multidimensional networks

This article presents a theoretical investigation of generalized encoded forms of networks in a uniform multidimensional space. First, we study encoded networks with (finite) arbitrary node dimensions (or aspects), such as time instants or layers. In particular, we study these networks that are formalized in the form of multiaspect graphs. In the context of node-aligned non-uniform (or node-unaligned non-uniform and uniform) multidimensional spaces, previous results has shown that, unlike classical graphs, the algorithmic information of a multidimensional network is not in general dominated by the algorithmic information of the binary sequence that determines the presence or absence of edges. In the present work, first we demonstrate the existence of such algorithmic information distortions for node-aligned uniform multidimensional networks. Secondly, we show that there are particular cases of infinite nesting families of finite uniform multidimensional networks such that each member of these families is incompressible. From these results, we also recover the network topological properties and equivalences in irreducible information content of multidimensional networks in comparison to their isomorphic classical graph counterpart in the previous literature. These results together establish a universal algorithmic approach and set limitations and conditions for irreducible information content analysis in comparing arbitrary networks with a large number of dimensions, such as multilayer networks.

cs.DM↗

arXiv2022

Approximations of Algorithmic and Structural Complexity Validate Cognitive-behavioural Experimental Results

Being able to objectively characterise the intrinsic complexity of behavioural patterns resulting from human or animal decisions is fundamental for deconvolving cognition and designing autonomous artificial intelligence systems. Yet complexity is difficult in practice, particularly when strings are short. By numerically approximating algorithmic (Kolmogorov) complexity (K), we establish an objective tool to characterise behavioural complexity. Next, we approximate structural (Bennett's Logical Depth) complexity (LD) to assess the amount of computation required for generating a behavioural string. We apply our toolbox to three landmark studies of animal behaviour of increasing sophistication and degree of environmental influence, including studies of foraging communication by ants, flight patterns of fruit flies, and tactical deception and competition (e.g., predator-prey) strategies. We find that ants harness the environmental condition in their internal decision process, modulating their behavioural complexity accordingly. Our analysis of flight (fruit flies) invalidated the common hypothesis that animals navigating in an environment devoid of stimuli adopt a random strategy. Fruit flies exposed to a featureless environment deviated the most from Levy flight, suggesting an algorithmic bias in their attempt to devise a useful (navigation) strategy. Similarly, a logical depth analysis of rats revealed that the structural complexity of the rat always ends up matching the structural complexity of the competitor, with the rats' behaviour simulating algorithmic randomness. Finally, we discuss how experiments on how humans perceive randomness suggest the existence of an algorithmic bias in our reasoning and decision processes, in line with our analysis of the animal experiments.

q-bio.QM↗