AI for Science

Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of imperfect detection, they have so far been analyzed only for simple gene-expression models that do not explicitly account for regulation. Here, we extend binomial models of capture to general gene regulatory networks to understand how imperfect capture reshapes the observed time-dependent statistics of molecular counts. Our results reveal when capture effects correspond to a renormalization of a subset of the kinetic rates and when they cannot be absorbed into effective rates, providing a systematic basis for interpreting noisy single-cell measurements. In particular, we show that rate renormalization depends on the level of regulatory detail in the model. For implicit regulatory models based on promoter state transitions, it arises whenever gene product synthesis does not trigger a promoter state change, as in the absence of promoter-proximal pausing or when pausing is short-lived. For models with explicit transcription factor binding, the same condition holds, together with sufficiently high transcription factor abundance, which in practice requires only a few tens of molecules per cell. In these cases, technical noise reduces the apparent mean burst size of synthesized gene products and accelerates the apparent rates of transcription factor binding reactions. This acceleration becomes stronger as the number of protein species and/or molecules involved in promoter switching increases. These effects hold for gene regulatory networks of arbitrary connectivity and remain valid under time-dependent kinetic rates.

Human bone marrow stromal cells (BMSC) include skeletal stem cells with ground-breaking therapeutic potential. However, BMSC colonies have very heterogeneous in vivo behaviour, due to their different potency; this unpredictability is the greatest hurdle to the development of skeletal regeneration therapies. Colony-level heterogeneity urges a fundamental question: how is it possible that one colony as a collective unit behaves differently from another one? If cell-to-cell variability were just an uncorrelated random process, a million cells in a transplant-bound colony would be enough to yield statistical homogeneity, hence washing out any colony-level traits. A possible answer is that the differences between two originating cells are transmitted to their progenies and collectively persist through an hereditary mechanism. But non-genetic inheritance remains an elusive notion, both at the experimental and at the theoretical level. Here, we prove that heterogeneity in the lineage topology of BMSC clonal colonies is determined by heritable traits that regulate cell-cycle exit. The cornerstone of this result is the definition of a novel entropy of the colony, which measures the hereditary ramifications in the distribution of inactive cells across different branches of the proliferation tree. We measure the entropy in 32 clonal colonies, obtained from single-cell lineage tracing experiments, and show that in the greatest majority of clones this entropy is decisively smaller than that of the corresponding non-hereditary lineage. This result indicates that hereditary epigenetic factors play a major role in determining cycle exit of bone marrow stromal cells.

The geometry of an object plays a vital role in modulating its interactions with the physical world. It nevertheless remains difficult to describe geometric information numerically for the purposes of statistical inference or classification tasks. Here, we introduce a new topological transform which leverages directional piecewise-linear Morse theory to quantify the geometry of an embedded object by cataloguing critical points across multiple height-functions. The output of this Morse transform records both the heights and the local topological type (peak, trough or saddle) of the critical points that characterise the underlying shape, retaining finer information than the Euler characteristic transform whilst naturally prioritising a shape's outermost regions. Crucially, this output can be further compressed into a rich but compact feature vector. We benchmark the Morse feature vector as a descriptor for ligand-based virtual screening (LBVS), which intrinsically depends on the shape of molecules. Under a common gradient-boosted tree classification pipeline, Morse descriptors achieve the highest mean AUROC when compared to other topological transform descriptors and to standard shape-based LBVS descriptors.

Data encountered in practice are frequently contaminated by additive noise, and wavelet shrinkage remains a fundamental tool for recovering underlying signals in nonparametric estimation. Classical procedures such as hard and soft thresholding decide whether to retain a wavelet coefficient almost entirely from its magnitude. Although effective in many settings, these rules can be too rigid for coefficients whose magnitudes fall in an intermediate region where the distinction between signal and noise is uncertain. We propose MLShrink, a two-threshold wavelet denoising procedure that combines wavelet shrinkage with machine learning. Coefficients below a lower threshold are discarded, coefficients above an upper threshold are retained, and coefficients in the intermediate band are classified using local wavelet-domain features. In this way, MLShrink preserves the simplicity of classical thresholding away from the decision boundary while allowing data-adaptive decisions for ambiguous coefficients. The paper also develops a theoretical framework tailored to this architecture. We show that MLShrink is a nonexpansive support-selection rule, derive an oracle-based risk decomposition showing that excess denoising risk is determined by classification errors on the undecided band, and establish an oracle-consistency result under suitable assumptions on classifier performance. Simulation experiments on standard benchmark signals indicate that MLShrink is competitive with several established wavelet shrinkage methods and is especially effective for signals with irregular, edge-rich, or non-smooth structure. These findings suggest that learned decisions on the intermediate threshold band provide a useful and interpretable connection between classical wavelet denoising and modern statistical learning.

Haematocrit influences blood viscosity and may affect coronary computational fluid dynamics (CFD). However, previous studies examined broad or pathological haematocrit ranges, and it remains unclear whether female-specific haematocrit variations within the physiological range produce meaningful changes in coronary haemodynamics. 15 female coronaries were analysed, including healthy arteries and diseased models with mild, moderate and severe stenosis. A haematocrit-dependent Carreau-Yasuda model was developed. CFD simulations were performed using the standard rheology model and a female-specific haematocrit-based model (40%). Time-averaged endothelial shear stress (TAESS), ESS gradient (ESSG), temporal shear variation index (TSVI), helicity, and low/high TAESS exposure were compared across coronary trees, arterial segments, bifurcations, stenosed vessels and corresponding narrowed regions. The female-specific model produced statistically significant differences from the standard model across all metrics and coronary regions (p < 0.05). However, the absolute differences were small, indicating a limited haemodynamic impact. Bland-Altman analysis showed narrow biases and limits of agreement. Linear regression demonstrated significant associations between inter-model differences and haemodynamic magnitude for TAESS, ESSG, helicity intensity, and adverse TAESS exposure, but the slopes were small. Similar findings were observed in stenosed arteries, where both models captured comparable flow disturbances across stenosis severities. Female-specific haematocrit variation within the physiological range is computationally detectable but haemodynamically negligible in coronary CFD. A standard rheology model is therefore likely sufficient for most coronary CFD studies, while personalised haematocrit modelling is more relevant for patients with abnormal haematocrit or rheology-focused studies.

The geochemical evolution of long-lived magma oceans is strongly regulated by volatile exchange between the molten mantle and the atmosphere. For planets inside the runaway-greenhouse limit, this coupled evolution can persist for billions of years. However, most existing studies assume Earth-like (oxidized) conditions and neglect the influence of redox state on melt thermodynamics and volatile release. We quantified how experimentally derived, oxygen-fugacity-dependent melting curves implemented within the coupled interior-atmosphere framework PROTEUS propagate into the thermal structure, melt fraction, and rheological evolution of rocky exoplanet interiors, applying this to the short-period super-Earth GJ 1132 b. We found strongly non-linear thermal responses to variations in melting curves. In volatile-poor systems, reduced melting curves promote earlier deep-mantle crystallisation relative to oxidised and Earth-like cases, favouring late-stage surface magma oceans sustained by greenhouse warming, while oxidized melting curves maintain higher melt fractions and a vertically extended magma ocean. Reduced mantles produce massive H$_2$-CO-rich atmospheres; oxidized mantles favour thinner H$_2$O-CO$_2$ envelopes. In volatile-rich systems, the interior reaches radiative equilibrium at high melt fractions, sustaining a steady-state global magma ocean in which melting curve variations do not significantly influence solidification timing. This indicates a hierarchical control: volatile inventory and surface oxygen fugacity act as the primary regulators of thermal state, while oxygen-fugacity-dependent melting relations provide a secondary modulation. These contrasting regimes produce distinct atmospheric compositions and formation timescales, offering testable spectral predictions for close-in rocky exoplanets evaluable with forthcoming JWST observations.

Human cognition depends on large scale communication constrained by white matter architecture. Although weak connections are abundant in mammalian connectomes, they have long been treated as noise and downweighted because of tractography uncertainty in the human brain, and their relevance to human cognition and large scale functional organization remains unresolved. Across multiple datasets and tractography pipelines, we show that, when tractography derived connectivity weights are interpreted through a nonlinear weighting framework, weak connections make measurable contributions to cognitive prediction, functional connectivity simulation, and structure-function coupling. These effects are selective: nonlinear weighting improves the prediction of general cognitive ability and memory more than that of crystallized intelligence or processing speed, consistent with the notion that weak connections preferentially expand the modal repertoire of brain networks to enhance both large scale integration and fine grained segregation, thereby supporting the functional balance essential for diverse cognitive abilities. Importantly, these effects are replicated in a reliability aware connectome generated by integrating two post tractography filtering methods, in which preserving weak links consistently outperforms conventional thresholding strategies. Finally, we show that weak connections contain functionally informative subsets organized along systems level and transcriptomic gradients. In particular, a specific class of weak connections, predominantly linking visual and motor systems with limbic regions and characterized by negative gene coexpression, exerts a disproportionately large influence on brain function.

Tree-like structures appear in many areas of science, and their shapes can help understand the underlying processes they drive or that give rise to them. By thinking of these structures as geometric graphs in $\mathbb{R}^3$, we gain access to tools from computational geometry and topology to study them. In this paper, we adopt the theory of quadratic forms to measure the directional spread of geometric graphs, and we introduce the hexplot model -- equipped with a metric derived from the Fisher metric on the standard triangle -- to visualize, measure, and collect statistics.

Tsetlin Machine (TM) is a logic-based machine learning approach that relies on simple bitwise operations and finite-state automata, which makes it attractive for edge AI deployments. Recent work has focused on co-processor and accelerator designs based on Tsetlin Machines (TMs). Although these designs achieve high performance, they typically depend on tightly coupled interfaces, microcode-style programming, and external host processors, limiting flexibility and ease of programming. In this work, we present a domain-specific RISC-V microprocessor architecture and design flow tailored for TM inference. Leveraging the modular structure of RISC-V, we design a reduced instruction subset processor that retains programmability while targeting improved performance and lower energy consumption for TM workloads. Instruction profiling is employed to guide instruction reduction, followed by datapath and control path simplifications tailored to TM inference. Both the baseline RV32IM core and the proposed reduced core are evaluated across multiple datasets and compared with Binarized Neural Networks (BNNs), which serve as a hardware-efficient baseline due to their reliance on bitwise operations during inference. Results show that TM achieves comparable or higher accuracy (e.g., up to 88.18% on CIFAR-2 compared to 60.0% for BNN) while reducing execution time by up to 98% across multiple datasets. Furthermore, the proposed design achieves an average $29.7\times$ reduction in energy consumption, demonstrating its effectiveness for programmable and efficient edge AI systems.

Graph neural networks (GNNs) provide a flexible framework for learning from scientific data linked through physical, biological, or functional relationships. One promising domain is plant physiology, where measured responses often arise from multiple interacting processes whose exact separation remains difficult even with manual intervention. In plant physiology, a key example is the A-Ci curve, which relates net CO2 assimilation rate (Anet) to leaf intercellular CO2 concentration (Ci) and is used to estimate photosynthetic parameters in leaf and crop-canopy models. However, reliable estimation requires identifying the active biochemical limitation state at each curve point, which remains a major source of uncertainty. Here, we formulate limitation-state identification along A-Ci curves as a graph-based node classification problem, with curve points as nodes. Domain-specific graph representations are created using distance-based k-nearest-neighbor (kNN) and auxiliary-signal-guided (ASG) connectivity, with edge attributes encoding pairwise relations. The framework was evaluated against conventional learning baselines, graph-based architectures, and an automated fitting-based benchmark. Results on a large synthetic dataset with known ground-truth limitation states show that graph-based models improve classification, particularly near biochemical transition regions. The best-performing configuration, SEAGAN (domain-Specific and Edge-Aware Graph Attention Network for Dynamic Plant Processes), integrates process-aware node features, edge attributes, kNN connectivity, and graph attention with weighted cross-entropy loss, achieving an F1-score of 0.857 and an accuracy of 0.882. The results show that representing A-Ci curves as graphs improves biochemical limitation-state analysis, with edge-aware attention over local kNN neighborhoods providing the most effective strategy.

Recent work on Kan-Do-Calculus (KDC) has established that the boundary between passive observation and active intervention in causal inference is a category-theoretic bi-adjunction, with interventions modeled by left Kan extensions and conditioning by right Kan extensions. This paper introduces two causal discovery algorithms under latent confounding, building on the information-geometric and categorical consequences of KDC. In smooth statistical settings, Radon-Nikodym derivatives between observational and interventional measures induce local causal vector fields; failures of these fields to close under Lie brackets become computable Frobenius residuals, which we interpret as witnesses of failed visible integrability and possible latent or unmodeled structure. Our first algorithm, BRIDGE (Bracket Residuals for Interventional Discovery and Geometric Estimation), combines an interventional density or Radon-Nikodym-ratio engine with a geometric screen that proposes a high-recall family of admissible arrows, identifies non-closing visible pairs as latent-obstruction candidates, and passes the reduced family to downstream score-based or differentiable discovery routines. The second algorithmic contribution, Spectral Kan-Do Flow Matching (SKFM), learns amortized intervention fields and factors latent curvature spectrally, exposing the direct Lie-space endpoint toward which BRIDGE points. A detailed set of experiments show that both algorithms are capable of discovering causal models with latent confounders while collapsing the super-exponential space of possible DAGs by many orders of magnitude. This paper introduces a new paradigm in causal discovery, where latent structure is inferred directly from the geometry of intervention-induced flows.

Real-time process monitoring requires methods that extract actionable information from high-dimensional time-series data. In this work, we present a new approach for process monitoring that combines tools of topological data analysis (TDA) and machine learning. In the proposed approach, we represent multivariate time-series data as manifolds and use topological descriptors to summarize the structure of such data; we then use a neural ordinary differential equation to learn the dynamic evolution of the topological structure of the system. Using real data from an industrial process, we show that this trajectory-based event detection approach is effective at detecting diverse types of events. We contrast this approach against reconstruction-based approaches such as principal component analysis and autoencoders and against a trajectory-based approach that uses Koopman autoencoders.

Dense Eisenstein--Jacobi (EJ) networks are degree-six algebraic interconnection networks whose finite quotient geometry is naturally represented by a hexagonal axial-coordinate ball. This paper studies non-redundant one-to-all broadcast repair in the dense EJ network generated by $α=(t+1)+tω$, where $t$ is the network diameter. We propose EJ-MOEM, a multi-orientation edge-minimum repair method that evaluates a constant-size family of hexagonal broadcast-tree orientations, selects a fault-aware candidate, contracts the fault-pruned tree into healthy components, and reconnects these components using external component-crossing repair edges. The resulting structure is a rooted spanning tree of the healthy subgraph: every healthy node receives the message exactly once, no faulty node is used, and the original healthy tree components are preserved. We prove that, for a chosen orientation whose fault-pruned component graph is connected, exactly $c-1$ external repair edges are necessary and sufficient, where $c$ is the number of healthy components. We also prove a depth-certificate theorem for EJ coordinate-reduction trees: every one-fault placement admits a repair of depth at most $t+1$, and every two-fault placement admits a repair of depth at most $t+2$. The proof uses the three-strip representation of EJ hexagons, a sector-suffix attachment lemma, a non-adjacent-sector separation lemma, and a six-direction shielding classification for paired cuts. Extended validation includes exhaustive one- and two-fault enumeration for $t=2,\ldots,12,14,16,18$ (up to $N=1027$ and 525,825 two-fault placements at $t=18$), structured theorem-critical tests through $t=30$, and large random tests through $t=200$, all with 100\% success and no violation of the theorem.

Circulant interconnection networks provide symmetric addressing, compact generator descriptions, and uniform local connectivity. This paper maps a degree--redundancy landscape for a fault-tolerant two-hop primitive in directed circulants: given $n$ nodes and degree budget $m$, how large can the worst-case shared-relay multiplicity $R(n,m)$ be? A node is a shared relay for an ordered terminal pair if it has outgoing links to both terminals; an $f$-relay-fault-tolerant circulant requires at least $f+1$ such relays for every pair. The underlying feasibility condition is a cyclic difference-multiplicity condition, which we use as a mathematical tool rather than claim as a new object. The contribution is the network-design framework around this tool: the parameters $R(n,m)$ and $D_f(n)$, a negative theorem for interval circulants, relay-table preprocessing and lookup algorithms, adversarial and random failure guarantees, load-balance scope, certified upper-bound interpretation of heuristic designs, exact small-$n$ calibration, a software lookup-versus-search microbenchmark, and a reproducible study of 526,539 generator sets. The results show that generator choice critically determines worst-case relay survivability: optimized threshold designs achieve $f$-relay-fault tolerance within about $1.16$--$1.63$ of the counting lower bound, while standard interval generators can fail structurally even at much larger degrees.

Eisenstein--Jacobi (EJ) networks are degree-six quotient-lattice interconnection networks. For a generator $α=a+bρ$, let $N=a^2+ab+b^2$ and $d=\gcd(a,b)$. If $d=1$, the three natural unit directions already give three edge-disjoint Hamiltonian cycles. If $d>1$, each unit direction splits into $d$ cycles and the EDHC problem becomes a cycle-splicing problem. Existing non-coprime EJ decompositions prove existence by using a rectangular representation and exchange schedules. This paper develops a different, local switch calculus in the natural Cayley geometry. The first two Hamiltonian cycles are built using the minimum possible $d-1$ intercomponent switches each, and the third factor is obtained as the unused edge complement. The contribution is deliberately not a new existence theorem for all non-coprime EJ networks; rather, it is a compact, formula-driven, minimal-switch decomposition for Euclidean-residue families whose complement incidence is proved symbolically. The proof separates four ingredients: component-label collapse, anchor cancellation, noncollision of lifted switch representatives, and connected complement incidence. No infinite-family theorem in this manuscript is proved by finite witnesses or by computational enumeration. The theorem scope is stated for the parameter ranges where an algebraic complement-incidence certificate is written down. Tables and CSV data are used only to verify and reproduce the formulas, never as proof of an infinite-family theorem.

We consider an intrusion detection task in which a defender must jointly optimize sensor placement locations and orientations to minimize the probability of missed detection of an intruder traversing a protected environment. We decompose this problem into a meta problem, termed SensorPlacement, and an embedded subproblem, termed OrientationScheduling. The OrientationScheduling subproblem, for a fixed sensor placement, is modeled as a 2-player zero-sum game between the defender and the intruder, where the defender seeks an orientation strategy for the deployed sensors to minimize the probability of missed detection, while the intruder seeks a path selection strategy to maximize it. Since the defender's strategy space grows combinatorially with the number of sensors and orientations, solving the game via standard linear programming becomes prohibitive. To this end, we develop an iterative and efficient equilibrium-seeking algorithm that exploits the structure of the game's payoff function and establishes theoretical guarantees for convergence to the Nash equilibrium (NE) of the game. This NE value is then used as a utility measure in the SensorPlacement meta problem. We show that this game-value-based utility function is weakly submodular over the set of sensor placements and propose a greedy placement algorithm with near-optimality guarantees. To our knowledge, this is the first unified framework to integrate game-theoretic utility design with (weak) submodular optimization, enabling principled joint optimization of sensor placement and orientation scheduling. Through extensive simulations, we demonstrate that the proposed approach achieves near-optimal detection performance while significantly reducing computation time compared to baselines.

Standard MCMC diagnostics ($\hat{R}$, effective sample size, divergence counts) detect whether a chain has mixed, but not why it has not. We ask whether the centring/non-centring obstruction in hierarchical models has a geometric cause beyond the metric. The joint parameter space is a fiber bundle (hyperparameters the base, group-level parameters the fibers), and the Fisher information metric induces an Ehresmann connection $A = -G_{FF}^{-1}G_{BF}$; the natural hypothesis is that the obstruction is its curvature, felt by the sampler as holonomy. We prove this false. The connection is flat for any smooth hierarchical posterior, not only the Gaussian case, because its horizontal leaves are the level sets of the fiber score $\partial_α\log p$: there is no geometric obstruction above the metric. What remains is statistical, not geometric, and the flat connection identifies it as a single quantity: the conditional dependence of fiber on base, governed per group by the prior fraction $π_j$, the classical pooling factor. From it the framework recovers the established picture, that prior-dominated groups mix slowly and that the optimal per-group non-centring weight follows in closed form, and a simulation study separates this base-fiber coupling from the funnel, a distinct base-space pathology, by their opposite dependence on the hierarchical variance. A direct attribution test confirms that NUTS does not transport the fiber: the chain-level footprint is excess conditional autocorrelation in prior-dominated groups, exactly as $π_j$ predicts. Genuine, even rotational, curvature does appear, but only for connections built from a sampler's working metric (a fixed mass matrix), where holonomy re-enters as an algorithmic rather than geometric phenomenon. The prior-fraction diagnostic is distributed as the R package fibr, with the geometric methods as accompanying reproduction code.

We introduce the CLUSTER algorithm (\textbf{c}oordinate-\textbf{l}evel \textbf{u}pdate \textbf{s}trategy for \textbf{t}rust-region step \textbf{e}valuation \textbf{r}efinement) for local derivative-free optimization problems where there is a cost to changing each parameter (or clusters of parameters). For example, this type of cost model is appropriate for optimizing robot-controlled laboratory experiments, in which a robot may incur a separate motion for each parameter cluster to be adjusted. We build off of a class of quadratic-interpolation optimization algorithms by Powell and Conn that are known to perform well for twice-differentiable objectives (e.g. low-noise experiments), and show that the CLUSTER variants improve performance on a variety of test problems (including an optics laboratory experiment) by around 50$\%$, and greatly outperform common competing algorithms for laboratory optimization (Bayesian optimization and Nelder--Mead). We also adapt the convergence proof of the Conn algorithm to obtain a similar convergence guarantee for CLUSTER-Conn.

In practical multispectral computed tomography (MSCT), the scanning geometric parameters under different X-ray energy spectra are often inconsistent, and the distributions of the energy spectra are even ray-dependent. However, existing algorithms cannot effectively and accurately solve the associated image reconstruction problem. To address this limitation, using the proposed aggregated energy spectra, we approximate the Jacobian matrix of the nonlinear forward operator at certain special points (e.g., the zero point) as a block product of a diagonal matrix composed of projection matrices and a very small-scale matrix, and then based on this matrix with a special structure, propose an efficient and accurate image reconstruction algorithm tailored for geometric-inconsistent MSCT with ray-dependent energy spectra. Under appropriate conditions, we establish the convergence theory for the proposed algorithm. Furthermore, numerical experiments using both noiseless and noisy projection data are conducted to verify the performance of the proposed algorithm, which demonstrate that the efficiency and accuracy of this algorithm are much higher than existing algorithms, offering the flexibility and scalability to accommodate various MSCT imaging configurations.

Cosmic-ray muon tomography records only a few detector-plane crossings per particle, while material information enters through stochastic scattering and energy loss along the path. Most pipelines first compress these hits to a per-muon scattering summary and assign a nominal momentum, moving the inverse problem away from the raw measurements. We introduce Raw-Hit Muon Tomography (RHMT), a measurement-domain formulation built directly on detector hits. RHMT-S projects out the unknown straight track and evaluates the remaining hit contrast with a Fermi--Eyges covariance; marginalizing the unknown scattering scale gives a blank-calibrated Student-$t$-type likelihood. RHMT-E fits the hits in a six-plane magnetic spectrometer to estimate each muon's log momentum loss and models it as a Bethe--Bloch line integral of the electron-density-related contrast $ρZ/A$. In a controlled Geant4 benchmark, RHMT-S improves the mean ROC-AUC over four-plane scattering baselines ($0.84$--$0.86$ versus $0.81$ for ASR), and RHMT-E provides a separate energy-loss contrast for aluminium, where scattering contrast is weak.

We include elliptical cross-sections to physically represent people, and irregular polygons to represent wheelchair users, in an anisotropic social force model whose velocity and angular dependence also captures the social tendency for people to avoid walking into one another. Physical interactions are included that depend on the area of overlap between people, or obstacles, to capture normal forces that resist compression and tangential forces that resist sliding motion. The model is further extended to include decision making capabilities, small social groups, the spread of panic, and herding behavior. A large box store is simulated during an evacuation where people move through the store, along the shortest path, to their desired exits. The effects of exit choice, or the perceived availability of exits, on exit times is elucidated. It is found that ignoring 'staff only' exits, and only exiting from the main entrances, can significantly increase average egress times.

The question of optimal experimental design has been addressed in a vast variety of contexts and answered using manifold approaches. Assuming additive white Gaussian noise, this work applies the Bayesian framework for design optimization to the posterior distribution after marginalization over linear parameters and discusses the implications. Examples of exponentially decaying signals with and without oscillations complement the discussion. Application of the examples considered include but are not limited to nuclear magnetic resonance and relaxometry experiments using solid-state spins sensors.

Extending earlier work in Physics-informed Meta-instrument for eXperiments (PiMiX) [1], PiMiX~2.0 is an artificial-intelligence (AI)-enhanced data-fusion and analysis framework that integrates multi-experiment multi-modal radiographic imaging and tomography (RadIT) with physics-informed reasoning and agentic AI workflows. The framework supports automated data ingestion, multimodal image processing from one or more experiments, three-dimensional (3D) and time-resolved three-dimensional (4D) reconstruction, and physics-aware interpretation of experimental observations. The PiMiX agents are designed for deployment on desktop and laptop systems commonly used in experimental workflows, while remaining scalable to high-performance computing environments for computationally intensive tasks. By coupling RadIT instrumentation and measurements with geometry, physics, computation, and statistical inference, PiMiX 2.0 aims to accelerate RadIT data processing, knowledge extraction, improve reproducibility, and enable more integrated analysis and workflows in high-temperature plasmas, nuclear fusion, advanced manufacturing, other static and dynamic experiments.

We present a study of charge sharing and electronic cross-talk in second-generation Large-Area Picosecond Photodetectors (LAPPD Gen 2). The LAPPD is a vacuum-based device consisting of a photocathode, two microchannel plates, and a resistive anode that capacitively couples to an 8 $\times$ 8 pixelated readout board (25.4 mm $\times$ 25.4 mm pixel area). Using a picosecond pulsed laser, we measure signal distributions across the resistive anode and quantify coupling between target and neighboring pixels. We further examine the relationship between dark-count rate and LAPPD voltage settings, identifying decay behavior characterized by fast, intermediate, and slow relaxation timescales. We additionally observe the LAPPD behaving as a resonant cavity by injecting electrical pulses into the readout board. To further interpret observed signals, we develop a pulse-classification method and identify additional features at approximately 60 ns and 110 ns. Finally, we implement a first-principles Monte Carlo simulation to model the radial and temporal distributions of observed signals, including contributions from electron backscatter and potential ion afterpulsing. The simulation shows reasonable agreement with the experimentally derived pulse classifications.

Altermagnets exhibit spin-split electronic structure without requiring spin-orbit coupling, but transport measurements generally mix intrinsic spin splitting with extrinsic scattering. We examine this identifiability problem for a two-dimensional d-wave altermagnet within a unified semiclassical framework spanning ballistic to diffusive transport. The spin-dependent Fermi-surface anisotropy produces a pronounced size effect, where vastly different longitudinal velocities cause the two spin channels to exhibit markedly different effective relaxation lengths within the same device geometry. However, the altermagnetic coupling $α$ and the momentum relaxation time $τ_0$ strongly compensate each other in longitudinal conductance, creating a severe parameter degeneracy. To lift this degeneracy, we formulate a physics-informed neural network (PINN) to act as a differentiable Boltzmann solver that strictly enforces contact injection, local particle conservation, and global current continuity. Driven by sparse conductance spectra, this neural solver leverages the Fermi-level dependence of transport to unlock the coupled parameters simultaneously, achieving sub-percent accuracy even under moderate measurement noise. These results show that combining the Fermi-level dependence of transport with strict physical constraints provides a robust route to separating spin splitting from scattering in altermagnetic conductors.

We study the collective dynamics of self-propelled spherocylinders carrying magnetic dipole moments in two dimensions. Magnetic interactions are modeled as two opposite monopoles $\pm Q$ separated by a distance $\ell$ along the particle director, a dumbbell model that remains well-defined at short range and introduces an explicit geometric lever arm for the magnetic torque. This approach, combined with the elongated particle geometry, produces a torque that competes with steric alignment in a manner inaccessible to point-dipole or disk models. By independently varying monopole separation and dipole strength (parameters that map directly onto the geometry and magnetization of cylindrical magnets) we show that the system navigates a rich landscape of collective states: gas, polar flock, chain, vortex-alignment, and locked-dimer phases. Our results establish that particle elongation and distributed magnetic charge together provide a minimal, experimentally accessible set of tuning knobs for controlling coherent states in magnetic active matter, with direct implications for the design of self-organized magnetic microswimmers and active colloidal assemblies.

We develop indexed Bellman information complexity, a representation-level theory of interactive decision making centered on information indices and reference histories. The representation strips away problem-specific syntax and retains only the ingredients needed for dynamic programming and information accounting, thereby unifying the earlier framework of indexed algorithmic information ratios (AIR). On the upper-bound side, regret is controlled by Bellman supersolutions or potential identities whose gradient bracket is paid for by indexed information. Upper-confidence-bound (UCB), estimation-to-decision/decision-estimation-coefficient (E2D/DEC), and adaptive-minimax-sampling or exploration-by-optimization (AMS/EBO) methods appear as three relaxations of this same identity. On the lower-bound side, the posterior-reference trajectory supplies both the information telescope and the ghost quantile of small-regret trajectories. The resulting critical radius in the lower bound is an effective-dimension-scale quantity, as in Fano and local-prior-mass lower bounds, rather than the constant radius of a two-point Le Cam argument. The examples show that DEC is best viewed as a one-step relaxation of indexed Bellman information complexity, not as a universally tight conversion mechanism. We illustrate the framework through several applications, with particular emphasis on kernel bandits. In this setting, the active action marginal provides a concrete basis for comparing UCB, E2D, and AMS/EBO.

This manuscript introduces a novel method to assess tissue oxygen concentration via the quantum entanglement (QE) of photons originating from positronium which is produced within the patient's body during positron emission tomography. We also investigate the possibility of assessing hypoxia by simultaneously detecting positronium lifetime and the positronium decay rate ratio. We introduce two distinct quantum sensing approaches. Method 1 utilizes the correlation between oxygen concentration and ortho-positronium (o-Ps) decay rates, relying on the simultaneous measurement of the mean o-Ps lifetime ($τ_{\mathrm{oPs}}$) and the $3γ$-to-$2γ$ annihilation rate ratio of o-Ps ($R_{\mathrm{oPs-3γ/2γ}}$). Method 2 introduces a novel hypothesis: that the degree of QE is sensitive to the relative contribution of annihilation mechanisms (pick-off vs. conversion), which in turn depends on oxygen concentration. We derive a formula for partial pressure of oxygen ($p\mathrm{O}_2$) as a function of $R_{\mathrm{oPs-3γ/2γ}}$ and $τ_{\mathrm{oPs}}$ and estimate the measurement accuracy required for these parameters - and for the degree of QE - to sense in-vivo oxygen pressure in the range between hypoxic and physoxic conditions. Theoretical models and quantitative estimates for $R_{\mathrm{oPs-3γ/2γ}}$, $τ_{\mathrm{oPs}}$ and for the degree of QE ($C_{\mathrm{QE}}$ ) as a function of $p\mathrm{O}_2$ are provided for water, isopropanol, cyclohexane, isooctane, and adipose tissue. In particular, applying the formulas derived under the working hypothesis that in pick-off process the photons are not entangled, we estimated that for $p\mathrm{O}_2 = 0$, the degree of quantum entanglement $C_{\mathrm{QE}}$ is equal to 0.890 for adipose, 0.886 for isopropanol, 0.867 for water, 0.818 for cyclohexane, and 0.784 for isooctane.

The article establishes a rigorous shift operator calculus for stationary time series modeling, addressing a certain gap in the literature. It provides proofs of existence and isometry for the transfer function operators $f(B)$ and $f(T)$ where $B$ is the bilateral shift operator and $T$ is the unilateral shift operator for different families of functions $f$. The article establishes convergence of the power series of $f(B)$ and $f(T)$ under the operator norm for the Wiener algebra $\mathbb{W}_+$, and convergence under strong operator topology for $f$ in $H^{\infty}$, based on the use of Abel sums. Based on this calculus, it unifies the notion of stationary process invertibility with the operator invertibility of the transfer function $f(T)$.

We give an explicit description of the BPS Lie algebra of any quiver with zero potential, by relating the perverse filtration on the cohomological Hall algebra with certain limit conditions on polynomials. Our results also give a partial description of the perverse filtration for arbitrary potential, which we conjecture is complete in the case of tripled quivers with canonical cubic potential.