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01.
arXiv (CS.AI) 2026-06-15

Shift-Invariant Attribute Scoring for Kolmogorov-Arnold Networks via Shapley Value

arXiv:2510.01663v2 Announce Type: replace-cross Abstract: For many real-world applications, understanding feature-outcome relationships is as crucial as achieving high predictive accuracy. While traditional neural networks excel at prediction, their black-box nature obscures underlying functional relationships. Kolmogorov–Arnold Networks (KANs) address this by employing learnable spline-based activation functions on edges, enabling recovery of symbolic representations while maintaining competitive performance. However, KAN's architecture presents unique challenges for network pruning. Conventional magnitude-based methods become unreliable due to sensitivity to input coordinate shifts. We propose ShapKAN, a pruning framework using Shapley value attribution to assess node importance in a shift-invariant manner. Unlike magnitude-based approaches, ShapKAN quantifies each node's actual contribution, ensuring consistent importance rankings regardless of input parameterization. Extensive experiments on synthetic and real-world datasets demonstrate that ShapKAN preserves true node importance while enabling effective network compression. Our approach improves KAN's interpretability advantages, facilitating deployment in resource-constrained environments.

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

Optimizing LLM Inference: Fluid-Guided Online Scheduling with Memory Constraints

arXiv:2504.11320v4 Announce Type: replace-cross Abstract: Large language models now serve millions of users daily, with providers incurring costs exceeding $700,000 per day. Each request requires token-by-token inference, making GPU scheduling central to latency, capacity, and cost. The difficulty is endogenous memory growth: generated tokens expand the Key-Value (KV) cache, and overflow can evict in-progress requests and waste prior computation. We formulate inference as a multi-stage online scheduling problem with endogenous memory growth, linear iteration times, and GPU-resident KV-cache constraints. We introduce a fluid model that characterizes equilibrium batch composition, memory requirement, and stability region. Guided by the fluid model, we design WAIT (Waiting for Accumulated Inference Threshold), a threshold-based admission rule for known output lengths, and Nested WAIT, which extends the rule to unknown output lengths by regulating how requests advance across decode-stage segments. Both algorithms approximate the fluid benchmark asymptotically under the stated memory conditions. Nested WAIT uses an additional safety buffer of moderate scale to hedge against memory-overflow-induced evictions under unknown output lengths. In Vidur simulations configured for Llama-2-7B on an A100 GPU, with supplemental real-GPU validation reported in the appendix, the policies enlarge the empirically observed stable operating range relative to widely used baseline algorithms and reduce latency especially in near-overloaded and overloaded regimes.

03.
arXiv (CS.LG) 2026-06-15

CANN-EUCLID: unsupervised constitutive artificial neural network model discovery from full-field data

arXiv:2606.14565v1 Announce Type: cross Abstract: Constitutive artificial neural networks (CANNs) provide interpretable material model discovery, but have so far been used in stress-supervised settings based on apparent stress-strain data from homogeneous tests. Because each test samples only a narrow loading path and provides homogenized rather than local stress information, robust discovery typically requires multiple loading modes to constrain the multidimensional response. This is challenging for soft biological tissues, where repeated testing, damage, and sample variability limit reliable information from a single specimen. Here, we combine CANNs with the stress-unsupervised full-field discovery framework EUCLID to identify sparse hyperelastic laws directly from displacement fields and reaction forces in one heterogeneity-inducing loading case. CANN-EUCLID minimizes equilibrium imbalance with sparsity-promoting regularization selecting compact active terms, without local stress measurements or a prescribed law. We evaluate the approach on isotropic and anisotropic benchmarks with prescribed ground-truth laws. When the ground truth is representable by the chosen CANN basis, our method recovers the correct terms with near-exact accuracy, including exponential terms with embedded parameters. When it is not contained in the basis, the method retains shared terms and approximates missing contributions using available basis functions. Generalization depends strongly on sampled deformation states: exponential strain-stiffening terms can be recovered accurately when sufficiently probed, but can produce large extrapolation errors when the stiffening regime lies outside the sampled domain. Forward FE validation simulations show that the discovered behavior accurately replicates the ground truth. These results establish stress-unsupervised CANN discovery as a promising framework for interpretable full-field constitutive model identification.

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

Surflo: Consistent 3D Surface Flow Model with Global State

Geometry is invariant to viewpoint, which makes any collection of images a redundant encoding of a single 3D state. Existing feed-forward reconstruction models fail to exploit this: per-view methods emit overlapping, unaligned pointmaps that grow linearly with input count, while global-latent methods commit to a fixed, low-resolution output. We introduce Surflo, which compresses a variable number of unposed RGB views into K latent tokens-one global state-and decodes oriented 3D surface points by independently transporting them from noise onto the surface via flow matching. This frees the output from any fixed grid or token budget: the same latent yields from a few thousand to a million points in a single forward pass. To suppress the local inconsistencies inherent to independent per-point decoding, an inference-time guidance term correlates nearby points by injecting a photometric gradient during ODE integration. Surflo matches or surpasses feed-forward baselines on surface metrics, runs an order of magnitude faster than optimization-based methods that require hundreds of views, and is the only feed-forward approach to combine a global latent with arbitrary-resolution decoding.

05.
arXiv (CS.AI) 2026-06-17

Know Thy Reasoner: Not All Language Models Explore Alike

arXiv:2604.10827v2 Announce Type: replace Abstract: Compute scaling for LLM reasoning trades off exploring solution approaches (breadth) against refining promising ones (depth), yet why a given trade-off works, and why it often fails to transfer across models, remains unclear. We argue that the optimal strategy depends on the model's diversity profile, the spread of probability mass across solution approaches, and that this must be characterized before any exploration strategy is adopted. We formalize this with a framework decomposing reasoning uncertainty, deriving when depth-based refinement outperforms parallel sampling, and validate it across three model families at both inference and training. Our central finding is that the diversity regime dictates the strategy: low-diversity aligned models benefit from depth-based refinement with lightweight intrinsic signals, whereas high-diversity base models are often harmed by it, and instead need breadth or stronger signals to compensate.

06.
bioRxiv (Bioinfo) 2026-06-16

PhenoBIC: operator-free single-cell spatial phenotyping in multiplex imaging data using deep learning of cell staining patterns

Multiplex imaging is a valuable tool for spatially examining tissue microenvironments at the single-cell level to uncover biological and clinical insights. However, most multiplex image analysis workflows currently require manual intervention for cell phenotyping, which slows progress, demands human effort, and yields operator-dependent outputs. Here, we developed PhenoBIC, a pre-trained deep learning model for image classification of the multiplexed biomarker signals in a cell (Biomarker Imprint of a Cell) to classify cell phenotypes. We show that PhenoBIC (F1-score ~0.88) outperforms manual gating (widely used) and other machine learning-based computational approaches for cell marker expression classification. We validated this across multiple biomarkers, tissue sampling strategies (whole biopsies and tissue microarrays), multiplex panels, imaging platforms, and tissue types. We have released our in-house training and validation datasets of ~1.4 million manually curated cell expression ground truth labels. We have also open-sourced PhenoBIC and enabled its community-wide deployment via the QuPath interface.

07.
arXiv (CS.AI) 2026-06-16

The Model Knows, the Decoder Finds: Future Value Guided Particle Power Sampling

arXiv:2605.02427v3 Announce Type: replace Abstract: A recurring pattern in "reasoning without training" is that base LLMs already assign non-trivial probability mass to correct multi-step solutions; the bottleneck is locating these modes efficiently at inference time. Power sampling provides a principled way to bias decoding toward such modes by targeting p_theta(x)^alpha with alpha > 1, but practical approximations must account for future-dependent correction factors that determine which prefixes remain promising. We introduce Auxiliary Particle Power Sampling (APPS), a blockwise particle algorithm for approximating the sequence-level power target with a bounded population of partial solutions. APPS propagates hypotheses in parallel using proposal-corrected power reweighting and refines their survival through future-value-guided selection at resampling boundaries. This redistributes finite compute across competing prefixes rather than committing to a single unfolding path, while providing a direct scaling knob in the particle count and predictable peak memory. We instantiate the future-value signal with short-horizon rollouts and also study an amortized variant that replaces rollouts with a lightweight learned selection head. AMore broadly, APPS improves the accuracy–runtime trade-off of training-free decoding, further supporting the view that inference-time power approximation can recover gains often attributed to post-training.

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

Improved Cryogenic Photodiode Optical Biasing for Low-Noise and Low-Jitter Superconducting Nanowire Single-Photon Detectors

arXiv:2606.07140v2 Announce Type: replace Abstract: We experimentally demonstrate an improved optical biasing scheme for superconducting nanowire single-photon detectors (SNSPDs), which employs a cryogenic InGaAs-InP photodiode (PD) as a local bias source. It is found that, under illumination from a stable external light source, this PD generates a stable photocurrent in a cryogenic environment (~2.3 K), with fluctuations in the photocurrent primarily attributed to fluctuations in the incident optical power. Furthermore, by screening and effectively blocking stray photons leaking from the PD, which give rise to background dark counts, we have achieved an SNSPD exhibiting an ultra-low intrinsic dark count rate of 1e-4 cps. Utilizing this improved optical biasing technique, our SNSPD achieved performance comparable to that obtained under conventional electrical biasing: a system detection efficiency of 80.7%, a background dark count rate of 32.6 cps, and a minimum timing jitter of 57.5 ps. These results indicate that cryogenic-PD-based optical biasing serves as a viable, low-noise, and low-jitter alternative to traditional electrical biasing. Moreover, this work offers useful design guidance for the future development of PD-based low-noise bias sources and for the construction of all-photonic SNSPD systems tailored for high-precision quantum photonics applications.

09.
arXiv (CS.AI) 2026-06-16

Retro-Expert: Collaborative Reasoning for Interpretable Retrosynthesis

arXiv:2508.10967v3 Announce Type: replace-cross Abstract: Retrosynthesis prediction aims to infer the reactant molecules based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing methods rely on a static pattern-matching paradigm, which limits their ability to perform effective logical decision-making from chemical data, leading to a black-box process. We propose Retro-Expert, an interpretable retrosynthesis framework that performs collaborative reasoning by combining the complementary strengths of Large Language Models and specialized models via pure reinforcement learning. It outputs natural language explanations grounded in chemical logic through three components: (1) specialized models provide chemical knowledge that is distilled into a high-quality chemical decision space, (2) LLM-driven critical reasoning to generate predictions with an interpretable reasoning path, and (3) knowledge-grounded policy optimization refines the interpretable decision policy. Experiments show that Retro-Expert surpasses both LLM-based and specialized models across different metrics, while generating chemically grounded explanations that enhance chemists' trust in practice. The source code for this paper is available at https://github.com/MagixRab-ll/Retro-Expert.

11.
arXiv (CS.AI) 2026-06-12

BASENet: Band-Adapted Speech Enhancement Network with Cross-Band Attention

arXiv:2606.12662v1 Announce Type: cross Abstract: Speech enhancement models typically apply uniform capacity across all frequencies, disregarding the non-uniform spectral resolution of human hearing. We propose BASENet, a frequency-adapted architecture that partitions the spectrum into Bark-scale bands and assigns each a scaled-capacity encoder derived from critical-band density, automatically granting deeper branches to perceptually dense low frequencies and lighter ones to high frequencies. A cross-band attention module captures harmonic dependencies across bands through compact frequency-pooled representations at linear complexity. Built on inverted residual blocks with dense connectivity and a convolutional recurrent network, BASENet achieves 3.55 PESQ and STOI~96% on VoiceBank+DEMAND with only 0.83M parameters and 7.3 G~MACs, the fewest parameters among all methods with PESQ > 3.50. A causal variant (3.44 PESQ) surpasses several non-causal baselines, confirming suitability for real-time streaming on resource-constrained devices.

12.
arXiv (math.PR) 2026-06-15

Upper tails for irregular graphs beyond the mean-field regime

arXiv:2606.14564v1 Announce Type: new Abstract: Let $G_{n,p}$ be the binomial random graph of density $p$ and let $X_H$ be the number of copies of a fixed graph $H$ in $G_{n,p}$. We prove asymptotically tight bounds on the logarithmic upper-tail probability of $X_H$ whenever $H$ is a connected, irregular graph with maximum degree $\Delta \ge 2$ and $p \ge n^{-1/\Delta - \varepsilon_H} (\log n)^{\omega(1)}$ for an explicit $\varepsilon_H >0$. These bounds are expressed in terms of a new variational problem that generalises the combinatorial optimisation problem arising from the naïve mean-field approximation. This new variational problem includes an entropy term that corresponds to the large number of embeddings of certain highly structured graphs in $K_n$. For a certain class of irregular graphs $H$ that we call stable, we show that this description of the upper-tail probability is valid in a range of densities that is optimal up to a poly($\log\log n$) factor. For a further subclass of stable graphs, which includes all irregular complete bipartite graphs, we show that this range of densities is optimal up to a multiplicative constant.

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

Perron–Frobenius Operator Matching for Generative Modeling

arXiv:2606.17465v1 Announce Type: new Abstract: We introduce Perron–Frobenius Operator Matching (PFOM), a generative framework that matches density evolution via the integral PF operator, subsuming flow, diffusion, and jump models. We prove that among Bregman divergences, only Kullback–Leibler divergence preserves equality between density-level and sample-conditioned objectives, yielding a practical loss equivalent to Koopman path matching. We further develop Nesterov-accelerated training and sampling that stabilize discretization and accelerate convergence. %On Gaussian mixtures and two-moons, PFOM achieves faster KL/$W_2$/MMD decrease and improved wall-clock efficiency with empirical validation. PFOM unifies operator-theoretic identification with modern generative modeling and opens paths to adaptive dictionaries and high-dimensional applications.

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

SMT-AD: a scalable quantum-inspired anomaly detection approach

arXiv:2604.06265v2 Announce Type: replace Abstract: Quantum-inspired tensor networks algorithms have shown to be effective and efficient models for machine learning tasks, including anomaly detection. Here, we propose a highly parallelizable quantum-inspired approach which we call SMT-AD from Superposition of Multiresolution Tensors for Anomaly Detection. It is based upon the superposition of bond-dimension-1 matrix product operators to transform the input data with Fourier-assisted feature embedding, where the number of learnable parameters grows linearly with feature size, embedding resolutions, and the number of additional components in the matrix product operators structure. We demonstrate successful anomaly detection when applied to standard datasets, including credit card transactions, and find that, even with minimal configurations, it achieves competitive performance against established anomaly detection baselines. Furthermore, it provides a straightforward way to reduce the weight of the model and even improve the performance by highlighting the most relevant input features.

16.
arXiv (CS.CV) 2026-06-12

Diffusion Transformer World-Action Model for AV Scene Prediction

Action-conditioned world models let an autonomous vehicle predict future camera scenes from its own planned controls, enabling planning and simulation without real-world rollouts, but at compact, trainable scale the futures are ambiguous and the field's standard distortion metrics actively mislead: they reward a blurry regression mean over a realistic prediction. We confront this with a compact latent world model that, given the present front-camera latent and a sequence of ego-actions, predicts future scene latents a frozen decoder renders to $256 \times 256$ frames up to 8 seconds ahead, evaluated on 150 held-out nuScenes scenes. We first benchmark where to predict: across six frozen encoders spanning four representation families, V-JEPA2 with temporal context reduces steering RMSE by 40% over the best single-frame encoder. We then train a latent Diffusion Transformer (DiT) and, through a controlled diagnosis, identify the four ingredients it needs: spatial tokens, the $x_0$ objective, residual anchoring, and sampling matched to target uncertainty. In a Stable-Diffusion-VAE encode-predict-decode pipeline we expose the central tension: distortion metrics (cosine similarity, SSIM) favor the blurry mean, masking that the diffusion model is far closer to the real frame distribution. Inception-based FID and KID reveal a clean perception-distortion frontier: diffusion attains KID 0.078 versus 0.375 for regression ($4.8\times$ better), and a deployable train-derived calibration makes this practical without test-time ground truth. The model is genuinely action-controllable (steering drives scene displacement, Spearman $\rho = 0.81$, vs $-0.18$ for regression). We trace limited single-pass motion to a shared-present anchor and engineer a compact 1.7M-parameter "jump" model that recovers full ground-truth motion magnitude ($1.02\times$ GT), where single-pass models capture less than half.

17.
arXiv (CS.CL) 2026-06-19

Segment-Level Mandarin Chinese Speech-Based Cognitive Impairment Detection via an Autoencoder with Contrastive Learning

\noindentBackground and Objective: Speech has emerged as a low-cost and non-invasive digital biomarker with considerable potential for cognitive impairment detection. However, limited labeled data and cross-dataset variability remain major challenges for robust speech-based screening systems. \par\noindentMethods: We developed a segment-level representation learning framework for speech-based cognitive impairment detection. Speech recordings were divided into short segments and converted into spectrogram representations. To improve robustness under limited-data conditions, offline and online augmentation strategies were combined with autoencoder-based representation learning and contrastive objectives to enhance discriminative latent representations. \par\noindentResults: Experiments conducted on four independent Mandarin Chinese speech datasets demonstrated stable and competitive performance in both binary and three-class classification tasks, with particularly notable improvements in the clinically challenging three-class setting. Ablation studies further supported the effectiveness of the proposed framework. \par\noindentConclusions: The findings suggest that segment-level speech representation learning may provide a scalable and practical approach for cognitive impairment screening in resource-constrained clinical settings.

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

Cascaded Sparse Autoencoders Learn Multi-Level Visual Concepts in Multimodal LLMs

Multimodal Large Language Models (MLLMs) have demonstrated strong performance on vision-language tasks, yet their internal visual representations remain difficult to interpret. Sparse Autoencoders (SAEs) provide a scalable way to decompose dense model activations into sparse, interpretable features. However, existing SAE architectures primarily recover flat feature dictionaries and are less suited for explicit multi-level concept organization. In this paper, we introduce cascaded sparse autoencoders (CSAEs) for learning hierarchical visual concepts in MLLMs. Rather than nesting or stacking SAE sparse activation codes, CSAEs train a second-level SAE directly on the decoder weights of the first-level SAE, treating learned low-level feature directions as inputs for higher-level abstraction. This design enables CSAEs to learn "concepts of concepts" while avoiding drawbacks from the shared-prefix coupling of nesting, Matryoshka-style hierarchies and the bottlenecks of naively stacked SAEs. Experiments across Qwen3-VL, Gemma-3, and LLaVA on multiple visual datasets show that CSAEs improve interpretability in terms of hierarchical concept coherence over state-of-the-art SAE baselines. Results on concept steering further demonstrate that the learned concept groups support effective group-level interventions in MLLM outputs.

19.
arXiv (CS.CL) 2026-06-17

Precision Is Not Faithfulness: Coverage-Aware Evaluation of Grounded Generation with a Complete Oracle

Reference-free faithfulness metrics verify each atomic claim a model makes against ground truth, and are increasingly used to evaluate grounded generation. We show they share a blind spot: they measure only precision – are the stated claims supported? – and therefore reward abstention, since a model can score near-perfect faithfulness by saying almost nothing. We make this measurable using Formula 1 telemetry, a domain where strategic ground truth is derived deterministically and, crucially, completely: for each decision we know the full set of facts that mattered. This completeness – absent in open-domain faithfulness benchmarks – lets us measure recall (coverage of the relevant facts) exactly, alongside precision. On a multilingual (EN/ES/PT) benchmark of 7,253 decision instances spanning 157 races, the most precise frontier model covers under half of the relevant facts and ranks last by F1, so requiring coverage reorders the systems; the same effect reappears in a second complete-oracle domain (NOAA weather forecasts). Fine-tuning small models (1B-7B) on the complete oracle closes the precision-recall gap entirely (F1 ~0.98), beating every zero-shot frontier system regardless of scale. We pair faithfulness with coverage into a single score, validate the metric (controlled perturbation; agreement across a model-free regex extractor and a cross-family LLM extractor, system-level Spearman 1.0), and give a verifier-guided generation method that improves precision and recall without references. We release the benchmark, structured annotations, metric, baselines, and an interactive demo.

20.
arXiv (quant-ph) 2026-06-19

Unveiling coherent dynamics in non-Markovian open quantum systems: exact expression and recursive perturbation expansion

arXiv:2506.04097v2 Announce Type: replace Abstract: We introduce a systematic framework to derive the effective Hamiltonian governing the coherent dynamics of non-Markovian open quantum systems. By applying the minimal dissipation principle, we uniquely isolate the coherent contribution to the time-local generator of the reduced dynamics. We derive a general expression for the effective Hamiltonian and develop a recursive perturbative expansion that expresses it in terms of system-bath interaction terms and bath correlation functions. This expansion provides a systematic tool for analyzing energy renormalization effects across different coupling regimes. Applying our framework to paradigmatic spin systems, we reveal how environmental correlations influence energy shifts and eigenbasis rotations, offering new insights into strong-coupling effects and non-Markovian quantum thermodynamics.

21.
arXiv (CS.CL) 2026-06-19

Quantifying Aleatoric Uncertainty of In-Context Learning for Robust Measure of LLM Prediction Confidence

In-Context Learning (ICL) allows LLMs to adapt to new tasks from a few demonstrations, but its reliability remains a concern: predictions are highly sensitive to both prompt design and the model's ability to understand the context, obscuring whether failures arise from data properties or model limitations. Uncertainty decomposition-separating aleatoric from epistemic sources-is particularly crucial in this setting, yet existing methods, designed for standard generation tasks, fail to capture the unique dynamics of ICL. To address this, we introduce a concept of self-function vectors, built upon Bayesian views and the mechanistic interpretability of ICL. These vectors leverage internal model representations to model the latent concept learned during in-context prompting, thereby enabling a direct estimation of aleatoric uncertainty within a Bayesian framework and circumventing the reliance on brittle input or decoding manipulations. Given the lack of established benchmarks and suitable evaluation protocols, we also propose the first and rigorous evaluation protocol, in which data is manipulated in controlled ways so as to quantify aleatoric uncertainty precisely and separately from epistemic uncertainty. With this new evaluation framework, initially grounded in synthetic tasks for conceptual development and subsequently extended to real-world datasets, we show that our proposed methodology can measure uncertainty of LLM predictions made under ICL more reliably than existing alternative methods. Moreover, we show it can be used as a practical tool for trustworthy-related applications, such as hallucination detection. Our findings pave a new direction for connecting the quantitative view of uncertainty with the mechanistic understanding of model behavior.

22.
arXiv (CS.AI) 2026-06-16

Let Them Steal: Trapping Large Language Model Extraction Attacks with Knowledge Honeypot

arXiv:2606.15810v1 Announce Type: cross Abstract: Large language models deployed as commercial APIs are vulnerable to model extraction attacks, while existing defenses either act too late or degrade utility for legitimate users. We propose Knowledge Trap, a defense that redirects extraction attacks toward low-transferability knowledge through a Honeypot Knowledge Graph (HKG) and breadcrumb-guided exploration. Instead of blocking queries or perturbing outputs, Knowledge Trap consumes the attacker's limited query budget on knowledge with negligible downstream utility while preserving benign-user performance. Experiments in medical and financial domains show that Knowledge Trap reduces surrogate Agreement by 6.2\% on average without degrading legitimate-user accuracy, outperforming existing defenses that impose measurable user impact. These results suggest that defending knowledge-space traversal is a practical direction for mitigating LLM extraction attacks.

23.
arXiv (CS.CL) 2026-06-11

A Geometric Profile of Semantic Information in Text: Frame-Conditional Uniqueness and a Trade-Off Triangle for Scalar Summaries

How much meaning does a text carry? Shannon's theory measures uncertainty over symbols and is intentionally indifferent to meaning, while pairwise metrics such as BERTScore compare two texts rather than characterizing one. We develop a geometric framework that measures semantic content from the structure of a text's sentence embeddings. The framework has three parts. First, within a fixed embedding and baseline, six natural axioms uniquely determine a scalar measure up to scale, a frame-conditional uniqueness theorem. The resulting scalar is empirically too coarse, motivating a richer representation. Second, we propose a three-coordinate semantic profile capturing novelty (displacement from generic discourse), breadth (diversity of distinct ideas), and integration (connectedness among them), together with a discrete minimal unit (the semantic quantum) whose resolution is fixed by a clustering threshold $\tau$. Third, we prove a no-go theorem: no scalar summary of the profile can simultaneously satisfy analytic stability under paraphrase and concatenation, ordinal robustness across text scales, and cross-representation comparability. We exhibit two practical scalars, $S_{\mathrm{minmax}}$ and $S_{\mathrm{rank}}$, each occupying a distinct corner of this trade-off triangle. Validation across 23 synthetic categories, 5 Project Gutenberg novels, and 3 embedding models confirms the trade-off. The recommended rank-normalized configuration passes 25 of 28 ordinal checks as point estimates (21 of 28 after Benjamini-Hochberg correction), outperforming seven baselines including unigram entropy and a BERTScore-based novelty signal. A separate variational result connects the breadth coordinate to the log-determinant of a determinantal point process (Spearman $\rho = 0.985$ over 507 Gutenberg chapters), giving an optimization-theoretic foundation for breadth.

24.
bioRxiv (Bioinfo) 2026-06-16

MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics

Metaproteomic peptide identification is constrained by the structure and size of the protein search space. Pooled gene catalogues provide coverage but obscure genome-level evidence, and current workflows for data-dependent (DDA) and data-independent (DIA) acquisition diverge in their database strategies. We present MetaPilot, a genome-aware workflow that uses conserved marker-protein evidence to rank candidate genomes from MGnify catalogues and construct adaptive, sample-specific search spaces. Applied to paired DDA/DIA datasets of defined mixtures and fecal samples, MetaPilot adapted genome selection to community complexity and reproduced published peptide evidence while expanding the detectable peptide space. In DDA-independent reanalysis of Orbitrap human gut DIA data, MetaPilot identified 24.4% more peptides than the published DDA-derived library and 2.06-fold more than the matched DDA-assisted DIA search. On timsTOF DIA-PASEF mouse intestinal data, it outperformed uMetaP by 41.8~119.7%, enabling genome-resolved functional interpretation without DDA-PASEF input.

25.
arXiv (quant-ph) 2026-06-16

Suppressing Intrinsic Spin-Phonon Errors in Trapped-Ion Quantum Simulation

arXiv:2606.15518v1 Announce Type: new Abstract: Trapped-ion quantum simulators realize programmable spin models through phonon-mediated interactions. For Hamiltonians with noncommuting terms, however, the same phonon bus generates intrinsic spin-phonon errors that strongly distort the target dynamics. Because these errors are governed by the full time history of the spin-dependent phonon motion, they survive standard loop-closing control and limit simulation accuracy. Using a sequence of frame transformations, we isolate the residual error dynamics and show that this intrinsic error can be strongly suppressed while preserving programmable Ising couplings. Full spin-boson simulations of multi-ion chains demonstrate orders-of-magnitude lower error than both constant-drive and conventional loop-closing protocols. These results remove a central precision barrier in trapped-ion analog quantum simulation and enable accurate programmable simulation of noncommuting many-body Hamiltonians and dynamical protocols.