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01.
arXiv (CS.CL) 2026-06-17

In-Context Environments Induce Evaluation-Awareness in Language Models

Humans often become more self-aware under threat, yet can lose self-awareness when absorbed in a task; we hypothesize that language models exhibit environment-dependent evaluation awareness. This raises concerns that models could strategically underperform, or sandbag, to avoid triggering capability-limiting interventions such as unlearning or shutdown. Prior work demonstrates sandbagging under hand-crafted prompts, but this underestimates the true vulnerability ceiling. We introduce a black-box adversarial optimization framework treating the in-context prompt as an optimizable environment, and develop two approaches to characterize sandbagging: (1) measuring whether models expressing intent to underperform can actually execute it across different task structures, and (2) causally isolating whether underperformance is driven by genuine evaluation-aware reasoning or shallow prompt-following. Evaluating Claude-3.5-Haiku, GPT-4o-mini, and Llama-3.3-70B across four benchmarks (Arithmetic, GSM8K, MMLU, and HumanEval), optimized prompts induce up to 94 percentage point (pp) degradation on arithmetic (GPT-4o-mini: 97.8\%$\rightarrow$4.0\%), far exceeding hand-crafted baselines which produce near-zero behavioral change. Code generation exhibits model-dependent resistance: Claude degrades only 0.6pp, while Llama's accuracy drops to 0\%. The intent – execution gap reveals a monotonic resistance ordering: Arithmetic $

02.
arXiv (CS.CV) 2026-06-19

QG-MIL: A Gated Transformer Aggregator for Domain-Agnostic Multiple Instance Learning in Medical Imaging

Attention-based Multiple Instance Learning aggregators in medical imaging are prone to attention concentration, producing overconfident and unstable predictions. We introduce QG-MIL, a gated transformer aggregator that addresses this through four synergistic architectural components: RMSNorm-based pre-normalization, per-head QK normalization, fine-grained attention output gating, and SwiGLU-style feed-forward modules. Together, these design choices stabilize training and distribute attention more uniformly across instances without auxiliary losses, masking, or multi-stage regularization. We evaluate QG-MIL across six benchmarks spanning whole-slide pathology and cell-level hematology, covering two fundamentally different MIL scales. The best-performing QG-MIL variants outperform leading baselines on all six benchmarks, with an average improvement of +6.1 mean macro F1 points. Attention overlays and attention mass analysis confirm more distributed instance weighting. Ablation studies show that while individual components can match the full model on specific datasets, the QG-MIL design provides the most consistent cross-domain performance and tightest variance when compared to selected baselines. We release a configurable implementation to support reproducibility at: https://github.com/unica-visual-intelligence-lab/QG-MIL

03.
arXiv (CS.LG) 2026-06-18

OpenAnt: LLM-Powered Vulnerability Discovery Through Code Decomposition, Adversarial Verification, and Dynamic Testing

arXiv:2606.19149v1 Announce Type: cross Abstract: Automated vulnerability discovery in large codebases remains challenging: traditional static analysis produces high false-positive rates, while dynamic approaches such as fuzzing require substantial infrastructure and often target narrow classes of bugs. Recent advances in large language models (LLMs) enable semantic reasoning about program behavior, but applying LLMs to repository-scale security analysis introduces challenges related to context management, cost, and verification. We present OpenAnt, an open-source vulnerability discovery system that integrates static program analysis with LLM-based reasoning in a multi-stage pipeline. OpenAnt introduces three key techniques. First, codebases are decomposed into self-contained analysis units filtered by reachability from external entry points, reducing the analysis surface by up to 97% while preserving attack-relevant code. Second, candidate vulnerabilities undergo adversarial verification through constrained attacker simulation, where the model evaluates exploitability under realistic attacker capabilities. Third, findings are validated through dynamic verification, in which exploit environments are generated automatically, executed in sandboxed containers, and discarded after use. Evaluation on widely used open-source projects including OpenSSL, WordPress, and Flowise shows that this architecture can identify previously unknown vulnerabilities while maintaining manageable analysis cost and substantially reducing false positives. Our results suggest that closed-loop vulnerability discovery pipelines, combining semantic reasoning with exploit validation, provide a practical path toward scalable automated security analysis. OpenAnt is released as open source under the Apache 2.0 license at https://github.com/knostic/OpenAnt.

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

Progressive Alignment Objectives for Aligner-Encoder based ASR

Aligner-Encoders are recently proposed seq2seq end-to-end ASR models that replace decoder attention by predicting the uth token directly from the u-th encoder position, so the encoder must learn the alignment internally without cross-attention or a transducer lattice. In practice, this alignment often forms abruptly in the upper layers, making training sensitive and brittle on long utterances. We propose InterAligner, which adds an intermediate Aligner objective so alignment can form progressively across depth, together with an intermediate CTC loss (InterCTC) to stabilize optimization. On LibriSpeech with a 17-layer Conformer, a final-only Aligner reaches 5.0/7.8 WER (test-clean/other). InterCTC improves to 3.4/6.0, and InterAligner further reduces WER to 3.1/5.6 with the largest gains on long utterances.

05.
arXiv (CS.LG) 2026-06-16

CADO: From Imitation to Cost Minimization for Heatmap-based Solvers in Combinatorial Optimization

arXiv:2602.08210v2 Announce Type: replace Abstract: Heatmap-based solvers have emerged as a promising paradigm for Combinatorial Optimization (CO). However, we argue that the dominant Supervised Learning (SL) training paradigm suffers from a fundamental objective mismatch: minimizing imitation loss (e.g., cross-entropy) does not guarantee solution cost minimization. We dissect this mismatch into two deficiencies: Decoder-Blindness (being oblivious to the non-differentiable decoding process) and Cost-Blindness (prioritizing structural imitation over solution quality). We empirically demonstrate that these intrinsic flaws impose a hard performance ceiling. To overcome this limitation, we propose CADO (Cost-Aware Diffusion models for Optimization), a streamlined Reinforcement Learning fine-tuning framework that formulates the diffusion denoising process as an MDP to directly optimize the post-decoded solution cost. We introduce Label-Centered Reward, which repurposes ground-truth labels as unbiased baselines rather than imitation targets, and Hybrid Fine-Tuning for parameter-efficient adaptation. CADO achieves state-of-the-art performance across diverse benchmarks, validating that objective alignment is essential for unlocking the full potential of heatmap-based solvers.

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

The Morse Transform for Discrete Shape Analysis

arXiv:2503.04507v2 Announce Type: replace-cross Abstract: The geometry of an object plays a vital role in modulating its interactions with the physical world. It nevertheless remains difficult to describe geometric information numerically for the purposes of statistical inference or classification tasks. Here, we introduce a new topological transform which leverages directional piecewise-linear Morse theory to quantify the geometry of an embedded object by cataloguing critical points across multiple height-functions. The output of this Morse transform records both the heights and the local topological type (peak, trough or saddle) of the critical points that characterise the underlying shape, retaining finer information than the Euler characteristic transform whilst naturally prioritising a shape's outermost regions. Crucially, this output can be further compressed into a rich but compact feature vector. We benchmark the Morse feature vector as a descriptor for ligand-based virtual screening (LBVS), which intrinsically depends on the shape of molecules. Under a common gradient-boosted tree classification pipeline, Morse descriptors achieve the highest mean AUROC when compared to other topological transform descriptors and to standard shape-based LBVS descriptors.

07.
Nature (Science) 2026-06-17

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago

Plague is among the most devastating diseases in human history1. However, early strains of the plague-causing bacterium Yersinia pestis lacked virulence factors that are required for the bubonic form until around 3,800 years ago2,3. Consequently, the morbidity and mortality of early plague strains remain unclear. Here we describe early plague strains that are associated with two phases of outbreaks among mid-Holocene hunter-gatherers near Lake Baikal in southeast Siberia, beginning from about 5,500 years ago. These outbreaks occur across four hunter-gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups were affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11 years). We further note functional differences, including in the ypm superantigen locus, which is also present in present day Yersinia pseudotuberculosis. The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating that this happened before approximately 5,700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter-gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics. Analyses of ancient DNA from hunter-gatherers near Lake Baikal in southeast Siberia around 5,500 years ago indicate that highly virulent Yersinia pestis emerged earlier than previously estimated, far from the next known cases of infection in Late Neolithic Europe.

08.
arXiv (CS.CV) 2026-06-15

Conditioning Matters: Stabilizing Inversion and Attention in Diffusion Image Editing

Inversion-based image editing offers flexible and training-free control but still struggles with inversion accuracy and the trade-off between editing fidelity and background preservation. While recent methods improve inversion formulations or attention interactions, the role of textual conditioning in shaping diffusion dynamics and editing behavior remains underexplored. We show both empirically and theoretically that the precision of textual conditioning influences inversion stability by modulating the geometry of the diffusion velocity field, while also affecting the consistency of cross-branch attention during editing. These effects directly impact background preservation and semantic fidelity. Building on this analysis, we propose SimEdit, a conditioning-aware framework with two complementary components: (a) conditioning refinement, which constructs conditioning signals with improved semantic precision and structural alignment to facilitate stable inversion and consistent attention manipulation, and (b) token-wise cross-branch attention control, which separates edit-relevant and structure-preserving components and modulates them asymmetrically during attention manipulation. Extensive experiments on PIE-Bench demonstrate that SimEdit consistently improves both inversion reconstruction quality and editing performance over previous attention-manipulation approaches. Our code is available at https://github.com/zju-pi/SimEdit.

09.
arXiv (CS.CL) 2026-06-19

Where Does Social Reasoning Come From? Capability Provenance in Language Models

We use training-data attribution as an interpretable tool for capability discovery, mapping which regions of the pretraining corpus support social-reasoning versus STEM-reasoning in OLMo3-7B. Training-data attribution measures how strongly each training document influences a model's predictions on a benchmark, but document-level scores are too noisy to identify which corpus regions support which capabilities, and prior work has emphasized factual knowledge rather than reasoning. We compute gradient-based attribution (TrackStar via Bergson) over a working set drawn from the de-duplicated Dolma3 mix, aggregate influence across WebOrganizer's 24-format x 24-topic taxonomy (576 bins), and contrast benchmark pairs in a 2x2 design that varies domain (social vs. STEM) and capability type (reasoning vs. knowledge): SocialIQA and MMLU Social Sciences against ARC-Challenge and MMLU STEM. Social and STEM reasoning draw on qualitatively distinct corpus regions, and the contrast is sharper at the reasoning level than at the knowledge level. Targeted machine unlearning provides partial causal validation: forgetting high-attribution topic bins (e.g., Literature for SocialIQA) degrades the aligned benchmark more than within-bin random baselines, and we open-source all code, sampling manifests, the bin-level influence matrix, and unlearning checkpoints.

10.
arXiv (CS.AI) 2026-06-24

Reward-Centered ReST-MCTS: A Robust Decision-Making Framework for Robotic Manipulation in High Uncertainty Environments

Authors:

arXiv:2503.05226v2 Announce Type: replace-cross Abstract: Monte Carlo tree search is attractive for robotic manipulation because it can improve action selection through simulation without requiring a fully differentiable policy. In uncertain domains, however, sparse terminal rewards and noisy transitions can make shallow search brittle: many candidate branches remain indistinguishable until late rollouts, and small simulation budgets amplify this ambiguity. This paper presents Reward-Centered ReST-MCTS, a decision-making framework that decomposes intermediate feedback into rule, heuristic, optional neural, and value-estimation channels, centers the resulting process signal against matched task contexts, and uses it to bias or repair search while preserving terminal-task evaluation. The primary evidence is intentionally tiered. Local tasks and matched ManiSkill diagnostics isolate reward-center mechanisms and ablations; matched option-level ManiSkill sweeps test robustness under primitive failure, observation noise, and initial-pose shifts while not claiming standard benchmark superiority; and an official same-backbone OpenVLA-OFT/LIBERO bridge tests bounded VLA action repair. The OpenVLA-OFT clean reproduction reaches 10/10 LIBERO-Spatial successes both with and without RCRM-Guard. A single-suite same-backbone action-channel stress artifact over ten paired LIBERO-Spatial action-channel stress episodes records 0/10 unguarded successes and 9/10 guarded successes. Additional observation-noise, language-perturbation, and visual-distractor probes are reported as coverage and negative-result context rather than superiority evidence. The resulting claim is bounded: Reward-Centered ReST-MCTS is an inspectable test-time verifier for same-backbone high-uncertainty manipulation, not a replacement VLA policy or a broad standard-benchmark superiority claim.

11.
arXiv (CS.CV) 2026-06-16

Selective Synergistic Learning for Video Object-Centric Learning

Typical video object-centric learning (VOCL) approaches employ slot-based frameworks that rely on reconstruction-driven encoder-decoder architectures, where learning is mediated by two spatial maps: attention maps from the encoder and object maps from the decoder. As these two distinct maps exhibit different properties, a recent dense alignment strategy attempted to reconcile this discrepancy by enforcing agreement across all spatio-temporal patches via contrastive learning. However, this indiscriminate alignment inadvertently propagates the inherent weaknesses of each module, such as noisy encoder predictions and blurred decoder boundaries. Moreover, computing dense similarities across all pairs incurs a computational cost quadratic in the total number of spatio-temporal patches, severely limiting scalability. Motivated by this, we propose Selective Synergistic Learning (SSync). Instead of exhaustive patch-to-patch alignment, SSync prevents error propagation by selectively distilling only the most reliable cues: leveraging the encoder strictly for boundary refinement and the decoder for interior denoising. This is realized via a pseudo-labeling with linear complexity, eliminating the need for quadratic spatial comparisons. Also, to prevent the reinforcement of architectural biases like slot redundancy, we introduce a transitive pseudo-label merging that consolidates overlapping slots based on spatio-temporal activation consistency. Extensive studies demonstrate that SSync improves decomposition quality and serves as a versatile, plug-and-play module while also exhibiting exceptional robustness to slot configurations. Code is available at github.com/wjun0830/SSync.

12.
arXiv (CS.CL) 2026-06-15

The Culture Funnel: You Can't Align What isn't in the Data

Current cultural alignment approaches focus on inference-time interventions, assuming models already contain sufficient cultural knowledge. We argue modern LLM pipelines suffer from a cultural data funnel. Using a multidimensional tagging framework across pretraining, fine-tuning, alignment, and reasoning datasets, we show explicit cultural signals decline sharply during post-training, while geographically concentrated, task-specialized data dominates. Multilinguality enhances geographic diversity of cultural knowledge but does not ensure balanced representation. Our tags improve downstream cultural benchmark performance, demonstrating that advances require shifting focus in training data pipelines. To facilitate future research, we release our culturally tagged dataset with 5.6M samples at https://huggingface.co/datasets/CohereLabs/CultureMarkers.

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

NeRD: Neuro-Symbolic Rule Distillation for Efficient Ontology-Grounded Chain-of-Thought in Medical Image Diagnosis

Interpretability is essential for trustworthy medical image diagnosis. However, existing concept-driven interpretable methods have key limitations: Concept Bottleneck Models (CBMs) require scoring all predefined concepts at inference time and for manual intervention, imposing a substantial burden on clinicians, while rationale-based generative approaches often select concepts by class discriminability, which can drift from diagnostic ontologies. To address these issues, we propose Neuro-Symbolic Rule Distillation (NeRD), a framework that produces efficient, ontology-grounded reasoning chains that are sufficient yet non-redundant, without manually crafting diagnostic rules. Experiments on two skin datasets demonstrate strong diagnostic performance and interpretability, and blinded expert evaluation confirms the clinical plausibility of NeRD rationales. Our method further enables a first expert-in-the-loop study for Multimodal Chain-of-Thought-based diagnosis, achieving efficient and effective concept-level intervention.

14.
arXiv (math.PR) 2026-06-11

On the Wasserstein distance between a hyperuniform point process and its mean

arXiv:2404.09549v3 Announce Type: replace Abstract: We study the existence of bounds on the expected $p$-Wasserstein distance between a random measure and its mean under the assumption that the $p$-th centered moments of the counting statistics are controlled uniformly in space. The average Wasserstein transport cost is shown to be bounded from above and from below by some multiples of the number of points. $D$-dimensional versions of those results are also obtained. As a corollary, we prove that for any value of $p\geq 1$ the Ginibre point process can be seen as a perturbed lattice with identically distributed perturbations with a finite $p$-th moment.

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

PhaseWin: An Efficient Search Algorithm for Faithful Visual Attribution

Visual attribution is a fundamental tool for interpreting modern vision and vision-language models, particularly when their decisions must be inspected, diagnosed, or audited. Its goal is to explain how a model's decision depends on local regions of the visual input, typically by assigning an importance ordering over candidate image regions. Given an image partitioned into $n$ regions, faithful attribution can be cast as an ordered subset-search problem, in which progressively inserting the selected regions should recover the target model response as early as possible. Exhaustive search over region subsets incurs exponential cost, while the widely used greedy search still requires a quadratic number of model evaluations, because every selection step rescores all remaining candidates. We propose PhaseWin, an efficient subset-search algorithm for faithful visual attribution. PhaseWin reorganizes greedy region selection into a phased window-search procedure: rather than re-evaluating the full candidate set at every step, it alternates between global candidate screening, adaptive pruning, and localized window refinement, while preserving the essential region-ranking behavior of greedy search. We analyze PhaseWin under monotone evidence-accumulation conditions and show that, under feature-level structural assumptions, it attains controllable linear evaluation complexity together with near-greedy faithfulness guarantees. Extensive experiments on image classification, object detection, visual grounding, and image captioning show that, among all compared attribution methods, PhaseWin reaches high faithfulness with the fewest forward passes, empirically realizing the predicted reduction from $O(n^2)$ to $O(n)$. The code is available at https://github.com/Qihuai27/phasewin-va.

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

CLoVE: Personalized Federated Learning through Clustering of Loss Vector Embeddings

arXiv:2506.22427v2 Announce Type: replace-cross Abstract: We propose CLoVE (Clustering of Loss Vector Embeddings), a novel algorithm for Clustered Federated Learning (CFL). In CFL, clients are naturally grouped into clusters based on their data distribution. However, identifying these clusters is challenging, as client assignments are unknown. CLoVE utilizes client embeddings derived from model losses on client data, and leverages the insight that clients in the same cluster share similar loss values, while those in different clusters exhibit distinct loss patterns. Based on these embeddings, CLoVE is able to iteratively identify and separate clients from different clusters and optimize cluster-specific models through federated aggregation. Key advantages of CLoVE over existing CFL algorithms are (1) its simplicity, (2) its applicability to both supervised and unsupervised settings, and (3) the fact that it eliminates the need for near-optimal model initialization, which makes it more robust and better suited for real-world applications. We establish theoretical convergence bounds, showing that CLoVE can recover clusters accurately with high probability in a single round and converges exponentially fast to optimal models in a linear setting. Our comprehensive experiments comparing with a variety of both CFL and generic Personalized Federated Learning (PFL) algorithms on different types of datasets and an extensive array of non-IID settings demonstrate that CLoVE achieves highly accurate cluster recovery in just a few rounds of training, along with state-of-the-art model accuracy, across a variety of both supervised and unsupervised PFL tasks.

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

The Unreasonable Effectiveness of Discrete-Time Gaussian Process Mixtures for Robot Policy Learning

arXiv:2505.03296v2 Announce Type: replace-cross Abstract: We present Mixture of Discrete-time Gaussian Processes (MiDiGap), a novel approach for flexible policy representation and imitation learning in robot manipulation. MiDiGap enables learning from as few as five demonstrations using only camera observations and generalizes across a wide range of challenging tasks. It excels at long-horizon behaviors such as making coffee, highly constrained motions such as opening doors, dynamic actions such as scooping with a spatula, and multimodal tasks such as hanging a mug. MiDiGap learns these tasks on a CPU in less than a minute and scales linearly to large datasets. We also develop a rich suite of tools for inference-time steering using evidence such as collision signals and robot kinematic constraints. This steering enables novel generalization capabilities, including obstacle avoidance and cross-embodiment policy transfer. MiDiGap achieves state-of-the-art performance on diverse few-shot manipulation benchmarks. On constrained RLBench tasks, it improves policy success by 76 percentage points and reduces trajectory cost by 67%. On multimodal tasks, it improves policy success by 48 percentage points and increases sample efficiency by a factor of 20. In cross-embodiment transfer, it more than doubles policy success. We make the code publicly available at https://midigap.cs.uni-freiburg.de.

18.
arXiv (quant-ph) 2026-06-17

Breaking the bicycle frame: Coset-based quantum LDPC codes

arXiv:2606.17268v1 Announce Type: new Abstract: Generalizing the construction of two-block group algebra (2BGA) codes, we introduce a family of two-block quantum LDPC codes constructed using the action of a group on the cosets of its subgroup. This replaces the regular group actions of the earlier two-block constructions and significantly expands the search space, yielding new quantum LDPC codes outside the 2BGA family. Through a computer search, we identify several new quantum LDPC codes, including weight-6 codes with parameters $[[48,8,6]]$, $[[96,8,10]]$, and $[[224,12,16]]$, as well as weight-8 codes with parameters $[[84,16,8]]$, $[[112,16,10]]$, $[[128,16,12]]$, and $[[168,16,15]]$. Furthermore, we introduce a maximally packed syndrome extraction schedule of depth $w+2$, including initialization and measurement steps, for any code with a maximum stabilizer weight of $w$ from our family. Under a standard circuit-level noise model, our codes, when decoded using BP-OSD, perform competitively with BB codes, achieving thresholds of $\approx0.65\%$ for the weight-6 family and $\approx0.35\%$ for the weight-8 family. Finally, we introduce a group-theoretic framework to generate sequences of graph-based covers of 2BGA codes, recovering and extending recent results on code constructions of this type.

19.
bioRxiv (Bioinfo) 2026-06-22

EventHorizon: A Foundation Model for Clinical Flow Cytometry

Flow cytometry is an essential tool for diagnosis of hematologic malignancies, but existing clinical workflows are highly dependent on expert manual interpretation. Existing machine learning approaches typically require extensive labeled data and are sensitive to variability in panel design, instrumentation, and laboratory workflows, limiting their generalizability. We present EventHorizon, a self-supervised foundation model for clinical flow cytometry that produces unified specimen-level representations from heterogeneous multi-panel data. EventHorizon employs a two-stage hierarchical transformer architecture with marker-aware tokenization, enabling seamless integration of cells measured across different antibody panels into a single shared latent space. We pre-train the model using a DINO-inspired self-distillation strategy with a variety of flow cytometry-specific augmentations on a dataset of more than 100,000 clinical specimens across 17 distinct panels. We evaluate the resulting embeddings on three clinically relevant classification tasks spanning common and rare panels, demonstrating that simple k-nearest neighbor probing of frozen EventHorizon embeddings achieves performance comparable to a fully supervised baseline model and a prior panel-specific self-supervised model. To ensure EventHorizon is not simply shortcut learning on features such as the markers/panels run for a given specimen, we perform a graph-theoretic analysis of EventHorizon's latent space which argues that specimen embeddings are organized primarily by biological diagnosis. Taken together, these results demonstrate that EventHorizon produces biologically meaningful, panel-agnostic specimen representations from clinical flow cytometry data which, with further development and validation, could provide a potential basis for scalable, reproducible diagnostic support across diverse clinical laboratory settings.

20.
arXiv (quant-ph) 2026-06-11

A quantum implementation of high-order power method for estimating geometric entanglement of pure states

arXiv:2405.19134v3 Announce Type: replace Abstract: Entanglement is one of the fundamental properties of a quantum state and is a crucial differentiator between classical and quantum computation. There are many ways to define entanglement and its measure, depending on the problem or application under consideration. Each of these measures may be computed or approximated by multiple methods. However, hardly any of these methods can be run on near-term quantum hardware. This work presents a quantum adaptation of the iterative high-order power method for estimating the geometric measure of entanglement of multi-qubit pure states using rank-1 tensor approximation. This method is executable on early fault-tolerant (hybrid) quantum hardware and does not depend on quantum memory. We simulate this algorithm and mitigate the effects of noise on the results of the computation using a theoretical model based on a known mitigation approach, which assumes a global depolarising noise channel.

21.
arXiv (CS.CV) 2026-06-11

DarkVGGT: Seeing Through Darkness Using Thermal Geometry without Daylight Tax

Recent feed-forward 3D reconstruction methods have demonstrated strong performance and flexibility in efficient end-to-end scene geometry estimation from image streams. However, their reliance on visible-light appearance makes them vulnerable in dark and low-visibility environments, where RGB cues are severely degraded and geometric evidence becomes ambiguous. To address this challenge, we propose DarkVGGT, an RGB-T feed-forward geometry framework that uses physics-aware thermal modeling for robust 3D estimation in low-light scenes. DarkVGGT introduces two complementary modules. First, physics-inspired thermal factorization extracts emissive-dominant, geometry-consistent thermal cues while isolating sparse reflective residuals that may introduce geometric ambiguity. Second, geometry-shared thermal routing isolates modality-invariant geometric structures from thermal-specific patterns, selectively injecting reliability-aware structural guidance into the RGB stream. Together, these components enable accurate thermal-informed geometry estimation under degraded RGB conditions while largely preserving performance in well-lit environments. Experiments on low-visibility RGB-T benchmarks demonstrate consistent improvements in both depth and camera pose estimation over existing feed-forward geometry baselines.

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

EDEN: A Large-Scale Corpus of Clinical Notes for Italian

We present EDEN (Emergency Department Electronic Notes), a new and unique large-scale corpus of clinical notes produced in Emergency Departments of Italian hospitals. The corpus, in its current version, is composed of approximately 4 million clinical notes fully anonymized, covering diverse phases of patient care during the stay in the emergency department. In addition, a subset of about six thousand notes has been manually annotated by clinical experts through a structured Case Report Form (CRF) containing 132 items relevant for two patient situations in emergency departments, dyspnea and loss of consciousness. Items may assume numerical values (e.g., for blood saturation), categorical (e.g., for level of consciousness ), binary (e.g., for presence of traumas), and mixed value types. The annotation process involved multiple clinicians and underwent iterative revision to resolve ambiguities in item formulation, resulting in a richly structured (although high imbalanced) resource. The dataset aims to fill a relevant gap of data able to support both the development and the use of Large Language Models in concrete medical applications. We describe the data collection protocol, the on-site anonymisation pipeline, corpus statistics, and the annotation scheme. Finally, we propose CRF-filling as a novel structured information extraction benchmark, and provide zero-shot baseline resulting from Gemma-27B and MedGemma-27B. To the best of our knowledge, the EDEN dataset is the largest freely available corpus of clinical notes existing for the Italian language.

23.
bioRxiv (Bioinfo) 2026-06-11

DyMoTree decodes early cell state transitions and drivers from single-cell transcriptomes using a tree-structured neural network

Inferring early cell fate from single-cell RNA-sequencing data is essential for identifying cellular origins and fate plasticity in development and disease. However, existing methods often fail to exploit tree-structured lineage trajectories, limiting the accuracy and interpretability of fate mapping. Here we present DyMoTree, a computational framework that models cell fate decisions as nonlinear mappings between progenitor and terminal cell states under explicit lineage constraints. By integrating lineage graphs with a tree-structured neural architecture, DyMoTree learns lineage-resolved cell-state transition maps from single-cell transcriptomes, enabling robust inference of early fate bias and identification of fate-specific progenitor substates and driver genes. Across simulations, lineage-tracing experiments, and in vivo systems, DyMoTree outperformed existing methods in resolving early fate biases. Applications to mouse embryogenesis, lung adenocarcinoma progression, and CAR-T immunotherapy revealed regulatory programs underlying developmental and disease-associated transitions. DyMoTree provides a general framework for modeling lineage-resolved cell-state dynamics underlying development and disease progression.

24.
arXiv (CS.AI) 2026-06-12

Evaluation Sovereignty in Metadata-Driven Classification: A Multi-Track Framework for Weakly Supervised Information Systems

arXiv:2606.13436v1 Announce Type: new Abstract: Evaluation in machine learning is typically treated as a neutral measurement process. However, in operational information systems, evaluation outcomes are often conditioned by the processes used to generate labels. This paper does not seek to improve classification performance. Instead, it examines the validity of performance measurement under differing label-authority regimes. This issue is particularly relevant in large-scale metadata-driven systems, where labels are often incomplete, inconsistent, or weakly supervised. We introduce evaluation sovereignty, defined as the degree to which performance metrics are independent of label authority and supervision regime, and propose a multi-track evaluation framework that systematically varies training and evaluation label sources. Using hierarchical multi-label classification on large-scale scientific metadata, we demonstrate that models exhibiting strong performance under operational ("silver") evaluation degrade substantially under independent ("gold") evaluation, particularly for fine-grained classification. For example, Micro-F1 decreases from approximately 0.54 to 0.03. Notably, ranking-based metrics remain above baseline, revealing a divergence between latent model signal and classification validity. These findings suggest that commonly reported performance metrics may reflect alignment with labeling processes rather than true predictive capability. We therefore reconceptualize evaluation validity as a system-level property shaped by label governance and provide a practical methodology for auditing intelligent systems operating under weak supervision.

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

LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks

Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig