Rhizomes play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant lineages, the genetic and developmental regulation of rhizomes remains poorly characterized. Here, we synthesize findings from in vitro induction studies, in vivo physiological and developmental analyses, quantitative trait loci (QTL) mapping, comparative transcriptomics, and limited functional studies to evaluate current knowledge and highlight outstanding questions in rhizome biology. Results show that phytohormones are central regulators of rhizome initiation and growth, with effects mediated in a context-dependent manner through interactions with environmental and developmental cues. Across rhizomatous species, traits such as rhizome initiation, branching, and elongation are typically under polygenic control, although comparatively simpler genetic architectures have been documented in emerging model systems like Mimulus. Transcriptomic analyses further highlight hormone signaling, stress-response, and carbohydrate metabolism pathways as key reg
The Abstraction and Reasoning Corpus (ARC), later renamed ARC-AGI, poses a fundamental challenge in artificial general intelligence (AGI), requiring solutions that exhibit robust abstraction and reasoning capabilities across diverse tasks, while only few (with median count of three) correct examples are presented. While ARC-AGI remains very challenging for artificial intelligence systems, it is rather easy for humans. This paper introduces ARC-NCA, a developmental approach leveraging standard Neural Cellular Automata (NCA) and NCA enhanced with hidden memories (EngramNCA) to tackle the ARC-AGI benchmark. NCAs are employed for their inherent ability to simulate complex dynamics and emergent patterns, mimicking developmental processes observed in biological systems. Developmental solutions may offer a promising avenue for enhancing AI's problem-solving capabilities beyond mere training data extrapolation. ARC-NCA demonstrates how integrating developmental principles into computational models can foster adaptive reasoning and abstraction. We show that our ARC-NCA proof-of-concept results may be comparable to, and sometimes surpass, that of ChatGPT 4.5, at a fraction of the cost.
How do the same mechanisms that faithfully regenerate complex developmental programs in spite of environmental and genetic perturbations also permit responsiveness to environmental signals, adaptation, and genetic evolution? Using the nematode Caenorhabditis elegans as a model, we explore the phenotypic space of growth and development in various genetic and environmental contexts. Our data are growth curves and developmental parameters obtained by automated microscopy. Using these, we show that among the traits that make up the developmental space, correlations within a particular context are predictive of correlations among different contexts. Further we find that the developmental variability of this animal can be captured on a relatively low dimensional phenoptypic manifold and that on this manifold, genetic and environmental contributions to plasticity can be deconvolved independently. Our perspective offers a new way of understanding the relationship between robustness and flexibility in complex systems, suggesting that projection and concentration of dimension can naturally align these forces as complementary rather than competing.
Artificial agents that support human group interactions hold great promise, especially in sensitive contexts such as well-being promotion and therapeutic interventions. However, current systems struggle to mediate group interactions involving people who are not neurotypical. This limitation arises because most AI detection models (e.g., for turn-taking) are trained on data from neurotypical populations. This work takes a step toward inclusive AI by addressing the challenge of eye contact detection, a core component of non-verbal communication, with and for people with Intellectual and Developmental Disabilities. First, we introduce a new dataset, Multi-party Interaction with Intellectual and Developmental Disabilities (MIDD), capturing atypical gaze and engagement patterns. Second, we present the results of a comparative analysis with neurotypical datasets, highlighting differences in class imbalance, speaking activity, gaze distribution, and interaction dynamics. Then, we evaluate classifiers ranging from SVMs to FSFNet, showing that fine-tuning on MIDD improves performance, though notable limitations remain. Finally, we present the insights gathered through a focus group with six
Gynandromorphs are creatures where at least two different body sections are a different sex. Bilateral gynandromorphs are half male and half female. Here we develop a theory of gynandromorph ontogeny based on developmental control networks. The theory explains the embryogenesis of all known variations of gynandromorphs found in multicellular organisms. The theory also predicts a large variety of more subtle gynandromorphic morphologies yet to be discovered. The network theory of gynandromorph development has direct relevance to understanding sexual dimorphism (differences in morphology between male and female organisms of the same species) and medical pathologies such as hemihyperplasia (asymmetric development of normally symmetric body parts in a unisexual individual). The network theory of gynandromorphs brings up fundamental open questions about developmental control in ontogeny. This in turn suggests a new theory of the origin and evolution of species that is based on cooperative interactions and conflicts between developmental control networks in the haploid genomes and epigenomes of potential sexual partners for reproduction. This network-based theory of the origin of species
Conversational AI is increasingly personalized around users' preferences, histories, goals, and knowledge, but much less around how users interpret and take up model outputs to construct and understand their reality. We draw on Robert Kegan's constructive-developmental theory as a complementary lens on this dimension. Existing methods for assessing developmental stage in the Keganian tradition rely either on expert interviews that do not scale or on sentence-completion instruments that are proprietary, lengthy, or invasive. To make this perspective tractable for LLM evaluation, we introduce the Developmental Sentence Completion Test (DSCT), a 20-item instrument designed to elicit developmental signal in self-administered text. Throughout, we treat the resulting labels as characterizations of stage-like structure in elicited responses, not as validated person-level developmental stage. We then ask how much of that signal can be recovered by LLMs across three elicited response regimes: simulated personas, real human respondents, and default model-generated answers. On simulated personas, top frontier models recover simulator-intended labels with high accuracy. On real human DSCT resp
Developmental plasticity plays a prominent role in shaping the brain's structure during ongoing learning in response to dynamically changing environments. However, the existing network compression methods for deep artificial neural networks (ANNs) and spiking neural networks (SNNs) draw little inspiration from brain's developmental plasticity mechanisms, thus limiting their ability to learn efficiently, rapidly, and accurately. This paper proposed a developmental plasticity-inspired adaptive pruning (DPAP) method, with inspiration from the adaptive developmental pruning of dendritic spines, synapses, and neurons according to the ``use it or lose it, gradually decay" principle. The proposed DPAP model considers multiple biologically realistic mechanisms (such as dendritic spine dynamic plasticity, activity-dependent neural spiking trace, and local synaptic plasticity), with additional adaptive pruning strategy, so that the network structure can be dynamically optimized during learning without any pre-training and retraining. Extensive comparative experiments show consistent and remarkable performance and speed boost with the extremely compressed networks on a diverse set of benchmar
For over a century, immunology has masterfully discovered and dissected the components of our immune system, yet its collective behavior remains fundamentally unpredictable. In this perspective, we argue that building on the learnings of reductionist biology and systems immunology, the field is poised for a third revolution. This new era will be driven by the convergence of purpose-built, large-scale causal experiments and predictive, generalizable AI models. Here, we propose the Predictive Immunology Loop as the unifying engine to harness this convergence. This closed loop iteratively uses AI to design maximally informative experiments and, in turn, leverages the resulting data to improve dynamic, in silico models of the human immune system across biological scales, culminating in a Virtual Immune System. This engine provides a natural roadmap for addressing immunology's grand challenges, from decoding molecular recognition to engineering tissue ecosystems. It also offers a framework to transform immunology from a descriptive discipline into one capable of forecasting and, ultimately, engineering human health.
In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and learning enhance nonheritable phenotypic variation, which in turn can accelerate evolutionary response. In this paper, I show how developmental variability alters evolutionary dynamics by smoothing the landscape that relates genotype to fitness. In a fitness landscape with multiple peaks and valleys, developmental variability can smooth the landscape to provide a directly increasing path of fitness to the highest peak. Developmental variability also allows initial survival of a genotype in response to novel or extreme environmental challenge, providing an opportunity for subsequent adaptation. This initial survival advantage arises from the way in which developmental variability smooths and broadens the fitness landscape. Ultimately, the synergism between developmental processes and genetic variation sets evolutionary rate.
Large language models (LLMs) achieve strong performance across many natural language processing tasks, yet their decision processes remain difficult to interpret. This lack of transparency creates challenges for trust, debugging, and deployment in real-world systems. This paper presents an applied comparative study of three explainability techniques: Integrated Gradients, Attention Rollout, and SHAP, on a fine-tuned DistilBERT model for SST-2 sentiment classification. Rather than proposing new methods, the focus is on evaluating the practical behavior of existing approaches under a consistent and reproducible setup. The results show that gradient-based attribution provides more stable and intuitive explanations, while attention-based methods are computationally efficient but less aligned with prediction-relevant features. Model-agnostic approaches offer flexibility but introduce higher computational cost and variability. This work highlights key trade-offs between explainability methods and emphasizes their role as diagnostic tools rather than definitive explanations. The findings provide practical insights for researchers and engineers working with transformer-based NLP systems. T
We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix (e.g. BLOSUM62). The kernel is used in learning machines to predict binding affinities of peptides to human leukocyte antigens DR (HLA-DR) molecules. On both fixed allele (Nielsen and Lund 2009) and pan-allele (Nielsen et.al. 2010) benchmark databases, our algorithm achieves the state-of-the-art performance. The kernel is also used to define a distance on an HLA-DR allele set based on which a clustering analysis precisely recovers the serotype classifications assigned by WHO (Nielsen and Lund 2009, and Marsh et.al. 2010). These results suggest that our kernel relates well the chain structure of both peptides and HLA-DR molecules to their biological functions, and that it offers a simple, powerful and promising methodology to immunology and amino acid chain studies.
Developmental psychologists have spent decades devising experiments to test the intelligence and knowledge of infants and children, tracing the origin of crucial concepts and capacities. Moreover, experimental techniques in developmental psychology have been carefully designed to discriminate the cognitive capacities that underlie particular behaviors. We propose that using classical experiments from child development is a particularly effective way to probe the computational abilities of AI models, in general, and LLMs in particular. First, the methodological techniques of developmental psychology, such as the use of novel stimuli to control for past experience or control conditions to determine whether children are using simple associations, can be equally helpful for assessing the capacities of LLMs. In parallel, testing LLMs in this way can tell us whether the information that is encoded in text is sufficient to enable particular responses, or whether those responses depend on other kinds of information, such as information from exploration of the physical world. In this work we adapt classical developmental experiments to evaluate the capabilities of LaMDA, a large language mo
This review synthesizes the nascent but critical field of developmental interpretability for Large Language Models. We chart the field's evolution from static, post-hoc analysis of trained models to a dynamic investigation of the training process itself. We begin by surveying the foundational methodologies, including representational probing, causal tracing, and circuit analysis, that enable researchers to deconstruct the learning process. The core of this review examines the developmental arc of LLM capabilities, detailing key findings on the formation and composition of computational circuits, the biphasic nature of knowledge acquisition, the transient dynamics of learning strategies like in-context learning, and the phenomenon of emergent abilities as phase transitions in training. We explore illuminating parallels with human cognitive and linguistic development, which provide valuable conceptual frameworks for understanding LLM learning. Finally, we argue that this developmental perspective is not merely an academic exercise but a cornerstone of proactive AI safety, offering a pathway to predict, monitor, and align the processes by which models acquire their capabilities. We co
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce a new information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns, and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction-diffusion models of self-organization. This paves a way towards a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and
This work simulates the developmental process of cortical neurogenesis, initiating from a single stem cell and governed by gene regulatory rules derived from mouse single-cell transcriptomic data. The developmental process spontaneously generates a heterogeneous population of 5,000 cells, yet yields only 85 mature neurons - merely 1.7% of the total population. These 85 neurons form a densely interconnected core of 200,400 synapses, corresponding to an average degree of 4,715 per neuron. At iteration zero, this minimal circuit performs at chance level on MNIST. However, after a single epoch of standard training, accuracy surges to over 90% - a gain exceeding 80 percentage points - with typical runs falling in the 89-94% range depending on developmental stochasticity. The identical circuit, without any architectural modification or data augmentation, achieves 40.53% on CIFAR-10 after one epoch. These findings demonstrate that developmental rules sculpt a domain-general topological substrate exceptionally amenable to rapid learning, suggesting that biological developmental processes inherently encode powerful structural priors for efficient computation.
In anticipation of the completion of the High-Luminosity Large Hadron Collider (HL-LHC) programme by the end of 2041, CERN is preparing to launch a new major facility in the mid-2040s. According to the 2020 update of the European Strategy for Particle Physics (ESPP), the highest-priority next collider is an electron-positron Higgs factory, followed in the longer term by a hadron-hadron collider at the highest achievable energy. The CERN directorate established a Future Colliders Comparative Evaluation working group in June 2023. This group brings together project leaders and domain experts to conduct a consistent evaluation of the Future Circular Collider (FCC) and alternative scenarios based on shared assumptions and standardized criteria. This report presents a comparative evaluation of proposed future collider projects submitted as input for the Update of the European Strategy for Particle Physics. These proposals are compared considering main performance parameters, environmental impact and sustainability, technical maturity, cost of construction and operation, required human resources, and realistic implementation timelines. An overview of the international collider projects w
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to establishing cell developmental trajectories within individual samples, necessitating biologists to manually link cells across samples to construct complete cross-sample evolutionary trajectories that consider cellular spatial dynamics. This process demands substantial human effort due to the complex spatial correspondence between each pair of samples. To address this challenge, we first proposed a GNN-based model to predict cross-sample cell developmental trajectories. We then developed TrajLens, a visual analytics system that supports biologists in exploring and refining the cell developmental trajectories based on predicted links. Specifically, we designed the visualization that integrates features on cell distribution and developmental direction across multiple samples, providing an overview of the spatial evolutionary patterns of cell populations along trajectories. Additionally, we included contour maps superimposed on the original cell distribution
Object detection in remotely sensed satellite pictures is fundamental in many fields such as biophysical, and environmental monitoring. While deep learning algorithms are constantly evolving, they have been mostly implemented and tested on popular ground-based taken photos. This paper critically evaluates and compares a suite of advanced object detection algorithms customized for the task of identifying aircraft within satellite imagery. Using the large HRPlanesV2 dataset, together with a rigorous validation with the GDIT dataset, this research encompasses an array of methodologies including YOLO versions 5 and 8, Faster RCNN, CenterNet, RetinaNet, RTMDet, and DETR, all trained from scratch. This exhaustive training and validation study reveal YOLOv5 as the preeminent model for the specific case of identifying airplanes from remote sensing data, showcasing high precision and adaptability across diverse imaging conditions. This research highlight the nuanced performance landscapes of these algorithms, with YOLOv5 emerging as a robust solution for aerial object detection, underlining its importance through superior mean average precision, Recall, and Intersection over Union scores. T
According to the World Health Organization, the population of children with developmental delays constitutes approximately 6% to 9% of the total population. Based on the number of newborns in Huaibei, Anhui Province, China, in 2023 (94,420), it is estimated that there are about 7,500 cases (suspected cases of developmental delays) of suspicious cases annually. Early identification and appropriate early intervention for these children can significantly reduce the wastage of medical resources and societal costs. International research indicates that the optimal period for intervention in children with developmental delays is before the age of six, with the golden treatment period being before three and a half years of age. Studies have shown that children with developmental delays who receive early intervention exhibit significant improvement in symptoms; some may even fully recover. This research adopts a hybrid model combining a CNN-Transformer model with Case-Based Reasoning (CBR) to enhance the screening efficiency for children with developmental delays. The CNN-Transformer model is an excellent model for image feature extraction and recognition, effectively identifying features
There is much to learn through synthesis of Developmental Biology, Cognitive Science and Computational Modeling. Our path forward involves a design for developmentally-inspired learning agents based on Braitenberg Vehicles. Continual developmental neurosimulation allows us to consider the role of developmental trajectories in bridging the related phenomena of nervous system morphogenesis, developmental learning, and plasticity. Being closely tied to continual learning, our approach is tightly integrated with developmental embodiment, and can be implemented using a type of agent called developmental Braitenberg Vehicles (dBVs). dBVs begin their lives as a set of undefined structures that transform into agent-based systems including a body, sensors, effectors, and nervous system. This phenotype is characterized in terms of developmental timing: with distinct morphogenetic, critical, and acquisition (developmental learning) periods. We further propose that network morphogenesis can be accomplished using a genetic algorithmic approach, while developmental learning can be implemented using a number of computational methodologies. This approach provides a framework for adaptive agent beh