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01.
arXiv (CS.CL) 2026-06-16

It's About Time: Temporal References in Emergent Communication

Emergent communication enables agents to develop bespoke languages that improve communication efficiency. Despite the known importance of temporal structure in natural language, there is no existing evidence of temporal references in emergent communication. This paper addresses this gap, by exploring how agents communicate about temporal relationships. We analyse three potential factors for the emergence of temporal references: environmental, external, and architectural. Our experiments demonstrate that altering the loss function is insufficient for temporal references to emerge; rather, architectural changes are necessary. A minimal change in agent architecture, using a different batching method, allows the emergence of temporal references. This modified design is compared with the standard architecture in a temporal referential games environment, which emphasises temporal relationships. The analysis shows that over 95% of the agents with the modified batching method develop temporal references, without changes to their loss function. We consider temporal referencing necessary for future improvements to the agents' communication efficiency, enabling future agents to use a closer to optimal coding as compared to purely compositional languages. These insights provide the basis for incorporation of temporal references into other emergent communication settings, and investigation of other aspects of language.

02.
arXiv (CS.AI) 2026-06-16

Learning in the Recurrent State: Gradient Descent with Linear Recurrent Networks

arXiv:2410.11687v3 Announce Type: replace-cross Abstract: Linear recurrent networks (LRNNs) offer linear-time sequence modeling, but standard recurrent updates do not directly expose the supervised products needed for in-context gradient descent. We propose a sufficient constructive inductive bias for LRNNs: equip a diagonal recurrent state with multiplicative readout and a short sliding-window cross-product self-attention update. The resulting architecture, Gradient-based Recurrent In-context Learner (GRIL), can implement minibatch gradient descent on a task-specific linear predictor during a single forward pass. The same design extends to multi-step updates and cross-entropy classification, with a limited MLP-based extension to non-linear regression. Empirically, trained GRILs recover the behavior and parameters predicted by the construction on synthetic ICL tasks, and the same architectural bias yields useful performance on Long Range Arena and language modelling. These results present windowed cross-product self-attention as a practical, testable inductive bias for LRNNs that learn in context through gradient-descent-like updates.

03.
arXiv (math.PR) 2026-06-16

Free energy of non-convex multi-species spin glasses with centered Ising spins

arXiv:2606.16636v1 Announce Type: new Abstract: We identify the limit free energy of all multi-species spin glasses with centered $\pm 1$ spins. The result was previously known only under a convexity assumption on the covariance function of the Hamiltonian. We also obtain a one-species reduction of the formula for balanced multi-species models.

04.
arXiv (CS.AI) 2026-06-12

CausalMoE: A Billion-Scale Multimodal Foundation Model for Granger Causal Discovery with Pattern-Routed Heterogeneous Experts

arXiv:2606.13024v1 Announce Type: cross Abstract: Granger Causal Discovery (GCD) is fundamental for analyzing temporal dependencies in complex systems. However, existing neural GCD methods predominantly rely on a "one-size-fits-all" paradigm, struggling to capture distribution shifts and dynamic regime changes inherent in real-world time series. This often leads to entangled representations and spurious causal graphs. In this paper, we propose CausalMoE, a billion-scale multimodal Granger causal foundation model that explicitly models patch-level heterogeneity. CausalMoE introduces a Pattern-Routed Mixture of Heterogeneous Experts, which dynamically identifies latent temporal patterns and routes patches to specialized domain experts, effectively decoupling regime-specific mechanisms from shared dynamics. To ensure interpretable graph recovery, we design a Causality-Aware Self-Attention mechanism operating across variables, yielding sparse Granger causal graphs via proximal optimization. Furthermore, CausalMoE is the first to integrate LLMs and VLMs to align numerical signals with textual and visual priors, regularizing causal estimation in complex scenarios. Extensive experiments demonstrate that CausalMoE establishes a new state-of-the-art on fully supervised benchmarks, while effectively generalizing to few-shot settings where traditional methods fail.

05.
PLOS Computational Biology 2026-06-05

StPedf: Cell trajectory inference of spatial transcriptomics via spatial proximity embedding and spatial density-adaptive fusion

作者:

by Yuan Zhang, Ziyan Sun, Zhixin Shi, Mengdi Nan, Yuhan Fu, Qing Ren, Jie Gao Spatial transcriptomics is transforming our multidimensional understanding of cellular spatial organization and its functional mechanisms in processes such as development and disease by systematically resolving the spatial heterogeneity of gene expression within tissues. To delve deeper into the dynamic processes underlying spatial expression patterns, spatial trajectory inference integrates genetic and spatial information to reconstruct the spatial developmental trajectories of cells within tissues. This approach reveals the patterns of differentiation and dynamic changes as cellular states evolve continuously along spatial axes. However, existing methods often struggle to uniformly model the complex, nonlinear interactions between high-dimensional gene expression and spatial coordinates. Here, we introduce StPedf, whose core lies in employing a neural network with a masking mechanism to capture complex nonlinear interactions between high-dimensional genes and spatial positions. It further leverages spatial proximity information as a guiding cue, dynamically and adaptively adjusting the embedding of gene and spatial information and the weighting of spatial proximity information based on spatial density. This enables trajectory inference guided by spatial information. This enables optimal transport to derive intercellular transition matrices, reconstruct cellular differentiation trajectories, and construct pseudo-spatiotemporal maps. StPedf demonstrates superior performance over existing methods on five structurally distinct simulated datasets. Using StPedf, we successfully mapped distinct lineages in the spatial trajectories of telencephalon regeneration in the Ambystoma mexicanum, multiple malignant lineages expanding within primary tumors, and developmental spatial trajectories and pseudo-spatiotemporal maps in human dorsolateral prefrontal cortex (DLPFC). StPedf significantly enhances the accuracy and interpretability of spatial trajectory inference, providing critical technical support for revealing the dynamic patterns of cellular fate transitions within tissue microenvironments.

06.
arXiv (quant-ph) 2026-06-12

Theoretical Study for Generating Optical GKP State via a Single-Photon-Added Squeezed Vacuum

arXiv:2606.12467v1 Announce Type: new Abstract: A theoretical framework is developed to analyze the generation of the optical GKP state using a single-photon-added squeezed vacuum. This state, defined by the squeezing parameter $r$, is injected into a 50:50 beam splitter, and the optical GKP state is obtained through conditional measurement at one output port. The single-photon-added squeezed vacuum is especially prominent in this context because it provides a simpler and more experimentally accessible ingredient than Schrodinger cat states, while conditional measurement ensures projection onto a state that closely approximates the finite-energy GKP form. Fidelity is employed to quantify this closeness, and the analysis demonstrates that the scheme achieves a maximum fidelity of 85% at a squeezing level of $3.76 \ dB$. This performance surpasses approaches based on squeezed optical odd Schrodinger cat states, underscoring the single-photon-added squeezed vacuum as a practical and effective pathway toward fault-tolerant photonic quantum computing.

07.
arXiv (quant-ph) 2026-06-17

DRAG-Compatible Leakage Suppression in Landau–Zener Control via Isoprobability Twins

arXiv:2506.19572v4 Announce Type: replace Abstract: Analytically solvable models – particularly the Landau-Majorana-Stückelberg-Zener (LMSZ) and Allen-Eberly-Hioe (AEH) models – underpin many quantum-gate implementations and population-transfer protocols. However, their canonical pulse shapes are incompatible with modern leakage-suppression techniques and some systems. Most notably, the constant Rabi envelope of the LMSZ pulse prevents many leakage-suppression approaches, which require smoothness. We address both limitations by developing the concept of isoprobability twin models: distinct pairs of Rabi frequency $\Omega(t)$ and detuning $\Delta(t)$ that yield identical post-pulse transition probabilities based on the Delos-Thorson transformation. In this work, we formalise the method by experimentally demonstrating the equivalence of multiple LMSZ and AEH twin models on IBM's ibm_kyiv processor. Finally, we show a staggering leakage reduction by more than 3 orders of magnitude using a custom DRAG implementation of a cosine LMSZ isoprobability model.

08.
arXiv (CS.LG) 2026-06-11

DeepRHP: A Hybrid Variational Autoencoder for Designing Random Heteropolymers as Protein Mimics

arXiv:2606.11651v1 Announce Type: new Abstract: Synthetic random heteropolymers (RHPs), consisting of a predefined set of monomers, offer an approach toward the design of protein-like materials. These RHPs, if designed appropriately, can mimic protein behavior and function. As such, there is a need for computational tools to efficiently guide RHP design. We bridge this gap by developing DeepRHP, a modified variational autoencoder (VAE) model under a semi-supervised framework. By equipping a classical VAE with an additional feature-based VAE, DeepRHP forces the latent space to capture structures of critical chemical features as well as individual RHP sequence patterns. In this sense, our method is versatile by allowing any relevant features to be incorporated in a hybrid manner. We demonstrate the effectiveness of DeepRHP by suggesting potential monomer compositions that stabilize membrane proteins (e.g. Aquaporin Z) in non-native environments and cross-validating our prediction with published results. The concordance between our model and true RHP function suggests strong potential in utilizing hybrid autoencoder architectures to guide RHP design for proteins and other biological compounds.

09.
arXiv (CS.AI) 2026-06-15

HarnessX: A Composable, Adaptive, and Evolvable Agent Harness Foundry

arXiv:2606.14249v1 Announce Type: new Abstract: AI agent performance depends critically on the runtime harness, comprising the prompts, tools, memory, and control flow that mediate how a model observes, reasons, and acts. Yet today's harnesses remain largely hand-crafted and static: each new model or task still demands bespoke scaffolding, and the rich traces produced during execution are rarely distilled back into systematic improvement. We introduce HarnessX, a foundry for composable, adaptive, and evolvable agent harnesses. HarnessX assembles typed harness primitives via a substitution algebra, adapts them through AEGIS, a trace-driven multi-agent evolution engine grounded in an operational mirror between symbolic adaptation and reinforcement learning, and closes the harness-model loop by turning trajectories into both harness updates and model training signal. Across five benchmarks (ALFWorld, GAIA, WebShop, tau^3-Bench, and SWE-bench Verified), HarnessX yields an average gain of +14.5% (up to +44.0%), with gains largest where baselines are lowest. These results suggest that agent progress need not come from model scaling alone: composing and evolving runtime interfaces from execution feedback is an actionable and complementary lever. The complete codebase will be open-sourced in a future release.

10.
arXiv (CS.CV) 2026-06-12

Revisiting Vehicle Color Recognition in Long-Tailed Surveillance Scenarios

Vehicle color recognition is an important cue for vehicle identification in surveillance systems, especially when license plates are illegible due to low resolution, occlusion, motion blur, or poor illumination. However, real-world vehicle color distributions are highly imbalanced, making overall accuracy insufficient to assess performance on rare but operationally relevant colors. This paper presents a comprehensive study of vehicle color recognition under severe class imbalance using UFPR-VeSV, a challenging real-world surveillance dataset. We investigate synthetic minority-class augmentation through two off-the-shelf generative strategies: text-conditioned image generation with RunDiffusion/JuggernautXL and image-conditioned color editing with Gemini 2.0 Flash. The curated synthetic data are combined with modern visual representations, loss reweighting, learning-rate scheduling, color-safe augmentation, foreground-aware preprocessing, and ensemble fusion. The bestperforming approach achieves 94.6% micro accuracy and 79.7% macro accuracy, improving macro accuracy by 8.2 percentage points over recent literature. A manual error analysis further shows that many remaining failures are visually ambiguous even for human annotators, highlighting the practical limits of color-based vehicle identification in unconstrained surveillance imagery. The generated images and source code are publicly available at https://github.com/viniciusorru/vcr-synthetic

11.
arXiv (math.PR) 2026-06-17

Limit theorems for descents and inversions of shelf-shuffles

arXiv:2510.00343v2 Announce Type: replace Abstract: We prove central limit theorems for the number of descents and inversions of permutations produced by shelf-shuffles. These are a model for casino card shuffling machines. We show the asymptotic normality of the number of descents in two limiting regimes depending on the ratio of cards to shelves. On the other hand, we study the inversions by employing a modification of the techniques from Islak's analysis of the statistics of riffle shuffles. In particular, we obtain a bound for the rate of convergence for inversions that is independent of the number of shelves.

12.
arXiv (CS.AI) 2026-06-17

Dissecting model behavior through agent trajectories

arXiv:2606.17454v1 Announce Type: new Abstract: AI agent performance is not just a modeling problem, it is fundamentally a systems problem. The advanced capabilities of models are realized through agent harnesses. Therefore, a gap between model assumptions and harness behavior can easily prevent the model's full capabilities from translating into agent performance. We formalize this as the `intent-execution' gap: the mismatch between what the model intends and what the harness executes, and vice versa. We argue that minimizing this intent-execution gap is as important as other aspects of harness design such as tools and execution loops. To illustrate the impact of this harness-model alignment, we develop a simple and customizable harness called `Simple Strands Agent' (SSA). SSA aims to find the bulk of common patterns which generalize across different model families (such as Claude, Gemini, GPT, Grok, Qwen), as well as a small number of model-specific preferences. We make two contributions: (i) we $reproduce or improve on the pass@1$ performance reported by diverse model-provider families on popular agentic benchmarks (SWE-Pro, SWE-Verified and Terminal-Bench-2), and (ii) building on an $analysis of 138k trajectories generated by SSA$, we look beyond the $\texttt{pass@1}$ numbers which tend to be relatively even across frontier models. By representing agent trajectories in code state-spaces, we observe model-level differences in problem-solving behavior. Finer-grained metrics such as edit frequency, testing activity, and phase-transitions reveal how individual models allocate effort across different stages of autonomous problem solving.

13.
arXiv (quant-ph) 2026-06-15

Path superposition activating perfect quantum teleportation ability for separable states

arXiv:2505.11398v2 Announce Type: replace Abstract: Quantum teleportation is a quintessential quantum communication protocol that enables the transmission of an arbitrary quantum state between two distant parties without physically transmitting the state with the help of shared entanglement and limited classical communication. We show that it is possible to relax the entanglement requirement in quantum teleportation if we have access to a certain strain of superposition of quantum processes. Two types of superposition of quantum processes are generally considered in the literature: superposition of paths identified with quantum maps and superposition of indefinite causal orders of the maps. We find that when superposition of paths is incorporated in the protocol, quantum teleportation with unit fidelity becomes possible with nonzero probability of 1/4 even when the two parties share certain classes of separable states, including pure product states. In contrast, the assistance of superposition of indefinite causal order of quantum maps in teleportation protocol does not enable any quantum advantage for shared pure product states. Furthermore, we show that separable Werner states can also yield quantum advantage in quantum teleportation assisted by the superposition of paths. Finally, we establish that the presence of quantum coherence in the control qubit is both necessary and sufficient to achieve quantum advantage in quantum teleportation assisted with superposition of paths. The results potentially uncover yet another role of quantum superposition, in general, in teleportation versus entanglement.

14.
arXiv (quant-ph) 2026-06-15

Tamed Feynman-Kac diffusion processes: Killing-branching intertwine

arXiv:2605.07824v2 Announce Type: replace-cross Abstract: Relaxation to equilibrium of a drifted Brownian motion is quantified by a transition probability density function, whose main (multiplicative) entry is an inferred Feynman-Kac kernel of the Schr\"{o}dinger semigroup operator. Although seemingly devoid of a natural probabilistic significance (except for its explicit path integral definition), the pertinent kernel relaxes to equilibrium as well. The implicit Feynman-Kac potential ${\cal{V}}(x)$, continuous, confining and bounded from below, may take negative values. If positive, ${\cal{V}}(x)$ can be interpreted as the killing rate of the decaying diffusion process. In case of relaxing F-K kernels the killing effects are tamed (often overcompensated). The taming inavoidably appears in conjunction with the existence of the negativity subdomains of ${\cal{V}}(x)$ in $R$. If locally ${\cal{V}}(x) < 0$, its sign inversion $- {\cal{V}}(x)$ can be interpreted as the branching (cloning, alternatively bifurcation) rate in the course of the other wise free random motion. The arising killed diffusion processes with branching, we interpret as the possible path-wise background of tamed (relaxing) Feynman-Kac diffusions. We present acomputer-assisted path-wise arguments, towards a consistency of the killing/branching taming scenario, for a number of nonlinear model systems in one space dimension. Special attention is paid to Feynman-Kac potential shapes in the double well form, where an analytic access to eigenvalues and eigenfunctions is scarce. Throughout the paper the dynamics refers to the positive real time. Since the Newton-type equations of motion for admissible classical trajectories have a Euclidean form (due to the sign inverted force term), we give a brief resume of a couple of their explicit solutions, without recourse to the Euclidean time intuitions, and the instanton lore of related quantum model systems.

15.
arXiv (CS.AI) 2026-06-17

Explicit Context-Driven Neural Acoustic Modeling for High-Fidelity RIR Generation

arXiv:2509.15210v2 Announce Type: replace-cross Abstract: Realistic sound simulation plays a critical role in many applications. A key element in sound simulation is the room impulse response (RIR), which characterizes how sound propagates within a given space. Recent studies have applied neural implicit methods to learn RIR using context information collected from the environment, such as scene images. However, these approaches do not effectively leverage explicit geometric information from the environment. To further exploit neural implicit models with direct geometric features, we present MiNAF, which queries a rough room mesh at given locations and extracts distance distributions as an explicit representation of local context. Our approach demonstrates that incorporating explicit local geometric features can better guide the model in generating more accurate RIR predictions. Through comparisons with conventional and state-of-the-art methods, we show that MiNAF performs competitively across various evaluation metrics.

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

Execution-State Capsules: Graph-Bound Execution-State Checkpoint and Restore for Low-Latency, Small-Batch, On-Device Physical-AI Serving

作者:

arXiv:2606.20537v1 Announce Type: new Abstract: Mainstream LLM serving systems reuse prefix work mainly through paged or radix key-value (KV) caches. This is highly effective for high-throughput, high-concurrency serving, but it manages only one positional fragment of execution state: the KV cache. We study the opposite regime: low-latency, small-batch, on-device physical-AI serving, where interactive LLM agents, speech systems, and robot policies repeatedly branch, reset, interrupt, and re-enter under tight responsiveness budgets. We introduce execution-state capsules, a graph-bound checkpoint and restore mechanism for the complete restorable state at a committed boundary. FlashRT is a white-box, backend-facing kernel runtime whose evaluated NVIDIA CUDA backend runs captured graph plans over contiguous static buffers with no block-table indirection. Because the live state is a closed set of named buffers, a capsule can snapshot, restore, fork, or roll back the whole execution boundary, including KV, recurrent state, convolution state, MTP state, and metadata. This moves reuse from token-addressed KV fragments to graph-bound execution-state boundaries. On an RTX 5090, capsule restore is byte-exact at the stored-state level and token-identical under greedy decode. A KV-only ablation diverges, showing that recurrent state is load-bearing. GPU-resident snapshot and restore are sub-millisecond, and TTFT speedup over cold prefill grows from 3.9x at 2k tokens to 27x at 16k tokens. On Jetson AGX Thor and DGX Spark, the same correctness and structural properties hold. Capsules are not a replacement for high-throughput KV-cache serving; they define a complementary latency-first serving point for explicit execution-state reuse.

17.
arXiv (math.PR) 2026-06-18

Functions of Bounded Variation and Point Processes

arXiv:2606.08304v2 Announce Type: replace-cross Abstract: We investigate the relationship between the analytical properties of functions of bounded variation and the statistical behavior of hyperuniform point processes. We establish several characterization formulas for the jump part of the gradient of a bounded variation function, extending and unifying previous results by Beretti–Gennaioli and Dávila. In particular, we provide new expressions for the $L^2$-jump of the gradient using both difference quotients and Fourier transform methods. Furthermore, we connect these analytic structures to the theory of hyperuniform point processes. By analyzing the variance of linear statistics associated with bounded variation functions, we provide asymptotic estimates that depend on the specific classification of the hyperuniformity of the point process. The results show how the regularity and jump discontinuities of a function dictate the growth rate of fluctuations in point processes. Finally, we introduce an averaged quadratic BMO-type oscillation functional over translated and rotated cube partitions, similar to the one recently studied by Ambrosio et al., and prove, using results from point process, that it converges to an explicit dimensional constant times the $L^2-$jump, giving in particular a further new characterization of the perimeter of a set.

18.
arXiv (CS.AI) 2026-06-15

Exact Linear Attention

作者:

arXiv:2605.18848v4 Announce Type: replace-cross Abstract: This paper introduces Exact Linear Attention (ELA), a mechanism that achieves linear computational complexity for Transformer attention by exploiting the exact decomposition property of kernel functions, thereby eliminating approximation error. We identify and address two key limitations of prior linear attention – gradient explosion and token attention dilution – by imposing kernel constraints that ensure non-negativity, discriminability, and geometric interpretability. Several kernel functions are proposed, including the Hadamard Exp Kernel, Summation Squared Euclidean Distance Kernel, and Subtraction Squared Euclidean Distance Kernel, each tailored for specific attention behaviors. Beyond the core attention formulation, the paper presents three engineering innovations: (1) a Hyper-Link structure that replaces traditional residual connections to mitigate gradient degradation; (2) a Memory Lobe module based on bidirectional linear attention, which captures "transformation flow" across layers to implement qualitative memory and an implicit reinforcement learning paradigm; and (3) a routing-score-based bias mechanism for Mixture-of-Experts (MoE) to improve interpretability and semantic alignment. Experimental results demonstrate that ELA achieves up to 6x faster decoding speed and 75% reduction in KV cache memory usage compared to full attention, while maintaining comparable or superior training performance. The proposed memory module accelerates convergence and enhances generalization. Furthermore, we extend the linear attention principle to vision models, yielding YOLO-LAT, which attains up to 4.3x GPU inference speedup and 7.9x parameter reduction with competitive detection accuracy. These results underline the broad applicability of exact linear attention for scaling Transformer models to ultra-long sequences and efficient visual tasks.

19.
arXiv (math.PR) 2026-06-16

Higher-order spectral perturbation expansions II: Kernel matrices and manifold learning

arXiv:2606.16373v1 Announce Type: cross Abstract: We study spectral concentration bounds for kernel matrices as approximation of the corresponding kernel integral operator. Results are established under weak assumptions on the data setting and the reproducing kernel relying only on a Mercer condition and a local Weyl law. This allows us to deal with key features of kernel matrices, such as large multiplicities, large effective dimension, and heavy-tailed distributions. Our results apply to infinite dimensional principal component analysis, manifold learning, and Bayesian nonparametric statistics. We illustrate this via two prototypical examples: The heat kernel on the sphere and a wavelet prior from Bayesian nonparametrics.

20.
arXiv (CS.AI) 2026-06-12

Emotional regulation improves deep learning-based image classification

arXiv:2606.13081v1 Announce Type: cross Abstract: Emotion significantly influences cognition, enhancing memory and learning under certain conditions. Drawing on this principle, emotion-augmented deep learning investigates how affective states can improve neural network architectures and learning paradigms, achieving better generalization than non-emotional models. However, existing methods often rely solely on objective neurophysiological factors, neglecting the role of subjectivity in emotion. To bridge this gap, the present study introduces Emotional Regulation, a novel framework for modeling emotion in deep learning through artificial subjective experience. The method employs pre-training based on affective stimuli, balancing non-emotional and emotionally-influenced responses in downstream task optimization. Extensive experimentation was conducted in image classification, pre-training ResNet and ViT architectures on four emotional datasets, using CIFAR-10 and -100 as target benchmarks. Results reveal improvements over the aforementioned backbones, providing evidence of Emotional Regulation as a promising method for defining emotion-augmented deep learning through artificial subjective experience. Furthermore, the proposed approach overcomes the related work in image classification based on CIFAR, revealing Emotional Regulation as the new state-of-the-art in emotion-augmented deep learning for large-scale vision datasets. The study also enforces evidence of the impact of affective states in improving machine learning tasks' optimization, encouraging further investigation on emotion-inspired architectures.

21.
arXiv (CS.CV) 2026-06-15

SA4Depth: Consistent Pose-Depth Scale Alignment for Self-Supervised Monocular Depth Estimation

Self-supervised depth estimation from monocular sequences relies on the joint learning of a depth and a pose network. Despite abundant research done to improve the depth network, efforts on the pose remain limited. In this context, even when depth is estimated up to scale, we highlight the importance of the alignment between the scene scales estimated by the pose and depth nets. Then, we introduce SA4Depth, an approach to improve this alignment and boost the depth predictions while keeping the inference time unchanged. Our proposed method uses the depth estimated during training to reproject learnable visual features across consecutive frames and refine the pose estimates by reducing feature alignment residuals. With our method, the estimated scene scales by the separate depth and pose networks are aligned, and the prediction scale consistency is improved across different sequences. Our differentiable refinement integrates seamlessly into existing self-supervised pipelines and substantially improves their depth estimates. We demonstrate this with extensive experiments both outdoors and indoors on KITTI, Cityscapes, and NYUv2. Additionally, results on KITTI Odometry confirm the effectiveness of our pose refinement. Our code is available at https://github.com/Runningchauncey/SA4Depth .

22.
bioRxiv (Bioinfo) 2026-06-16

scIsoAgent enables autonomous isoform-resolved characterization and sequence-informed interpretation of long-read single-cell transcriptomes

Alternative isoform usage can alter gene function independently of total gene expression, creating a need to resolve transcript isoforms at single-cell resolution. Long-read single-cell RNA sequencing meets this need by linking cellular identity to transcript isoforms and sequence-level features. Realizing its full biological value requires reproducible workflows that connect specialized long-read analysis with biological interpretation. Existing large language model (LLM)-based biomedical agents support general omics analysis, but are not designed for isoform-resolved long-read single-cell workflows. Here, we present scIsoAgent, an autonomous LLM-powered scientific agent for long-read single-cell RNA-seq analysis. scIsoAgent turns heterogeneous long-read single-cell inputs into traceable isoform-resolved workflows, using stage-aware planning and persistent computational context to support both execution and interpretation. Across complementary evaluations, this design improved the continuity from analysis planning to executable, interactive workflows compared with general-purpose LLM baselines. In real-data reanalysis, scIsoAgent recovered major findings from published long-read single-cell resources and extended a representative differential transcript usage event into a sequence-informed functional hypothesis. By linking full-length isoform sequences with model-inferred transcript properties, scIsoAgent connects observed isoform usage with potential sequence-level functional consequences. These results demonstrate that autonomous scientific agents can transform fragmented long-read single-cell analysis into coherent, reproducible workflows for isoform-resolved discovery and biological interpretation.

23.
arXiv (CS.AI) 2026-06-18

TransitNet: A Compact Attention-Augmented Deep Learning Framework for Low-SNR Transit Blind Searches

arXiv:2606.18932v1 Announce Type: cross Abstract: Motivated by the observational incompleteness of intermediate-to-long-period Earth-size planets, we present TransitNet, a compact attention-augmented deep-learning framework for low-SNR transit blind searches. To enable realistic method development and objective threshold calibration under blind-search conditions, we develop a unified dataset construction, benchmarking, and threshold-selection framework. On recovery benchmarks constructed from unseen Kepler targets, TransitNet attains 95.2 percent accuracy in the challenging SNR range of 6 to 8 and outperforms both TLS and BLS, achieving ROC-AUC and PR-AP values of 0.974 and 0.982, respectively. In an injected Earth-size and sub-Earth-size transit recovery experiment, TransitNet achieves a recovery rate of 93.0 percent, substantially exceeding those of TLS (63.1 percent) and BLS (60.0 percent). In addition to detection, TransitNet provides attention-based estimates of transit windows and midpoints. On an independent evaluation set, 97.4 percent of injected transits are fully covered by the estimated transit window. Applied to real Kepler observations, the model successfully recovers all 34 selected confirmed Kepler planets, with a mean absolute transit midpoint error of 1.24 hours. The model combines a compact footprint of about 1.5 MB with high inference efficiency, yielding speed-ups of about 12 to 25 times relative to CPU-TLS and about 4 to 5 times relative to CPU-BLS. These results demonstrate that TransitNet provides an accurate, scalable, and computationally efficient framework for low-SNR transit blind searches in the tested regime and motivate its extension to longer-period Earth-size planet searches.

24.
arXiv (CS.CV) 2026-06-15

Interpretable Alzheimer's Diagnosis via Multimodal Fusion of Regional Brain Experts

Accurate and early diagnosis of Alzheimer's disease (AD) is critical for effective intervention and requires integrating complementary information from multimodal neuroimaging data. However, conventional fusion approaches often rely on simple concatenation of features, which cannot adaptively balance the contributions of biomarkers such as amyloid PET and MRI across brain regions. In this work, we propose MREF-AD, a Multimodal Regional Expert Fusion model for AD diagnosis. It is a Mixture-of-Experts (MoE) framework that models mesoscopic brain regions within each modality as independent experts and employs a gating network to learn subject-specific fusion weights. Utilizing tabular neuroimaging and demographic information from the Alzheimer's Disease Neuroimaging Initiative (ADNI), MREF-AD achieves competitive performance over strong classic and deep baselines while providing interpretable, modality- and region-level insight into how structural and molecular imaging jointly contribute to AD diagnosis. The source code is available at https://github.com/PennShenLab/mref-ad.

25.
arXiv (CS.CV) 2026-06-19

Thinking in Boxes: 3D Editing in Real Images Made Easy

Text and 2D-conditioning interfaces provide weak, ambiguous control over spatial transformations in image editing – particularly under large object motions and camera changes. Prior work has used 3D primitives such as boxes, but only as loose conditioning signals indicating approximate object location rather than specifying the transformation. We instead use 3D boxes as structured specifications: the user provides the input and output boxes of the edit, casting editing as a well-posed geometry problem. This ``thinking in boxes'' interface, where each box face is color-coded to convey 3D orientation, gives precise control over translation, rotation, scaling, and viewpoint changes in real images while preserving scene and object identity, and recovering previously unseen object regions. To ground transformations in scene appearance, we introduce a depth-aligned planar floor as a global reference frame, shaded with depth-aware cues. Conditioned on this structure, an image generator produces consistent results under large transformations. Trained in two stages – on synthetic multi-object scenes and a small set of real-world videos from Objectron – the system generalizes to complex, in-the-wild real images. Our method operates directly on real photographs and substantially outperforms recent state-of-the-art methods on large 3D edits.