Morphogenesis

LLM agents solve complex tasks by iteratively changing files, invoking local tools, and interacting with remote services, which modifies state across their local environment and remote services. Today, agents and users must manage these changes explicitly, whether reverting exploratory actions or recovering from erroneous ones. Doing so safely requires coordinated actions, yet current agent harnesses lack unified abstractions and mechanisms for managing local and remote state consistently and efficiently. We describe Planarian, an agent runtime with state management that enables agents and users to recover from erroneous actions and explore alternative executions over consistent local and remote environment state. Planarian introduces the abstraction of agent statepoints, which are consistent, restorable point-in-time versions of the environment state. Planarian exposes three state-management primitives to agents and users: (i) snapshot creates a new statepoint spanning local and remote state without requiring external services to support checkpoints: it relies on efficient incremental process and file system snapshotting to capture local sandboxed state, and transparently records compensating actions to undo remote state changes; (ii) rollback restores the environment to a previous statepoint by reverting to a prior local checkpoint and replaying compensating actions for remote state changes; and (iii) fork creates multiple isolated branches from a statepoint, enabling the agent to explore alternatives in parallel. We show that Planarian enables agents to undo mistakes and explore alternatives in parallel, improving task quality by up to 15x, and allows users to recover from erroneous actions with only 3% overhead.

Learning population dynamics from temporally sparse, unpaired distribution snapshots is a fundamental challenge in developmental biology. Recent approaches based on neural differential equations and flow matching can interpolate between observed population snapshots, but may struggle to extrapolate beyond the training horizon and often lack an explicit mechanism for modeling developmental branching. We propose KoopCell, a unified generative framework based on Koopman-Mori-Zwanzig theory that jointly learns representations and predictive linear latent dynamics. Theoretically, using the weak continuity equation, we derive a closed-form least-squares estimator for the Koopman generator from distribution snapshots and establish convergence guarantees under suitable assumptions. To model branching dynamics, we further develop KoopCell-M, which incorporates non-Markovian memory into the latent Koopman dynamics through a Markovian embedding. Experiments on synthetic systems and three scRNA-seq datasets demonstrate the ability of our framework to recover Koopman spectra, model branching through memory, and scale to predicting high-dimensional gene expression distributions, achieving state-of-the-art performance among the evaluated methods.

Continual learning, the ability to learn from sequential experience while retaining and adapting prior knowledge, is central to intelligent systems operating in changing environments. However, conventional continual learning is typically studied with offline task-wise training and clear task boundaries, leaving a substantial gap from general continual learning under online, uncertain, and evolving data streams. In this regime, intelligent systems must separate conflicting experience to reduce interference while integrating compatible experience to promote generalization. Inspired by the organization of the Drosophila learning and memory system, we identify a hierarchical modular principle that coordinates both functions through expert specialization and ensemble integration. We instantiate this principle as lightweight modular adaptation of pretrained foundation models, combining brain-inspired random expansion for expert routing and diversified modular integration across spatial and temporal scales. Across visual recognition, vision-language understanding, ego-exo video understanding, and embodied vision-language-action learning, our method consistently improves learning under online and uncertain data streams, with gains exceeding 50 percentage points over replay-free alternatives in embodied manipulation. These findings support hierarchical modularity as a biologically grounded path for learning from dynamic experience.

Artificial ontogeny, developmental encodings, robot reproduction, and inherited controllers are established research directions, yet a narrower question remains: can a newborn artificial agent exhibit measurable biparental heredity before learning, and can that dependence be isolated causally rather than inferred only from parent-offspring resemblance? We introduce Machine Zygote, a computational germline-soma architecture designed to test this question. Two parental germlines are independently mutated and recombined into a zygote that parameterizes development of an initially generic eight-module soma, which is then frozen and evaluated without learning. A preregistered 4 x 4 diallel of 640 offspring shows significant dam and sire dependence for five of six behavioral traits after Holm correction, with parental and interaction components accounting for 36-53 percent of modeled variance across five principal traits. In matched-background interventions (n=60), substituting one parental germline while holding recombination and stochastic background fixed causes phenotype shifts exceeding a same-parent re-mutation control for five of six traits for both parental channels. Recombination also yields excess transgressive offspring for speed and gait frequency. A preregistered developmental-dependence hypothesis is not supported: a quasistatic no-dynamics ablation preserves the mean phenotype distribution while altering parental variance structure. Thus the study supports causal biparental pre-learning heredity in this simulation, but not the stronger claim that recurrent developmental dynamics are necessary. It does not establish physical heredity, biological genetics, or autonomous evolution. The contribution is an intervention-centered framework and reproducible benchmark for separating heredity, development, stochastic variation, and post-birth learning.

The larval stage of Drosophila melanogaster is a compact model system for neuroscience whose genetic toolkit allows fluorescent markers to be expressed in defined neural populations, and comparing the resulting expression patterns across animals requires every brain to be registered into a shared anatomical reference space. Existing pipelines for this task are predominantly based on classical registration methods, which perform a new optimization for each volume, often require per-case parameter tuning, and can take minutes per brain, limiting their use as a routine preprocessing step. We present a trained deep registration pipeline that deformably aligns a larval brain to a reference template in a single forward pass at high spatial resolution, on volumes that hold several times more voxels than those learned 3D registration is normally reported on, together with the preprocessing and anatomy-anchored evaluation pipeline required to apply it. Against eleven classical and seven further learned baselines on a held-out collection acquired with different acquisition and quality strata, the proposed pipeline is the most accurate, improving on the strongest classical baseline by 23 percentage points of anatomical landmark-local mutual information. It registers a volume one to two orders of magnitude faster than the classical deformable pipelines, and it retains more of its accuracy than any other method as acquisition quality degrades. The network, its trained weights and the full pipeline are released as the open-source deep larval brain registration framework: https://github.com/agentdr1/deep-larval-brain-reg

Biological specimen records collected by natural history institutions constitute a rich source of temporal geographic knowledge, capturing biodiversity information about regional landscapes as they were recorded at different times. Using digitised data from the Allan Herbarium (New Zealand), this study identifies place names in these specimen locality descriptions that are absent from current gazetteers; we refer to these as non-gazetteer place names (NGPs). These place names are typically historical, vernacular, or colloquial and were used as landmarks to describe a specimen's location at the time of collection. We then investigate the problem of georeferencing the NGPs using only the limited information available in the specimen records. To resolve this, we leverage repeated occurrences of the same place name across specimen records with different specimen locations and spatial relation terms, extracting and inverting these relations to derive constraints on NGP locations. This approach is instantiated within deterministic, probabilistic, and LLM-based methods, enabling a comparative analysis of their strengths and limitations for text-based spatial inference. On a pseudo-NGP benchmark, probabilistic inference achieves the highest accuracy (median error 1.43 km; A@1 km 36%), while the LLM yields competitive but less precise estimates (median error 1.80 km; A@1 km 31%), indicating that, despite advances in LLMs, traditional modelling remains advantageous when high spatial precision is required.

Modern neuroscience relies on integrating multi-scale, multimodal datasets to uncover the neural principles underlying intelligence. However, analytical challenges posed by highly heterogeneous data and fragmented workflows increasingly constrain discoveries. Here we introduce SeekBrain, an autonomous multi-agent framework designed to accelerate neuroscience discovery through domain-grounded hierarchical planning and cross-modal data analysis. SeekBrain dynamically constructs a repertoire of analysis recipes extracted from code-paper pairs. By coupling this codified expertise with agentic planning and execution engines, the framework scalably generates hypotheses and analytical pipelines on demand. Systematic evaluation on the expert-annotated BrainArena benchmark demonstrates that SeekBrain substantially outperforms state-of-the-art agent baselines across various analysis tasks. Crucially, when deployed in real-world research, SeekBrain integrated behavioral, neural, and anatomical data to reveal structured, distributed neural representations of larval zebrafish behavior and a shared axis of regional decoding strength across the brain in a mouse decision-making task. These results establish SeekBrain as a scalable and practical tool for accelerating data-driven discoveries in neuroscience.

Neurological disorders are a leading cause of global disability and are increasingly linked to environmental chemical exposures. Yet neurotoxicity assessment still relies on hand-scored morphological readouts that are subjective and poorly predictive of behavioral outcomes. Caenorhabditis elegans provides a genetically tractable, 3R-compliant alternative, but quantifying neuronal phenotypes from confocal microscopy at scale remains computationally challenging: existing vision foundation models, trained on natural or radiological images, cannot resolve the sparse signals and multi-scale lesions of neuronal imaging. Here, we introduce a dedicated self-supervised vision model for C. elegans dopaminergic neurons, together with CeNeuMorph, a multi-grained confocal benchmark of 27,117 annotated images. Specifically, moving beyond standard Masked Autoencoders, we propose a scale-adaptive masked image modeling strategy that jointly learns representations across resolutions and patch sizes under a fixed token budget. By decoupling structural semantic learning from rigid grid constraints, the model effectively resolves the full spectrum of neurodegenerative lesions - ranging from fine dendritic beading to gross soma shrinkage - within a tractable computational framework. Finally, our model surpasses both generalist and biomedical foundation models across classification, segmentation and detection tasks. Fusing visual features with morphological descriptors enables prediction of dopamine-dependent behavioral deficits ($R^2=0.498$). Screening 180 agrochemicals, we identify the benzimidazole moiety as a previously unrecognized determinant of dopaminergic neurotoxicity. Together, the work demonstrates how scale-adaptive self-supervised learning can connect morphology to function for a scalable alternative to mammalian in vivo models for neurotoxicity assessment and drug discovery.

A walking fly steers toward a goal direction, held as a bump of activity across the FC2 neurons of the fan-shaped body. These neurons also inhibit one another over distance, more strongly the farther apart they are, a feedback proposed to keep the fly on a single goal. We asked, from the connectome, what circuit produces this inhibition, and whether it lets FC2 actively choose one goal among competitors (a winner-take-all) or simply keeps a goal set elsewhere as one clean bump. Tracing the wiring in a single FlyWire brain, we find the inhibition is almost entirely global: four FB5A cells inhibit every FC2 neuron roughly equally, with a smaller, distance-dependent contribution from hDelta interneurons and a negligible direct component. A ring-attractor winner-take-all (the kind the compass uses) requires local recurrent excitation that the FC2 wiring lacks, so this geometry cannot build one; and across a range of dynamical models, including a spiking network, no version of the circuit locks onto a winner at the connectome-scaled reference coupling. FC2 therefore normalizes an externally set goal rather than selecting it, with FB5A likely acting as the global normalizer, much as the APL neuron does in the mushroom body. We are explicit about two open points: a different mechanism, mutual inhibition between two competing goals (which hDelta supplies), could in principle select at very strong coupling, and we bound rather than exclude it; and FB5A's inhibitory identity is a low-confidence prediction of the connectome's transmitter classifier, not yet measured, and likely not GABAergic. We then ask where the goal is actually set: the connectome nominates an upstream hDelta network and rules out the leading proposed alternative, whose neurons supply under 0.2% of FC2's input. Finally, we propose a direct experiment, silencing FB5A while imaging FC2, that would test the account.

We propose and evaluate three hierarchical ensemble setups for zebrafish phenotype classification from embryo images. In all setups, stage 1 uses a single four-class classifier to assign images to one of the exclusive phenotypes: Normal, Chorion, Dead, or Other. Images classified as Other are then processed in stage 2, where the ensemble design differs across setups: a single multi-label classifier, two specialized multi-label classifiers, or an ensemble of binary classifiers. We compare these setups using three backbone architectures: ResNet18, ViT, and ConvNeXt. Overall, ConvNeXt achieves the best performance across setups, while the specialized hierarchical ensemble in setup 2 provides the best balance in terms of F1-score. The results show that the proposed specialised hierarchical ensembles are effective for zebrafish phenotype recognition, and suggest that ConvNeXt is particularly useful backbone model.

We present PinFT, a miniature five-axis capacitive force/torque sensor designed for direct tip-level integration into tweezer-like tools. The sensor employs a compact three-PCB stack with segmented plated through-hole electrodes and a silicone elastomer dielectric, enabling five-degree-of-freedom force and torque sensing ($F_x$, $F_y$, $F_z$, $T_x$, $T_y$) through displacement of a central 2,mm-diameter stainless steel pin. The fabricated prototype was calibrated using a higher-order polynomial mapping, yielding mean absolute errors of approximately 0.23,N for forces and 2.5,mN$\cdot$m for torques, with coefficients of determination ($R^2$) exceeding 0.97 across all axes. To demonstrate practical utility, a 3D-printed tweezer integrating PinFT sensors at both tips was mounted on a parallel-jaw gripper and evaluated across three representative manipulation tasks: grasping a sub-millimeter SMD capacitor, pulling a simulated hair from a silicone substrate, and tearing a compliant silicone specimen. In all cases, per-tip force sensing reliably captured characteristic force signatures that distinguish successful manipulation from failure events -- including slip and object ejection -- using gradient-based features derived from internal grasp force and net interaction force. These results demonstrate that direct, per-tip force sensing enables standard parallel-jaw grippers to monitor and interpret fine manipulation tasks performed through a handheld tweezer.

Self-organization is an emergent property of life, driven by the collective behavior of individual components acting on local information. Biological neurons, through local interactions transmitted through synapses, are able to learn efficiently and can adapt their connections over an organism's lifespan. Motivated by these desirable properties of adaptability and local interaction, neural cellular automata (NCA) models have been successful at learning morphogenesis solely through local update rules, demonstrating stability over many updates and robustness to perturbations. In this work, we introduce Meta Neural Cellular Automata (MetaNCA), a framework that learns local rules which self-organize the weights of artificial neural networks. A learned rule network iteratively updates the weights of a task network using only local interactions on the computation graph. We propose a novel Weight Transformer architecture for the local rule network, which uses linear attention to aggregate signals from neighboring weights and hidden states. Once trained, the rule network generates task networks of diverse architectures without backpropagation. We show that MetaNCA generates weights for feedforward MLPs, CNNs, and ResNets on MNIST and CIFAR-100, scaling to networks of 2 million parameters. We further show that MetaNCA generalizes to architectures not seen during meta-training, and that architectural diversity in the training phase strengthens this generalization.

Zebrafish embryos are a valuable model for drug discovery due to their optical transparency and genetic similarity to humans. However, current evaluations rely on manual inspection, which is costly and labor-intensive. While machine learning offers automation potential, progress is limited by the lack of comprehensive datasets. To address this, we introduce a large-scale dataset of high-resolution microscopic image sequences capturing zebrafish embryonic development under both control conditions and exposure to compounds (3,4-dichloroaniline). This dataset, with expert annotations at fine-grained temporal levels, supports two benchmarking tasks: (1) fertility classification, assessing zebrafish egg viability (130,368 images), and (2) toxicity assessment, detecting malformations induced by toxic exposure over time (55,296 images). Alongside the dataset, we present the first transformer-based baseline model that integrates spatiotemporal features to predict developmental abnormalities at early stages. Experimental results present the model's effectiveness, achieving 98% accuracy in fertility classification and 92% in toxicity assessment. These findings underscore the potential of automated approaches to enhance zebrafish-based toxicity analysis.

In this paper, we explore deep learning techniques for individual identification of animals based on their skin patterns. Individual identification is crucial in biodiversity monitoring, since it enables analysis of decline or growth of populations, or intra-species interactions within populations. Models trained for the task of individual identification often do not focus on the skin pattern of animals, but on background details or body shape details. These characteristics are not individually specific, or can change drastically through time. We focus on techniques that will make machine learning models more responsive to skin pattern structure when extracting individual visual embeddings from images. For this, we explore image inpainting of task-specific masks as an auxiliary task to enhance ML-based individual identification from animal skin patterns. We propose a comparative analysis among four models as an encoder backbone for the individual identification task. We focus on the case study of zebrafish, which is a widely recognized biological model organism, and which exhibits individually identifying skin patterns. To evaluate encoder backbone performance, we present standard metrics for classification accuracy, embedding clustering metrics, and GradCAM visualizations.

Many disciplines need quantitative models that synthesize experimental data across multiple instances of the same general system. For example, neuroscientists must combine data from the brains of many individual animals to understand the species' brain in general. However, typical machine learning models treat one system instance at a time. Here we introduce a machine learning framework, deep probabilistic model synthesis (DPMS), that leverages system properties auxiliary to the model to combine data across system instances. DPMS specifically uses variational inference to learn a conditional prior distribution and instance-specific posterior distributions over model parameters that respectively tie together the system instances and capture their unique structure. DPMS can synthesize a wide variety of model classes, such as those for regression, classification, and dimensionality reduction, and we demonstrate its ability to improve upon single-instance models on synthetic data and whole-brain neural activity data from larval zebrafish.