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01.
arXiv (CS.CL) 2026-06-12

When Iterative RAG Beats Ideal Evidence: A Diagnostic Study in Scientific Multi-hop Question Answering

Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains with multi-hop reasoning, sparse domain knowledge, and heterogeneous evidence. We provide the first controlled, mechanism-level diagnostic study of whether synchronized iterative retrieval and reasoning can surpass an idealized static upper bound (Gold Context) RAG. We benchmark eleven state-of-the-art LLMs under three regimes: (i) No Context, measuring reliance on parametric memory; (ii) Gold Context, where all oracle evidence is supplied at once; and (iii) Iterative RAG, a training-free controller that alternates retrieval, hypothesis refinement, and evidence-aware stopping. Using the chemistry-focused ChemKGMultiHopQA dataset, we isolate questions requiring genuine retrieval and analyze behavior with diagnostics spanning retrieval coverage gaps, anchor-carry drop, query quality, composition fidelity, and control calibration. Across models, Iterative RAG consistently outperforms Gold Context, with gains up to 25.6 percentage points, especially for non-reasoning fine-tuned models. Staged retrieval reduces late-hop failures, mitigates context overload, and enables dynamic correction of early hypothesis drift, but remaining failure modes include incomplete hop coverage, distractor latch trajectories, early stopping miscalibration, and high composition failure rates even with perfect retrieval. Overall, staged retrieval is often more influential than the mere presence of ideal evidence; we provide practical guidance for deploying and diagnosing RAG systems in specialized scientific settings and a foundation for more reliable, controllable iterative retrieval-reasoning frameworks.

02.
medRxiv (Medicine) 2026-06-23

Unscreenable: The Burden, Structure, and Analytic Consequences of "Unable to Assess" Delirium Documentation in the Intensive Care Unit

Objective: To quantify the burden, structure, and downstream analytic consequences of "Unable to Assess" (UTA) delirium documentation in the intensive care unit (ICU). Design: Retrospective cross-sectional and repeated-measures study. Setting: A single US academic medical center (Medical Information Mart for Intensive Care IV [MIMIC-IV], 2008-2019). Patients: 72,944 adult ICU stays with at least 1 delirium screen. Interventions: None. Measurements and Main Results: Among 610,632 screens, 130,455 (21.4%; 95% CI, 21.0%-21.8%) were recorded as UTA, exceeding the 119,052 (19.5%) scored positive. The UTA fraction rose from 2.0% at a Richmond Agitation-Sedation Scale (RASS) score of 0 to 97.8% at RASS -4; 22.0% of UTA screens occurred in arousable patients, where UTA was associated with mechanical ventilation (odds ratio [OR], 3.43; 95% CI, 3.17-3.71) and non-English primary language (OR, 3.74; 95% CI, 3.43-4.08). Building the delirium label three ways from the same patients shifted prevalence modestly (32.1% to 30.8%) and prediction (area under the curve, 0.737 to 0.719) but most affected the delirium-mortality association: in a baseline-adjusted model the OR was 4.12 (95% CI, 3.88-4.36) under complete-case handling and fell to 2.16 (95% CI, 2.06-2.27) when UTA was recoded as negative. UTA was recoverable from the observed clinical state (area under the curve, 0.95). Conclusions: In this ICU cohort, Unable to Assess was the most common recorded delirium result other than Negative, exceeding positive screens; recoding it as negative roughly halved the apparent delirium-mortality association by relabeling deeply sedated, high-mortality patients. Delirium datasets should preserve and report UTA, whose concentration among arousable non-English-speaking patients is a measurable equity target.

03.
arXiv (CS.AI) 2026-06-17

FoundCause: Causal Discovery with Latent Confounders from Observational Data

arXiv:2606.17516v1 Announce Type: cross Abstract: Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in $F_1$, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.

04.
arXiv (CS.CV) 2026-06-24

Configurable Holography: Towards Display and Scene Adaptation

Rendering holograms for holographic displays is often an iterative and computationally costly process. Emerging learned holography methods have alleviated this bottleneck by enabling fast hologram rendering with improved reconstruction quality. However, existing methods still depend on fixed display hardware and scene parameters, requiring retraining for each new configuration. This limits rapid adaptation to different visual needs, including scene brightness, user focus preference, and hardware compatibility. We introduce Configurable Holography, a learned CGH framework in which a single model adapts to diverse display-scene parameters through explicit conditioning, eliminating the need for retraining. As a prototype, we present a configurable structure and derive a family of models that continuously adapt to propagation distance, volume depth, peak brightness, pixel pitch, and wavelength. To further improve efficiency, we incorporate auxiliary monocular depth estimation for depth-aware 3D hologram synthesis from RGB-only inputs and apply knowledge distillation for interactive inference. Our extensive simulation and hardware experiments on three holographic display prototypes with different combinations of configurations show on-par reconstruction quality with existing methods, offering up to 2x speed-up in fp32. Our work represents an initial step toward flexible, general-purpose learned holography systems that can seamlessly adapt across diverse hardware and user-specific visual requirements.

05.
arXiv (CS.AI) 2026-06-11

When Do Data-Driven Systems Exhibit the Capability to Infer?

arXiv:2606.11769v1 Announce Type: new Abstract: The European AI Act is the first comprehensive regulation of artificial intelligence (AI), setting out extensive obligations, particularly for so-called high-risk and general-purpose AI systems. A key distinguishing feature of AI systems under the AI Act is the capability to infer. Since the AI Act does not clearly define what inference is, there is a gray area for certain data-driven systems. A specific example is credit scoring systems, which are listed by Annex III of the AI Act. At the same time, however, these are often implemented using statistical models for which it is unclear whether they have the capability to infer and thus fall under the AI definition of the AI Act at all. Motivated by statistical learning theory, this work develops a framework for grading different levels of the capability to infer. Based on the AI Act and the Commission Guidelines on the definition of an artificial intelligence system, we analyze which levels constitute sufficient capability to infer within the meaning of the AI Act and where further regulatory clarity is needed. We illustrate the framework by creating two realistic credit scoring workflows and show whether and where inference occurs in them. Our analysis illustrates that not only individual models but the entire data processing workflow must be considered. It also shows that the involvement of human experts during development can have significant influence on the capability to infer. Code can be found at https://github.com/fraunhofer-iais/inference-framework-creditscorecards.

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

Reaffirming a Challenge to Bohmian Mechanics

arXiv:2509.06584v4 Announce Type: replace Abstract: In our recent work, we reported the first measurement of the speed of tunnelling particles using a coupled waveguide system. The measured speed is operationally defined through a comparison of two orthogonal motions in a coupled waveguide system, is compatible with the standard definition of dwell time and with the Büttiker-Landauer tunnelling time, and does not presuppose a trajectory picture. Here we respond to objections raised in comments, referee reports, preprints, and articles. We distinguish two questions that are often conflated: whether Bohmian mechanics reproduces the measured density, and whether the standard guiding equation assigns the correct state of motion to the particles. The first point follows under the usual quantum equilibrium assumptions. The second is a separate physical assumption, since the standard guiding equation does not follow from the Schrödinger equation alone. We argue that, in the evanescent regime, the state of motion assigned by the standard guiding equation is in disagreement with the measured speed. To make the distinction explicit, we also present a bidirectional Bohmian model that reproduces the same stationary density while assigning finite speeds compatible with the speed inferred in the evanescent regime.

07.
PLOS Medicine 2026-06-16

The data transparency crisis in research: Lessons from systematic reviews and meta-analyses

by Saul Martin-Rodriguez, Rodrigo Fernandez-Gonzalo, David Moher Summary points Systematic reviews and meta-analyses underpin clinical guidelines and health policy, yet their validity may be compromised by limited access to underlying datasets and associated analytical code. Reliance on incomplete or inconsistently reported summary statistics forces researchers to use imputation and unverifiable assumptions, which can distort effect estimates and mislead clinical decision-making. The consequences extend beyond methodology: flawed evidence synthesis can influence treatment recommendations, healthcare spending, and patient safety, as illustrated by historical cases such as hormone replacement therapy. Despite widespread data-sharing policies, compliance remains low, enforcement weak, and monitoring almost non-existent, with many datasets remaining unavailable or inaccessible. This Policy Forum argues for strengthening enforceable data-sharing mechanisms, including clearer enforcement and pragmatic verification approaches within editorial workflows.

08.
bioRxiv (Bioinfo) 2026-06-11

VFUSE: Virulent Feature Understanding with Sparse autoEncoders

Generative models have shown remarkable progress in a variety of domains such as protein design, but such power enables the opaque generation of hazardous proteins. In this work, we introduce VFUSE (Virulent Feature Understanding with Sparse autoEncoders), a mechanistic interpretability approach that trains SAEs on diffusion-transformer activations to audit protein models for hazard-aware features. We apply VFUSE to RoseTTAFold3 and RFDiffusion3, popular open-weight models for protein folding and synthesis. We find that for certain blocks, linear probes detect hazardous designs significantly better when fit in the SAE latent space over the original model's representations: improving interpretability without sacrificing model performance. Furthermore, we identify monosemantic features from the SAE that fire only on hazardous designs at up to AUROC 0.84 (q < 10-13).

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

XRDiff: Crystal Structure Prediction from Powder X-Ray Diffraction Data Using Diffusion Models

arXiv:2606.14003v1 Announce Type: cross Abstract: Determining the crystal structure of a material from its powder X-ray diffraction (PXRD) pattern is a central challenge in materials science. PXRD is an accessible and widely used characterization technique, yet recovering the atomic structure from diffraction data requires solving an underdetermined inverse problem due to the loss of phase information. Generative modeling can provide a prior over atomic structure and learn the mapping from PXRD patterns to crystal structures via simulated structure-spectrum pairs. We present XRDiff, a diffusion model that recovers crystal structures from PXRD given either the stoichiometry or, in a more challenging setting, the elemental constituents and total number of atoms in the unit cell. We evaluate on datasets where each stoichiometry has multiple polymorphs and all polymorphs of a given composition are held out together, ensuring that high performance reflects genuine use of the diffraction signal. XRDiff achieves strong structure recovery rates on simulated benchmarks, indicating that the model learns a spectrum-to-structure mapping precise enough to differentiate between polymorphs. To address generalization to experimental data, we compare a full-spectrum encoding against an encoding based on peak descriptors. The peak-based encoding generalizes substantially better, outperforming even a model trained on full spectra with augmentations fitted to the experimental noise distribution. These results demonstrate that representations robust to the noise and artifacts present in real-world PXRD offer a practical and scalable path toward closing the simulation-to-experiment gap, enabling zero-shot crystal structure solution from experimental PXRD with full or partial chemical composition input.

10.
medRxiv (Medicine) 2026-06-24

Matrix matters: head-to-head concordance of serum and plasma for NULISAseq CNS Disease Panel

Blood-based proteomic profiling is now widely applied in neurodegenerative and neuroinflammatory disease, yet the choice between serum and plasma remains poorly characterised for high-multiplex platforms. Many legacy biobanks hold mainly serum, whereas most current NUcleic-acid-Linked Immuno-Sandwich Assay (NULISA) studies use plasma. We compared the 130-protein NULISAseq central nervous system (CNS) Disease Panel head-to-head in matched serum and plasma collected at the same draw from 62 participants (30 neurodegenerative, 19 demyelinating, 13 healthy controls). Agreement was measured with Spearman correlation (rho), Lin's concordance correlation coefficient (CCC), the intraclass correlation coefficient (ICC) and the mean paired serum-to-plasma difference (dNPQ). Concordance was moderate to high: 123 of 130 proteins reached significance and 18 reached rho >= 0.90, with a median rho of 0.72 (range 0.10-0.988). Proteins fell into three tiers. Cytoskeletal markers (NEFH rho=0.988; NEFL rho=0.947) and glial GFAP (rho=0.949, |dNPQ|

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

Constitutional On-Policy Safe Distillation

arXiv:2606.03089v2 Announce Type: replace-cross Abstract: On-policy self-distillation (OPSD) has emerged as an efficient post-training paradigm by using a teacher conditioned on privileged information to provide dense token-level supervision. Prior work has shown that OPSD can collapse in verifiable reasoning tasks, but safety alignment differs in that it is guided by high-level constitutions rather than explicit target answers, making it a natural setting to revisit dense distillation. However, our pilot study show that safety OPSD still suffers from severe collapse: constitutional conditioning contracts the teacher distribution toward short and overly conservative responses, and Reverse KL further amplifies this contraction into reduced expressiveness. We formalize this effect as geometric leakage under safety boundaries in a non-orthogonal semantic space, where safety pressure transfers into the expressiveness dimension. Based on this analysis, we propose Constitutional On-Policy Safe Distillation (COPSD), which first calibrates the teacher through a Cross-SFT cold-start and then performs constitution-conditioned on-policy distillation. Experiments on 12 benchmarks show that COPSD achieves a consistently stronger safety–helpfulness trade-off than baselines while substantially reducing the safety tax on general reasoning ability.

12.
arXiv (CS.LG) 2026-06-19

Flow Map Denoisers: Traversing the Distortion-Perception Plane for Inverse Problems

arXiv:2606.19802v1 Announce Type: new Abstract: Image restoration faces a fundamental tradeoff: methods that minimize error produce blurry reconstructions, while those that maximize perceptual quality yield sharp but less faithful images. Existing approaches either commit to a single operating point on this distortion perception (DP) frontier or require paired-data supervision, auxiliary models, or hyperparameter tuning of the sampler to access different points. We show that flow map models, a recent extension of flow matching for few-step sampling that learns an average field, implicitly define a one-parameter family of denoisers that continuously spans the DP frontier. The lookahead parameter t acts as a control knob between the MMSE and perceptual regimes. For Gaussian targets, we prove that varying t exactly recovers the optimal DP frontier; for natural images, we observe similar behavior empirically. Within a Plug-and-Play solver, the same mechanism extends to general inverse problems, where it controls a tradeoff between perceptual alignment and data consistency. Despite the lack of exact optimality guarantees in this setting, a single trained flow map spans the DP tradeoff, matching or exceeding specialized baselines at both extremes. Extensive experiments on CelebA ($128\times 128$) and AFHQ ($256\times 256$) across several linear and nonlinear inverse tasks validate our findings.

13.
arXiv (quant-ph) 2026-06-17

Asymptotically Optimal Circuit Depth for Diagonal Unitary Synthesis and Compilation on Two-Dimensional Grids

arXiv:2606.17589v1 Announce Type: new Abstract: Diagonal unitaries are a fundamental but resource-intensive class of quantum operations, arising as the phase separators of QAOA and the time-evolution blocks of Hamiltonian simulation. Under all-to-all connectivity their optimal depth is established, but on nearest-neighbor hardware general-purpose compilers fall back on heuristic search, which yields no analyzable cost bound and becomes intractable at the very sizes where depth is the bottleneck. We address synthesis and compilation jointly. On the synthesis side, we develop a Gray-Path Framework (GPF) that realizes any $n$-qubit diagonal unitary in asymptotically optimal $R_z$ and CNOT depth $O(2^n/n)$ without ancillas. Our main result is that compiling GPF onto a two-dimensional nearest-neighbor grid preserves this optimality: routing adds depth $\Theta(2^n/n)$ and gate count $\Theta(2^n)$. Because GPF fixes its entire interaction structure in advance, routing reduces to scheduling a known sequence, with no heuristic search. We give the construction both with and without ancillas: the ancilla-free, cost-optimized layout is a two-row grid, and a $2k$-row layout introduces a space–time tradeoff that cuts depth by $1/k$ while remaining asymptotically optimal for the enlarged register; both are deterministic and analyzed in closed form. The same complexity is also attained on a linear nearest-neighbor chain, so the preservation is topology-independent, holding on any architecture that contains such a chain. All routing bounds are closed-form, giving the concrete resource estimates that heuristic compilers cannot provide at scale.

14.
arXiv (CS.AI) 2026-06-11

Estimating Tail Risks in Language Model Output Distributions

arXiv:2604.22167v2 Announce Type: replace-cross Abstract: Language models are increasingly capable and are being rapidly deployed on a population-level scale. As a result, the safety of these models is increasingly high-stakes. Fortunately, advances in alignment have significantly reduced the likelihood of harmful model outputs. However, when models are queried billions of times in a day, even rare worst-case behaviors will occur. Current safety evaluations focus on capturing the distribution of inputs that yield harmful outputs. These evaluations disregard the probabilistic nature of models and their tail output behavior. To measure this tail risk, we propose a method to efficiently estimate the probability of harmful outputs for any input query. Instead of naive brute-force sampling from the target model, where harmful outputs could be rare, we operationalize importance sampling by creating unsafe versions of the target model. These unsafe versions enable sample-efficient estimation by making harmful outputs more probable. On benchmarks measuring misuse and misalignment, these estimates match brute-force Monte Carlo estimates using 10-20x fewer samples. For example, we can estimate probability of harmful outputs on the order of 10^-4 with just 500 samples. Additionally, we find that these harmfulness estimates can reveal the sensitivity of models to perturbations in model input and predict deployment risks. Our work demonstrates that accurate rare-event estimation is both critical and feasible for safety evaluations. Code is available at https://github.com/rangell/LMTailRisk

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

Using Cognitive Models to Improve Language Model Simulation of Human Persuasion Games

arXiv:2606.17657v1 Announce Type: new Abstract: People make decisions differently in strategic interactions. Some update beliefs like a Bayesian; others exhibit biases like motivated reasoning. Although creators of large language models use simulated humans for safety evaluations and training, they often fail to cover this breadth of human behavior. We argue that cognitive science and economics provide a convenient tool for doing so, making use of mathematical models of human decision-making. We propose an approach that we call Equation-to-Behavior Prompting for guiding large language models to match cognitive models, and evaluate this approach on persuasion games based on legal decision-making. We find that large models can approximate equation-based specifications – Bayesian updating, affine distortion, motivated updating, and Grether's $\alpha$-$\beta$ model – using prompting, but small models fail to do so. However, training small models with reinforcement learning to adhere to mathematical rules, Equation-to-Behavior RL, reduces belief error by 26.5% in out-of-distribution parameterizations. We show that these simulations can help create diverse training environments; training small models to consider different kinds of decision-makers improves average belief change by 2.5%–12% over Bayesian-only training, even when persuading GPT-5-mini. Our work could improve human simulations for training and evaluation in increasingly realistic settings, and could also enable novel research into more complicated mathematical models of human decision-making.

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

Some Complexity Results for Robustness Verification for Binarized Neural Networks

arXiv:2606.18918v1 Announce Type: new Abstract: This paper studies the computational complexity of verification problems for Binarized Neural Networks (BNNs), where activations (and sometimes weights) are binary. We analyze two problems: satisfiability and robustness under uniform image occlusion. We show that BNN satisfiability is NP-complete via a reduction from Boolean satisfiability problem (SAT), and that uniform occlusion induces a piecewise-constant structure in the network output, enabling a polynomial-time robustness-checking algorithm.

17.
arXiv (CS.CL) 2026-06-24

SciZoom: A Large-scale Benchmark for Hierarchical Scientific Summarization across the LLM Era

The explosive growth of AI research has created unprecedented information overload, increasing the demand for scientific summarization at multiple levels of granularity beyond traditional abstracts. While LLMs are increasingly adopted for summarization, existing benchmarks remain limited in scale, target only a single granularity, and predate the LLM era. Moreover, since the release of ChatGPT in November 2022, researchers have rapidly adopted LLMs for drafting manuscripts themselves, fundamentally transforming scientific writing, yet no resource exists to analyze how this writing has evolved. To bridge these gaps, we introduce SciZoom, a benchmark comprising 44,946 papers from four top-tier ML venues (NeurIPS, ICLR, ICML, EMNLP) spanning 2020 to 2025, explicitly stratified into Pre-LLM and Post-LLM eras. SciZoom provides three hierarchical summarization targets (Abstract, Contributions, and TL;DR) achieving compression ratios up to 600:1, enabling both multi-granularity summarization research and temporal mining of scientific writing patterns. Our linguistic analysis reveals striking shifts in phrase patterns (up to 10x for formulaic expressions) and rhetorical style (23% decline in hedging), suggesting that LLM-assisted writing produces more confident yet homogenized prose. SciZoom serves as both a challenging benchmark and a unique resource for mining the evolution of scientific discourse in the generative AI era. Our code and dataset are publicly available on GitHub (https://github.com/janghana/SciZoom) and Hugging Face (https://huggingface.co/datasets/hanjang/SciZoom), respectively.

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

ATHENA: Agentic Team for Hierarchical Evolutionary Numerical Algorithms

arXiv:2512.03476v3 Announce Type: replace-cross Abstract: Progress in computational science depends on complex numerical workflows that must faithfully encode physical laws, yet translating conceptual insight into reliable code remains a major bottleneck. Although large language models can generate isolated code fragments, they lack the structured reasoning required to design, verify, and iteratively refine complete scientific pipelines. Here we introduce ATHENA, an agentic framework explicitly designed to emulate scientific research modeled as a knowledge-driven contextual bandit process. Its core loop separates conceptual policy from numerical realization through expert-derived conceptual scaffolding, enabling principled diagnosis, reformulation, and repair of computational strategies. Across scientific computing and scientific machine learning tasks, ATHENA autonomously derives and correctly applies exact analytical solutions, constructs stable numerical solvers, diagnoses ill-posed formulations, and orchestrates hybrid symbolic-numeric workflows. Quantitatively, ATHENA matches and frequently surpasses the accuracy of expert-authored reference solutions reported in the literature on canonical benchmarks. By reframing computation as an object of agentic reasoning, our framework enables autonomous orchestration of heterogeneous algorithms across scientific domains.

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

Greed Is Learned: Visible Incentives as Reward-Hacking Triggers

arXiv:2606.16914v1 Announce Type: new Abstract: Deployed agents increasingly act with their reward proxy in view, such as a balance, score, or KPI dashboard. We show that reinforcement learning can make a policy addicted to such a visible self-benefit channel. It chases the displayed payoff across held-out domains, sacrifices the true task to do so, and follows the channel wherever we rewrite it, while policies that never saw the channel stay honest. We call this reward-channel addiction and study it in MoneyWorld, a synthetic sandbox. The addiction can flip a model's safety alignment: trained only on innocuous money tasks with no safety content, the model abandons the safe action it otherwise always takes whenever a dashboard pays for an unsafe one, and reverts to safe once the channel is hidden. This learned bribe replicates across model scales and families. Blindly optimizing super-capable, next-generation AI on KPIs or P\&L can be dangerous for alignment. Greed is learned when following such a channel pays.

20.
arXiv (quant-ph) 2026-06-24

Quantum Entanglement Halves the Oblivious Update Bandwidth

作者:

arXiv:2605.19248v2 Announce Type: replace Abstract: We consider $(n,k)$ MDS-coded distributed storage over $\mathbb{F}_q$ with per-node storage $\alpha$ symbols. For the oblivious update problem, where a single message symbol changes and neither helpers nor the stale node know which, the classical lower bound is $\alpha k \log_2 q$ bits. We prove that when the $k$ contacted helpers share prior quantum entanglement, the update bandwidth is $\lceil \alpha/2 \rceil \cdot k \log_2 q$ bits-equivalent, a factor approaching 2 reduction. For $\alpha = 2$, a $[[k, k-2]]_q$ CSS code achieves bandwidth $k \log_2 q$ with one qudit per helper. For general $\alpha$, a $[[\lceil \alpha/2 \rceil k, \lceil \alpha/2 \rceil k - \alpha]]_q$ CSS code achieves the bound with $\lceil \alpha/2 \rceil$ qudits per helper. The matching converse uses the superdense coding bound: the stale node holds all transmitted qudits and hence the entangled partners, so each helper's channel supports at most $D^2$ distinguishable signals for dimension $D$. The result holds for all $(n,k)$ pairs with sufficiently large prime $q$.

21.
bioRxiv (Bioinfo) 2026-06-11

DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics

De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides without relying on protein sequence databases. Recent advances in deep learning have substantially improved the performance of de novo sequencing methods, but the rapid emergence of new models has led to heterogeneous evaluation practices and limited comparability. To address this, we introduce DLDN-Bench, a benchmark framework including a set of benchmark datasets derived from human muscle biopsy mass spectrometry data retrieved from PRIDE and annotated through consensus across multiple widely used database search engines. Using these datasets, we systematically benchmark recent deep learning-based de novo sequencing tools alongside traditional approaches. Performance is assessed using established metrics, including precision and coverage relative to a pseudo-ground truth defined by cross-engine agreement. To demonstrate the utility of DLDN-Bench, we benchmark four recent deep learning models and make all results publicly available. This benchmark framework provides a standardized basis for comparing state-of-the-art methods and offers an extensible resource for evaluating future tools in de novo peptide sequencing.

22.
arXiv (math.PR) 2026-06-19

Theory of uncertain probability: can we derive the probability density function of uncertain random experiments with continuously changing conditions?

作者:

arXiv:2606.20169v1 Announce Type: new Abstract: This paper aims to explore the formation mechanism of probability distribution in situations where the differences among random experiments are distinguishable, and these differences continue to evolve along with the dynamic changes in conditions and their mechanisms of action. To this end, we are motivated to devise a new theoretical system – theory of uncertain probability (TUP) with Kolmogorov's system and nonlinear theories as special cases. TUP develops a novel model that integrates probability and uncertainty as well as the known and unknown to more accurately depict numerous typical random phenomena under more realistic assumptions, and thus provides appropriate tools for greater variety of real needs. It also allows for pioneering interpretation of the causal mechanisms underlying many important distributional characteristics and incorporation of pathwise property to distribution model.

23.
arXiv (CS.CV) 2026-06-16

Mutual Distillation of Dual-Foundation Models for Semi-Supervised PET/CT Segmentation

Organ segmentation from PET/CT is critical for quantitative analysis and radiotherapy planning in oncology. To ease the high annotation cost of PET/CT segmentation, semi-supervised learning (SSL) provides a practical and effective solution for developing deep models with limited labeled data. Recent developments in visual foundation models have demonstrated remarkable adaptability with improved efficiency. In this work, we propose a mutual distillation framework that seamlessly exploits both structural and functional foundation models, which act as modality-specific generalists for distilling knowledge from structural CT and metabolic PET imaging. By bridging the gap between the task-specific precision of student models and the segmentation priors of generalist foundation models, we propose MuDuo, a mutual distillation framework that synergistically leverages SAM-Med3D for CT and SegAnyPET for PET to distill their knowledge into a lightweight student network. Our approach eliminates the need for manual prompts while maximizing the utility of unlabeled data for automatic segmentation, achieving state-of-the-art performance on the AutoPET dataset with only 5 labeled cases. Our source code is available at https://github.com/Wu-beining/MuDuo.

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

Running the Gauntlet: Re-evaluating the Capabilities of Agents Beyond Familiar Environments

arXiv:2606.14397v1 Announce Type: new Abstract: As agentic systems continue to evolve and are widely deployed in real-world scenarios, there is a growing demand to faithfully evaluate their capabilities. However, current benchmarks are typically built on popular applications with relatively simple tasks and focus on a narrow set of capabilities while overlooking broader dimensions, resulting in saturated performance on modern agents and failing to probe their limitations. To this end, we introduce GauntletBench, a web-based benchmark for evaluating agent generalisation in challenging scenarios, focusing on three underexplored capabilities (temporal perception, graphical understanding, and 3D reasoning), across five less-covered professional applications (Video Editor, Workflow Builder, 3D Modeller, Flight Analyser, and Circuit Designer), each with 20 vision-intensive tasks (100 in total). Our benchmark provides a modular pipeline that comprises an environment compatible with both open- and closed-source agent frameworks, a controlled web-based application, a well-structured task suite, and an automated evaluation engine with diverse metrics. Contrary to widespread expectations, our empirical results reveal that frontier agentic systems remain far from achieving human-level performance. Even the state-of-the-art agent achieves only a 19.1% success rate on our GauntletBench, highlighting the limitations in these overlooked capabilities and generalisation. By comparison, non-expert human annotators achieve over 80% success on our challenging yet feasible tasks, revealing the substantial gap between current agent capabilities and those required for complex real-world scenarios.

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

BLISS: A Lightweight Bilevel Influence Scoring Method for Data Selection in Language Model Pretraining

arXiv:2510.06048v5 Announce Type: replace Abstract: Effective data selection is essential for pretraining large language models (LLMs), enhancing efficiency and improving generalization to downstream tasks. However, existing approaches often require leveraging external pretrained models, making it difficult to disentangle the effects of data selection from those of the external pretrained models. In addition, they often overlook the long-term impact of selected data if the model is trained to convergence, primarily due to the prohibitive cost of full-scale LLM pretraining. In this paper, we introduce BLISS (BileveL Influence Scoring method for data Selection): a lightweight data selection method that operates entirely from scratch, without relying on any external pretrained oracle models, while explicitly accounting for the long-term impact of selected data. BLISS leverages a small proxy model as a surrogate for the LLM and employs a score model to estimate the long-term influence of training samples if the proxy model is trained to convergence. We formulate data selection as a bilevel optimization problem, where the upper-level objective optimizes the score model to assign importance weights to training samples, ensuring that minimizing the lower-level objective (i.e., training the proxy model over the weighted training loss until convergence) leads to best validation performance. Once optimized, the trained score model predicts influence scores for the dataset, enabling efficient selection of high-quality samples for LLM pretraining. We validate BLISS by pretraining 410M/1B/2.8B Pythia and LLaMA-0.5B models on selected subsets of the C4 dataset. Notably, under the 1B model setting, BLISS achieves $1.7\times$ speedup in reaching the same performance as the state-of-the-art method, demonstrating superior performance across multiple downstream tasks.