We present a novel multiscale algorithm for directly recovering the atomic model structure of a protein from single-particle cryo-EM data. Our algorithm is able to estimate protein structures to state-of-the-art accuracy for high-noise and low-contrast data. It is also robust to misspecifications in the TEM image formation model. These desirable properties are primarily due to the use of an explicit representation of the protein backbone in terms of bonds, torsion angles and bond angles, which supplies rich prior information to the structure recovery process. We apply our method on three protein cryo-EM datasets, generated using an electron microscope digital twin, and show that using a multiscale approach yields an improvement of the root-mean-square deviation (RMSD) and template modelling (TM) scores with respect to the ground truth. Furthermore, there is evidence that larger-scale structures are being prioritised with the multiscale algorithm, which reduces the possibility of convergence to bad local minima.

High-throughput chromatin accessibility assays such as ATAC-seq generate thousands of candidate regulatory elements (peaks), yet no standardized tool exists for assembling the diverse quantitative features needed to prioritize peaks for functional validation. Here we present PyPeakRankR, an open-source Python package that extracts peak-level features, namely BigWig signal summaries, GC content, PhyloP conservation scores, distribution moments (kurtosis, skewness, bimodality), and cell-type specificity rankings, into a single reproducible peak by feature matrix stored as a tab-separated values (TSV) file. PyPeakRankR separates deterministic feature extraction from downstream ranking, enabling transparent benchmarking of prioritization strategies on the same upstream data. The package provides both a command-line interface and a matching Python API, supports cross-assembly scoring via liftOver, and runs in minutes on thousands of peaks. PyPeakRankR was validated in the Brain Initiative Cell Census Network (BICCN) community challenge, where its predecessor PeakRankR ranked among the top 3 of 16 methods for cell-type specific enhancer prediction. In a recent basal ganglia study, PyPeakRankR was used within the Cross-species Enhancer Ranking Pipeline (CERP) to identify enhancer-AAV tools achieving greater than 70% on-target specificity across cell types. PyPeakRankR is freely available under the MIT license at https://github.com/AllenInstitute/PeakRankR/tree/python-package.

Electron-microscopy reconstruction now yields complete synaptic wiring diagrams, or connectomes, of entire small brains, including the larval Drosophila, the first insect brain reconstructed in full. How far a wiring diagram alone fixes a circuit's activity, as opposed to the finer physiological detail it does not record, is debated. We run a complete connectome as a fixed, rate-based dynamical operator in which no single-neuron parameter is fitted, so that, at one fixed dynamical regime, the model's behavior reflects the wiring and its connection strengths rather than tuned single-neuron physiology, and compare it against a hierarchy of randomized networks that each preserve a coarser description of the wiring. The model's overall dynamical regime, how strongly and how richly it responds, is mostly statistical: networks keeping only the connectome's coarse wiring statistics reproduce it. The wiring beyond these statistics instead sets where activity travels and which circuits shape it. Sparse input is confined to a compact olfactory pathway that randomized networks flood, and the mushroom body, the insect learning center, takes an outsized role in the leading adjoint-side modes, the directions that weigh which neurons shape the recurrent dynamics. Coarse statistics set the regime; the precise pattern of connections sets the geometry, a separation that clarifies which connectome-based claims rest on wiring alone.

Subjective tinnitus - the perception of sound in the absence of an external acoustic stimulus - remains one of the most debated phenomena in auditory neuroscience. In 2016, the stochastic resonance (SR) model was introduced as an alternative account of tinnitus-related neuronal hyperactivity, proposing that internally generated neural noise is adaptively upregulated to restore information transmission after hearing loss. Rather than interpreting increased spontaneous activity as maladaptive, the model reframed it as a functional mechanism that enhances signal detection near sensory thresholds, with tinnitus emerging as a side effect of adaptive sensory optimization. Over the past decade, this framework has evolved from a phenomenological hypothesis into a broader neurocomputational theory linking information theory, adaptive signal detection, multichannel auditory processing, and cross-modal plasticity. Computational modeling, large-scale clinical analyses, and animal experiments have provided converging support for key predictions, including improved detectability under specific noise conditions and frequency-specific phantom percepts. The framework has also inspired a therapeutic approach based on spectrally matched near-threshold noise stimulation and has recently been integrated into a unified account of auditory phantom perception that combines stochastic resonance, central gain, homeostatic plasticity, and predictive coding. This review provides a chronological overview of the development of the stochastic resonance model, summarizes major theoretical and empirical advances, and outlines future directions for mechanistic validation and clinical translation. By redefining tinnitus as a consequence of adaptive sensory computation, the model shifts the conceptual focus from pathological dysfunction toward principles of information optimization in neural systems.

Skeletal muscle undergo remarkable changes during aging including anatomical, ultrastructural, and moreover biochemical. The aging associated reduction of muscle mass, termed as sarcopenia, is a major factor in geriatric functional decline and frailty, contributing to the lowering of self-confidence. In an adult skeletal muscle fibers, sarcoplasmic reticulum (SR) and mitochondria exhibit most intricate and precise distribution along with the sarcolemmal (forming T-tubule), which is critical for muscle function. In healthy young muscle tissue, the close physical proximity of SR and mitochondrial membranes shows contacts called mitochondria-associated membranes (MAMs). Recent literature highlights the role of MAMs network in smooth functioning of muscle by regulating localization of Ca2+-signaling, lipid transport, and other signalling molecules like reactive oxygen species. Several tethering mechanisms are proposed to stabilize the MAMs network, the classical ones being the mitofusins (MFN1 and MFN2). Emerging consensus suggest that MAMs in the skeletal muscle facilitate accuracy of excitation-metabolic coupling ensuring spatial energy supply. However, upon aging the precision of SR and mitochondria co-localization as well as crosstalk seems to be affected. In this review, we have critically examined the current literature about MAMs network structure and function during health and diseases mainly from an aging perspective. We have further evaluated the role of exercise, nutritional, nutraceutical and pharmacological approaches in lowering MAMs loss in an effort to retard aging progression. Retention of skeletal muscle health and performance is a major factor in achieving the goal of healthy aging.

Spinal cord stimulation with implantable leads is a valuable therapy used to treat a variety of chronic pain conditions. However, lead migration is a common complication causing loss of efficacy. Previous reports have characterized lead migration using radiographs, but methods are not consistent and lack rigorous validation. The purpose of this study was to develop a technique to perform radiographic measurements of the position of epidural spinal cord leads within the lumbosacral spinal canal and establish its accuracy, repeatability, and reproducibility. Computed tomography scans were acquired from three clinical trial participants implanted percutaneously with two eight-contact cylindrical leads; from these, electrode positions were established using three-dimensional measurements, and digitally reconstructed radiographs were created. Two operators applied a digitization and measurement protocol for each lead. Bland-Altman plots were created to determine smallest detectable change, and a gage repeatability and reproducibility analysis was performed. Smallest detectable change was found to be less than the distance between adjacent electrodes and variability introduced by repeatability and reproducibility was less than 10% of the total study variability. We conclude that the method developed to measure lead electrode position has sufficient accuracy and acceptable repeatability and reproducibility.

Tau PET imaging is central to tracking Alzheimer's disease progression, but systematic differences between scanners, protocols, and radiotracers across sites introduce nonbiological variability that inflates biomarker variance, reduces sensitivity to disease effects, and can bias downstream clinical assessments. Harmonization methods aim to remove these site-induced shifts while preserving biologically meaningful signal, yet existing approaches struggle when source and target cohorts differ in subgroup composition, risking conflation of site effects with biological variation such as tau-positivity status. We propose the Feynman Kac Reweighted Schröodinger Bridge Matching (FKRSBM) model to address this problem. Rather than routing data through a Gaussian noise prior as in diffusion-based methods, FKRSBM learns a direct stochastic transport process between source and target distributions via entropy-regularized optimal transport. To enforce biologically consistent transport, FKRSBM incorporates a subgroup-aware endpoint proposal derived from a Feynman Kac reweighting of the reference bridge measure, implemented entirely through stratified importance sampling at the data level and requiring no changes to the underlying bridge-matching solver or network architecture. For surface-based neuroimaging, FKRSBM employs a spherical convolutional backbone operating on cortical meshes to perform vertex-level harmonization. We evaluate the method on tau PET SUVR maps, harmonizing PI-2620 data from the HABS-HD cohort into the AV-1451 domain of ADNI. Compared against ComBat, CycleGAN, a diffusion-based method (DF), and unregularized Diffusion Schröodinger Bridge Matching (DSBM), FKRSBM achieves superior distributional alignment, reduced tau-positivity sign mismatch, stronger APOE subgroup alignment, and improved downstream disease classification performance.

The growing energy demand for computation is becoming increasingly unsustainable. Thermodynamic computing, which harnesses physical thermal fluctuations as a computational resource rather than suppressing them, offers orders-of-magnitude energy savings for probabilistic and combinatorial tasks. Pharmaceutical R&D, heavily reliant on computational optimization and sampling, is a natural application domain. Here we present what is, to our knowledge, the first concrete pharmaceutical application mapped to thermodynamic hardware with energy estimates grounded in prototype measurements. We reduce mRNA codon optimization, a combinatorial problem routinely solved in drug development, to sampling from an Ising model, making it directly executable on a thermodynamic sampling unit (TSU). Benchmarking three approaches (Potts sampling, Ising sampling, and a genetic algorithm baseline) on the SARS-CoV-2 spike protein, we find that all achieve comparable optimization quality (scores ~234-240), but energy estimates based on validated hardware models indicate that a TSU could solve this problem using approximately 10e6 times less energy than a conventional GPU. All code is released under an open-source license.

Antimicrobial resistance causes to over a million deaths annually. Antimicrobial peptides (AMPs) are a promising solution, but generative AMP models are not yet ready to design peptides with non-natural amino acids and/or chemical modifications, which are essential for real-world peptide drugs. We present AMPGAN v3, a multi-objective conditional GAN that expands the generative vocabulary to D-amino acids and N/C-terminus modifications such as amidation. By separating adversarial and activity-aware supervision across two specialized discriminators, AMPGAN v3 substantially improves training stability and outperforms prior generative AMP models on external classifiers. We validated five candidates spanning three structural classes in vitro; two showed activity against Gram-positive strains, with the best candidate reaching MIC 8 μg/mL against B. subtilis. To support downstream curation, we further present PepCraft, a multi-agent framework for end-to-end AMP discovery in which a Planning Agent orchestrates specialized executors for generation, filtering, and verification. Its prioritization recommendations align with our in vitro outcomes. Together, these contributions let us examine, on a small but real scale, how generative and agentic AI compose in therapeutic peptide discovery. Code: https://github.com/marszzibros/AMPGANv3

Radiology report evaluation must distinguish clinical compatibility from surface similarity, because negation, laterality, or normal-abnormal polarity can reverse a finding. We propose RadSEM (Radiology Sentence-Level Evaluation Metric), a constrained LLM-assisted metric for reference-based evaluation of radiology Findings. RadSEM rewrites reference and generated reports into ordered atomic finding sentences, each expressing one site-finding proposition. It then performs contradiction-constrained many-to-many matching: incompatible pairs such as "effusion" and "no effusion" receive no credit, while compatible granularity differences can receive partial credit. A deterministic stage weights pairs by part-whole and abnormal-detail relationships, counts unmatched findings, and produces an abnormal-focused weighted F1 score. Thus, the LLM supports structured rewriting and local alignment rather than acting as an opaque judge. We evaluate RadSEM with SSREE, a controlled monotonicity stress test built from 2,448 de-identified reports expanded into five graded corruption levels. RadSEM achieves Kendall tau_b of 0.957, all-pairs concordance of 97.8%, adjacent concordance of 95.0%, and strict five-level ordering for 81.9% of reports, outperforming radiology-specific and general text metrics while avoiding the failure in which polarity-inverted reports regain lexical overlap. On the same SSREE set, RadSEM outperforms the Ref-anchored RadSEM-Alt policy, improving adjacent concordance from 90.7% to 95.0% and strict ordering from 67.2% to 81.9%. On a 599-triplet synonym/antonym subset, RadSEM prefers synonyms in 597 cases (99.67%). These results suggest that explicit finding units, contradiction-aware matching, and abnormal-focused deterministic scoring make report scoring more interpretable and sensitive to clinically meaningful errors. Code is available at https://github.com/jdh-algo/RadSEM.

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis. Accurate forecast of the outcomes of a MD simulation is not only an attractive scientific challenge but also has substantial practical value. In this work, we developed a data-driven framework, termed ASTEROID (Advanced Spatiotemporal TransformER fOr Inferring Dynamics), that can directly predict multi-step atomic coordinates, avoiding conventional iterative integration. For this purpose, our ASTEROID reformulates MD trajectories as high-dimensional spatiotemporal sequences and integrates the Spatiotemporal Information (STI) Transformation equation into a Transformer architecture. The core innovation of ASTEROID lies in its ability to model multiscale spatiotemporal dependencies. In particular, for spatial dependencies, a local-global self-attention mechanism captures both short- and long-range interactions. For temporal dependencies, an encoder-decoder structure integrates global context with autoregressive forecasting. ASTEROID was evaluated on several quantum-mechanics derived molecular datasets. Our results indicate that ASTEROID achieved not only a higher level of accuracy in multi-step prediction than existing methods on various benchmarks, but also significantly reduced computational cost of conventional MD simulation. Moreover, the model supports iterative multi-step forecasting over an extended time scale. This work establishes a robust and generalizable data-driven paradigm for accelerating MD simulations.

Rolling over is one of the earliest milestones in infant motor development, reflecting the emergence of coordinated, whole-body sensorimotor control. Here, we conduct a computational study of infant rolling using MIMo, a virtual infant embodiment equipped with proprioception and vestibular sensation. MIMo learns supine-to-prone rolls with reinforcement learning. Interestingly, the learned behaviors capture developmental trends and coordination patterns consistent with those reported in real infants, including improved performance and faster execution with age. Our results explain how infant capabilities and constraints can give rise to realistic behaviors in artificial agents, with a particular emphasis on how motor development is shaped by the changing body morphology. This work highlights the role of embodied computational models as a powerful tool for studying sensorimotor development.

Foundation models (FMs) have emerged as powerful representation extractors for medical data, yet their generalizability to datasets under distribution shift remains underexplored. This work systematically evaluates FM-based representations on a suite of computational pathology tasks across two real-world commercial cohorts, IH-BC and IH-NSCLC, drawn from the licensed in-house (IH) oncology dataset. The analysis focuses on two modalities, whole-slide images and transcriptomic profiles, drawn from the IH multimodal data. We first benchmark unimodal probing performance across five FMs on eight downstream classification tasks, and find that image and omics representations carry complementary predictive signals. Then we investigate whether multimodal fusion can yield additional gains over unimodal baselines by comparing three image-omics fusion strategies built on paired representations. The trustworthiness of selected unimodal and multimodal pipelines is further assessed through conformal prediction. Our results show that FM representations achieve competitive performance on out-of-distribution data and that multimodal fusion helps mainly when no single modality dominates the signal. Conformal prediction reveals that in the majority of cases where a point prediction fails, the true diagnosis remains recoverable within the prediction set, reinforcing the value of uncertainty-aware inference for clinical support.

Prey aggregation is widely regarded as a defense against predation, yet we show that in disease-structured populations subject to predator-induced fear and demographic Allee thresholds, aggregation can paradoxically accelerate ecosystem collapse. We develop and analyze a susceptible-infectious-predator model incorporating dual fear responses -- together with a sublinear aggregation-based predation term and an Allee effect. Critically, we derive an explicit upper bound on the extinction time that decreases as predator pressure increases or aggregation strengthens, quantifying for the first time how behavioral and demographic parameters jointly determine the speed of ecological collapse. This finite-time extinction subsequently triggers a cascade collapse of the infected prey and predator populations, driving the entire ecological community to extinction. Bifurcation analysis reveals transcritical, saddle-node, and Hopf bifurcations as fear intensity, aggregation strength, and Allee threshold vary. Two-parameter continuation further identifies the precise regions of the fear--Allee parameter plane in which stable coexistence, oscillatory coexistence, predator exclusion, and finite-time extinction occur, demonstrating that stronger aggregation monotonically enlarges the finite-time extinction region while weaker aggregation supports a richer landscape of coexistence dynamics. These results demonstrate that behavioral defenses operating at the population level can generate abrupt ecological tipping points when they interact with disease dynamics and demographic vulnerability.

We formulate and analyze a sex- and stage-structured model for Anopheles dynamics under the sterile insect technique (SIT), motivated by the need for tools robust to insecticide resistance and outdoor transmission. The model tracks aquatic stages, adult males, unmated females, and females mated with wild or sterile males; includes egg-laying capacity and larval competition; and uses a refractory period followed by density-dependent mate search. The resulting Holling type-II mating term generates a mate-finding Allee effect. After establishing well-posedness, we prove that this Allee effect makes the mosquito-free equilibrium locally stable for all admissible parameters and globally asymptotically stable when a quick-mate-search reproduction number $R_0^q$ is below one. When $R_0^q>1$, habitat capacity is large, and larval competition is weak, two positive equilibria arise through a saddle-node bifurcation: a stable natural equilibrium and an unstable Allee equilibrium separating persistence from extinction. For a reduced model, a Goh-Volterra Lyapunov functional estimates the persistence basin. We then show how constant and population-responsive sterile-male releases reshape this bistability. Sufficiently large releases annihilate the positive equilibria in a second saddle-node bifurcation, while a sufficiently large constant release drives local elimination from every admissible initial state. Thus SIT need only push the population across the Allee separatrix, after which mate-finding failure can complete extinction. In a free-horizon optimization framework with an Allee-threshold stopping rule, a hybrid release strategy reduces the sterile-male requirement by about $5\%$ relative to the best constant-only strategy and $39\%$ relative to the best population-responsive-only strategy. These results recast the Allee effect as a control lever for vector suppression.

We ask whether knotting can be recognised using persistent homology. Starting from a point-cloud representation of a curve, we compute one-dimensional persistent homology, extract cycle representatives, and assign a hypergraph curvature-based score to these cycles. Motivated by proteins but tested more broadly, the method reveals systematic differences between knotted and unknotted structures in both protein families and synthetic examples. This suggests that knotting leaves a detectable persistent-homology-based signature.

Collective migration of heterogeneous cell populations is central to many biological and physiological processes, including development and immune response. Recent experimental and theoretical advances have shown how asymmetric interactions with self-generated chemical gradients shape the spatial distribution of distinct cell types within migrating collectives. However, the principles governing robust spatial organisation of heterogeneous cell populations remain poorly understood. Here, we use asymptotic analysis to systematically derive a nonlinear analytical theory for heterogeneous cell collectives guided by self-generated chemotaxis. Our theory disentangles how heterogeneity in cell diffusivity, chemoattractant consumption, and chemotactic sensitivity shape the density profiles of migrating heterogeneous collectives, revealing four distinct dynamical behaviours that together capture all possible regimes. We calibrate our framework to experimental data on the co-migration of dendritic and T cells. We predict that this system operates in a parameter regime that balances intercellular mixing with T-cell localisation at the leading front of the migrating collective. Our theory reveals that this behaviour is enabled by intermediate long-range chemoattractant signalling generated through strong chemoattractant consumption by dendritic cells. Overall, our framework provides general principles for understanding how non-reciprocal chemical interactions shape robust collective migration in heterogeneous cell populations.

Exploration in deep reinforcement learning (RL) is commonly implemented as temporally uncorrelated white noise. However, recent works show that temporally correlated colored noise can improve exploration efficiency by producing smooth trajectories with better coverage of the state space. We inquire whether action noise inspired by infant spontaneous movements can also improve exploration in deep RL. We find that the power spectral densities of babies' end-effector velocities follow a colored noise process where the spectral exponent increases with age. Inspired by this developmental pattern, we introduce a mechanism that progressively increases the temporal auto-correlation of exploration noise during RL training, matching the infant statistics. Experiments across several RL environments show that infant-inspired noise produces structured exploratory behavior and can improve learning efficiency compared to conventional exploration strategies. These findings suggest that human motor and cognitive development can provide useful guidance for designing learning mechanisms in artificial agents. Our code is available at https://github.com/trieschlab/baby-noise-rl.

Warm-blooded vertebrates accumulate approximately conserved numbers of physiological cycles over a natural lifetime: of order $10^9$ heartbeats and $10^8$--$3\times10^8$ breaths. These regularities are not exact constants, but their persistence across orders-of-magnitude variation in body mass, metabolic power, physiological frequency, and lifespan suggests that biological time is not measured by chronological duration alone. We develop the Principle of Biological Time Equivalence (PBTE), a thermodynamic framework in which lifetime cycle count is determined by the ratio between total lifetime entropy production and the entropy cost of one physiological cycle. Starting from the open-system entropy balance $\dot S=\dot e_p-\dot h_d$, we define the entropy cost per cycle as $σ_0=dΣ/dN$, where $dΣ$ is the entropy produced as the physiological clock advances by $dN$ cycles. For an adult homeostatic regime, this gives the cycle-count relation $N_\star=Σ/\langleσ_0\rangle$, with $Σ=\int_0^L \dot e_p(t)\,dt$, where $N_\star$ is the lifetime cycle count, $Σ$ is total lifetime entropy production, and $\langleσ_0\rangle$ is the lifetime-averaged entropy cost per cycle. In the homeostatic limit, $\dot e_p\simeq P/T$, so direct measurement of metabolic power $P$, body temperature $T$, and physiological frequency $f$ gives $σ_0\simeq P/(Tf)$. PBTE converts the empirical lifetime-cycle invariants into entropy-cost invariants. Under Kleiber metabolic scaling and quarter-power physiological-frequency scaling, the mass-specific entropy cost satisfies $\barσ_0=P/(TfM)\propto M^{3/4+1/4-1}=M^0$, providing a thermodynamic interpretation of allometric mass cancellation.

Nearby neurons in cortex share similar response profiles, producing systematic spatial organization across sensory and cognitive systems. Recent topographic models reproduce aspects of this structure but remain unimodal and spatially constrain each layer separately, yielding fragmented maps that capture neither the contiguity of cortical processing streams nor their integration across modalities. We introduce Topo-Omni, a topographic multimodal model in which visual, auditory, and language/cognitive processing share a single contiguous in-silico sheet. Built by fine-tuning a pretrained foundation model with a spatial smoothness objective, this architecture develops clusters across modalities that are consistent with human neuroimaging, from sensory to cognitive systems. Driving or suppressing a cluster selectively biases or impairs perception, paralleling human intervention studies. Finally, we use our model to screen for novel clusters in-silico and discover new natural landscape and animal networks which we validate in human data. A single spatial principle thus organizes representations across modalities and processing stages, yielding testable hypotheses about cortical organization.

The study of representations is widespread across fields, including neuroscience, psychology, and artificial intelligence. While representations are often studied and compared through similarities between stimuli, current methods provide only limited access to the dimensions that shape these representations and are often limited in interpretability. To overcome these challenges, here we introduce Similarity-Based Representation Factorization (SRF), a general computational method for recovering low-dimensional, non-negative, interpretable embeddings from similarity matrices derived from measured data. Across simulations and many neural, behavioral, and computational datasets, SRF recovers interpretable dimensions from diverse forms of representational data, even for very sparsely sampled, incomplete data. The dimensions derived from these datasets match those obtained by task-specific models, predict independent behavioral properties, improve exploratory analysis, and offer higher power for confirmatory hypothesis testing than comparing similarity matrices. Together, these results establish SRF as a general-purpose method with broad applications for uncovering, understanding, and using the dimensions underlying representations.

Motion retargeting from humans to human-like artificial agents is becoming increasingly important as humanoid robots grow more capable. However, most existing approaches focus only on reproducing kinematics and ignore the rich sensorimotor experience associated with human movement. In this work, we present a framework for simulating the multimodal sensorimotor experiences of infants using physical and virtual humanoids. From a single video, our method reconstructs the infant's body configuration by extracting its skeletal structure and estimating the full 3D pose from each frame. Then we map the reconstructed motion onto several developmental platforms: the physical iCub robot and the virtual simulators pyCub, EMFANT and MIMo. Replaying the retargeted motions on these embodiments produces simulated multisensory streams including proprioception (joints and muscles), touch, and vision. For the best-matching embodiment, the retargeting achieves sub-centimeter accuracy and enables a rich multimodal analysis of infant development as well as enhanced automated annotation of behaviors. This framework provides a unique window into the infant's sensorimotor experience, offering new tools for robotics, developmental science, and early detection of neurodevelopmental disorders. The code is available at https://github.com/ctu-vras/motion-retargeting/.

Intersectional biases in healthcare data can produce compound disparities in clinical machine learning models, yet most fairness evaluations assess demographic attributes independently. FairLogue, a toolkit for intersectional fairness auditing, was applied across multiple clinical prediction tasks to evaluate disparities across combined demographic groups. Using the All of Us dataset, two published models were selected for replication and evaluation: (A) prediction of selective serotonin reuptake inhibitor associated bleeding events and (B) two-year stroke risk in patients with atrial fibrillation. Observational fairness metrics were computed across race, gender, and intersectional subgroups, followed by counterfactual analysis to evaluate whether disparities were attributable to group membership. Intersectional evaluation revealed larger disparities than single-axis analyses; however, counterfactual diagnostics indicated that most observed disparities were comparable to those expected under randomized group membership. These results highlight the importance of intersectional fairness auditing and demonstrate how FairLogue provides deeper insight into bias in clinical machine learning systems.

Most functional magnetic resonance imaging studies rely on estimates of hierarchically organized functional brain networks whose segregation and integration reflect the cognitive and behavioral changes in humans. However, most existing methods for estimating the community structure of networks from both individual and group-level analysis methods do not account for the variability between subjects. In this paper, we develop a new multilayer community detection method based on Bayesian latent block model (LBM). The method can robustly detect the community structure of weighted functional networks with an unknown number of communities at both individual and group levels and retain the variability of the individual networks. For validation, we propose a new community structure-based multivariate Gaussian generative model to simulate synthetic signal. Our simulation study shows that the community memberships estimated by hierarchical Bayesian inference are consistent with the predefined node labels in the generative model. The method is also tested via split-half reproducibility using working memory task fMRI data of 100 unrelated healthy subjects from the Human Connectome Project. Analyses using both synthetic and real data show that our proposed method is more accurate and reliable compared with the commonly used (multilayer) modularity models.

Our subjective experience of color is typically described by abstract properties such as hue, saturation, and brightness that do not directly correspond to sensory signals arising from cones in the retina. Along the hue dimension, certain colors -- red, green, blue, and yellow -- appear unique in that they are not perceived as a combination of other colors, and the pairs red-green and blue-yellow appear opposites. However, the anatomical and physiological correlates of these 'unique hues' within the brain and the reason for their existence remain a mystery. Here, we demonstrate a direct connection between these hues and the statistics of the natural visual environment. Analysis of simulated cone responses on a dataset of 503 calibrated natural images reveals a strongly non-Gaussian distribution in 3D color space, with heavy tails in distinct, asymmetrically arranged directions. A sparse coding model is then adapted to this data so as to minimize the total sum of coefficients on the basis vectors for representing the data. A six basis-vector model converges to the four unique hues in addition to black and white. Moreover, we find that the nonlinear nature of inference in the sparse coding model yields both excitatory and inhibitory interactions among latent variables; the former facilitates combining adjacent pairs of unique hues to encode intermediate hues situated between them, while the latter enforces mutual exclusivity between opposite unique hues. Together, these findings shed new light on the distribution of color in the natural environment and provide a linking principle between this structure and the phenomenology of color appearance.

Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but existing methods typically analyze these modalities in isolation or at limited resolution. We address the problem by introducing SPATIA, a multi-level generative and predictive model that learns unified, spatially aware representations by fusing morphology, gene expression, and spatial context from the cell to the tissue level. SPATIA also incorporates a spatially conditioned generative framework with confidence-aware OT reweighting and morphology-profile alignment for modeling target-state morphology distributions. Specifically, we propose a confidence-aware flow matching objective that reweights weak optimal-transport pairs based on uncertainty. We further apply morphology-profile alignment to encourage biologically meaningful image generation, enabling the modeling of microenvironment-dependent phenotypic transitions. We assembled a multi-scale dataset consisting of 25.9 million cell-gene pairs across 17 tissues. We benchmark SPATIA against 18 models across 12 tasks, spanning categories such as phenotype generation, annotation, clustering, gene imputation, and cross-modal prediction. SPATIA achieves improved performance over state-of-the-art models, improving generative fidelity by 8% and predictive accuracy by up to 3%.

Predicting transcriptional responses to genetic perturbations is a central problem in functional genomics. In practice, perturbation responses are rarely gene-independent but instead manifest as coordinated, program-level transcriptional changes among functionally related genes. However, most existing methods do not explicitly model such coordination, due to gene-wise modeling paradigms and reliance on static biological priors that cannot capture dynamic program reorganization. To address these limitations, we propose scBIG, a module-inductive perturbation prediction framework that explicitly models coordinated gene programs. scBIG induces coherent gene programs from data via Gene-Relation Clustering, captures inter-program interactions through a Gene-Cluster-Aware Encoder, and preserves modular coordination using structure-aware alignment objectives. These structured representations are then modeled using conditional flow matching to enable flexible and generalizable perturbation prediction. Extensive experiments on multiple single-cell perturbation benchmarks show that scBIG consistently outperforms state-of-the-art methods, particularly on unseen and combinatorial perturbation settings, achieving an average improvement of 6.7% over the strongest baselines. The code is available at https://github.com/ttruan2426-dot/scBIG.

Living cells exhibit nonequilibrium dynamics that shape intracellular processes across length scales, from nanoscale molecular assembly to the organization of macroscopic organelles. While dynamics at micrometer scales are known to be constrained by the actin meshwork at low frequencies, the physical principles governing active fluctuations at the nanoscale remain elusive. Here, we present an analytical framework integrating fluorescence correlation spectroscopy with nonequilibrium modeling to delineate the physical scaling of intracellular mechanics. Applying this framework to fibroblasts, we demonstrate that, in contrast to larger components, nanoscale active fluctuations remain prominent at high frequencies and are predominantly driven by local nonmuscle myosin II activity, establishing a distinct functional hierarchy in intracellular mechanics: local active forces promote rapid spatial exploration for nanoscale molecules, whereas macroscopic actin constraints ensure the structural stability required for larger molecular complexes and organelles. To integrate these scale-dependent behaviors within a single physical framework, we formulated a model that captures the transition of active fluctuations across length scales, revealing that the physical properties of the cytoplasm are governed by the balance between active driving forces and passive structural constraints. Furthermore, applying this model to cellular senescence reveals a reduction in nonequilibrium complexity associated with cytoskeletal rigidification. Thus, our findings bridge the dimensional gap between local molecular kinetics and macroscopic constraints, providing a fundamental physical basis for understanding the hierarchical organization of intracellular dynamics.

Topological analyses of brain functional connectivity usually reduce each pair of channels to a single scalar dependence, typically the Pearson correlation, and so cannot resolve the frequency-specific synchronisation that organises electrophysiology. We propose a topological summary that keeps the frequency information. The spectral landscape indexes the persistence landscape of Bubenik (2015) by Fourier frequency, building each filtration from a coherence-based distance, so that it is a function of both the filtration scale and the frequency. It is Lipschitz-stable in the coherence matrix and feeds a functional two-sample test over a chosen frequency band, whose limiting null distribution and consistency follow from standard functional-data arguments. In simulations the test recovers a topological difference in the band where it lives while holding its nominal level under the null. Applied to electroencephalography from 53 control and 51 ADHD children, a global test rejects equality of the two groups' cycle topology at the 95% level (p = 0.019); a band-by-band follow-up localises the difference to the gamma and theta bands, although none survives family-wise correction at this sample size. The pattern is consistent with the established role of these bands in ADHD.