arXiv subjects

Sergi Valverde

Publications and source records attributed to Sergi Valverde.

At least 19 recordsLinked to original sources

arXiv2026

Human--LLM Collaboration Is Transforming Complexity Metrics in Scientific Texts

While human language has long been studied as a complex system, Large Language Models (LLMs) are rapidly becoming contributors to its dynamics. Because LLMs are trained on human language use, their effects on the broader human-AI linguistic ecosystem are likely subtle at first. As their use becomes more widespread, however, LLMs may alter emergent properties of language, particularly as models increasingly train on mixed human-LLM textual data. Here, we draw on complexity science to look for subtle LLM effects in millions of arXiv abstracts from 2010 to 2025. The year 2023, when LLMs rapidly became widely used, serves as a landmark in a natural experiment. While we find a sharp increase in a composite LLM-associated style index after early 2023, we observe only subtle changes in the exponents of Zipf's law and Heaps' law. More compelling, however, are two subtle changes in complexity metrics that emerge from 2023 onward. First, turnover among top-ranked words increases sharply. Second, the positive relationship between the LLM-associated style index and three complexity metrics--vocabulary size and the exponents of Heaps' and Zipf's laws--becomes flatter after 2022. Together, these patterns are consistent with changes in the emergent properties of scientific text in a mixed human-AI linguistic ecosystem.

cs.CY↗

arXiv2025

The Evolutionary Ecology of Software: Constraints, Innovation, and the AI Disruption

This chapter investigates the evolutionary ecology of software, focusing on the symbiotic relationship between software and innovation. An interplay between constraints, tinkering, and frequency-dependent selection drives the complex evolutionary trajectories of these socio-technological systems. Our approach integrates agent-based modeling and case studies, drawing on complex network analysis and evolutionary theory to explore how software evolves under the competing forces of novelty generation and imitation. By examining the evolution of programming languages and their impact on developer practices, we illustrate how technological artifacts co-evolve with and shape societal norms, cultural dynamics, and human interactions. This ecological perspective also informs our analysis of the emerging role of AI-driven development tools in software evolution. While large language models (LLMs) provide unprecedented access to information, their widespread adoption introduces new evolutionary pressures that may contribute to cultural stagnation, much like the decline of diversity in past software ecosystems. Understanding the evolutionary pressures introduced by AI-mediated software production is critical for anticipating broader patterns of cultural change, technological adaptation, and the future of software innovation.

cs.SE↗

arXiv2024

Networks: The Visual Language of Complexity

Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to represent inter-dependencies among many system components, facilitating the study of both local and global properties. However, it is unclear whether we can define a universal theoretical framework for evolving networks. While basic growth mechanisms, like preferential attachment, recapitulate common properties such as the power-law degree distribution, they fall short in capturing other system-specific properties. Tinkering, on the other hand, has shown to be very successful in generating modular or nested structures "for-free", highlighting the role of internal, non-adaptive mechanisms in the evolution of complexity. Different network extensions, like hypergraphs, have been recently developed to integrate exogenous factors in evolutionary models, as pairwise interactions are insufficient to capture environmentally-mediated species associations. As we confront global societal and climatic challenges, the study of network and hypergraphs provides valuable insights, emphasizing the importance of scientific exploration in understanding and managing complexity.

cond-mat.dis-nn↗

arXiv2023

Is disruption decreasing, or is it accelerating?

A recent highly-publicized study by Park et al. (Nature 613: 138-144, 2023), claiming that science has become less disruptive over recent decades, represents an extraordinary achievement but with deceptive results. The measure of disruption, CD-5, in this study does not account for differences in citation amid decades of exponential growth in publication rate. In order to account for both the exponential growth as well as the differential impact of research works over time, here we apply a weighted disruption index to the same dataset. We find that, among research papers in the dataset, this weighted disruption index has been close to its expected neutral value over the last fifty years and has even increased modestly since 2000. We also show how the proportional decrease in unique words (highlighted by Park et al. (2023) is expected in an exponentially growing corpus. Finding little evidence for recent decrease in disruption, we suggest that it is actually increasing.

cs.DL↗

arXiv2021

QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at: https://github.com/RagMeh11/QU-BraTS.

eess.IV↗

arXiv2019

Evolving complexity: how tinkering shapes cells, software and ecological networks

A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not reducible to the properties of the individual parts. Can the topological organisation of these webs provide some insight into their evolutionary origins? Both biological and artificial networks share some common architectural traits. They are often heterogeneous and sparse, and most exhibit the small-world property or the presence of modular or hierarchical patterns. These properties have often been attributed to the selection of functionally meaningful traits. However, the proper formulation of generative network models suggests a rather different picture. Against the standard selection-optimisation argument, some networks reveal the inevitable generation of complex patterns resulting from reuse and can be modelled using duplication-rewiring rules. These give rise to the heterogeneous, scale-free and modular architectures observed in the real case studies. Tinkering is a universal mechanism that drives not only biological evolution but also the large-scale dynamics of some technological designs. Here we examine the evidence for tinkering in cellular, technological and ecological webs and its impact in shaping their architecture and deeply affecting their functional properties. Our analysis suggests to seriously reconsider the role played by selection forces or design principles as main drivers of network evolution.

q-bio.PE↗

arXiv2019

Acute and sub-acute stroke lesion segmentation from multimodal MRI

Acute stroke lesion segmentation tasks are of great clinical interest as they can help doctors make better informed treatment decisions. Magnetic resonance imaging (MRI) is time demanding but can provide images that are considered gold standard for diagnosis. Automated stroke lesion segmentation can provide with an estimate of the location and volume of the lesioned tissue, which can help in the clinical practice to better assess and evaluate the risks of each treatment. We propose a deep learning methodology for acute and sub-acute stroke lesion segmentation using multimodal MR imaging. The proposed method is evaluated using two public datasets from the 2015 Ischemic Stroke Lesion Segmentation challenge (ISLES 2015). These involve the tasks of sub-acute stroke lesion segmentation (SISS) and acute stroke penumbra estimation (SPES) from diffusion, perfusion and anatomical MRI modalities. The performance is compared against state-of-the-art methods with a blind online testing set evaluation on each of the challenges. At the time of submitting this manuscript, our approach is the first method in the online rankings for the SISS (DSC=0.59$\pm$0.31) and SPES sub-tasks (DSC=0.84$\pm$0.10). When compared with the rest of submitted strategies, we achieve top rank performance with a lower Hausdorff distance. Better segmentation results are obtained by leveraging the anatomy and pathophysiology of acute stroke lesions and using a combined approach to minimize the effects of class imbalance. The same training procedure is used for both tasks, showing the proposed methodology can generalize well enough to deal with different unrelated tasks and imaging modalities without training hyper-parameter tuning. A public version of the proposed method has been released to the scientific community at https://github.com/NIC-VICOROB/stroke-mri-segmentation.

cs.CV↗

arXiv2019

Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. Automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their method on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge (https://wmh.isi.uu.nl/). Sixty T1+FLAIR images from three MR scanners were released with manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. Segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: (1) Dice similarity coefficient, (2) modified Hausdorff distance (95th percentile), (3) absolute log-transformed volume difference, (4) sensitivity for detecting individual lesions, and (5) F1-score for individual lesions. Additionally, methods were ranked on their inter-scanner robustness. Twenty participants submitted their method for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation.

cs.CV↗

arXiv2019

Multiple Sclerosis Lesion Synthesis in MRI using an encoder-decoder U-NET

In this paper, we propose generating synthetic multiple sclerosis (MS) lesions on MRI images with the final aim to improve the performance of supervised machine learning algorithms, therefore avoiding the problem of the lack of available ground truth. We propose a two-input two-output fully convolutional neural network model for MS lesion synthesis in MRI images. The lesion information is encoded as discrete binary intensity level masks passed to the model and stacked with the input images. The model is trained end-to-end without the need for manually annotating the lesions in the training set. We then perform the generation of synthetic lesions on healthy images via registration of patient images, which are subsequently used for data augmentation to increase the performance for supervised MS lesion detection algorithms. Our pipeline is evaluated on MS patient data from an in-house clinical dataset and the public ISBI2015 challenge dataset. The evaluation is based on measuring the similarities between the real and the synthetic images as well as in terms of lesion detection performance by segmenting both the original and synthetic images individually using a state-of-the-art segmentation framework. We also demonstrate the usage of synthetic MS lesions generated on healthy images as data augmentation. We analyze a scenario of limited training data (one-image training) to demonstrate the effect of the data augmentation on both datasets. Our results significantly show the effectiveness of the usage of synthetic MS lesion images. For the ISBI2015 challenge, our one-image model trained using only a single image plus the synthetic data augmentation strategy showed a performance similar to that of other CNN methods that were fully trained using the entire training set, yielding a comparable human expert rater performance

cs.CV↗

arXiv2018

Survival prediction using ensemble tumor segmentation and transfer learning

Segmenting tumors and their subregions is a challenging task as demonstrated by the annual BraTS challenge. Moreover, predicting the survival of the patient using mainly imaging features, while being a desirable outcome to evaluate the treatment of the patient, it is also a difficult task. In this paper, we present a cascaded pipeline to segment the tumor and its subregions and then we use these results and other clinical features together with image features coming from a pretrained VGG-16 network to predict the survival of the patient. Preliminary results with the training and validation dataset show a promising start in terms of segmentation, while the prediction values could be improved with further testing on the feature extraction part of the network.

q-bio.QM↗

arXiv2018

Chromatic transitions in the emergence of syntax networks

The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from a scale-free graphs associated to the adult, complex grammar. Here we explore the evolution of syntax networks through language acquisition using the {\em chromatic number}, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display nontrivial and sensible differences. In a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.

q-bio.NC↗

arXiv2018

Deep convolutional neural networks for brain image analysis on magnetic resonance imaging: a review

In recent years, deep convolutional neural networks (CNNs) have shown record-shattering performance in a variety of computer vision problems, such as visual object recognition, detection and segmentation. These methods have also been utilised in medical image analysis domain for lesion segmentation, anatomical segmentation and classification. We present an extensive literature review of CNN techniques applied in brain magnetic resonance imaging (MRI) analysis, focusing on the architectures, pre-processing, data-preparation and post-processing strategies available in these works. The aim of this study is three-fold. Our primary goal is to report how different CNN architectures have evolved, discuss state-of-the-art strategies, condense their results obtained using public datasets and examine their pros and cons. Second, this paper is intended to be a detailed reference of the research activity in deep CNN for brain MRI analysis. Finally, we present a perspective on the future of CNNs in which we hint some of the research directions in subsequent years.

cs.CV↗

arXiv2018

One-shot domain adaptation in multiple sclerosis lesion segmentation using convolutional neural networks

In recent years, several convolutional neural network (CNN) methods have been proposed for the automated white matter lesion segmentation of multiple sclerosis (MS) patient images, due to their superior performance compared with those of other state-of-the-art methods. However, the accuracies of CNN methods tend to decrease significantly when evaluated on different image domains compared with those used for training, which demonstrates the lack of adaptability of CNNs to unseen imaging data. In this study, we analyzed the effect of intensity domain adaptation on our recently proposed CNN-based MS lesion segmentation method. Given a source model trained on two public MS datasets, we investigated the transferability of the CNN model when applied to other MRI scanners and protocols, evaluating the minimum number of annotated images needed from the new domain and the minimum number of layers needed to re-train to obtain comparable accuracy. Our analysis comprised MS patient data from both a clinical center and the public ISBI2015 challenge database, which permitted us to compare the domain adaptation capability of our model to that of other state-of-the-art methods. For the ISBI2015 challenge, our one-shot domain adaptation model trained using only a single image showed a performance similar to that of other CNN methods that were fully trained using the entire available training set, yielding a comparable human expert rater performance. We believe that our experiments will encourage the MS community to incorporate its use in different clinical settings with reduced amounts of annotated data. This approach could be meaningful not only in terms of the accuracy in delineating MS lesions but also in the related reductions in time and economic costs derived from manual lesion labeling.

cs.CV↗

arXiv2018

Quantitative analysis of patch-based fully convolutional neural networks for tissue segmentation on brain magnetic resonance imaging

Accurate brain tissue segmentation in Magnetic Resonance Imaging (MRI) has attracted the attention of medical doctors and researchers since variations in tissue volume help in diagnosing and monitoring neurological diseases. Several proposals have been designed throughout the years comprising conventional machine learning strategies as well as convolutional neural networks (CNN) approaches. In particular, in this paper, we analyse a sub-group of deep learning methods producing dense predictions. This branch, referred in the literature as Fully CNN (FCNN), is of interest as these architectures can process an input volume in less time than CNNs and local spatial dependencies may be encoded since several voxels are classified at once. Our study focuses on understanding architectural strengths and weaknesses of literature-like approaches. Hence, we implement eight FCNN architectures inspired by robust state-of-the-art methods on brain segmentation related tasks. We evaluate them using the IBSR18, MICCAI2012 and iSeg2017 datasets as they contain infant and adult data and exhibit varied voxel spacing, image quality, number of scans and available imaging modalities. The discussion is driven in three directions: comparison between 2D and 3D approaches, the importance of multiple modalities and overlapping as a sampling strategy for training and testing models. To encourage other researchers to explore the evaluation framework, a public version is accessible to download from our research website.

cs.CV↗

arXiv2017

Automated sub-cortical brain structure segmentation combining spatial and deep convolutional features

Sub-cortical brain structure segmentation in Magnetic Resonance Images (MRI) has attracted the interest of the research community for a long time because morphological changes in these structures are related to different neurodegenerative disorders. However, manual segmentation of these structures can be tedious and prone to variability, highlighting the need for robust automated segmentation methods. In this paper, we present a novel convolutional neural network based approach for accurate segmentation of the sub-cortical brain structures that combines both convolutional and prior spatial features for improving the segmentation accuracy. In order to increase the accuracy of the automated segmentation, we propose to train the network using a restricted sample selection to force the network to learn the most difficult parts of the structures. We evaluate the accuracy of the proposed method on the public MICCAI 2012 challenge and IBSR 18 datasets, comparing it with different available state-of-the-art methods and other recently proposed deep learning approaches. On the MICCAI 2012 dataset, our method shows an excellent performance comparable to the best challenge participant strategy, while performing significantly better than state-of-the-art techniques such as FreeSurfer and FIRST. On the IBSR 18 dataset, our method also exhibits a significant increase in the performance with respect to not only FreeSurfer and FIRST, but also comparable or better results than other recent deep learning approaches. Moreover, our experiments show that both the addition of the spatial priors and the restricted sampling strategy have a significant effect on the accuracy of the proposed method. In order to encourage the reproducibility and the use of the proposed method, a public version of our approach is available to download for the neuroimaging community.

cs.CV↗

arXiv2017

Improving automated multiple sclerosis lesion segmentation with a cascaded 3D convolutional neural network approach

In this paper, we present a novel automated method for White Matter (WM) lesion segmentation of Multiple Sclerosis (MS) patient images. Our approach is based on a cascade of two 3D patch-wise convolutional neural networks (CNN). The first network is trained to be more sensitive revealing possible candidate lesion voxels while the second network is trained to reduce the number of misclassified voxels coming from the first network. This cascaded CNN architecture tends to learn well from small sets of training data, which can be very interesting in practice, given the difficulty to obtain manual label annotations and the large amount of available unlabeled Magnetic Resonance Imaging (MRI) data. We evaluate the accuracy of the proposed method on the public MS lesion segmentation challenge MICCAI2008 dataset, comparing it with respect to other state-of-the-art MS lesion segmentation tools. Furthermore, the proposed method is also evaluated on two private MS clinical datasets, where the performance of our method is also compared with different recent public available state-of-the-art MS lesion segmentation methods. At the time of writing this paper, our method is the best ranked approach on the MICCAI2008 challenge, outperforming the rest of 60 participant methods when using all the available input modalities (T1-w, T2-w and FLAIR), while still in the top-rank (3rd position) when using only T1-w and FLAIR modalities. On clinical MS data, our approach exhibits a significant increase in the accuracy segmenting of WM lesions when compared with the rest of evaluated methods, highly correlating ($r \ge 0.97$) also with the expected lesion volume.

cs.CV↗

arXiv2016

Is nestedness in mutualistic networks an evolutionary spandrel?

Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species. The architecture of these webs seems to pervade some of their robust and fragile behaviour. Recent work indicates that there is a strong correlation between the patterning of animal-plant interactions and their phylogenetic organisation. Here we show that such pattern and other reported regularities from mutualistic webs can be properly explained by means of a very simple model of speciation and divergence. This model also predicts a co-extinction dynamics under species loss consistent with the presence of an evolutionary signal. The agreement between observed and model networks suggests that some patterns displayed by real mutualistic webs might actually represent evolutionary spandrels.

q-bio.PE↗

arXiv2015

Emergence of proto-organisms from bistable stochastic differentiation and adhesion

The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but little is known about the potential origins of multicellular aggregates before genetic programs took full control of developmental processes. Such aggregates should involve spatial organisation of differentiated cells and the modification of flows and concentrations of metabolites within well defined boundaries. Here we show that, in an environment where limited nutrients and toxic metabolites are introduced, a population of cells capable of stochastic differentiation and differential adhesion can develop into multicellular aggregates with a complex internal structure. The morphospace of possible patterns is shown to be very rich, including proto-organisms that display a high degree of organisational complexity, far beyond simple heterogeneous populations of cells. Our findings reveal that there is a potentially enormous richness of organismal complexity between simple mixed cooperators and embodied living organisms.

q-bio.PE↗