Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

01.
arXiv (CS.CV) 2026-06-18

A Multi-Domain Benchmark for Detecting AI-Generated Text-Rich Images from GPT-Image-2

Text-rich images often contain privacy-sensitive, transactional, or decision-relevant information. As recent multimodal image generation models become increasingly capable of synthesizing realistic textual content and structured visual designs, detecting AI-generated text-rich images has become an important challenge for digital trust and content authenticity. Existing benchmarks, however, largely focus on object-centric images and provide limited coverage of scenarios where textual semantics and layout organization are central. In this paper, we introduce a multi-domain benchmark for detecting text-rich images generated by OpenAI's GPT Image 2. The benchmark contains 8,602 images across six representative categories: commercial posters, infographics, academic posters, receipts, tables, and UI screenshots. Using this benchmark, we evaluate five representative AI-generated image detectors in a zero-shot setting and analyze their overall, category-wise, and post-processing robustness. Our results show that detector performance is highly domain-dependent: methods that perform well in some categories often fail on others, and even the strongest conventional detector exhibits severe sensitivity to JPEG compression. We further conduct an exploratory evaluation with a multimodal vision-language model, revealing both its promise and its limitations on structured formats. These findings highlight the need for text- and layout-aware detection methods for modern AI-generated images. Our dataset is released at XXX.

02.
arXiv (quant-ph) 2026-06-12

Beyond-Third-Order Quantum Coherence in Two-Dimensional Spectroscopy via Order-Selective Isolation

arXiv:2606.12794v1 Announce Type: new Abstract: A central challenge in nonlinear spectroscopy is the order-selective readout of weak higher-order responses that spectrally overlap with dominant lower-order signals. This bottleneck is particularly severe in two-dimensional (2D) spectroscopy, where extending conventional phase-cycling schemes to higher orders rapidly increases measurement and analysis complexity. Here we introduce a computation-assisted strategy that combines rotating-frame acquisition with a frame-shift tracking algorithm to separate signals by their frame-dependent spectral shifts. In a rubidium vapor experiment, we use this approach to isolate a 7th-order nonlinear contribution from coexisting 3rd-order components, enabling direct access to higher-order quantum-coherence dynamics without sacrificing operation at comparatively high pulse intensities. The method is broadly compatible with multidimensional spectroscopy platforms and provides a practical route to probing many-body and collective ultrafast dynamics beyond third order.

03.
arXiv (CS.CV) 2026-06-11

STEAM: Squeeze and Transform Enhanced Attention Module

Channel and spatial attention mechanisms introduced in earlier work enhance the representational capabilities of deep convolutional neural networks (CNNs) but often increase parameter and computational costs. While recent approaches focus solely on efficient feature context modeling for channel attention, we aim to model both channel and spatial attention comprehensively with minimal parameters and reduced computation. Leveraging the principles of relational modeling in graphs, we introduce a constant-parameter module, STEAM: Squeeze and Transform Enhanced Attention Module, which integrates channel and spatial attention to enhance the representation power of CNNs. To our knowledge, we are the first to propose a graph-based approach for modeling both channel and spatial attention, utilizing concepts from multi-head graph transformers. Additionally, we introduce Output Guided Pooling (OGP), which efficiently captures spatial context to further enhance spatial attention. We extensively evaluate STEAM for large-scale image classification, object detection and instance segmentation on standard benchmark datasets. STEAM achieves a \(2\%\) increase in accuracy over the standard ResNet-50 model with only a meager increase in GFLOPs. Furthermore, STEAM outperforms the leading modules, ECA and GCT, in terms of accuracy while achieving a threefold reduction in GFLOPs. The code will be made available upon acceptance.

04.
arXiv (CS.LG) 2026-06-19

MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

arXiv:2606.19624v1 Announce Type: new Abstract: Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.

05.
Nature (Science) 2026-06-17

Revealing competitive interfacial reactions in high-energy Li–S batteries

Authors:

Charge transfer at solid–liquid interfaces plays a critical role in various energy-storage systems1, particularly under dynamically varying reactant concentrations. Deciphering these intricate reaction pathways remains a substantial challenge, notably in lithium–sulfur (Li–S) batteries, in which achieving high energy density requires efficient conversion of highly concentrated lithium polysulfides (LiPSs)2,3. However, the mechanisms governing lithium sulfide (Li2S) deposition and dissolution under lean electrolyte conditions remain poorly understood. Here, using in situ liquid-cell electron microscopy, we directly visualize concentration-driven phase segregation at the electrode–electrolyte interface. Within these high-concentration interfacial layers (HCILs), competitive surface and solution dictate the charge-transfer dynamics and ultimately govern Li2S deposition at different phase boundaries. Density functional theory (DFT) calculations reveal that the aggregation of LiPSs alters molecular geometry, electronic properties and orbital hybridization, collectively facilitating charge transfer through highly concentrated LiPSs clusters. Guided by these insights, we design optimized electrodes that balance interfacial reaction pathways, enabling fast charging (4 C, 26.8 mA cm−2) and achieving high energy densities exceeding 400 Wh kg−1. These findings provide mechanistic understanding of interfacial reactions under practical working conditions and offer a design strategy to advance Li–S batteries. Visualization of concentration-driven phase segregation within high-concentration interfacial layers in the context of high-energy lithium–sulfur batteries using liquid-cell electrochemical transmission electron microscopy reveals competitive interfacial reactions under lean electrolyte conditions at different phase boundaries.

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

SAFformer:Improving Spiking Transformer via Active Predictive Filtering

Spiking Neural Networks (SNNs) offer notable advantages in biological plausibility and energy efficiency, making them promising candidates for building low-power Transformers. However, existing Spiking Transformers largely adhere to a passive reactive paradigm, which struggles to focus on task-relevant information and incurs substantial computational overhead when processing redundant visual data. To overcome this fundamental yet underexplored limitation, we propose SAFformer, a novel Spiking Transformer architecture based on an active predictive filtering paradigm. Inspired by the brain's predictive coding mechanism, SAFformer actively suppresses predictable signals and focuses on salient visual features. Extensive experiments show that SAFformer establishes new state-of-the-art performance on CIFAR-10/100 and CIFAR10-DVS. Remarkably, on ImageNet-1K, it achieves 80.44% Top-1 accuracy with only 26.58M parameters and an energy consumption of 5.88 mJ, demonstrating an exceptional balance between accuracy and efficiency.

07.
Nature (Science) 2026-06-08

Targeting Cancer-Specific Mutations with RNA-Triggered Chromatin Shredding

Authors:

Genetic mutations that drive cancer often occur in tumor suppressor proteins, including the p53 transcription factor which is altered in ~40-50% of cases1,2. However, current therapies fail to target most such mutations because the mutant proteins typically lack defined drug-binding pockets, and restoring the endogenous function has proven challenging. Here, we programmed CRISPR-Cas12a2, an RNA-guided nuclease with trans-nucleolytic cleavage activities3,4, to selectively kill cancer cells by targeting cancer-specific transcripts. This approach limits cell growth by inducing trans shredding of chromatin, triggering DNA damage responses and cell death. Unlike existing methods, RNA-guided Cas12a2 senses cellular RNA signatures, enabling precise targeting of undruggable mutations. Transcript-activated chromatin shredding provides a new approach to precision disease treatments for undruggable targets.

08.
arXiv (CS.LG) 2026-06-19

Evaluating deep learning models for fault diagnosis of a rotating machinery with epistemic and aleatoric uncertainty

arXiv:2412.18980v2 Announce Type: replace Abstract: Uncertainty-aware deep learning (DL) models recently gained attention in fault diagnosis as a way to promote the reliable detection of faults when out-of-distribution (OOD) data arise from unseen faults (epistemic uncertainty) or the presence of noise (aleatoric uncertainty). In this paper, we present the first comprehensive comparative study of state-of-the-art uncertainty-aware DL architectures for fault diagnosis in rotating machinery, where different scenarios affected by epistemic uncertainty and different types of aleatoric uncertainty are investigated. The selected architectures include sampling by dropout, Bayesian neural networks, and deep ensembles. Moreover, to distinguish between in-distribution and OOD data in the different scenarios two uncertainty thresholds, one of which is introduced in this paper, are alternatively applied. Our empirical findings offer guidance to practitioners and researchers who have to deploy real-world uncertainty-aware fault diagnosis systems. In particular, they reveal that, in the presence of epistemic uncertainty, all DL models are capable of effectively detecting, on average, a substantial portion of OOD data across all the scenarios. However, deep ensemble models show superior performance, independently of the uncertainty threshold used for discrimination. In the presence of aleatoric uncertainty, the noise level plays an important role. Specifically, low noise levels hinder the models' ability to effectively detect OOD data. Even in this case, however, deep ensemble models exhibit a milder degradation in performance, dominating the others. These achievements, combined with their shorter inference time, make deep ensemble architectures the preferred choice.

09.
PLOS Computational Biology 2026-06-01

On real-time calibrated prediction for complex model-based decision support in pandemics: Part 2

by Trevelyan J. McKinley, Daniel B. Williamson, Xiaoyu Xiong, James M. Salter, Robert Challen, Leon Danon, Ben Youngman, Doug McNeall Calibration of complex stochastic infectious disease models is challenging. These often have high-dimensional input and output spaces, with the models exhibiting complex, non-linear dynamics. Coupled with a paucity of necessary data, this results in a large number of non-ignorable hidden states that must be handled by the inference routine. Likelihood-based approaches to this missing data problem are very flexible, but challenging to scale, due to having to monitor and update these hidden states. Methods based on simulating the hidden states directly from the model-of-interest have an advantage that they are often more straightforward to code, and thus are easier to implement and adapt in real-time. However, these often require evaluating very large numbers of simulations, rendering them infeasible for many large-scale problems. We present a framework for using emulation-based methods to calibrate a large-scale, stochastic, age-structured, spatial meta-population model of COVID-19 transmission in England and Wales. By embedding a model discrepancy process into the simulation model, and combining this with particle filtering, we show that it is possible to calibrate complex models to high-dimensional data by emulating the log-likelihood surface instead of individual data points. The use of embedded model discrepancy also helps to alleviate other key challenges, such as the introduction of infection across space and time. We conclude with a discussion of major challenges remaining and key areas for future work.

10.
arXiv (CS.CV) 2026-06-18

Pyramid Self-Contrastive Learning for Single-shot Test-time Ultrasound Image Denoising

The inherent electronic and speckle noise complicates clinical interpretation of ultrasound images. Conventional denoising methods rely on explicit noise assumptions whose validity diminishes under composite noise conditions. Learning-based methods are usually pretrained in a limited image domain using a labeled dataset, which implies inevitable domain shift in complex in vivo environments. This study proposes a Pyramid Self-Contrastive Learning (PSCL) framework for test-time ultrasound image denoising without pretraining. Given multiple noisy samples from only one-shot imaging, PSCL disentangles anatomical similarity and noise randomness into separate pyramid latent spaces. The clean image is then decoded from the anatomy space while discarding the noise space. We first apply PSCL to synthetic aperture ultrasound (SAU), where an Aperture-to-Aperture loop serves as a self-supervised proxy task to ensure denoising fidelity. Simulation experiments, including noise levels from 0 to 30 dB and inclusion geometries from simple to complex, demonstrated improvements of 69.3% in SNR and 34.4% in CNR. The in vivo results showed 84.8% SNR and 25.7% CNR gains using only two aperture data of the heart in six echocardiographic views, liver, and kidney. PSCL delivers clear images across diverse imaging targets and configurations, paving the way for more reliable anatomical visualization without domain shift and pretraining costs.

11.
arXiv (CS.CV) 2026-06-15

HiST: A Hierarchical Sparse Transformer for Cross-Modal Spatial Transcriptomics Modeling

Spatial transcriptomics (ST) links gene expression with tissue morphology but remains expensive and low-throughput, motivating surrogates that infer expression from routine histology. Whole-slide H&E-to-ST inference pairs a gigapixel image with gene measurements at a sparse, irregular set of locations, making multiscale modeling challenging without incurring dense-grid overhead or quadratic token mixing. We propose HiST, a hierarchical sparse transformer that treats measured locations as a lattice-indexed sparse field and builds a dyadic encoder–decoder directly on the active tissue footprint. HiST combines sparse window attention for local geometric correspondence with resolution-changing operators for rapid multiscale context integration. For a fixed window size, the dominant runtime and memory scale with the number of observed locations rather than the dense slide area. To mitigate slide-specific acquisition variation, HiST adds a bottlenecked global conditioning pathway via a slide calibration token that summarizes slide-level context and conditions local representations. On a multi-organ benchmark spanning diverse tissues and acquisition sources, HiST improves predictive performance over recent baselines while reducing runtime and peak memory.

12.
arXiv (CS.AI) 2026-06-18

InstructTime++: Time Series Classification with Multimodal Language Modeling via Implicit Feature Enhancement

arXiv:2601.14968v2 Announce Type: replace-cross Abstract: Most existing time series classification methods adopt a discriminative paradigm that maps input sequences directly to one-hot encoded class labels. While effective, this paradigm struggles to incorporate contextual features and fails to capture semantic relationships among classes. To address these limitations, we propose InstructTime, a novel framework that reformulates time series classification as a multimodal generative task. Specifically, continuous numerical sequences, contextual textual features, and task instructions are treated as multimodal inputs, while class labels are generated as textual outputs by tuned language models. To bridge the modality gap, InstructTime introduces a time series discretization module that converts continuous sequences into discrete temporal tokens, together with an alignment projection layer and a generative self-supervised pre-training strategy to enhance cross-modal representation alignment. Building upon this framework, we further propose InstructTime++, which extends InstructTime by incorporating implicit feature modeling to compensate for the limited inductive bias of language models. InstructTime++ leverages specialized toolkits to mine informative implicit patterns from raw time series and contextual inputs, including statistical feature extraction and vision-language-based image captioning, and translates them into textual descriptions for seamless integration. Extensive experiments on multiple benchmark datasets demonstrate the superior performance of InstructTime++.

13.
arXiv (CS.LG) 2026-06-16

Analytic Torsion and Spectral Gap Capture Persistent-Laplacian Performance

arXiv:2606.16990v1 Announce Type: new Abstract: While persistent Laplacians (PL) offer a richer geometric representation of data than persistent homology, utilizing their full eigenspectrum for learning tasks is often hampered by high dimensionality and the ``varying length'' problem across different filtration scales. We propose a compact spectral representation that distills the persistent Laplacian into three mathematically grounded invariants: Betti numbers, the spectral gap, and analytic torsion. Across benchmark datasets including MNIST, QM-3D, and SKEMPI WT, we demonstrate that this reduced feature space captures the essential predictive signal of the full spectrum, and in some cases outperforms it, while significantly reducing computational overhead and preventing the noise introduced by higher-frequency eigenvalues. Our results suggest that these invariants provide a principled, fixed-length interface between spectral geometry and topological learning.

14.
arXiv (CS.CL) 2026-06-15

Verbatim Chunks Beat Extracted Artifacts: A Controlled Ablation of Memory Representations for Long LLM Conversations

Authors:

A growing class of conversational-memory systems compresses dialogue history into structured artifacts – extracted facts, decisions, or events – on the premise that distilled structure retrieves better than raw text. We test this premise with a controlled ablation: within one fixed retrieval-rerank-reasoning pipeline, we swap only the stored representation – LLM-extracted typed artifacts versus verbatim conversation chunks – holding the model, retriever, reranker, and judge constant. Verbatim chunks win by 15.9 points on LoCoMo (43.9% vs. 28.0%) and 22.0 points on LongMemEval-S (67.4% vs. 45.4%); a 1-hop semantic graph does not recover the gap, and five confound controls reproduce the effect. The mechanism is lossy distillation: extraction discards verbatim detail that chunks retain for free, and the extracted-artifact pipeline never beats naive RAG in overall accuracy. Concurrent positive results with near-verbatim, provenance-preserving units fit the same account: retrieval accuracy tracks how far the representation departs from the source. For the extraction designs we test, structured memory should augment verbatim text rather than replace it: a chunks $\cup$ artifacts union store matches chunks on both benchmarks while artifacts alone forfeit the gap. Code and data: https://github.com/tao-hpu/cog-canvas

15.
arXiv (CS.CL) 2026-06-16

Vernier: Probing Representational Misalignment Behind Lexical Gaps in Causal Reasoning

Authors:

Instruction-tuned language models can answer the same causal-reasoning question differently after its English variable names are replaced by type-preserving placeholders, although the structural causal model and the gold answer are unchanged. We ask whether this lexical gap reflects information loss in the placeholder view or a misaligned read-out from a representation that still carries answer-relevant content. Vernier uses a paired-view weight update as an instrument and then inspects the mechanism left after the gap closes. In the working regimes, the evidence favours representational misalignment. A variable-name probe becomes more accurate on the placeholder view, and activation patching on Qwen-7B, Qwen-14B, and Llama-3.1-8B shows that the decision-token representation can transfer answer identity between views. The update that realigns the views is counterfactual augmentation over original and placeholder prompts, while the answer-subspace KL mainly sharpens intermediate answer-belief agreement. Success is bounded by model family, scale, and task. CRASS transfer is reliable across Qwen scales and Llama, e-CARE remains weak, and preliminary non-causal rename tasks show a similar qualitative pattern.

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

In-Context Learning Is Provably Bayesian Inference: A Generalization Theory for Meta-Learning

arXiv:2510.10981v3 Announce Type: replace-cross Abstract: This paper develops a finite-sample statistical theory for in-context learning (ICL), analyzed within a meta-learning framework that accommodates mixtures of diverse task types. We introduce a principled risk decomposition that separates the total ICL risk into two orthogonal components: Bayes Gap and Posterior Variance. The Bayes Gap quantifies how well the trained model approximates the Bayes-optimal in-context predictor. For a uniform-attention Transformer, we derive a non-asymptotic upper bound on this gap, which explicitly clarifies the dependence on the number of pretraining prompts and their context length. The Posterior Variance is a model-independent risk representing the intrinsic task uncertainty. Our key finding is that this term is determined solely by the difficulty of the true underlying task, while the uncertainty arising from the task mixture vanishes exponentially fast with only a few in-context examples. Together, these results provide a unified view of ICL: the Transformer selects the optimal meta-algorithm during pretraining and rapidly converges to the optimal algorithm for the true task at test time.

17.
arXiv (CS.CV) 2026-06-16

An Adaptive Data cleaning Framework for Noisy Label Detection

Deep neural networks (DNNs) excel in computer vision tasks given large annotated datasets. In real-world applications, however, labels are often corrupted by ambiguity, human error, or dynamic environments. Over-parameterized DNNs easily memorize these noisy labels during training, degrading model accuracy and generalization. Existing data-cleaning and sample-selection strategies often rely on manually specified thresholds, prior knowledge of the noise ratio, or a single metric (either learning dynamics or geometric structure), making them unstable in complex data regimes. This paper proposes a self-adaptive data-cleaning framework that integrates local, global, and learning dynamics cues for robust noisy-label detection. Samples are mapped into a unified low-dimensional feature space through a modular feature concatenation paradigm. We provide two instantiations: a 2D metric integrating class-adaptive KNN-based local disagreement with k-means-based global centroid distance, and a 3D multi-metric that additionally incorporates a z-normalized score. Unlike conventional 1D Gaussian Mixture Models applied to a single scalar metric, our framework performs multi-metric clustering on the feature space to adaptively partition samples into clean-dominant and noise-dominant components without requiring manual thresholds or noise priors. Experiments on CIFAR-10, MNIST, and ImageNet-100 with 5% to 40% symmetric label noise show high recall across settings, including near-perfect recall (>=98%) on ImageNet-100 at 40% noise. Subsequent training yields accuracy gains across evaluated settings, especially under severe corruption on ImageNet-100. These findings suggest that multi-metric integration provides a threshold-free, practical, and low-tuning strategy for noisy label detection.

18.
PLOS Computational Biology 2026-06-15

Environmental “knees” and “wiggles” as strong stabilizers of species’ range limits set by interspecific competition

by Farshad Shirani, Benjamin G. Freeman Whether interspecific competition is a major contributing factor to setting species’ range limits has been debated for a long time. Theoretical studies have proposed that the interactions between interspecific competition and disruptive gene flow along an environmental gradient can halt range expansion of ecologically similar species where they meet. However, the stability of such range limits has not been well addressed. We use a deterministic mathematical model of adaptive range evolution over a continuous habitat to show that the range limits set by interspecific competition are unlikely to be evolutionarily stable if the environmental optima for fitness-related traits vary (almost) linearly in space. That is, in a linear environment without a dispersal barrier or a third (or more) species, the range borders formed between two competing species constantly move towards the weaker species. We demonstrate that environmental nonlinearities such as “knees” and “wiggles”—wherein an isolated sharp change or a step-like change occurs in the steepness of a trait optimum—can strongly stabilize competitively formed range limits. The stabilization mechanism relies on the contrast that such nonlinearities create in the level of disruptive gene flow to the peripheral population of each species, and succeeds when an additional process, such as Allee effects, prevents the establishment of an infinitesimal population in the presence of an abundant competitor. We show that the stability of the range limits at these nonlinearities is robust against moderate environmental disturbances. Whether strong disturbances such as rapid high-amplitude climate changes can destabilize such range limits depends on how the competitive dominance of the species changes across the nonlinearity. Therefore, our findings underscore the importance of assessing species’ competitive ability when predicting responses to climate change, and identify geographic regions where established range limits are likely to persist as well as regions where shifting limits may eventually stabilize.

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

Adaptive Oscillatory-State Alignment for Time Series Forecasting

arXiv:2606.06010v2 Announce Type: replace Abstract: Long-term time series forecasting benefits from inductive biases that expose recurring temporal structure. Existing periodic forecasting methods typically model recurrence through predefined periods, global spectral components, or fixed learnable templates. However, real-world temporal dynamics are rarely rigidly periodic: around a nominal cycle, oscillatory behavior often exhibits non-rigid periodicity (NRP), where cycle magnitude, cycle alignment, and local cycle duration vary over time. Under these conditions, fixed-template periodic modeling can become fundamentally mismatched to the underlying temporal states. We propose AOSNet, a Hilbert-guided forecasting framework that reformulates periodic forecasting from fixed template matching to adaptive oscillatory-state alignment. AOSNet extracts analytic-signal descriptors from both the observed sequence and a learnable global oscillatory prior, then adaptively aligns local states through a descriptor-conditioned gate that selectively preserves reliable observations while softly correcting mismatched regions. The learned prior serves not as a rigid repeated template but as a flexible oscillatory reference interpreted through local state dynamics. Experiments on eight public benchmarks and two cloud workload traces demonstrate leading or highly competitive accuracy with a compact model size and low inference latency, supporting repeated forecasting settings such as capacity planning and autoscaling. Controlled synthetic studies that isolate cycle-magnitude and cycle-alignment variation and combine them with cycle-duration changes show that the advantage of oscillatory-state alignment increases as NRP intensifies.

20.
arXiv (CS.LG) 2026-06-18

AGDN: Learning to Solve Traveling Salesman Problem with Anisotropic Graph Diffusion Network

arXiv:2606.19185v1 Announce Type: new Abstract: The Traveling Salesman Problem (TSP) is a cornerstone of combinatorial optimization and arises in many practical scenarios. Although graph-based learning approaches have been explored for TSP, the question of how to exploit graph structure more effectively remains open. We present the Anisotropic Graph Diffusion Network (AGDN), a new Graph Neural Network framework designed to solve TSP. Our method tackles two central difficulties: (1) the lack of informative topological prior in fully connected TSP graphs, and (2) losing connected nodes in the optimal solution after the commonly used graph sparsification techniques. To overcome these issues, we construct a MixScore transition matrix that merges node similarity with pairwise distance, and we develop an anisotropic graph diffusion strategy that supports efficient information exchange across multiple hops. Comprehensive experiments spanning diverse instance sizes and node distributions show that AGDN consistently outperforms existing methods while keeping computation time competitive. Furthermore, AGDN generalizes well to problem sizes and distributions beyond those seen during training. The implementation is publicly available at: https://github.com/LabRAI/AGDN.

21.
bioRxiv (Bioinfo) 2026-06-18

A Two-Stage Interpretable Framework for Predicting Plant-Derived Small RNA Targets on Human 3'UTRs

Authors:

Can plant-derived small RNAs target human mRNA 3'UTRs via complementary base pairing and produce experimentally detectable regulatory effects? This question concerns not only the fundamental feasibility of cross-kingdom RNA regulation but also the technological pathway for screening plant-derived active small nucleic acids. Existing miRNA target prediction tools are predominantly designed for endogenous miRNA-mRNA systems, exhibiting notable limitations when applied to cross-species small RNA inputs and small-sample wet-lab experimental adaptation. In this study, we developed a two-layer prediction framework, MetaLulu-AI. The first layer builds upon publicly available human miRNA-mRNA 3'UTR interaction data, utilizing XGBoost to learn foundational binding rules on human 3'UTRs based on 41 interpretable computational features, including seed region pairing types, local context sequence composition, site positioning, and RNA secondary structures. The second layer is tailored to the experimental system of plant-derived small RNAs and human target genes. It introduces 40 experimental samples using significant changes in endogenous protein expression as the regulatory standard (determined by Western blot or ELISA 48 hours post-transfection of small RNAs via Lipo3000). Using 52-dimensional computational features and the optimal transcript scores from the first layer as inputs, this layer employs TabPFN for experimental label adaptation. The first-layer dataset consists of 38,752 training samples, 5,536 validation samples, and 11,073 testing samples (totaling 55,361), with a positive-to-negative sample ratio of approximately 1:5.4. On the randomly split test set, the model achieved an AUC of 0.9686, a recall of 0.8523, a precision of 0.8080, and an accuracy of 0.9452 (at a decision threshold of 0.4797). Group-based splitting revealed that the model maintains high discriminative power for unseen genes (AUC = 0.9541), though its generalization ability for completely unseen miRNAs decreases (AUC = 0.7390). For the 40 experimental samples in the second layer, the TabPFN model achieved an average AUC of 0.7406 {+/-} 0.092 across ten repeated 70/30 random splits, outperforming the baseline of directly using the first-layer scores (0.3563 {+/-} 0.149); the average AUC in a 5-fold cross-validation was 0.770 {+/-} 0.177. SHAP analysis demonstrated a clear divergence in the discriminative basis of the two models: the first layer relies more heavily on the thermodynamics of the small RNA itself and the quality of canonical seed sites, whereas the second layer focuses more on the local UTR environment and statistical site features. Although the current second-layer results are constrained by sample size and gene coverage, this framework serves as a preliminary observation of the adaptation mechanism for cross-kingdom regulation experiments, and motivating future large-scale validation. Under stricter leave-one-gene-out and leave-one-small-RNA-out evaluation, the adapter exceeded the first-layer score baseline but only matched the majority-class baseline, underscoring that entity-level generalization is not yet established.

22.
arXiv (CS.CV) 2026-06-12

PROBE: Probabilistic Occupancy BEV Encoding with Analytical Translation Robustness for 3D Place Recognition

We present PROBE (PRobabilistic Occupancy BEV Encoding), a learning-free LiDAR place recognition descriptor that models each BEV cell's occupancy as a Bernoulli random variable. Rather than relying on discrete point-cloud perturbations, PROBE analytically marginalizes over continuous Cartesian translations via the polar Jacobian, yielding a distance-adaptive angular uncertainty $\sigma_\theta = \sigma_t / r$ in $\mathcal{O}(R{\cdot}S)$ time. The primary parameter $\sigma_t$ represents the expected translational uncertainty in meters, a sensor-independent physical quantity that enhances cross-sensor generalization while reducing the need for extensive per-dataset tuning. Pairwise similarity combines a Bernoulli-KL Jaccard with exponential uncertainty gating and FFT-based height cosine similarity for rotation alignment. Evaluated on four datasets spanning four diverse LiDAR types, PROBE achieves the highest accuracy among handcrafted descriptors in multi-session evaluation and competitive single-session performance relative to both handcrafted and supervised baselines. The source code and supplementary materials are available at https://sites.google.com/view/probe-pr.

23.
arXiv (quant-ph) 2026-06-12

Symmetry-Accelerated Classical Simulation of Clifford-Dominated Circuits

arXiv:2510.18977v2 Announce Type: replace Abstract: Classical simulation of quantum circuits plays a crucial role in validating quantum hardware and delineating the boundaries of quantum advantage. Among the most effective simulation techniques are those based on the stabilizer extent, which quantifies the overhead of representing non-Clifford operations as linear combinations of Clifford unitaries. However, finding optimal decompositions rapidly becomes intractable as it constitutes a superexponentially large optimization problem. In this work, we exploit symmetries in the computation of the stabilizer extent, proving that for real, diagonal, and real-diagonal unitaries, the optimization can be restricted to the corresponding subgroups of the Clifford group without loss of optimality. This ``strong symmetry reduction'' drastically reduces computational cost, enabling optimal decompositions of unitaries on up to seven qubits using a standard laptop – far beyond previous two-qubit limits. Additionally, we employ a ``weak symmetry reduction'' method that leverages additional invariances to shrink the search space further. Applying these results, we demonstrate exponential runtime improvements in classical simulations of quantum Fourier transform circuits and measurement-based quantum computations on the Union Jack lattice, as well as new insights into the nonstabilizer properties of multicontrolled phase gates and unitaries generating hypergraph states. Our findings establish symmetry exploitation as a powerful route to scale classical simulation techniques and deepen the resource-theoretic understanding of quantum advantage.

24.
arXiv (CS.AI) 2026-06-16

PrologMCP: A Standardized Prolog Tool Interface for LLM Agents

arXiv:2606.14935v1 Announce Type: new Abstract: Frontier reasoning-tuned language models still fail on deductive tasks at depth, and the cost of improved performance through extended internal reasoning scales poorly. Symbolic delegation offers a complementary route: a language model translates the problem, while a solver performs the inference. However, current autoformalization pipelines for logic programming are typically bespoke integrations tied to particular tasks or agents. We introduce PrologMCP, a task-agnostic, open-source server that exposes Prolog as a stateful tool through the Model Context Protocol (MCP). Its compact tool interface, structured error reporting, and per-session isolation make the translate-run-inspect-repair loop a reusable primitive for MCP-capable agents. We evaluate a formalizer agent enhanced with PrologMCP against standard and reasoning LLMs (Claude Sonnet 4.6, GPT-4.1, and o4-mini) on two subsets of PARARULE-Plus: a general-purpose sample and a more challenging one targeting a specific failure mode of natural-language reasoning. On the general sample, the formalizer matches or exceeds reasoning LLMs (accuracy 1.00 vs.\ 1.00 / 0.998), with the largest gains over standard models (0.762 for GPT-4.1). On the challenging subset, the formalizer remains near-perfect (1.00 / 0.99) while reasoning LLMs drop to 0.95 / 0.94. These results suggest that delegating inference to Prolog via MCP is a robust and inspectable alternative to extended natural-language reasoning.

25.
arXiv (CS.AI) 2026-06-17

Trustworthy Self-Composable Big-Data-as-a-Service: An LLM-Orchestrated Multi-Agent Framework for Automated Data Engineering, AutoML, MLOps Deployment, and Drift-Aware Lifecycle Optimization

arXiv:2606.17915v1 Announce Type: cross Abstract: Big-Data-as-a-Service (BDaaS) platforms require re liable automation across data ingestion, cleaning, feature engi neering, model development, deployment, and post-deployment monitoring. However, existing LLM-based data science agents and AutoML systems mainly focus on isolated workflow stages, leaving limited support for lifecycle-level orchestration, artifact governance, human oversight, and drift-aware adaptation. This paper proposes a trustworthy self-composable BDaaS frame work based on LLM-orchestrated multi-agent collaboration. The proposed architecture decomposes the BDaaS lifecycle into specialized agents for data ingestion, data cleaning, feature engineering, AutoML training, model evaluation, MLOps de ployment, monitoring, and drift detection. A central LLM or chestration layer coordinates agent execution, validates interme diate outputs, manages workflow context, and enables dynamic workflow composition. The framework also incorporates shared artifact governance, reproducibility support, human-in-the-loop checkpoints, and drift-aware feedback loops. A prototype-based evaluation is conducted using controlled tabular benchmark datasets with missing values, categorical variables, outliers, class imbalance, and simulated covariate drift. Compared with manual ML, AutoML-only, and single-agent LLM baselines, the pro posed multi-agent BDaaS pipeline achieves competitive predictive performance while improving lifecycle-level reliability, including workflow completion, artifact traceability, deployment readiness, reproducibility, and drift recovery. The results suggest that LLM-orchestrated multi-agent systems can extend conventional AutoML toward trustworthy, adaptive, and production-oriented BDaaS lifecycle automation.