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

A Benchmark and Framework for Evaluating Next Action Predictions in Spreadsheets

arXiv:2606.13802v1 Announce Type: cross Abstract: Predictive code completion greatly accelerates how quickly developers work. In spreadsheets, despite being much more common, such auto-completion features are virtually non-existent. To address this gap, we introduce a benchmark for systems that observe a sequence of user actions in a spreadsheet and predict future actions. Two challenges are (1) the absence of edit histories in public spreadsheet corpora and (2) the complex space of spreadsheet actions (spatial, temporal, composite). To address (1), we manually curate 52 sequences of 12K actions that recreate spreadsheets from public corpora, seeded by parametrized heuristics and LLM refinement. To address (2), we propose an online evaluation that expects a prediction after each user action, accepts or rejects that prediction, updates the future actions upon acceptance, and repeats this until the target spreadsheet is obtained. We use multiple baseline predictors (including zero-shot LLMs, fine-tuned SLMs, and classical models) and analyze different properties that our benchmark teaches us, including but not limited to: properties of saved actions and false positives, efficiency, effect of user profiles, effect of triggers, and effect of context.

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

Coulomb crystallization of xenon highly charged ions in a laser-cooled Ca+ matrix

arXiv:2512.12266v2 Announce Type: replace-cross Abstract: We report on the sympathetic cooling and Coulomb crystallization of xenon highly charged ions (HCIs) with laser-cooled Ca$^+$ ions. The HCIs are produced in a compact electron beam ion trap, then charge selected, decelerated, and finally injected into a cryogenic linear Paul trap. There, they are captured into $^{40}$Ca$^+$ Coulomb crystals, and co-crystallized within them, causing dark voids in their fluorescence images. Fine control over the number of trapped ions and HCIs allows us to realize mixed-species crystals with arbitrary ordering patterns. By investigating Xe$^{q+}$–Ca$^+$ strings, we confirm the HCI charge states, measure their lifetime and characterize the mixed-species motional modes. Our system effectively combines the established quantum control toolbox for Ca$^+$ with the rich set of atomic properties of Xe highly charged ions, providing a resourceful platform for optical frequency metrology, searches for signatures of new physics, and quantum information science.

03.
arXiv (quant-ph) 2026-06-12

Reservoir-controlled electromagnetically induced gratings in a weakly driven two-level medium

arXiv:2606.13085v1 Announce Type: cross Abstract: We theoretically investigate the transmission and diffraction of a weak probe field from an electromagnetically induced grating formed in a weakly driven two-level medium coupled to engineered quantum reservoirs. Using a perturbative solution of the optical Bloch equations in the weak-driving regime, we analyze how normal-vacuum, thermal, and broadband squeezed-vacuum environments modify the probe susceptibility and consequently reshape both the spatial transmission function and the far-field diffraction patterns. We show that reservoir statistics have a pronounced impact on the diffraction response by altering the amplitude and phase of the induced grating. Thermal reservoirs enhance the transmission modulation and increase the intensity of the dominant diffraction orders, whereas squeezed-vacuum reservoirs generate strongly phase-sensitive modifications that selectively redistribute optical power among diffraction channels. We further demonstrate that the detuning between the squeezed reservoir and the driving field provides an efficient mechanism for controlling diffraction directionality, leading to substantial amplification of selected angular orders. In two-dimensional geometries, squeezed-vacuum correlations produce highly structured phase landscapes and strongly anisotropic diffraction patterns, enabling directional enhancement of specific diffraction channels while suppressing others. These results establish reservoir engineering as a versatile approach for controlling transmission, diffraction efficiency, and angular selectivity in minimal two-level systems, with potential applications in programmable photonic devices, beam steering, and quantum optical platforms.

04.
Science (Express) 2026-06-02

Another red alert for American science | Science

作者: 未知作者

Although research has bipartisan support in the US Congress, and trust in science is above 75% across the country, the Trump administration seems as determined as ever to mortally wound the nation’s scientific enterprise. After the scientific community persuaded Congress to restore most of the president’s draconian cuts to research funding last year, the White House Office of Management and Budget (OMB), under Russell Vought, has found new ways to circumvent the will of Congress and starve American science. At the beginning of this year, OMB dragged its feet in releasing instructions to federal agencies for how to distribute the funding appropriated by Congress, leading to lags in dispersal. Now, OMB has proposed revising the rules that govern how federal dollars are spent. The changes would inevitably lead to unlegislated reductions in funding and damage US leadership in science, both in academia and industry.

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

Incentives and Evidence in Learned Service Orchestration

arXiv:2606.16555v1 Announce Type: cross Abstract: Reinforcement learning for service orchestration has been the subject of sustained research for over a decade, yet it is not used in production at scale. The usual explanation is that learned controllers degrade under delayed and noisy telemetry, workload shifts, and uncontrolled tenants. We test whether existing evidence supports that explanation. We evaluate three highly influential RL-based orchestration systems spanning resource allocation, DAG scheduling, and autoscaling, using pre-registered predictions about comparative degradation under production-relevant perturbations and paired inference with family-wise error correction. Across the tests, most predicted performance reversals do not occur. Diagnostic analyses show that these outcomes often reflect comparator collapse, artefact limitations, or evaluation choices rather than evidence that learned controllers tolerate the perturbations. One apparent advantage under observation lag is roughly fortyfold compared to a Kubernetes HPA-equivalent controller. Another widely cited result cannot be reconstructed from its released artefact, and the strongest reproducible margin is far smaller than the published results. Conclusions also reverse under changes in perturbation magnitude and evaluation mode. Based on these results and broader patterns in the literature, we identify an institutional problem. Publication and review incentives favour benchmark gains against convenient comparators, even when those gains provide little evidence of deployment performance. We argue that the problem is not solely technical. Rather, it is institutional, so learned orchestration needs production-grade comparators, registered perturbation models, separate operational metrics, and publication criteria that reward reproducible operational evidence. Without these changes, the literature can grow without establishing whether learning improves orchestration.

06.
medRxiv (Medicine) 2026-06-12

Integrative Mechanisms of Early Clinical and Research Training (ECART) in Orthopaedic Medical Education: A Qualitative Single-Case Study

Background: Early clinical exposure and student participation in research are important components of medical training. They may support learning motivation, evidence literacy, and self-directed learning. In many programmes, however, clinical training and research training remain separated. Few studies have explained, within a real teaching team, how learners turn clinical phenomena into researchable questions and how research participation can reshape their clinical understanding. Early Clinical and Research Training (ECART) is a clinical-research integration approach developed by an orthopaedic team at the Second Hospital of Shandong University. Methods: We conducted a theory-informed, interpretivist qualitative single-case study. The case was an orthopaedic clinical-research team at the Second Hospital of Shandong University. Participants included medical undergraduates, academic degree graduate students, professional degree graduate students, clinical teachers, and research platform leads. We used purposive sampling with maximum variation. Data were collected through semi-structured interviews and de-identified teaching documents. Data were analysed using the framework method and were interpreted with a Context-Activity-Mechanism-Outcome (CAMO) logic. Results: The analysis showed that ECART was not simply early entry into the clinic or early entry into the laboratory. It was a team-based learning process centred on real medical problems. Four themes were identified. First, early clinical exposure helped learners make real problems visible and nameable, rather than merely increasing exposure. Second, clinical-research connection followed different pathways. Professional degree graduate students often started from clinical uncertainties in residency training and case management, and moved toward evidence-informed small projects. Academic degree graduate students often started from literature gaps, experimental findings, and mechanistic hypotheses, and then used clinical feedback to calibrate meaning. Third, research training, through literature reading, group meetings, experimental design, data review, and mentor questioning, helped learners move from completing tasks to explaining problems. Fourth, sustained ECART depended on a tiered team ecology formed by clinical teachers, research mentors, research platforms, and senior peers. Based on these findings, we refined the ECART programme theory: real medical problems are translated through explanation, searching, experimentalisation, and feedback-based reinterpretation into research questions that learners can understand, discuss, and test. This process supports problem formation, evidence awareness, mechanistic reasoning, translational judgement, and career clarification. Conclusion: ECART is best understood as a clinical-research integrated learning ecology that emerges from real team practice, rather than as a fixed standardised course. Its educational value lies in a recurring cycle of real problems, research translation, multi-source feedback, and clinical reinterpretation. This framework may inform the design, evaluation, and contextual adaptation of clinical-research integration pathways in medical education.

07.
arXiv (CS.AI) 2026-06-17

Agentic AI-based Framework for Mitigating Premature Diagnostic Handoff and Silent Hallucination in Healthcare Applications

arXiv:2606.18068v1 Announce Type: new Abstract: Recent advances in Large Language Models (LLMs) and multi-agent systems have driven the rise of Agentic AI, showing promise for medical reasoning. However, open-ended conversational agents remain prone to two critical failure modes: premature diagnostic handoff and silent clinical hallucinations that may go undetected before reaching the patient. In this work, we propose a multi-agent framework that addresses both issues by replacing ``LLM-as-a-judge'' routing with deterministic orchestration constraints. The framework incorporates two safety mechanisms. First, a neuro-symbolic state-tracking gate enforces completeness of the OLDCARTS clinical protocol (Onset, Location, Duration, Character, Aggravating/Alleviating factors, Radiation, Timing, and Severity) by blocking diagnostic transitions until all required dimensions are collected. Second, an epistemic uncertainty quantification (UQ) gate computes semantic entropy (H) across K=5 independent diagnostic samples to identify and intercept divergent outputs before delivery. We evaluate the system using simulated patient agents powered by the llama-3.1-70b-instruct model on 150 test cases. The full architecture achieves 49.3% diagnostic precision, representing an absolute improvement of 11.3 percentage points over an unconstrained baseline. Additionally, we observe a statistically significant negative correlation (r = -0.181, p < 0.05) between OLDCARTS completeness (\sigma) and semantic entropy (H), suggesting that structured information gathering is associated with reduced diagnostic uncertainty.

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

Optimising Entanglement Distillation Policies

arXiv:2606.14908v1 Announce Type: new Abstract: Entanglement distillation is a fundamental operation in quantum information processing used to obtain higher-fidelity entangled pairs from a supply of less entangled quantum states using local operations aided by classical communication (LOCC). In a physically relevant setting, where states with an initial fidelity of $f_0$, probabilistically generated over multiple, $m$, memory pairs distributed between two parties, Alice and Bob, are pairwise distilled, the optimal policy identifies the system-configuration dependent sequence of entanglement generation and distillation operations that need to be performed in order to minimize the expected time to reach some target fidelity $f_T>f_0$. Here, we formulate and systematically analyze this task as a Markov decision problem and using a value iteration algorithm, obtain optimal deterministic policies that minimize the expected waiting time required to reach a target fidelity. Our results show that the expected waiting time under the optimal policy decreases with increasing generation probability $p$ and number of quantum memories $m$ - as expected. In contrast, it exhibits non-monotonic behavior with respect to $f_0$ for a fixed fidelity gap, $(\Delta f = f_T-f_0)$. While the optimal policy consistently outperforms baseline policies such as the greedy, nested and entanglement pumping policies, its relative advantage is regime-dependent, being determined by the system parameters ($p,f_0,f_T,m$), and exhibits a nontrivial dependence on the fidelity gap $\Delta f$. Our results highlight the value of formulating entanglement distillation as a Markov decision problem, enabling the systematic design of policies that achieve target fidelity thresholds for quantum information tasks in realistic resource-constrained settings.

09.
arXiv (CS.AI) 2026-06-12

What Type of Inference is Active Inference?

arXiv:2606.04935v2 Announce Type: replace Abstract: Active inference casts decision-making as inference, with the Expected Free Energy (EFE) unifying goal-directed and information-seeking behavior. Recent work showed that EFE minimization can be written as Variational Free Energy (VFE) minimization on a generative model augmented with epistemic priors. We prove that the VFE of the augmented model can be rewritten as the VFE of the predictive model plus explicit entropy-correction terms, making the EFE contribution transparent. We then show that proper EFE-based planning requires combining these epistemic corrections with a planning correction that turns marginal inference into policy optimization, yielding a full variational characterization of EFE-based planning. This clarifies which corrections are needed for cross-entropy planning and for full EFE-based planning. The same entropy-corrected formulation leads to a detailed message-passing scheme for EFE-based planning together with simpler ablations. Experiments on three grid-world environments show that full EFE-based planning outperforms ablations that omit either the planning correction or the epistemic corrections.

10.
arXiv (CS.AI) 2026-06-16

When in Doubt, Plan It Out: Committed Small Language Model Deliberation for Reactive Reinforcement Learning

arXiv:2606.16995v1 Announce Type: new Abstract: Reinforcement Learning (RL) policies often degrade in unfamiliar environments because they lack explicit deliberation. We propose Plan, Align, Commit, Think (PACT), a hybrid architecture that combines a fast, reactive RL policy with a slow, deliberative Small Language Model (SLM) planner. PACT invokes the SLM asynchronously to generate and validate candidate action plans. Once a plan is verified through simulation as safe, feasible, and complete, it is executed directly, bypassing the RL policy without retraining or modifying it. Evaluated on three FrozenLake configurations of increasing difficulty, PACT outperforms all baselines while relying on a 2B-parameter SLM backbone, suggesting that deliberative planning and reactive execution are more powerful in concert than either is alone in these settings.

11.
arXiv (CS.CV) 2026-06-19

PCFootprint: A Large-Scale Dataset and Benchmark for Vectorized Building Footprint Extraction from Aerial LiDAR Point Clouds

Building footprint extraction is a fundamental task in photogrammetry, remote sensing, and computer vision. Recent image-based methods have achieved remarkable progress in extracting vectorized footprints from high-resolution optical imagery. However, optical imagery inherently susceptible to occlusions, perspective distortions, and residual relief displacement, yielding incomplete or misaligned footprint extraction. Furthermore, the lack of explicit elevation information limits its direct applicability to Level of Detail building modeling. In this paper, we present PCFootprint, the first large-scale public dataset for footprint extraction from airborne laser scanning point clouds. PCFootprint comprises \num{33000} tiles derived from the Estonian Land and Spatial Development Board, covering diverse urban and rural landscapes. Each tile spans \qtyproduct{128 x 128}{\m} with systematically aligned vectorized footprints aligned to point clouds. The dataset includes a \num{3000} tiles cross-domain test set for evaluating generalization across geographic regions. We establish comprehensive benchmarks by evaluating mainstream methods. Experimental results reveal significant challenges including high intra-class variance, data imbalance, and noise across complex geospatial environments. We believe PCFootprint will advance future research in building modeling, urban scene understanding, and geospatial analysis. The PCFootprint dataset is publicly available at \url{https://huggingface.co/datasets/Haoyuan-Shen/PCFootprint}.

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

Generalizing GNNs with Tokenized Mixture of Experts

arXiv:2602.09258v2 Announce Type: replace Abstract: Deployed graph neural networks (GNNs) are frozen at deployment yet must fit clean data, generalize under distribution shifts, and remain stable to perturbations. We show that static inference induces a fundamental tradeoff: improving stability requires reducing reliance on shift-sensitive features, leaving an irreducible worst-case generalization floor. Instance-conditional routing can break this ceiling, but is fragile because shifts can mislead routing and perturbations can make routing fluctuate. We capture these effects via two decompositions separating coverage vs selection, and base sensitivity vs fluctuation amplification. Based on these insights, we propose STEM-GNN, a pretrain-then-finetune framework with a mixture-of-experts encoder for diverse computation paths, a vector-quantized token interface to stabilize encoder-to-head signals, and a Lipschitz-regularized head to bound output amplification. Across nine node, link, and graph benchmarks, STEM-GNN achieves a stronger three-way balance, improving robustness to degree/homophily shifts and to feature/edge corruptions while remaining competitive on clean graphs.

13.
arXiv (quant-ph) 2026-06-12

Quantum-Driven Neuromorphic Computing for Million-Qubit-Scale Workloads

arXiv:2606.12968v1 Announce Type: new Abstract: We introduce Apollo, a 10000 node p-qubit neuromorphic processor fabricated in 16 nm mixed signal CMOS and operating fully at room temperature with a typical analog core power envelope of about 0.5 W. Its fundamental element, the p-qubit, is a bistable stochastic unit whose continuous time state fluctuations are driven by integrated quantum entropy units that inject true quantum derived randomness. This enables ultrafast stochastic transitions at low energy while preserving a classical state representation. Apollo combines these p-qubits with a high degree Hyperion 256 interconnect topology, allowing efficient embedding of dense Ising and QUBO problems with substantially reduced minor embedding overhead compared with sparse annealing platforms. We show that, through the Suzuki Trotter correspondence, the equilibrium statistics and annealing dynamics of the p-qubit network reproduce key properties of transverse field quantum annealing without cryogenic cooling, long lived coherence, or microwave control. Beyond device level validation, Apollo is evaluated on a three dimensional spin glass benchmark previously used to study quantum advantage in superconducting annealers. Across 300 disorder realizations, Apollo reaches substantially lower ground state energies than reported cryogenic quantum annealing hardware, while remaining distinct from classical simulated annealing and simulated quantum annealing. A 350 nm release candidate device experimentally validates the core p-qubit dynamics, thermodynamic sampling correctness, and continuous time annealing behavior. These results establish Apollo as a room temperature, industrially scalable platform for quantum driven energy based optimization, probabilistic inference, generative modeling, and hybrid classical quantum workflows.

14.
arXiv (CS.AI) 2026-06-16

MUZZLE: Adaptive Agentic Red-Teaming of Web Agents Against Indirect Prompt Injection Attacks

arXiv:2602.09222v2 Announce Type: replace-cross Abstract: Large language model (LLM) based web agents are increasingly deployed to automate complex online tasks by directly interacting with web sites and performing actions on users' behalf. While these agents offer powerful capabilities, their design exposes them to indirect prompt injection attacks embedded in untrusted web content, enabling adversaries to hijack agent behavior and violate user intent. Despite growing awareness of this threat, existing evaluations rely on fixed attack templates, manually selected injection surfaces, or narrowly scoped scenarios, limiting their ability to capture realistic, adaptive attacks encountered in practice. We present MUZZLE, an automated agentic framework for evaluating the security of web agents against indirect prompt injection attacks. MUZZLE utilizes the agent's trajectories to automatically identify high-salience injection surfaces, and adaptively generate context-aware malicious instructions that target violations of confidentiality, integrity, and availability. Unlike prior approaches, MUZZLE adapts its attack strategy based on the agent's observed execution trajectory and iteratively refines attacks using feedback from failed executions. We evaluate MUZZLE across diverse web applications, user tasks, and agent configurations, demonstrating its ability to automatically and adaptively assess the security of web agents with minimal human intervention. Our results show that MUZZLE effectively discovers 44 new attacks on 4 web applications with 10 adversarial objectives that violate confidentiality, availability, or privacy properties across different LLMs and agent scaffolds. MUZZLE also identifies novel attack strategies, including 3 cross-application prompt injection attacks and an agent-tailored phishing scenario.

15.
bioRxiv (Bioinfo) 2026-06-15

DAQplugin: Deep Learning based Real-time Model Evaluation Plugin for ChimeraX

Although an increasing number of protein structures are determined by cryogenic electron microscopy (cryo-EM), protein structure modeling frequently suffers from residue misassignments and sequence register shifts, particularly in regions with ambiguous density. Here, we present DAQplugin, a ChimeraX plugin that performs real-time evaluation of protein models against cryo-EM density maps using the deep-learning-based residue-wise model quality (DAQ) score. Unlike existing validation tools that are typically applied after model construction, DAQplugin enables real-time deep-learning-based validation during model building and refinement. To our knowledge, DAQplugin is the first tool that provides real-time deep-learning based validation of protein models for cryo-EM map within an interactive modeling environment. In addition to identifying potential modeling errors, DAQplugin also provides guidance for correcting sequence register shifts by suggesting alternative residue placements along the backbone. The computation in this plugin is designed to run efficiently on general CPUs without requiring GPU hardware. Using DAQplugin, users can perform deep-learning-based validation on standard laptops during interactive model building, model-map fitting, and refinement. DAQplugin is able to facilitate more accurate interpretation of cryo-EM density maps and improve the reliability assessment of protein structure models.

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

PATCH: Action-Chunk-Conditioned Latent Patch Innovation Monitoring for Robot Manipulation

Learning-based manipulation policies have made substantial progress in real-world robot manipulation, particularly for short-horizon action generation. However, deployment in open workspaces remains fragile under unexpected local scene dynamics, such as moving objects, transient occlusions, or disturbances near the intended motion. Existing runtime monitors often rely on global observation anomalies, policy uncertainty, or frame-level visual changes, and struggle to distinguish task-relevant execution risk from benign visual variation. We introduce PATCH, an action-chunk-conditioned latent patch innovation monitor for deployment-time intervention. Given the active action chunk, PATCH defines a projected execution corridor, predicts latent patch evolution inside it, and accumulates persistent residuals unexplained by the robot's own motion. These residuals form a localized intervention signal that allows PATCH-Router to pause execution, select an available recovery source, and resume the original policy once localized innovation subsides. Experiments on real robot rollout data show that PATCH produces more stable and context-relevant triggers than competing runtime monitors. Real-robot deployment further demonstrates monitor-driven intervention and policy resumption for disturbance-aware manipulation. Project Page: https://yananzhou5555.github.io/PATCH/.

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

When CQs Go Wrong: Challenges in CQ Verification with OE-Assist

arXiv:2606.24619v1 Announce Type: new Abstract: Competency Questions (CQs) are the central component of CQ-verification, an established process in which an ontology is evaluated against a set of natural language questions to determine whether the intended purpose of the ontology has been properly modelled. However, CQ-verification is often time-consuming and error-prone, as it requires careful interpretation of linguistic nuances and precise alignment with formal ontology constructs. Ambiguities and complexity in CQs can further complicate this process, leading to inconsistent modelling decisions and verification outcomes. In this paper, we investigate what makes a CQ challenging and possible solutions to enhance the users' performance in the CQ-verification process. We experimented with the data of 19 participants who performed CQ-verification on 20 tasks using an LLM assistant to support ontology evaluation. The results show the necessity of a tool to refine CQs before publishing them to avoid ambiguity or excessive complexity in later phases of the ontology engineering process.

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

SCAR: Semantic Continuity-Aware Retrieval for Efficient Context Expansion in RAG

Fixed-length chunking in Retrieval-Augmented Generation (RAG) often leads to boundary fragmentation, where critical evidence is split across segments, degrading retrieval recall. While static windowing and parent retrieval improve recall, they introduce significant token overhead. We propose SCAR (Semantic Continuity-Aware Retrieval), an adaptive retrieval policy that selectively expands neighboring chunks by weighing query-neighbor relevance against a structural continuity penalty. SCAR uses a relative expansion threshold tied to each retrieved chunk's own query-relevance, yielding an approximately scale-invariant decision rule that transfers across embedding models without recalibration. Across four diverse corpora (RFC, GDPR, a 10-K report, and a Merger agreement; N=320 queries; 160 boundary-fragmented), SCAR achieves 92.8% recall on boundary-fragmented queries with only 7.84 chunks, a 22.9% reduction compared to static windowing (10.16 chunks). Paired bootstrap tests (B=10,000) confirm the chunk reduction is highly significant (p

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

Does Text Actually Help? Uncovering and Resolving Text Collapse in Multimodal Time Series Forecasting

arXiv:2606.19413v1 Announce Type: new Abstract: Multimodal time series forecasting, which pairs numerical sequences with domain-relevant textual reports, promises to inject world knowledge into forecasting pipelines. However, we uncover a critical failure mode in existing frameworks that we term text collapse: the text branch converges to a content-independent transformation, contributing negligible discriminative signal regardless of the input description. We argue that text collapse is a consequence of a fundamental asymmetry in time series forecasting: the numerical input is strongly autocorrelated with the output, making the numerical backbone inherently dominant, while the text branch, despite carrying complementary and often critical information, is insufficiently utilized, leading to its systematic underexploitation. To address this, we propose REST-TS (Residual-Exclusive Supervision for Text in Time Series), which turns the asymmetry into a design principle: the numerical backbone produces its own independent numerical forecast, and the text branch is exclusively supervised to predict the structured components of the residual, the prediction gap that numbers cannot explain. Because no numerical pathway can reduce these losses, the text branch must extract genuine content from the input description. Evaluated across diverse real-world domains and backbone architectures, REST-TS achieves state-of-the-art performance and consistently demonstrates greater text-branch utilization than existing frameworks, providing strong empirical evidence that supervising the text branch on the residual compels it to extract genuine content from the input.

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

Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment

arXiv:2606.18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation. Yet these distributions are learned from broad unlabeled corpora and are not naturally conditioned on task-specific biological contexts such as interaction partners, cellular environments, or therapeutic interventions. Existing contextual matching methods often distort this interface through pooled embeddings, contrastive latent spaces, or task-specific prediction heads. We introduce LOGICA (Logit-space Contrastive Alignment), a framework for context-conditioned prediction that performs contrastive learning directly in output-logit space. Using gated cross-modal adapters compatible with each model's native token head, LOGICA preserves the pretrained likelihood interface and converts contextualized token log-likelihoods into matching scores. Alignment is defined through context-sensitive token probabilities rather than proximity in a shared embedding space, enabling learning from sparse paired data across models with distinct vocabularies, without a shared tokenizer or decoder. LOGICA is particularly effective for mutation-local variant ranking, where comparisons reduce to context-conditioned likelihoods of mutant tokens at perturbed sites. Across protein–ligand binding, TCR–peptide activity, and drug-conditioned resistance prediction, LOGICA improves over prior state-of-the-art methods, including matched latent-contrastive and conditional MLM baselines, while retaining a token-level interface for interpretation and generation. On held-out-gene single-mutation drug-resistance prediction, LOGICA improves AUC from near-random latent-space baselines of $\sim$0.55 to $\sim$0.65.

21.
arXiv (CS.CL) 2026-06-24

PEARL: Self-Evolving Assistant for Time Management with Reinforcement Learning

Overlapping calendar invitations force busy professionals to repeatedly decide which meetings to attend, reschedule, or decline. We refer to this preference-driven decision process as calendar conflict resolution. Automating this decision process is crucial yet challenging. Scheduling logistics can drain hours, and human delegation often fails at scale, which motivates us to ask: Can we trust large language models (LLMs) or language agents to manage time? To enable a systematic study of this question, we introduce CalConflictBench, a benchmark for long-horizon calendar conflict resolution. In CalConflictBench, conflicts are presented to agents round-by-round over a calendar year, requiring them to infer and adapt to user preferences progressively. Our experiments show that current LLM agents perform poorly with high error rates, e.g., Qwen-3-30B-Think has an average error rate of 35%. To address this gap, we propose PEARL, a reinforcement-learning framework that (i) augments the language agent with an external preference memory that stores and updates inferred strategies (e.g., attendee priorities, topic importance, time/location preferences), and (ii) optimizes the agent with round-wise rewards that directly supervise decision correctness, ranking quality, and memory usage across rounds. Experiments on CalConflictBench show that PEARL achieves an error reduction rate of 0.76 and a 55% improvement in average error rate compared to the strongest baseline.

22.
arXiv (CS.CV) 2026-06-19

Occ-VLM: Occupancy Grounded Vision Language Model for Indoor Scene Understanding

Recently, vision-language models (VLMs) have made significant progress in 3D scene understanding, driving advances in applications such as embodied intelligence and robotic vision. However, existing approaches typically either rely directly on explicit 3D inputs (e.g., point clouds or RGB-D sequences), or introduce an additional 3D geometry encoder to derive 3D-aware visual tokens from 2D images. Such designs structurally decouple 3D geometric perception from the rich 2D semantics learned via vision-language pre-training, hindering the development of a unified 3D vision-language representation. In this work, we propose Occ-VLM, a novel framework for 3D scene understanding that operates purely on posed RGB images and employs a single 2D vision encoder. Specifically, Occ-VLM reconstructs 3D scene occupancy as an auxiliary geometric prior, which is utilized to spatially associate foreground 2D tokens with 3D space. These tokens are then decoded by a Large Language Model (LLM) for unified scene understanding. Extensive experiments demonstrate that Occ-VLM achieves both accurate geometric perception and robust vision-language reasoning: it attains state-of-the-art performance on multi-view occupancy prediction, while performing on par with 3D-input VLMs on 3D Visual Question Answering (VQA) and 3D dense captioning benchmarks.

23.
arXiv (CS.LG) 2026-06-12

Generative Modeling of Bach-Style Symbolic Music: A Comparative Study of Autoregressive, Latent-Variable, and Adversarial Approaches

arXiv:2606.13626v1 Announce Type: cross Abstract: We study generative modeling of Bach-style symbolic piano music using a shared MIDI corpus and three model families: autoregressive LSTMs with attention, latent-variable models including recurrent VAEs and vector-quantized VAEs, and generative adversarial networks. We compare their ability to model polyphonic note sequences, learn useful latent representations, and generate stylistically coherent compositions. Our experiments show that the autoregressive LSTM with attention produces the most musically coherent samples, while vector quantization helps mitigate posterior collapse and yields more structured outputs than conventional recurrent VAEs. The adversarial approach captures local pitch patterns but remains difficult to train and generalizes less reliably to Bach's style. These results highlight the relative strengths and failure modes of autoregressive, latent-variable, and adversarial approaches for symbolic music generation.

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

FactoryLLM: A Safe and Open-Source AI Playground for Evaluating LLMs in Smart Factories

arXiv:2606.14119v1 Announce Type: new Abstract: Fault diagnostics and recovery in smart factories is challenging because critical information is dispersed across manuals of multiple machines which are interconnected through the manufacturing process. Large Language Models (LLMs) can provide a promising approach. In this paper, we propose FactoryLLM, a safe and open-source AI playground designed for evaluating different LLM-based retrieval-augmented generation (RAG) models by analysing documents from multiple machines across the manufacturing process. FactoryLLM enables the user to configure the LLM, and assess performance when reasoning over multiple documents, through a dual evaluation setup using both RAGAS and NVIDIA's LLM-as-a-Judge metrics. FactoryLLM is safe because it allows users to run local or open-source LLMs without sharing sensitive industrial data, providing a controlled environment for experimentation. We demonstrate the efficacy of FactoryLLM through a case study which involves an Autonomous Intelligent Vehicle and its Mobile Planner software, evaluating three LLMs across 30 maintenance queries derived from approximately 600 pages of cross-machine documentation. The results suggest that FactoryLLM is effective in cross-machine document reasoning: every model achieved a groundedness score above 0.88. The full code and documentation for community to test FactoryLLM with their manufacturing specific scenarios are publicly available.

25.
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.