arXiv preprints from January 1, 2026 through September 8, 2026 — 10:49:43 EST
Full-length RNAs, particularly messenger RNAs, often exceed the context lengths used to pretrain existing RNA foundation models, limiting complete-transcript modeling at single-nucleotide resolution. We present RIBOSPAN, a 1.61-billion-parameter bidirectional RNA foundation model natively pretrained with context lengths up to 10,240...
Our capacity to maintain focus on task-relevant goals over time is constrained because attentional states wax and wane moment to moment. One theoretical account posits that temporal filling-in - filling temporal blank intervals between target stimuli - reduces attentional fluctuations to enhance sustained attention. This proposal,...
Cooperation is ubiquitous in both natural and human societies, yet its evolutionary basis remains a major challenge. A long-standing puzzle is whether having more information leads to better decision-making and thus a higher level of cooperation. To address this question, we adopt a recently developed reinforcement learning framework...
Stochastic reaction networks are continuous-time Markov chain models for interacting populations, with applications in biochemistry, epidemiology, ecology, and related areas. We study finite-difference sensitivity estimation when a single estimator requires several nearby parameterized paths. Existing variance-reducing couplings are...
The origin of life is the first, arguably, the most important and also the most enigmatic major transition in evolution (MTE). As all MTE, the transition at the origin of life can be constructively addressed only within the conceptual framework of multilevel selection. The two levels of selection relevant for the origin of life are...
Vibrational spectroscopy reports on molecular structure with chemical-bond specificity, but in biological systems the vibrational signals of a target chromophore are typically buried under contributions from the surrounding matrix. Resonance Raman (RR) spectroscopy addresses this problem by matching the excitation wavelength to an...
We develop a stochastic framework for a broad class of heterogeneous SIR epidemic models. In the finite-population construction, each initially susceptible individual is assigned a fixed nonnegative susceptibility, and infection occurs when the accumulated population-level infection pressure exceeds an individual random threshold....
Ion channels and pumps drive ion-selective currents through cell membranes at localized sites, yet a cell's electrical state is routinely summarized by a single transmembrane voltage. Combining theory and numerical simulations, we resolve the spatiotemporal dynamics of charge reorganization driven by a localized current on a spherical...
Pathologic complete response (pCR) is a strong neoadjuvant endpoint, yet 5-15% of complete responders recur and clinical/genomic variables do not reliably identify them. We tested whether pretreatment dynamic contrast-enhanced MRI entropy - intratumoral enhancement heterogeneity - resolves response quality hidden within pCR and...
Reengineered biological systems have the potential to revolutionize chemical and material production, enhance critical mineral recovery, serve as threat sensors and improve human health. Unfortunately, the extreme complexity of organisms has made it difficult to achieve this potential in all but the simplest cases. Recent...
Single-particle cryo-electron microscopy (cryo-EM) pose estimation is traditionally solved anew for each dataset, where iterative refinement is done from scratch while the estimator learns to store the molecule in its weights. In this work, we show that pose inference is a generalizable, specimen-agnostic operation when conditioned...
We study the evolution of cooperation in a finite haploid population whose individuals carry both a strategy and a phenotype on a finite periodic space. Cooperators help with a probability that decays exponentially with phenotypic distance, generating graded phenotype-dependent assortment. Under weak selection and a large-population...
Hippocampal replay is a phenomenon observed in mammals and songbirds where neural activation sequences experienced during wakeful periods are repeated during rest or sleep. This mechanism is believed to play a crucial role in episodic memory consolidation, retrieval, and planning. Interestingly, replay can occur in both forward and...
The 5' untranslated region is a major determinant of translation initiation, and its effect becomes especially important in modified mRNA sequences, where start-codon context, cap-proximal secondary structure, upstream AUGs and upstream open reading frames, and nucleotide chemistry can alter ribosome scanning and initiation...
Network Hamiltonian Models (NHMs) provide an efficient framework for modeling the aggregation of interacting particles (e.g., the condensation of proteins into gel-like, oligomeric, or fibrillar states), representing the system as a network whose edges represent bound interactions. Terms within the network Hamiltonian represent...
Purpose: Nocturnal hypoglycemia (NH) remains a challenge for individuals with type 1 diabetes (T1D), particularly those who are physically active or on multiple daily injections (MDI). We leveraged an explainable evidential neural network model that forecasts minimum overnight glucose to identify NH risk factors and generate...
We establish the existence of a stochastic flow on $L^{\infty} (\mathbb{T})$ for the stochastic Allen-Cahn equation with multiplicative noise \[ (\partial_t - \partial_x^2) u = u - u^3 + σ(u) ξ\quad \text{on} \quad \mathbb{R}_+ \times \mathbb{T}, \] where $ξ$ is space-time white noise and $σ: \mathbb{R} \rightarrow \mathbb{R}$ is...
We prove Dennin's conjecture (Conjecture 8.9 of arXiv:2506.21052) that his variant of dual RSK correspondence is symmetric when restricted to biGrassmannian permutations. For a binary matrix $A$, let $A^\dagger$ denote its transpose-complement, and let $\operatorname{ins}(A)$ and $\operatorname{rec}(A)$ denote its insertion and...
For every integer $d\geq 1$, we construct a countably infinite set $X_d\subset\mathbb{R}^d$ in affine general position, with all pairwise distances rational. When $d$ is odd, $X_d$ may also be chosen so that no $d+2$ points lie on a common sphere. The construction is uniform in $d$: positive Chebyshev square decompositions produce...
We investigate which 3-manifolds bound 4-manifolds that are homeomorphic but not stably diffeomorphic, where stabilising means taking connected sum with copies of $S^2\times S^2$. We show that every closed, orientable 3-manifold admits such fillings, as do certain families of nonorientable 3-manifolds. In contrast we show that for a...
We establish a general structure theorem for local quantum Cuntz--Krieger families associated to finite quantum graphs whose relations are analogous to those of the partial isometries generating an ordinary graph $C^*$-algebra, with the quantum edge correspondence governing composition. We apply this structure theorem to the quantum...
We prove the wall-crossing formula conjectured by Gross--Joyce--Tanaka for equivariant enumerative invariants of CY4 categories equipped with framing functors. We also establish a version for stable pairs with fixed-determinant obstruction theories, as used in earlier applications by the first-named author. The main technical...
The probabilistic formulation of principal component analysis promises statistically grounded solutions to the problem of selecting the number of principal components. However, developing tractable model selection methods is complicated by the fact that the probabilistic principal component analysis (PPCA) model exhibits non-standard...
We establish a Demailly-Kollár type continuity theorem for plurisubharmonic functions with respect to adapted measures on normal complex analytic klt pairs. As applications, we prove the equality of the analytic and divisorial versions of the alpha and delta invariants on compact normal Kähler klt pairs, thereby completing a program...
Let $λ(n)=(-1)^{Ω(n)}$ be the Liouville function. Pilatte proved a fixed power saving for the logarithmically weighted two-point correlation at shift one. More recently, Tao and Teräväinen obtained power-logarithmic two-point estimates uniform over polylogarithmically growing shifts and coefficients outside a common exceptional set of...