Brain functional connectivity alterations, that is, pathological changes in the signal exchange between areas of the brain, occur in several neurological diseases, including neurodegenerative and neuropsychiatric ones. They consist in changes in how brain functional networks operate. By conceptualising a brain space as a space whose points are connectome configurations representing brain functional states, changes in brain network functionality can be represented by paths between these points. Paths from a healthy state to a diseased one, or between diseased states as instances of disease progression, are modelled as the action of the Krankheit-Operator, which produces changes from a brain functional state to another. This study proposes a formal representation of the space of brain states and presents its computational definition. References to patients affected by Parkinson's disease, schizophrenia, and Alzheimer-Perusini's disease are included to discuss the proposed approach and possible developments of the research toward a generalisation.

Electroencephalographic (EEG) signals provide macroscopic observables of complex neural dynamics. We introduce a horizon-inspired framework in which measured EEG signals are modeled as projections of a complex wave-like representation constrained by an effective boundary analogous to an event horizon. In this formulation the signal amplitude obeys a renormalization-group scaling relation while EEG spectral entropy parameterizes the accessibility of observable modes. The resulting solutions generate oscillatory structures whose geometry and spectral signatures can be explored through signal analysis and sonification. This mapping between entropy-based neural observables and wave-like signal representations provides a physically motivated framework linking entropy measures, scale-dependent dynamics, and observable neural oscillations, and suggests testable connections between spectral entropy and the amplitude scaling of EEG modes.

Fluorescence-based Ca$^{2+}$-imaging is a powerful tool for studying localized neuronal activity, including miniature Synaptic Calcium Transients, providing real-time insights into synaptic activity. These transients induce only subtle changes in the fluorescence signal, often barely above baseline, which poses a significant challenge for automated synaptic transient detection and segmentation. Detecting astronomical transients similarly requires efficient algorithms that will remain robust over a large field of view with varying noise properties. We leverage techniques used in astronomical transient detection for miniature Synaptic Calcium Transient detection in fluorescence microscopy. We present Astro-BEATS, an automatic miniature Synaptic Calcium Transient segmentation algorithm that incorporates image estimation and source-finding techniques used in astronomy and designed for Ca$^{2+}$-imaging videos. Astro-BEATS outperforms current threshold-based approaches for synaptic Ca$^{2+}$ transient detection and segmentation. The produced segmentation masks can be used to train a supervised deep learning algorithm for improved synaptic Ca$^{2+}$ transient detection in Ca$^{2+}$-imaging data. The speed of Astro-BEATS and its applicability to previously unseen datasets without re-optimization makes it particularly useful for generating training datasets for deep learning-based approaches.

Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret because current benchmarks may overestimate generalization across RNA families. We present the Comprehensive Hierarchical Annotation of Non-coding RNA Groups (CHANRG), a benchmark of 170{,}083 structurally non-redundant RNAs curated from more than 10 million sequences in Rfam~15.0 using structure-aware deduplication, genome-aware split design and multiscale structural evaluation. Across 29 predictors, foundation-model methods achieved the highest held-out accuracy but lost most of that advantage out of distribution, whereas structured decoders and direct neural predictors remained markedly more robust. This gap persisted after controlling for sequence length and reflected both loss of structural coverage and incorrect higher-order wiring. Together, CHANRG and a padding-free, symmetry-aware evaluation stack provide a stricter and batch-invariant framework for developing RNA structure predictors with demonstrable out-of-distribution robustness.

Aphasia, a language impairment primarily resulting from stroke or brain injury, profoundly disrupts communication and everyday functioning. Despite advances in speech therapy, barriers such as limited therapist availability and the scarcity of personalized, culturally relevant tools continue to hinder optimal rehabilitation outcomes. This paper reviews recent developments in neurocognitive research and language technologies that contribute to the diagnosis and therapy of aphasia. Drawing on findings from our ethnographic field study, we introduce two digital therapy prototypes designed to reflect local linguistic diversity and enhance patient engagement. We also show how insights from neuroscience and the local context guided the design of these tools to better meet patient and therapist needs. Our work highlights the potential of adaptive, AI-enhanced assistive technologies to complement conventional therapy and broaden access to therapy. We conclude by outlining future research directions for advancing personalized and scalable aphasia rehabilitation.

Accurate prediction of synthetic lethality (SL) is important for guiding the development of cancer drugs and therapies. SL prediction faces significant challenges in the effective fusion of heterogeneous multi-source data. Existing multimodal methods often suffer from "modality laziness" due to disparate convergence speeds, which hinders the exploitation of complementary information. This is also one reason why most existing SL prediction models cannot perform well on both pan-cancer and single-cancer SL pair prediction. In this study, we propose SynLeaF, a dual-stage multimodal fusion framework for SL prediction across pan- and single-cancer contexts. The framework employs a VAE-based cross-encoder with a product of experts mechanism to fuse four omics data types (gene expression, mutation, methylation, and CNV), while simultaneously utilizing a relational graph convolutional network to capture structured gene representations from biomedical knowledge graphs. To mitigate modality laziness, SynLeaF introduces a dual-stage training mechanism employing featurelevel knowledge distillation with adaptive uni-modal teacher and ensemble strategies. In extensive experiments across eight specific cancer types and a pancancer dataset, SynLeaF achieves superior performance in 17 out of 19 scenarios. Ablation studies and gradient analyses further validate the critical contributions of the proposed fusion and distillation mechanisms to model robustness and generalization. To facilitate community use, a web server is available at this https URL.

Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent advances, significant challenges remain, including the treatment of batch effects, the handling of mixed cell-type signals, and the imputation of poorly measured or missing gene expression. This work addresses these challenges by introducing a novel Subspace Tensor Orthogonal Rotation Model (STORM) that aligns multiple slices which vary in their spatial dimensions and geometry by considering them at the level of physical patterns or microenvironments. To this end, STORM presents an irregular tensor factorization technique for decomposing a collection of gene expression matrices and integrating them into a shared latent space for downstream analysis. In contrast to black-box deep learning approaches, the proposed model is inherently interpretable. Numerical experiments demonstrate state-of-the-art performance in vertical and horizontal batch integration, cell-type deconvolution, and unmeasured gene imputation for spatial transcriptomics data.

We consider the SEIRS epidemiology model with such features of the COVID-19 outbreak as: abundance of unidentified infected individuals, limited time of immunity and a possibility of vaccination. The control of the pandemic dynamics is possible by restricting the transmission rate, increasing identification and isolation rate of infected individuals, and via vaccination. For the compartmental version of this model, we found stable disease-free and endemic stationary states. The basic reproductive number is analysed with respect to balancing quarantine and vaccination measures. The positions and heights of the first peak of outbreak are obtained numerically and fitted to simple in usage algebraic forms. Lattice-based realization of this model is studied by means of the asynchronous cellular automaton algorithm. This permitted to study the effect of social distancing by varying the neighbourhood size of the model. The attempt is made to match the quarantine and vaccination effects.

Musculoskeletal injuries (MSI) in Thoroughbred racehorses are a leading cause of death and premature retirement in racehorses and are heavily influenced by training practices. Greater distances of high-speed galloping accumulated during racing campaigns are associated with MSI. Bone injury is the most common MSI, and understanding how training practices influence bone damage accumulation is critical for improving both horse welfare and racing outcomes. This study builds on an existing mathematical model of bone adaptation and damage to investigate the impact of different training programs on bone injury risk. Several training programs (three progressive, four race-fit, six rest programs and two with rest replaced by low-intensity training) were constructed to reflect representative practices undertaken by professional trainers in Victoria, Australia. Training programs varied in training volume, rest frequency and program duration. Lower volume training programs that included high-speed training, achieved sufficient bone adaptation with less accumulation of bone damage, and subsequently lower risk of bone failure. In addition, incorporating more frequent rests (at least 2 per year) and/or longer rest periods (at least 6 weeks) reduced bone damage due to the extended opportunity to remove and repair bone damage. These results provide an in-silico mathematical model of the bone response to training, demonstrating the effects of training programs on bone adaptation, damage formation and repair. The findings can guide the design of training programs that balance both bone adaptation and bone health throughout horses racing career.

Background: Autism spectrum disorder (ASD) is characterized by significant clinical and biological heterogeneity. Conventional group-mean analyses of eye movements often mask individual atypicalities, potentially overlooking critical pathological signatures. This study aimed to identify idiosyncratic oculomotor patterns in ASD using an "outlier analysis" of smooth pursuit eye movement (SPEM). Methods: We recorded SPEM during a slow Lissajous pursuit task in 18 adults with ASD and 39 typically developed (TD) individuals. To quantify individual deviations, we derived an "outlier score" based on the Mahalanobis distance. This score was calculated from a feature vector, optimized via Principal Component Analysis (PCA), comprising the temporal lag ($\Delta$t) and the spatial deviation ($\Delta$s). An outlier was statistically defined as a score exceeding $\sqrt{10}$ (approximately 3.16$\sigma$) relative to the TD normative distribution. Results: While the TD group exhibited a low outlier rate of 5.1\%, the ASD group demonstrated a significantly higher prevalence of 38.9\% (7/18) (binomial P = 0.0034). Furthermore, the mean outlier score was significantly elevated in the ASD group (3.00 $\pm$ 2.62) compared to the TD group (1.52 $\pm$ 0.80; P = 0.002). Notably, these extreme deviations were captured even when conventional mean-based comparisons showed limited sensitivity. Conclusions: Our outlier analysis successfully visualized the high degree of idiosyncratic atypicality in ASD oculomotor control. By shifting the focus from group averages to individual deviations, this approach provides a sensitive metric for capturing the inherent heterogeneity of ASD, offering a potential baseline for identifying clinical subtypes.

The incorporation of neuroimaging techniques such as electroenchephalography (EEG) and functional near-infrared spectroscopy (fNIRS) has provided new opportunities for the analysis of dynamic brain processes involved in cognitive and motor functions. Despite the great contribution of the open-access neuroimaging datasets to neuroscience studies, they have mainly remained on a single modality and isolated task paradigms performed in a controlled environments. These limitations restrict the analysis of multi-task effects in real-world applications, thus creating a gap in the understanding of how cognitive and motor processes interact in daily life activities. To address these limitations, we present a multi-modal dataset containing neurophysiological (EEG, fNIRS), physiological (ECG), behavioral, and subjective measures collected from 30 healthy participants over three sessions. This dataset includes a hierarchical series of seven tasks ranging from single cognitive and motor activities, such as N-back, motor, passive motor, mental arithmetic and motor imagery, to combined cognitive-motor interactions simulating real life scenarios. This raw dataset provides a resource for developing advanced preprocessing methods and analysis pipelines, with potential applications in brain-computer interfaces, neurorehabilitation, and other fields requiring an understanding of multi-tasks brain dynamics. this https URL

Alzheimer's disease (AD) develops over a prolonged preclinical phase, during which neuropathological changes accumulate long before cognitive symptoms appear. Identifying cognitive functions affected at early stages is critical for the preclinical detection of asymptomatic individuals at-risk of AD. Early risk identification could enable timely interventions aimed at mitigating the development of significant future cognitive impairment. While episodic memory decline typically appears after substantial medial temporal lobe damage, spatial navigation has emerged as a particularly sensitive cognitive function in preclinical AD. In this review, we provide an overview of spatial navigation computations and the tasks used to assess them, highlighting how spatial navigation relies on neural circuits corresponding to the earliest sites of AD pathology. We synthesize evidence from cognitively unimpaired individuals with AD biomarkers, i.e. individuals at-risk of AD, and discuss future research directions. Overall, performance on spatial navigation tasks, particularly path integration and wayfinding, correlates with plasma and CSF biomarkers of AD pathology, notably p-tau. Spatial navigation assessment can represent a sensitive and scalable approach for early detection of individuals at-risk of AD in preclinical stages, and will inform future interventions to mitigate the progression toward clinically significant cognitive impairment.

Mechanical loading in articular cartilage drives interstitial fluid flow through the porous collagen proteoglycan matrix, generating electrokinetic signals. We investigate whether the structural organization of cartilage histology can be translated into a computational representation capable of predicting its electrokinetic behavior. Histological pictures were analyzed to build a pore-network graph representing potential pathways for interstitial fluid transport. Pressure driven flow was simulated using hydraulic conductance relations, while electrical potentials were estimated through electrokinetic coupling between pressure gradients and ion displacement. Simulations comparing networks derived from healthy and degenerative cartilage showed that pathological structures exhibited fragmented connectivity and lower predicted signal amplitudes, whereas physiological architecture generated more coherent transport trajectories and stronger electrical responses. Our simulations yield testable predictions, depth-dependent electrical signals across cartilage layers with directional anisotropy relative to collagen orientation. Potential applications include improved experimental assessment of cartilage transport biomechanics and integration of microstructural imaging with computational models of charged porous biomaterials.

The disjunction effect in human decision making is often taken to show that the classical law of total probability is violated, motivating quantum-like models. We re-examine this claim for the Prisoner's Dilemma disjunction effect. Under the mental-event reading of the opponent-choice events, the conventional classical decision-process model implicitly builds in a certainty-only premise: its standard partition assumptions leave no room for ambiguity, forcing every participant to be certain that the opponent will defect or will cooperate. We relax this by introducing a new classical model in which each participant carries a continuous expectation parameter representing the anticipated likelihood of opponent defection, and the participant pool is partitioned by expectation level; the resulting ambiguity set is precisely the union of the interior expectation bins. In contrast, under the quantum-like event semantics, ambiguous pure states are generic (dense and of full unitarily invariant measure on the unit sphere), so "certainty states" are mathematically exceptional. We prove that an instance of our classical model can realize any empirically observed triple of defection rates across the three information conditions, including strong disjunction-effect patterns, while strictly obeying the classical law of total probability. We further prove that for any such triple produced by a standard quantum-like model of the same experiment, there exists a classical instance reproducing it exactly. In this sense, classical and quantum-like approaches have the same observable-rate expressiveness; their substantive difference lies in how ambiguity is represented and in their respective event semantics, not in a breakdown of classical probability.

This proof-of-concept study introduces a novel multimodal framework combining synchronized EEG-fNIRS modalities with neuronal avalanche analysis to identify early network dysfunction in Alzheimer's disease. The approach leverages complementary neural signals to examine motor network dynamics during execution and imagery tasks within an interactive task environment. Preliminary analysis of a small pilot cohort (N=4 subjects, including one with Mild Cognitive Impairment) validated the technical feasibility of the multimodal framework and revealed observable condition-dependent patterns in network organization. Two primary observations emerged: a reduced neural contrast between motor execution and imagery states, and increased trial-to-trial variability in network organization in the MCI participant. These initial results successfully validate the technical pipeline and provide hypothesis-generating observations for future statistically powered studies. The convergence of findings across modalities suggests that multimodal assessment of network flexibility may help detect functional changes in early Alzheimer's continuum, supporting the future development of this BCI-inspired framework into an engaging diagnostic tool.

The development of new drugs is a tedious, time-consuming, and expensive process, for which the average costs are estimated to be up to around $2.5 billion. The first step in this long process is the design of the new drug, for which de novo drug design, assisted by artificial intelligence, has blossomed in recent years and revolutionized the field. In particular, generative artificial intelligence has delivered promising results in drug discovery and development, reducing costs and the time to solution. However, classical generative models, such as generative adversarial networks (GANs), are difficult to train due to barren plateaus and prone to mode collapse. Quantum computing may be an avenue to overcome these issues and provide models with fewer parameters, thereby enhancing the generalizability of GANs. We propose a new style-based quantum GAN (QGAN) architecture for drug design that implements noise encoding at every rotational gate of the circuit and a gradient penalty in the loss function to mitigate mode collapse. Our pipeline employs a variational autoencoder to represent the molecular structure in a latent space, which is then used as input to our QGAN. Our baseline model runs on up to 15 qubits to validate our architecture on quantum simulators, and a 156-qubit IBM Heron quantum computer in the five-qubit setup is used for inference to investigate the effects of using real quantum hardware on the analysis. We benchmark our results against classical models as provided by the MOSES benchmark suite.

We introduce the Dual-View Pheromone Pathway Network (DPPN), an architecture that routes sparse attention through a persistent pheromone field over latent slot transitions, and use it to discover two independent requirements for persistent structural memory in neural networks. Through five progressively refined experiments using up to 10 seeds per condition across 5 model variants and 4 transfer targets, we identify a core principle: persistent memory requires a stable coordinate system, and any coordinate system learned jointly with the model is inherently unstable. We characterize three obstacles -- pheromone saturation, surface-structure entanglement, and coordinate incompatibility -- and show that neither contrastive updates, multi-source distillation, Hungarian alignment, nor semantic decomposition resolves the instability when embeddings are learned from scratch. Fixed random Fourier features provide extrinsic coordinates that are stable, structure-blind, and informative, but coordinate stability alone is insufficient: routing-bias pheromone does not transfer (10 seeds, p>0.05). DPPN outperforms transformer and random sparse baselines for within-task learning (AULC 0.700 vs 0.680 vs 0.670). Replacing routing bias with learning-rate modulation eliminates negative transfer: warm pheromone as a learning-rate prior achieves +0.003 on same-family tasks (17 seeds, p<0.05) while never reducing performance. A structure completion function over extrinsic coordinates produces +0.006 same-family bonus beyond regularization, showing the catch-22 between stability and informativeness is partially permeable to learned functions. The contribution is two independent requirements for persistent structural memory: (a) coordinate stability and (b) graceful transfer mechanism.

Biological AI models increasingly predict complex cellular responses, yet their learned representations remain disconnected from the molecular processes they aim to capture. We present CDT-III, which extends mechanism-oriented AI across the full central dogma: DNA, RNA, and protein. Its two-stage Virtual Cell Embedder architecture mirrors the spatial compartmentalization of the cell: VCE-N models transcription in the nucleus and VCE-C models translation in the cytosol. On five held-out genes, CDT-III achieves per-gene RNA r=0.843 and protein r=0.969. Adding protein prediction improves RNA performance (r=0.804 to 0.843), demonstrating that downstream tasks regularize upstream representations. Protein supervision sharpens DNA-level interpretability, increasing CTCF enrichment by 30%. Applied to in silico CD52 knockdown approximating Alemtuzumab, the model predicts 29/29 protein changes correctly and rediscovers 5 of 7 known clinical side effects without clinical data. Gradient-based side effect profiling requires only unperturbed baseline data (r=0.939), enabling screening of all 2,361 genes without new experiments.

Understanding how electric fields destabilize biological membranes is important for electroporation-based technologies and bioelectronic interfaces. However, theoretical descriptions of this phenomenon remain fragmented. Existing theories treat either electrostatics in membranes of finite thickness or electrohydrodynamic flows at idealized zero-thickness interfaces, leaving unresolved a unified description that simultaneously incorporates finite membrane thickness, surface charge, and bulk electrohydrodynamics. Here, we apply a recently-developed, dimension-reduction framework that captures the coupled electrohydrodynamic and mechanical effects governing height fluctuations of a charged lipid bilayer of thickness $\delta$ in an electrolyte characterized by Debye screening length $\lambda$. We derive voltage- and charge-dependent renormalizations of the effective surface tension and bending rigidity, along with a dispersion relation governing undulatory instabilities. A wide range of prior theoretical results arise as limiting cases of our more general theory when finite-thickness effects are neglected or screening is asymptotically strong. The key new contribution arises from traction moments generated across the finite membrane thickness, which are absent in zero-thickness descriptions. Under physiological screening ($\delta/\lambda\sim 4$), these contributions account for more than $>70\%$ of the total electrostatic correction to both surface tension and bending rigidity. The theory further reveals that surface charges can stabilize the membrane at physiological ionic strengths, increasing the effective tension and shifting electroporation thresholds in a manner that depends on charge asymmetry between the leaflets.

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug to its protein target. A major drawback of the approaches is that they require exceptional computing capabilities to consider for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently proposed learning paradigm that is able to leverage low-precision binary vector arithmetic to build efficient representations of the data that can be obtained without the need for gradient-based optimization approaches that are required in many conventional machine learning and deep learning approaches. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated for a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encoding algorithms that leverage the extended connectivity fingerprint (ECFP) algorithm. We show that HDC-based inference methods are as much as 90 times more efficient than more complex representative machine learning methods and achieve an acceleration of nearly 9 orders of magnitude as compared to inference with molecular docking. We demonstrate multiple approaches for the encoding of molecular data for HDC and examine their relative performance on a range of challenging molecular property prediction and drug-protein binding classification tasks. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools.

Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence space for categorization of aggregate morphology remains intractable. We introduce PepMorph, an end-to-end peptide discovery pipeline that generates novel sequences that are not only prone to aggregate but whose self-assembly is steered toward fibrillar or spherical morphologies by conditioning on isolated peptide descriptors that serve as morphology proxies. To this end, we compiled a new dataset by leveraging existing aggregation propensity datasets and extracting geometric and physicochemical descriptors. This dataset is then used to train a Transformer-based Conditional Variational Autoencoder with a masking mechanism, which generates novel peptides under arbitrary conditioning. After filtering to ensure design specifications and validation of generated sequences through coarse-grained molecular dynamics (CG-MD) simulations, PepMorph yielded 83% success rate under our CG-MD validation protocol and morphology criterion for the targeted class, showcasing its promise as a framework for application-driven peptide discovery.

Waning immunity and reinfection are critical features of many infectious diseases, but epidemiological models often fail to capture the intricate interaction between an individual's history of immunity and their current infection status; when they do, the approach is usually overly simplistic. We develop a novel dual-age structured model that simultaneously tracks immunity age (time since the last recovery from infection) and infection age (time since infection) to analyze epidemic dynamics under conditions of waning immunity and reinfection. The model is formulated as a system of age-structured partial differential equations that describe susceptible and infected populations stratified by both immunity and infection ages. We derive basic reproduction numbers associated with the model and numerically solve the system using a second-order Runge-Kutta scheme along the characteristic lines. We further extend the model to explore vaccination interventions, specifically targeting individuals according to their immunity age. Numerical results reveal that higher contact rates produce larger amplitude oscillations with longer interepidemic periods. The relationship between initial infection levels and long-term epidemic behavior is nonmonotonic. Vaccination efficiency depends critically on the viral load profile across immunity and infection age, with more pronounced viral load distributions requiring higher vaccination rates for disease elimination. Most efficient vaccination strategies begin with intermediate immunity ages rather than targeting only fully susceptible individuals. The structured dual-age framework provides a flexible approach to analyzing the dynamics of reinfection and evaluating targeted vaccination strategies based on the history of immunity.

Mental events are considered to supervene on physical events. A supervenient event does not change without a corresponding change in the underlying subvenient physical events. Since wholes and their parts exhibit the same supervenience-subvenience relations, inter-level causation has been expected to serve as a model for mental causation. We proposed an inter-level causation mechanism to construct a model of consciousness and an agent's self-determination. However, a significant gap exists between this mechanism and cognitive functions. Here, we demonstrate how to integrate the inter-level causation mechanism with the widely known dual-process theories. We assume that the supervenience level is composed of multiple supervenient functions (i.e., neural networks), and we argue that inter-level causation can be achieved by controlling the feedback error defined through changing algebraic expressions combining these functions. Using inter-level causation allows for a dual laws model in which each level possesses its own distinct dynamics. In this framework, the feedback error is determined independently by two processes: (1) the selection of equations combining supervenient functions, and (2) the negative feedback error reduction to satisfy the equations through adjustments of neurons and synapses. We interpret these two independent feedback controls as Type 1 and Type 2 processes in the dual process theories. As a result, theories of consciousness, agency, and dual process theory are unified into a single framework, and the characteristic features of Type 1 and Type 2 processes are naturally derived.

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse DNA elements, potentially enabling various genomic prediction, interpretation and design tasks. Despite their potential, existing benchmarks do not adequately assess the capabilities of DNALMs on key downstream applications involving an important class of non-coding DNA elements critical for regulating gene activity. In this study, we introduce DART-Eval, a suite of representative benchmarks specifically focused on regulatory DNA to evaluate model performance across zero-shot, probed, and fine-tuned scenarios against contemporary ab initio models as baselines. Our benchmarks target biologically meaningful downstream tasks such as functional sequence feature discovery, predicting cell-type specific regulatory activity, and counterfactual prediction of the impacts of genetic variants. We find that current DNALMs exhibit inconsistent performance and do not offer compelling gains over alternative baseline models for most tasks, while requiring significantly more computational resources. We discuss potentially promising modeling, data curation, and evaluation strategies for the next generation of DNALMs. Our code is available at this https URL.

Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges. Transformer-based models have made significant advances in this domain but are often limited by their quadratic complexity and suboptimal handling of long-range dependencies. In this work, we introduce GeneMamba, a scalable and efficient foundation model for single-cell transcriptomics built on state space modeling. Leveraging the Bi-Mamba architecture, GeneMamba captures bidirectional gene context with linear-time complexity, offering substantial computational gains over transformer baselines. The model is pretrained on nearly 30 million cells and incorporates biologically informed objectives, including pathway-aware contrastive loss and rank-based gene encoding. We evaluate GeneMamba across diverse tasks, including multi-batch integration, cell type annotation, and gene-gene correlation, demonstrating strong performance, interpretability, and robustness. These results position GeneMamba as a practical and powerful alternative to transformer-based methods, advancing the development of biologically grounded, scalable tools for large-scale single-cell data analysis.

Agent-based modeling (ABM) is a powerful tool for understanding self-organizing biological systems, but it is computationally intensive and often not analytically tractable. Equation learning (EQL) methods can derive continuum models from ABM data, but they typically require extensive simulations for each parameter set, raising concerns about generalizability. In this work, we extend EQL to Multi-experiment equation learning (ME-EQL) by introducing two methods: one-at-a-time ME-EQL (OAT ME-EQL), which learns individual models for each parameter set and connects them via interpolation, and embedded structure ME-EQL (ES ME-EQL), which builds a unified model library across parameters. We demonstrate these methods using a birth--death mean-field model and an on-lattice agent-based model of birth, death, and migration with spatial structure. Our results show that both methods significantly reduce the relative error in recovering parameters from agent-based simulations, with OAT ME-EQL offering better generalizability across parameter space. Our findings highlight the potential of equation learning from multiple experiments to enhance the generalizability and interpretability of learned models for complex biological systems.

Accurate and reliable forecasting models are critical for guiding public health responses and policy decisions during pandemics such as COVID-19. Retrospective evaluation of model performance is essential for improving epidemic forecasting capabilities. In this study, we used COVID-19 wastewater data from CDC's National Wastewater Surveillance System to generate sequential weekly retrospective forecasts for the United States from March 2022 through September 2024, both at the national level and for four major regions (Northeast, Midwest, South, and West). We produced 133 weekly forecasts using 11 models, including ARIMA, generalized additive models (GAM), simple linear regression (SLR), Prophet, and the n-sub-epidemic framework (top-ranked, weighted-ensemble, and unweighted-ensemble variants). Forecast performance was assessed using mean absolute error (MAE), mean squared error (MSE), weighted interval score (WIS), and 95% prediction interval coverage. The n-sub-epidemic unweighted ensembles outperformed all other models at 3-4-week horizons, particularly at the national level and in the Midwest and West. ARIMA and GAM performed best at 1-2-week horizons in most regions, whereas Prophet and SLR consistently underperformed across regions and horizons. These findings highlight the value of region-specific modeling strategies and demonstrate the utility of the n-sub-epidemic framework for real-time outbreak forecasting using wastewater surveillance data.

First-passage times are often the most relevant aspect of a complex Markovian network, because they signify when information processing has resulted in a definite decision. Previous studies have shown that for kinetic proofreading networks in the limit of large network size the first-passage time distribution converges either to a delta or to an exponential distribution. Remarkably, these two forms correspond to the two extreme distributions of minimal and maximal entropy for a fixed mean, respectively. Here we build on the connection between first-passage times and graph theory to show that these two limits are not model-specific, but arise generically in Markovian networks from the distribution of the eigenvalues of the generator matrix. A deterministic peak emerges when infinitely many eigenvalues contribute, while the exponential limit arises from a single dominant eigenvalue. We also show that the exponential limit emerges robustly for reversible networks when a backward bias exists. In contrast, the deterministic limit is not obtained from a simple reversal of this condition, but under structurally tighter conditions, revealing a fundamental asymmetry between both regimes. Our theoretical analysis is illustrated and validated by computer simulations of one-step master equations and random networks.