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01.
arXiv (CS.AI) 2026-06-19

The Scaffold Effect: How Prompt Framing Drives Apparent Multimodal Gains in Clinical VLM Evaluation

arXiv:2603.28387v2 Announce Type: replace Abstract: Trustworthy clinical AI requires that performance gains reflect genuine evidence integration rather than surface-level artifacts. We evaluate 12 open-weight vision-language models (VLMs) on binary classification across two clinical neuroimaging cohorts, \textsc{FOR2107} (affective disorders) and \textsc{OASIS-3} (cognitive decline). Both datasets come with structural MRI data that carries no reliable individual-level diagnostic signal. Under these conditions, smaller VLMs exhibit gains of up to 58\% F1 upon introduction of neuroimaging context, with distilled models becoming competitive with counterparts an order of magnitude larger. A contrastive confidence analysis reveals that merely mentioning MRI availability in the task prompt accounts for 70-80\% of this shift, independent of whether imaging data is present, a domain-specific instance of modality collapse we term the scaffold effect. Expert evaluation reveals fabrication of neuroimaging-grounded justifications across all conditions, and preference alignment, while eliminating MRI-referencing behavior, collapses both conditions toward random baseline. Our findings demonstrate that surface evaluations are inadequate indicators of multimodal reasoning, with direct implications for the deployment of VLMs in clinical settings.

02.
arXiv (math.PR) 2026-06-18

Multi-floor generalization of TASEP

arXiv:2603.13610v2 Announce Type: replace Abstract: We consider an interacting particle system, which generalizes the classical totally asymmetric simple exclusion process (TASEP), in that each site can contain up to a fixed finite number of particles, and the particle movement is governed by a back-pressure (BP) algorithm (also often called MaxWeight). There are $N$ sites (with $N$ finite or infinite), each may contain at most $c$ particles, $1 \le c < \infty$. New particles enter the system at the left-most site $1$ as a Poisson process of rate $\alpha\le 1$, unless site $1$ has $c$ particles. Particles (if any) are removed from the right-most site $N$ as a Poisson process of rate $\beta \le 1$. The left-to-right movement of particles between neighboring sites is governed by the BP rule: one particle moves from site $n$ to $n+1$ at epochs of a rate $1$ Poisson process, as long as the former site has strictly more particles than the latter. When $c=1$, this is the standard TASEP. Our main results address the asymptotics of the stationary distribution of a finite system, and especially the limit of the flux (current) as $N\to\infty$. In particular, we prove that interesting non-trivial phase transitions take place in a system with $c>1$. For example, if $c>1$ and $1/2 \le \beta \le 1$, the maximum limiting flux $1/4$ is achieved as long as $\alpha \ge \alpha_c^*$, where $\alpha_c^* < 1/2$ is some non-trivial threshold. (For the standard TASEP the threshold is $1/2$.) We also put forward a general conjecture about the stationary distribution asymptotics under an arbitrary parameter setting. We illustrate our formal results and the conjecture by simulations, and identify interesting directions for further research.

03.
medRxiv (Medicine) 2026-06-16

AI-assisted continuous-time modelling of metastatic breast cancer reveals subtype-specific spatiotemporal organ interactions

Metastatic breast cancer is one of the leading causes of premature mortality among women worldwide. A major barrier to optimal care is the marked heterogeneity in both the temporal dynamics of metastatic spread and the organ-specific spatial distribution of metastases. Existing analyses do not adequately capture this complexity, as they either neglect temporal dependencies or assume independence between metastasic sites. As a result, it remains unclear how established metastases influence subsequent organ-specific dissemination. We address this question using patient-level longitudinal trajectories from a large multicentre real-world metastatic breast cancer registry, combined with an AI-assisted disease-progression modelling framework based on continuous-time Markov chains that represent combinations of metastatic sites and the non-uniform and practice-driven timing of radiologic response assessments, as encountered in routine clinical care. We present a stochastic model determined by progression rates, which are parameterised to capture baseline organ-specific transition risks, patient-level covariates, and pairwise inter-organ interaction effects. High-dimensional treatment information is incorporated using an large language model based encoding. We find that metastatic spread follows non-independent, subtype-specific spatiotemporal patterns, with subtype-specific inter-organ interaction patterns that shape progression. Visceral metastases, particularly lung and liver metastasis, are associated with an increased hazard of subsequent brain metastasis, with effects varying across hormone receptor-positive, HER2-positive, and triple-negative subtypes. Together, these findings define a clinically relevant spatiotemporal architecture of metastatic progression in breast cancer. This framework enables refined mechanism-informed risk stratification and provides a data-driven rationale for targeted and risk-adapted – rather than symptom-triggered – surveillance strategies.

04.
medRxiv (Medicine) 2026-06-24

Mask-Based Breath Sampling for Detection of Pseudomonas aeruginosa in Adults with Cystic Fibrosis and Bronchiectasis

Background: Monitoring Pseudomonas aeruginosa (P. aeruginosa) infection in people with cystic fibrosis (pwCF) is essential for early detection, targeted treatment, and prevention of chronification. Sputum culture is the current standard, yet many patients, particularly those receiving CFTR modulator therapy, struggle to expectorate sputum. Microbial aerosols from the respiratory tract offer a non-invasive alternative. This proof-of-principle study assessed the accuracy and feasibility of the AveloMask, a novel breath aerosol collection kit paired with qPCR detection. Methods: Adult pwCF and bronchiectasis patients attending routine monitoring visits and healthy controls were enrolled in a cross-sectional study. Participants wore the mask for 30 minutes, followed by 20 instructed coughs. Mask filters were tested with a triplex qPCR assay targeting P. aeruginosa specific ecfX and gyrB, and human RPP30 as an endogenous control. Accuracy was evaluated using a composite reference standard (sputum culture and PCR). Results: Of 25 patients enrolled, 23 were included in the analyses. Sensitivity was 12/19 (63.2%) for breath qPCR versus 15/19 (78.9%) for sputum culture. Breath qPCR missed 5 cases detected by sputum culture but detected 2 sputum culture-negative/qPCR-positive cases. Specificity of breath qPCR was 100% in 4 patients and 15 healthy controls. RPP30 was detected in all mask samples. AveloMask was perceived as easy to use, with many patients preferring it over sputum collection. Discussion: Mask-based breath collection demonstrated promising diagnostic accuracy for detection of P. aeruginosa. Breath sampling may complement or partially substitute sputum-based diagnostics, especially in patients unable to expectorate. Further studies are needed to define its clinical role.

05.
arXiv (CS.AI) 2026-06-25

Surrogate models for Rock-Fluid Interaction: A Grid-Size-Invariant Approach

arXiv:2602.22188v2 Announce Type: replace-cross Abstract: Modelling rock-fluid interaction requires solving a set of partial differential equations (PDEs) to predict the flow behaviour and the reactions of the fluid with the rock on the interfaces. Conventional high-fidelity numerical models require a high resolution to obtain reliable results, resulting in huge computational expense. This restricts the applicability of these models for multi-query problems, such as uncertainty quantification and optimisation, which require running numerous scenarios. As a cheaper alternative to high-fidelity models, this work develops eight surrogate models for predicting the fluid flow in porous media. Four of these are reduced-order models (ROM) based on one neural network for compression and another for prediction. The other four are single neural networks with the property of grid-size invariance; a term which we use to refer to image-to-image models that are capable of inferring on computational domains that are larger than those used during training. In addition to the novel grid-size-invariant framework for surrogate models, we compare the predictive performance of UNet and UNet++ architectures, and demonstrate that UNet++ outperforms UNet for surrogate models. Furthermore, we show that the grid-size-invariant approach is a reliable way to reduce memory consumption during training, resulting in good correlation between predicted and ground-truth values and outperforming the ROMs analysed. The application analysed is particularly challenging because fluid-induced rock dissolution results in a non-static solid field and, consequently, it cannot be used to help in adjustments of the future prediction.

06.
PLOS Computational Biology 2026-06-22

A lactylation- and autophagy-associated prognostic signature reveals LSEC-derived CLEC3B as a novel mediator of hepatocellular carcinoma suppression

Authors:

by Youai Song, Yinkuan Ning, Meihui Li, Jianwei Lan, Liangchen Lei, Yufei Han, Zhuo Meng, Binjie Li, Pengpeng Liu, Quanyan Liu The crosstalk between lactylation and autophagy within the hepatocellular carcinoma (HCC) microenvironment is a burgeoning field with profound implications. By integrating multi-omics data from public cohorts, we delineated two molecular subtypes of HCC with divergent clinical outcomes and established a lactylation-autophagy-related prognostic signature. This signature highlighted CLEC3B as a pivotal gene. Subsequent single-cell RNA sequencing and experimental validation unequivocally pinpointed liver sinusoidal endothelial cells (LSECs) as the principal cellular source of CLEC3B, which was significantly downregulated in HCC tissues. Functionally, conditioned media derived from CLEC3B-overexpressing LSECs potently inhibited HCC cell proliferation. Mechanistic investigations revealed that this tumor-suppressive effect was orchestrated through the concurrent suppression of autophagy and diminution of lactylation levels. Our findings position LSEC-secreted CLEC3B as a novel metabolic mediator in HCC, bridging two key pathways in tumor suppression, and endorse its clinical value both as a prognostic indicator and a promising therapeutic target.

07.
arXiv (CS.CL) 2026-06-15

Non-Parametric Machine Text Detection via Multi-View Gaussian Processes

Adversarial conditions such as paraphrasing and targeted style transfer sharply degrade the accuracy of machine text detectors. A document, however, carries multiple complementary signals (e.g., stylistic features, likelihood and rank-order features, and structural features), and an attack that suppresses one may leave others intact. While a parametric classifier can learn to combine these features given sufficient supervision, classifiers are prone to making confidently incorrect predictions when the distribution shifts (e.g., novel attacks or unseen language models). To address this, we propose a multi-view, non-parametric detection framework that extracts complementary feature views from the same document and aggregates per-view evidence through a Gaussian process ensemble. By aggregating evidence across views, an adversary must simultaneously defeat multiple independent axes of detection, substantially raising the cost of evasion. The Gaussian process formulation additionally provides calibrated probabilities and principled abstention on out-of-distribution inputs, supporting reliable deployment in high-stakes settings. We evaluate on three benchmarks spanning diverse generators and attacks: the DetectRL and RAID benchmarks, and the PAN2025 shared task and demonstrate that our multi-view detector maintains strong performance under the considered attacks, outperforming existing approaches against held out attacks.

08.
arXiv (quant-ph) 2026-06-16

Trainable Quantum Channels as Computational Primitives for Quantum Learning

arXiv:2606.15808v1 Announce Type: new Abstract: Variational quantum learning is traditionally constrained to unitary dynamics, often treating quantum channels as detrimental noise. In this work, we reformulate the quantum channels as trainable computational primitives and establish a non-unitary quantum machine learning framework grounded in open-system dynamics. We demonstrate that the outputs of channel-enhanced quantum models form a structured superposition of multiple functional components. Each component is governed by an effective observable whose spectrum can be adaptively modulated during training, a significant departure from the spectral invariance in unitary transformations. Moreover, the proposed framework generalizes conventional unitary quantum models by retaining them as a special case while introducing additional non-unitary degrees of freedom. Furthermore, we reveal that trainable quantum channels enrich the optimization geometry through ensemble-averaged gradient and additional optimization directions induced by the Kraus operators. Empirical evaluations on classification tasks using trainable amplitude-damping and phase-damping channels confirm enhanced optimization dynamics and predictive performance. Our work provides a principled approach for leveraging quantum channels as trainable resources and advances the design of high-performance quantum learning architectures.

09.
arXiv (math.PR) 2026-06-11

Persistent Homology of the Planar Wiener Sausage: Brownian Scaling and a Logarithmic Expectation Law

arXiv:2606.11248v1 Announce Type: new Abstract: We study degree-one persistent homology of the planar Wiener-sausage filtration generated by standard Brownian motion without drift. In the drifted case, regeneration along the drift direction leads to linear-in-time laws for persistent-homological observables. In the recurrent zero-drift case, this renewal structure disappears. The organizing mechanism is instead Brownian self-similarity: the persistence diagram at time $T$ is equal in law to the image of the unit-time diagram under spatial dilation by $\sqrt T$. Consequently, large-time questions on fixed radius windows are transformed into small-radius questions for the unit-time Brownian trace. Let $B$ be standard planar Brownian motion, let $K_T=B\left(\left[0,T\right]\right)$, and let $K_T^{\left(r\right)}$ be the radius-$r$ Wiener sausage. Since $K_T^{\left(r\right)}$ is connected, its first Betti number $\beta_1^T\left(r\right)$ is the number of bounded complementary components of $K_T^{\left(r\right)}$. For a bounded nonnegative Borel function $\psi$ supported in a compact interval $\left[a,b\right]\subset\left(0,\infty\right)$, we consider the smoothed Betti-curve observable $\left[r_0,r_1\right] \mathrm{\Phi}_\psi \left(T\right) = \int_{r_0}^{r_1} \beta_1^T \left( r \right) \psi \left( r \right) dr$. We prove that there exist absolute constants 0

10.
Nature (Science) 2026-06-09

A unicellular relative links aggregative multicellularity to animal origins

Authors:

How animals evolved complex multicellularity from their unicellular ancestors remains unanswered. Unicellular relatives of animals exhibit simple multicellularity through clonal division, formation of multinucleate coenocytes, or aggregation. 1 Therefore, animal multicellularity may have evolved from one (or a combination) of these behaviours. Aggregation has classically been dismissed as a means to complex multicellularity. 2 However, aggregation occurs in many extant animal cells and has also been recently described in three close unicellular relatives of animals (the choanoflagellates Salpingoeca rosetta and Choanoeca flexa, and the filasterean Capsaspora owczarzaki). 3-5 It is unclear whether aggregation in these species is derived or ancestral, and its relevance for animal origins remains unknown. To fill this gap, we investigated whether an additional close unicellular relative of animals can undergo aggregation. We discovered that the marine free-living bacterivorous filasterean Ministeria vibrans 6 forms homogeneous aggregates with reproducible kinetics that have long-term stability, and that improved feeding and mating may be evolutionary drivers of this aggregation. Notably, we found that homologs of many animal multicellularity genes involved in cell adhesion, signalling, and transcriptional regulation were deployed during the aggregation process, indicating that they may have been used for aggregation in the unicellular ancestors of animals before being co-opted into animal multicellular development. Thus, our results imply that aggregative multicellularity was key to the development of the multicellular animal genetic toolkit.

11.
arXiv (CS.CV) 2026-06-24

Mamba-FSCIL: Dynamic Adaptation with Selective State Space Model for Few-Shot Class-Incremental Learning

Few-shot class-incremental learning (FSCIL) aims to incrementally learn novel classes from limited examples while preserving knowledge of previously learned classes. Existing methods face a critical dilemma: static architectures rely on a constant parameter space to learn from data that arrive sequentially, making them prone to overfitting to the current session, while dynamic architectures continually expand the parameter space, leading to increased complexity. In this study, we explore the potential of Selective State Space Models (SSMs) for FSCIL. Mamba leverages its input-dependent parameters to dynamically adjust its processing patterns and generate content-aware scan patterns without session-wise projector expansion. This enables it to configure distinct processing for base and novel classes, helping preserve existing knowledge while adapting to new ones. To leverage Mamba's potential for FSCIL, we design two key modules: First, we propose a dual selective SSM projector that generates input-conditioned state-space parameters from intermediate features for dynamic adaptation. The dual design structurally decouples base and novel-class processing, employing a frozen base branch to maintain stable base-class features and a dynamic incremental branch that adaptively learns distinctive feature shifts for novel classes. Second, we develop a class-sensitive selective scan mechanism to guide dynamic adaptation of the incremental branch. It reduces the disruption to base-class representations caused by training on novel data, and meanwhile, encourages the selective scan to perform in distinct patterns between base and novel classes. Extensive experiments on miniImageNet, CIFAR-100, and CUB-200 demonstrate that Mamba-FSCIL achieves state-of-the-art performance.

12.
arXiv (math.PR) 2026-06-12

Temporal Conductance and Bounds on the Voter Model for Dynamic Networks

arXiv:2606.13374v1 Announce Type: cross Abstract: The voter model is a classical stochastic process that models how opinions might spread through a network: at each step, every node lazily adopts the opinion of a random neighbour; eventually all nodes share the same opinion (consensus). Stronger connectivity should yield faster consensus. Berenbrink, Giakkoupis, Kermarrec, and Mallmann-Trenn (ICALP 2016) make this precise via the network's conductance: if the network has $m$ edges, minimum degree $d_{\min}$, and conductance at least $\phi$, then the voter model reaches consensus in expected $O(m/(d_{\min}\phi))$ steps. Their results extend to dynamic networks with fixed vertex degrees by considering the network's conductance at each time step. We introduce temporal conductance $\Phi$, a more general connectivity measure for dynamic networks. Unlike static conductance, which collapses to $0$ whenever some snapshot is disconnected, $\Phi$ captures connectivity through edges that appear at different times. We generalise the results of Berenbrink et al. from static conductance to temporal conductance, showing that the expected consensus time of the standard voter model is at most $O(m/(d_{\min}\Phi))$. Moreover, we prove that this bound is tight up to constant factors. We expect temporal conductance to be a useful primitive for analysing other dynamics on temporal networks, and potentially time-inhomogeneous Markov chains more generally.

13.
arXiv (CS.LG) 2026-06-17

Amortizing Maximum Inner Product Search with Learned Support Functions

arXiv:2603.08001v2 Announce Type: replace Abstract: Maximum inner product search (MIPS) is a crucial subroutine in machine learning, requiring the identification of a vector taken within a database (the keys) that best aligns with a given query. We propose amortized MIPS: a regression-based approach that trains neural networks to directly predict MIPS solutions, amortizing the cost of repeatedly solving MIPS for queries drawn from a known distribution over a fixed key database. Our key insight is that the MIPS value function is the support function of the set of keys, a well-studied convex function whose gradient yields the optimal key. This motivates two complementary amortized models: SupportNet, an input-convex neural network trained to regress the support function, and KeyNet, a vector-valued network that directly regresses the optimal key. SupportNet can serve as a cluster router, steering queries toward relevant database partitions, while KeyNet can be used as a drop-in replacement for the original query, fed directly to off-the-shelf indexing pipelines. Our experiments on the BEIR benchmark show that, for document embeddings, learned \SupportNet{}s and \KeyNet{}s significantly improve IVF match rates when accounting for compute effort, whether measured in FLOPs, number of probes, or wall-clock time. Our code is available at: https://github.com/apple/ml-amips.

14.
arXiv (CS.AI) 2026-06-18

TxBench-PP: Analyzing AI Agent Performance on Small-Molecule Preclinical Pharmacology

arXiv:2606.19245v1 Announce Type: new Abstract: Artificial intelligence (AI) agents promise to accelerate drug discovery by compressing interpretation and decision-making loops, but practical deployment requires trusted evaluation on realistic program decisions. We introduce TherapeuticsBench Preclinical Pharmacology (TxBench-PP), a verifiable benchmark for small-molecule preclinical pharmacology and the first focused slice of a broader TherapeuticsBench effort across drug-discovery stages and therapeutic modalities. TxBench-PP tests whether agents can recover accurate conclusions from real-world assay data rather than memorized facts from literature. The benchmark contains 100 evaluations indexed by program stage, assay type, and task structure, spanning mechanism-of-action (MoA) and pharmacodynamic (PD) reasoning, compound-target engagement, causal target validation, developability and safety, and translational efficacy. Agents receive realistic workflow snapshots, inspect files in a coding environment, and return structured answers graded deterministically. Across 16 model-harness configurations, comprising 11 models and 4,800 trajectories, no system reliably recovered preclinical pharmacology decisions. The strongest configuration, Claude Opus 4.8 / Pi, passed 59.3\% of endpoint attempts (178/300; 95\% CI, 51.1-67.6), followed by GPT-5.5 / Pi at 55.3\% (166/300; 47.0-63.6).

15.
arXiv (CS.AI) 2026-06-19

Beyond Entropy: Learning from Token-Level Distributional Deviations for LLM Reasoning

arXiv:2606.19771v1 Announce Type: new Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has significantly advanced Large Language Model (LLM) reasoning; however, it faces a fundamental optimization instability: uniform token updates precipitate entropy collapse, leading to premature convergence to suboptimal strategies, whereas excessive Shannon Entropy maximization can cause entropy explosion, driving blind exploration toward incoherent reasoning chains. To resolve this dichotomy, we introduce the Independent Combinatorial Tokens (ICT) framework, which shifts the optimization focus from scalar uncertainty to the distributional properties of token logits. By leveraging the Jensen-Shannon (JS) divergence between token logits distributions, ICT identifies tokens with distinctive distributional patterns as critical branching points for guiding effective exploration in LLM reasoning. Our theoretical analysis, grounded in both Shannon and second-order Rényi entropy, proves that selectively updating on these tokens regulates policy concentration: it reduces the overall distribution uncertainty measured by Shannon entropy, while controlling probability concentration captured by second-order Rényi entropy. This dual effect prevents over-concentrated token generation from weakening exploration and effectively stabilizes the training landscape. Empirical results demonstrate that updating only the top 10% of unique tokens on Qwen2.5 (0.5B/1.5B/7B) models yields an average pass@4 improvement of 4.58%, with a maximum gain of 14.9%, over GRPO, 20-Entropy, and STAPO baselines across seven benchmarks spanning math, commonsense, and Olympiad-level problems.

16.
medRxiv (Medicine) 2026-06-11

Parent and physiotherapist perceptions about movement skills of young children with juvenile idiopathic arthritis

Objective: The onset of juvenile idiopathic arthritis (JIA) in the early years ([&le;]5 years) may negatively impact movement skill (encompassing related concepts of gross motor skills, fundamental movement skills, and functional ability) development. Few studies have explored the perceptions and needs of parents and physiotherapists towards children's difficulty with these movement skills, essential to identify potential areas for added support. The objective of this study is to understand the perceptions of physiotherapists and parents towards movement skills of children with JIA. Methods: Seventeen parents and 24 physiotherapists completed an online questionnaire consisting of multiple choice and open-ended questions about the movement skills of young children with JIA. Demographic and multiple choice questions were quantitively analysed using descriptive statistics. Open-ended responses were analyzed using qualitative conventional content analysis. Results: About half (47%) of parents perceived their children to have movement difficulties, and 75% of physiotherapists described the movement skills of children with JIA as worse than other children of the same age. Our qualitative analysis revealed three general themes including: functional task difficulties; clinical variability in movement skills; and psychosocial components of movement skill difficulties. Conclusion: This study provides an analysis of perceptions of physiotherapists and parents towards the movement skills of young children with JIA. A significant proportion of parents and physiotherapists identify movement difficulties among children with JIA that impact daily life. Future interventions co-designed with both parents and care providers targeting movement skills are needed.

17.
arXiv (CS.LG) 2026-06-11

Projected random forests and conformal prediction of circular data

arXiv:2410.24145v3 Announce Type: replace-cross Abstract: We apply conformal prediction techniques to regression problems with circular responses, producing prediction sets with adaptive arc length and finite-sample coverage guarantees for any circular predictive model under the assumption of data exchangeability. Leveraging the high performance of existing predictive models designed for linear responses, we analyze a general projection procedure that converts any linear-response regression model into one suitable for circular responses. When random forests are used as base models in this projection procedure, we leverage the random forest out-of-bag mechanism to eliminate the need for a separate calibration sample in the construction of prediction sets. On synthetic and real datasets, the resulting projected random forest model produces more efficient out-of-bag conformal prediction sets, with shorter median arc length, than the split conformal prediction sets generated by two existing alternative models.

18.
arXiv (CS.AI) 2026-06-16

PH-KAN: Port-Hamiltonian Kolmogorov-Arnold Network

arXiv:2606.14708v1 Announce Type: cross Abstract: Data-driven machine learning approaches have become increasingly attractive for nonlinear system identification, but standard models often fail to preserve the underlying physical structure and remain difficult to interpret, especially when no analytical model is available. In this context, port-Hamiltonian (pH) models provide a natural physics-informed representation. However, when these models are parameterized with standard multilayer perceptrons (MLPs), the learned constitutive components often remain poorly interpretable. In this paper, we propose a structure-preserving identification framework for nonlinear port-Hamiltonian systems based on Kolmogorov-Arnold Networks (KANs). The proposed PH-KAN model parameterizes the interconnection matrix, dissipation matrix, Hamiltonian, and input mapping using dedicated KAN blocks, while enforcing the port-Hamiltonian constraints by construction. This yields constitutive representations in which the nonlinear functions defining the identified pH components can be explicitly inspected, leading to a more interpretable model than with standard MLP-based parameterizations.

19.
arXiv (CS.LG) 2026-06-16

Dynestyx: A Probabilistic Programming Library for Dynamical Systems

arXiv:2606.16985v1 Announce Type: cross Abstract: State-space models (SSMs) are the standard formalism for Bayesian treatment of dynamical systems, with natural applications in statistics, signal processing, and machine learning. Despite their importance in both theory and application, dynamical systems have proven difficult to incorporate in modern probabilistic programming languages (PPLs), making state-of-the-art methods less accessible to practitioners and introducing friction in following the "Bayesian workflow." We introduce dynestyx, a probabilistic programming library with first-class support for SSMs, including state-of-the-art methods in the estimation of both states and parameters. Through a single, unified interface, users may specify arbitrary priors for discrete-time or continuous-time dynamical systems, perform inference over mixed-effect data, and make state and parameter estimates with principled uncertainty quantification.

20.
arXiv (quant-ph) 2026-06-16

Phase controlled spectral topology, dynamic stability and sensitivity in Non-Hermitian Cavity Magnonics

arXiv:2606.16522v1 Announce Type: new Abstract: We theoretically investigate a non-Hermitian cavity-magnon platform in which coherent photonmagnon interactions and reservoir-mediated dissipative coupling interfere through a single externally tunable phase. We show that this interference phase provides a universal control parameter that continuously rotates the effective coupling between Hermitian and anti-Hermitian regimes, enabling dynamic transitions between level repulsion and level attraction without modifying intrinsic system parameters. The resulting phase-controlled non-Hermitian topology gives rise to exceptional points, linewidth engineering, and zero-damping conditions. Owing to the propagation-direction dependence of the dissipative interaction, the system further exhibits strong nonreciprocal transport and phase-tunable isolation arising from asymmetric hybridization of the cavity and magnon modes. Beyond its spectral and transport properties, we establish a direct connection between nonHermitian spectral topology and nonequilibrium population dynamics. The interference phase governs the stability of the hybrid modes, driving transitions between stable relaxation, critical slowing down near exceptional points, oscillatory energy exchange, and exponentially amplified dynamics. We further demonstrate that the same phase-controlled exceptional topology can be exploited for enhanced sensing, where the eigenvalue response exhibits the characteristic square-root scaling associated with exceptional-point physics. Our results provide a unified framework linking spectral topology, directional transport, dynamical stability, and sensing functionality through reservoirengineered interference in cavity magnonic systems.

21.
arXiv (CS.CV) 2026-06-16

LOCUS: Local Visual Cue Search for Enhancing Fine-Grained Perception in Multimodal Large Language Models

Multimodal Large Language Models (MLLMs) remain unreliable on fine-grained visual perception, even when high-resolution inputs preserve the necessary local details. We identify this limitation as visual context rot: decisive evidence may exist in the full image, yet fail to be reliably selected and used amid redundant visual context. We propose LOCUS (LOcal visual CUe Search), a training framework that teaches MLLMs to internalize local evidence search through a verifiable proxy task. During training, LOCUS provides a local crop as a visual cue and optimizes the model to recover its spatial support in the full image using an IoU-based reward. The visual cue is used only during training, leaving the standard image-question inference interface unchanged. Experiments across fine-grained perception, hallucination, general understanding, and reasoning benchmarks show that LOCUS improves localization-sensitive visual understanding while preserving broad capabilities. Attention analyses further indicate stronger focus on task-relevant evidence regions, suggesting that training-time visual cue search provides an effective route to internalized fine-grained evidence selection.

22.
bioRxiv (Bioinfo) 2026-06-24

InVitroGap: an open-source tool for automated quantification of wound closure in the in vitro scratch assay

Abstract Background and Objective: Scratch assays are widely used to study wound closure in vitro, but quantitative image analysis remains constrained by manual variability, proprietary workflows, and tools requiring programming expertise. We developed InVitroGap, a Python-based application with a browser-accessible interface for automated quantification of scratch assay closure from sequential microscopy images. Methods: RCC-ER and Renca cells were seeded in 96-well ImageLock plates and scratched using a WoundMaker device for uniform linear wounds or a 200 uL pipette tip for crisscross wounds. Phase-contrast time-lapse images acquired at 0, 24, and 48 h with an IncuCyte SX5 system were independently analyzed using IncuCyte 2023A Rev2 and InVitroGap. The InVitroGap pipeline combines Gaussian smoothing, gradient-based texture mapping, adaptive percentile thresholding, and morphological post-processing to quantify wound confluence and relative wound density (RWD). Agreement was evaluated using paired comparisons, Pearson and Spearman correlations, Bland-Altman analysis, and mean absolute error (MAE). Results: InVitroGap measurements closely tracked IncuCyte outputs across both cell lines, with no significant between-method differences (p > 0.05), strong pooled correlations (R square = 0.964 for RWD; R square = 0.983 for wound confluence), and small mean biases (absolute bias [&le;] 1.64%). The tool successfully processed crisscross wounds from brightfield image series, and a complete four-timepoint series was analyzed in approximately 10 seconds, with robust performance across distinct cell morphologies and wound geometries. Conclusions: InVitroGap provides a transparent, computationally efficient, and platform-independent alternative for scratch assay analysis, delivering performance comparable to commercial systems while remaining freely accessible at https://invitrogap.vercel.app/.

23.
arXiv (CS.LG) 2026-06-25

LLM Program Optimization via Retrieval Augmented Search

arXiv:2501.18916v2 Announce Type: replace Abstract: Recent work has demonstrated the potential of large language models (LLMs) for program optimization, a key challenge in programming languages. We propose a blackbox adaptation method called Retrieval Augmented Search (RAS) that performs beam search over candidate optimizations; at each step, it retrieves in-context examples from a given training dataset of slow-fast program pairs to guide the LLM. Critically, we find that performing contextual retrieval based on an LLM-generated natural language description significantly outperforms retrieval based on the source code. We also propose AEGIS, a method for improving interpretability by decomposing training examples into ''atomic edits'' that are significantly more incremental in nature. We show that RAS performs up to 2.06$\times$ better than prior state-of-the-art blackbox adaptation strategies on optimizing C++ programs, and that AEGIS performs up to 1.37$\times$ better while making significantly smaller edits. We also show that using RAS improves the mean runtime percentile of Python programs by 10.27 compared to baselines.

24.
arXiv (CS.CL) 2026-06-18

PEC-Home: Interpretation of Progressively Elliptical Commands in Smart Homes

Recent advancements in Large Language Models (LLMs) have empowered home assistants with natural language interaction capabilities. However, current assistants overlook the progressive omission that occurs in human dialogue as shared context accumulates, leading to more elliptical expressions for efficient communication. Thus, current assistants still struggle to interpret such elliptical expressions accurately, which limits their effectiveness in real-world applications. In practical smart home scenarios, assistants face two major challenges caused by elliptical commands: (1) referential ambiguity caused by different environmental expectations among multiple users; and (2) intention ambiguity resulting from user preferences that evolve over time or change with the environment. To address these challenges, we introduce PEC-Home, the first simulated home dataset specifically designed for interpreting progressively elliptical commands in smart homes. Extensive experiments on various LLMs, including GPT-4o, show that existing home assistants struggle to execute user-intended operations based solely on elliptical commands. Even when equipped with tools for storing and retrieving user dialogue history, execution accuracy remains below that achieved with complete commands.}.

25.
arXiv (CS.AI) 2026-06-24

IPO Finance Agent: Evaluation of LLM Financial Analysts beyond Finance Agent v2, with Automated Rubric Generation – the Case of the SpaceX (SPCX) IPO

arXiv:2606.23032v2 Announce Type: replace Abstract: Finance Agent v2 (by Vals AI) has emerged as the reference benchmark for evaluating both Anthropic Claude and OpenAI ChatGPT frontier language models on financial tasks. However, it narrowly deals with periodic reporting from publicly traded companies (SEC 10-K and 10-Q filings), and its agentic harness relies on naive, unenriched chunk retrieval. Neither the task design nor the retrieval approach addresses the distinct challenges of IPO due diligence. SEC S-1 filings combine historical financial statements, governance structures, pro forma and common-control accounting treatments, capital-formation narratives, and underwriting-sensitive risk disclosures within substantially longer documents than typical periodic filings. That is why we introduce IPO Finance Agent, which extends the Finance Agent v2 framework along two directions: task domain and retrieval architecture. During our experiments, the original Finance Agent v2 harness basically failed to deliver any output related to the SpaceX S-1 filing, due to document length. We therefore had to improve the agentic harness with contextual retrieval, a more realistic and industry-standard approach for long documents. We also built a dataset of 1,000 IPO-diligence questions, and publicly release 70 questions on the SpaceX (SPCX) S-1 filing to support reproducibility, while the remainder are held private to guard against benchmark contamination. In addition, we introduce an evaluator-optimizer pipeline to automatically generate evaluation rubrics for the benchmark: candidate facts are extracted from model answers, consolidated into draft criteria, then automatically audited for omissions, hallucinations, mistiered items, and redundancy, with LLM feedback driving iterative repair, targeted enrichment, and deduplication. Human experts only review final rubrics before deployment. Results show that the best-performing evaluated model, Alibaba Qwen 3.7 Max, reaches 79.4% accuracy at 0.30 USD per query, and the most cost-efficient model on the resulting Pareto frontier, Xiaomi MiMo-2.5 Pro, reaches slightly lower accuracy (76.8%) at 0.05 USD per query. Both exceed the current Finance Agent v2 leaderboard ceiling-Google Gemini 3.5 Flash at 57.9% for 2.51 USD per querywhile undercutting even FABv2's cheapest entry (MiniMax M3: 48.3% at 0.32 USD) on cost-efficiency. Code and data are released on GitHub: https://github.com/benstaf/ipoagent