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

Optical Implementation of Equilibrium Propagation Using Spatial Photonic Ising Machines

arXiv:2606.13454v1 Announce Type: cross Abstract: Equilibrium Propagation offers a compelling alternative to traditional machine learning for training energy-based networks. Here we demonstrate a hybrid optical-digital implementation of EP using a Spatial Photonic Ising Machine (SPIM). The SPIM exploits the gauge transformation method to optically encode both continuous neuron states and rank-1 binary trainable patterns as phase modulations via a spatial light modulator, with inference realized using a finite difference scheme. The experimental system is evaluated on the Wine classification dataset. The potential of this approach, including the use of continuous couplings and structured coupling matrices, is evaluated numerically on the more complex MNIST dataset. Our work provides a concrete pathway toward energy-efficient physical implementations of Equilibrium Propagation.

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

TetriServe: Efficiently Serving Mixed DiT Workloads

arXiv:2510.01565v4 Announce Type: replace Abstract: Diffusion Transformer (DiT) models excel at generating high-quality images through iterative denoising steps, but serving them under strict Service Level Objectives (SLOs) is challenging due to their high computational cost, particularly at larger resolutions. Existing serving systems use fixed-degree sequence parallelism, which is inefficient for heterogeneous workloads with mixed resolutions and deadlines, leading to poor GPU utilization and low SLO attainment. In this paper, we propose step-level sequence parallelism to dynamically adjust the degree of parallelism of individual requests according to their deadlines. We present TetriServe, a DiT serving system that implements this strategy for highly efficient image generation. Specifically, TetriServe introduces a novel round-based scheduling mechanism that improves SLO attainment by (1) discretizing time into fixed rounds to make deadline-aware scheduling tractable, (2) adapting parallelism at the step level and minimizing GPU hour consumption, and (3) jointly packing requests to minimize late completions. Extensive evaluation on state-of-the-art DiT models shows that TetriServe achieves up to 32% higher SLO attainment compared to existing solutions without degrading image quality.

03.
arXiv (CS.LG) 2026-06-25

Cellular Predictions on the Move: What about Data?

arXiv:2606.25709v1 Announce Type: new Abstract: Mobile cellular load forecasting is native to network resource optimization and delivery of services with reliability, latency and quality guarantees. The mainstream of machine learning research in the area is focused primarily on developing powerful learning structures for improved prediction accuracy. The data used for forecasting traditionally belong to the cellular domain and at most contain exogenous information about the surroundings of the base stations. We approach the prediction task from the perspective of data as a vital component of any data learning process. We hypothesize that substantial improvements could be achieved when the data inform on the processes that create the cellular load. Specifically, we propose to characterize the population dynamics – the potential number of cellular traffic sources and their mobility – in addition to employing historical time series of mobile data traffic. We validate our hypothesis for the rarely examined highway scenario. Comprehensive experiments show forecasting improvements on the order of $60\%$ due to the use of these data alone.

04.
Nature Medicine 2026-06-24

Automated reanalysis of genomic data for rare disease diagnostics at scale

Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necessary to ensure scalability, adoption and sustainability of iterative reanalysis. We developed Talos, an open-source tool that automates variant prioritization by integrating dynamically updated gene−disease and variant-level evidence with inheritance-aware filtering and validated its performance using data from 1,089 individuals with rare disease. Trio-based analysis identified 90% of known diagnoses, returning 1.3 variants per case on average. Variant burden reduced to one variant per 200 cases on iterative monthly reanalysis. Application to an unselected cohort of 4,735 undiagnosed individuals identified 241 diagnoses (5.1% yield): 78 (32%) due to new gene−disease relationships, 54 (22%) due to new variant-level evidence and 109 (45%) due to improved analysis strategies. Our automated, iterative reanalysis model demonstrates the feasibility of delivering frequent, systematic reanalysis at scale. Talos, a new tool for the automated analysis of genomic data, demonstrates the feasibility and diagnostic utility of systematic reanalyses of data in rare diseases.

05.
arXiv (CS.CL) 2026-06-15

Poker Arena: Multi-Axis Profiling of Strategic Reasoning and Memory in LLMs

Strategic reasoning under uncertainty underpins consequential decisions in negotiation, finance, and policy, but prevailing game-play benchmarks collapse heterogeneous reasoning dimensions into a single scalar, leaving the capability structure of frontier LLMs unexamined. We introduce Poker Arena, a no-limit Texas Hold'em tournament platform that couples a three-layer memory architecture (within-hand, session, and cross-session) with a nine-axis cognitive profile decomposing strategic reasoning into interpretable dimensions such as bet-sizing calibration and positional awareness. We evaluate seven frontier models across 50 sessions of 1,000 hands and a controlled memory ablation; tournament chips and aggregate axis score order the field differently: Claude Opus 4.6 wins +$15,730 chips with 14 first-place finishes, yet ranks only fifth of seven on mean axis score, while persistent memory helps some models and hurts others. These findings show that multi-axis evaluation surfaces capability structure that scalar leaderboards systematically misrank, with cross-dimensional consistency outweighing peak performance on any single axis.

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

LLMs Can Better Capture Human Judgments–With the Right Prompts

Are large language models (LLMs) bad at capturing human judgment? Two commonly stated limitations are that LLMs fail to capture full distributions of responses, and that their judgments are unstable across wording variations. We demonstrate simple prompting strategies that mitigate these limitations. Across two datasets–a U.S.-representative set of 144 moral scenarios and 38 moral beliefs from the International Social Survey Programme's Family and Changing Gender Roles module covering 32 countries–we show how simple elicitation techniques help improve AI-human alignment. First, prompting models to report standard deviations and response proportions recovers the full range of human responses better than common strategies. Second, ensuring scenarios are clear to human participants–as reflected in human confusion ratings–boosts model alignment, and LLMs can track human confusion ratings. At the same time, we find that LLMs' estimates of their own error are poorly calibrated, though they can predict human variability relatively well. These results suggest that asking better questions to LLMs can yield better answers.

07.
arXiv (quant-ph) 2026-06-15

Quantum sensing through bosonic-fermionic Bell-state transitions in two-photon interference

arXiv:2606.14408v1 Announce Type: new Abstract: Hong-Ou-Mandel (HOM) interference has become a central resource for quantum sensing and metrology owing to its sensitivity to temporal delay and photon indistinguishability. However, existing HOM-based sensing schemes generally rely on inserting a sample into one arm of the interferometer, making the measurement vulnerable to optical loss, alignment instability, and bandwidth-dependent distortion of the interference profile. Here, we demonstrate a symmetry-controlled quantum sensing scheme based on continuous transitions between symmetric (bosonic-like) and antisymmetric (fermionic-like) Bell states in two-photon interference. By imprinting a geometric phase onto the classical pump beam and transferring it to polarization-entangled photons generated via spontaneous parametric down-conversion, we coherently tune the exchange symmetry of the entangled state without altering the temporal or spectral indistinguishability of the photons. The HOM response evolves continuously from bunching to antibunching with a sine square phase dependence, producing a coincidence modulation of approximately 10 * 10^4 counts s^-1 counts/s. In contrast to conventional HOM sensing, the phase-modulation linewidth remains fixed at pi/2, independent of photon bandwidth. Using a birefringent crystal placed directly in the pump beam, we measure thermo-dispersive birefringence with a resolution of the order of 10^{-6} over a broad temperature range. Our results establish exchange symmetry as a controllable resource for robust quantum sensing and symmetry-engineered photonic quantum information processing.

08.
arXiv (quant-ph) 2026-06-17

Pulse-optimised circuit elements for scalable and noise-resilient quantum chemistry

arXiv:2606.17357v1 Announce Type: new Abstract: Useful chemistry calculations on near-term quantum processors are hindered by current algorithmic runtimes. We develop a methodology to significantly reduce these runtimes. Typically, variational quantum eigensolver (VQE) algorithms are implemented as sequences of primitive gates. Our methodology instead relies on gradient-ascent pulse engineering to construct hardware-tailored pulses for the direct implementation of VQEs. As problem sizes increase, it quickly becomes intractable to optimise a pulse that implements an entire VQE ansatz circuit. However, leading VQEs are constructed in a modular fashion. A problem-tailored VQE is assembled from parameterised circuit elements that simulate hopping between two or four electronic spin orbitals. We show that these circuit elements can be implemented more efficiently using hardware-tailored pulses. We numerically demonstrate our methodology on a silicon spin-qubit quantum processor. We find that common circuit elements, known as single- and double-qubit excitations, can be implemented in less than 289 ns and 927 ns, respectively. Compared with conventional gate-based implementations, our pulse-accelerated qubit excitations provide a scalable approach for faster and therefore more noise-robust quantum chemistry simulations by reducing VQE runtimes by up to a factor of 15.3.

09.
arXiv (CS.CL) 2026-06-11

Debiasing Without Protected Attributes: Latent Concept Erasure from Textual Profiles

Most fairness research in NLP assumes direct access to protected attributes such as gender, race, or nationality. In practice, however, such information is often unavailable due to privacy constraints, missing metadata, or legal restrictions, even though models may infer it from indirect textual cues. This raises a key question: can debiasing succeed without direct access to sensitive attributes? We propose H-SAL, which performs post-hoc concept and attribute erasure using self-description text as an implicit debiasing signal. To support this setting, we introduce a multi-domain Stack Exchange-based fairness benchmark for helpfulness prediction that includes both explicit and implicit signals, enabling comparison between standard debiasing with protected labels and debiasing without access to sensitive information. Across encoder and decoder-only language models, we find that implicit self-description often matches or outperforms explicit-label-based debiasing. Our results broaden representation-level fairness research and provide a new benchmark for studying debiasing under realistic data constraints.

10.
medRxiv (Medicine) 2026-06-22

Regional Service-System Conditions Associated with Facility-Linked Home-Based Specialist Care in Japan: A Claims-Based Ecological Study of Home Dialysis

Background Complex chronic care is increasingly delivered in patients' homes while remaining linked to specialist facilities for training, monitoring, and backup care. Home dialysis provides a useful case because peritoneal dialysis (PD) and home hemodialysis (HHD) share a home-facility delivery structure but differ in technical and operational requirements. This study examined regional service-system conditions associated with the presence and scale of PD and HHD in Japan. Methods This ecological study used publicly available claims, administrative, census, and geospatial data harmonized to 334 Secondary Medical Areas. Regional indicators were organized into four domains: dialysis service delivery, implementation support for home-based care, hospital backup capacity, and living and sociodemographic context. Diffusion was examined using claims-based indicators of regional presence and post-presence scale, analyzed separately for PD and HHD with Firth penalized logistic regression and zero-truncated negative binomial regression, respectively. Results PD was observed in 271 regions and HHD in 109. Patterns of associated regional conditions differed by modality and stage. PD was associated mainly with existing dialysis-service organization, whereas HHD was associated with broader regional supports, including home-care delivery, living infrastructure, transition support, and hospital-system indicators. Conditions associated with presence differed from those associated with scale. Cross-modality associations suggested that shared regional factors may shape the distribution of both modalities. Conclusions Regional conditions for home dialysis diffusion in Japan differed by modality and stage. PD was linked mainly to existing dialysis-service organization, whereas HHD was linked to multi-domain regional support for technically demanding home treatment. Under standardized reimbursement, local service-system capacity may remain important for modality- and stage-specific diffusion of home dialysis.

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

A Tool for the Synthesis of Adaptive Probabilistic Processors Based on the Ising Model

arXiv:2606.19533v1 Announce Type: cross Abstract: This work presents a tool for the synthesis and simulation of probabilistic architectures for solving combinatorial optimization problems by mapping them to the Ising model. The proposed approach automatically constructs the Ising Hamiltonian and determines the number of probabilistic elements (p-bits) based on problem characteristics such as size and topology. Furthermore, the tool introduces an adaptive strategy for selecting the most suitable update algorithm among Gibbs Sampling, Simulated Annealing (SA), Simulated Quantum Annealing (SQA), and cluster-based methods. Experimental results using benchmark problems demonstrate improved convergence behavior and flexibility compared to fixed approaches. The proposed framework enables systematic evaluation of probabilistic computing strategies and supports the development of future hardware implementations based on MTJs and p-bits.

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

PatchWorld: Gradient-Free Optimization of Executable World Models

Text-agent environments are typically modeled as partially observable Markov decision processes (POMDPs), assuming that the simulator's latent state and transition dynamics are hidden from the agent. Yet little work has examined whether executable code can be induced to serve as a world model for prediction and planning under partial observability. We introduce PatchWorld, a gradient-free framework that turns offline trajectories into executable Python world models through counterexample-guided code repair. Instead of predicting the next observation with a black-box model, PatchWorld induces symbolic belief-state programs whose action updates can be inspected, replayed, and locally patched. Across seven AgentGym environments, PatchWorld-Simple achieves the highest code-based planning score among evaluated methods, reaching 76.4\% macro success in live one-step lookahead while invoking no LLM calls inside the world-model prediction module itself. We further find that a human-specified residual-memory bias improves surface observation fidelity but weakens decision utility. This exposes a tradeoff in executable world models, since improving observation fidelity can come at the expense of action-discriminative dynamics, and vice versa. Code is available at https://github.com/HKBU-KnowComp/PatchWorld.

13.
arXiv (CS.LG) 2026-06-24

Forget Without Compromise: Nexus Sampling for Streaming KV-Cache Eviction Under Fixed Budgets

arXiv:2606.23961v1 Announce Type: new Abstract: Long-context and agentic LLM workloads push the KV cache past any fixed memory budget, forcing the inference stack to permanently evict tokens at every step of a continuous-inference stream. Existing methods all share the same template, a per-step direct-attention score followed by deterministic top-$K$ selection, which converts a single below-cutoff step into an irreversible verdict and permanently erases any subtly important token that direct attention cannot single out from noise. To address this challenge, we propose Nexus Sampling, a training-free eviction method that pairs Nexus scoring, an iterative walk over direct attention that surfaces bridge tokens, with weighted reservoir sampling, which retains tokens with inclusion probability in place of deterministic top-$K$. Theoretically, we show that Nexus Sampling dominates deterministic top-$K$ in long-run survival of subtly important tokens. Empirically, at 80% KV cache eviction, Nexus Sampling matches dense attention within 1% on LongBench while outperforming top-$K$ baselines on retrieval-heavy tasks, with up to 10x smaller per-sequence cache memory.

14.
arXiv (CS.LG) 2026-06-12

Learning with Simulators: No Regret in a Computationally Bounded World

arXiv:2606.13576v1 Announce Type: new Abstract: Understanding the minimal assumptions necessary for generalization is the fundamental question in learning theory. Unfortunately, most results rely heavily on independence (or some proxy thereof) of the data-generating process, while results for strongly dependent data are far more limited. Towards addressing this gap, we introduce the framework of simulatable processes, where the learner has access to a simulator that approximates the distribution generating the data (which may be an arbitrarily complex and dependent process). Surprisingly, given access to such a simulator, we show that we can recover the same learning guarantees as in the classical setting with independent data, namely, error bounds that depend on the VC dimension. Further, we use this framework to study the power of conditional sampling and show strict statistical and computational advantages in this setting. As a highlight of our framework, we exhibit a single algorithm that simultaneously learns any given VC class under all processes samplable in bounded polynomial time, with regret controlled by the time-bounded Kolmogorov complexity of the process. This provides a significant conceptual broadening of the classical PAC model.

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

ViT-FREE: Efficient Face Recognition via Early Exiting and Synthetic Adaptation

Vision Transformers (ViTs) have gained significant attention in computer vision and shown strong potential for face recognition (FR). However, their high computational cost makes deployment on resource-constrained devices challenging, motivating the need for methods that balance efficiency and accuracy. In this work, we investigate early exiting in pretrained ViTs as a simple yet effective training-free strategy for efficient FR inference. Leveraging the uniform feature dimensionality across transformer encoder blocks, we introduce ViT-FREE, a multi-exit framework that enables face verification directly from intermediate representations without modifying or retraining the backbone model, and thus, reducing inference cost. Empirically, we show that patch embeddings and attention maps evolve progressively across depth, exhibiting high similarity between consecutive ViT blocks and increasing alignment with the final representation. This indicates gradual feature refinement and attention convergence, suggesting that intermediate layers already provide stable and discriminative representations suitable for early exiting. Through extensive experiments on multiple FR benchmarks, we systematically analyze the accuracy-efficiency trade-off across exit depths. Our results demonstrate that later exits achieve a highly favorable balance, with exiting at layer 10 yielding up to a 20% speedup while incurring only a 1.5 drop in verification performance on benchmarks such as IJB-C. Also, we propose ViT-FREE_FT, a lightweight exit-specific fine-tuning strategy that adapts only the projection layers using a small synthetic dataset while keeping the transformer backbone frozen. This approach improves the performance of shallow exits while preserving the efficiency benefits and leaving deeper exits largely unaffected.

16.
arXiv (quant-ph) 2026-06-19

Quantifying Imaginarity in Neutrino Systems

arXiv:2412.01871v2 Announce Type: replace-cross Abstract: It is a fundamental question why quantum mechanics employs complex numbers rather than solely real numbers. In this work, we conduct the first analysis of imaginarity quantification in neutrino flavor and spin-flavor oscillations. As quantum systems in coherent superposition, neutrinos are ideal candidates for quantifying imaginarity within the resource theoretic framework, using measures such as the $\ell_1$-norm and the relative entropy of imaginarity. We show that in the case of two-flavor mixing, these measures of imaginarity are nonzero. The measures of imaginarity reach their extreme values when the probabilistic features of quantum theory are fully maximized, i.e., both the transitional and survival probabilities are approximately equal. Our study reveals that the imaginarity, as a resource, can be harnessed not solely from the presence of a complex phase in the mixing matrix but also from the intrinsic quantum dynamics of time evolution itself. We further extend our analysis to explore the dynamics of three-flavor neutrino mixing, incorporating the effects of a nonzero $CP$ phase.

17.
medRxiv (Medicine) 2026-06-17

Treatment of Multi-Drug-Resistant Tuberculosis with Second-Line All-Oral Drugs in Ghana: Incidence of Adverse Events.

Introduction: The treatment of multidrug-resistant tuberculosis (MDR-TB) remains challenging due to the toxicity of second-line medications and suboptimal treatment outcomes. This study aimed to determine the incidence of adverse events and identify factors associated with these events in patients undergoing treatment for MDR-TB with second-line all-oral drugs in Ghana. Methods: This retrospective cohort study reviewed the medical records of 384 MDR-TB patients treated with second-line all-oral drugs at selected health facilities in Ghana, including the Greater Accra Regional Hospital, Eastern Regional Hospital, and Kumasi South Hospital. Data were extracted using the Kobo Collect tool, capturing patient demographics, baseline clinical and laboratory characteristics, treatment regimens, and adverse events. The study period spanned from 2020 to August 2024. Results: The study included a total of 384 MDR-TB patients, with a mean age of 45 years (SD = 15). The majority of patients were male (65.78%), and most were within the 45-64 years age group (33.85%), followed by those aged 25-44 years (31.25%). Regionally, the highest number of cases were reported from the Greater Accra Region (39.06%), followed by the Eastern Region (31.25%) and Kumasi South Hospital (29.69%). Approximately one in four patients (25%) presented with comorbidities, with HIV being the most common (19.5%). The most frequently reported adverse events were diarrhea (14%), dizziness (13.7%), and vomiting (12.3%). Most of these were mild to moderate in severity and tended to decrease as treatment progressed. Severe adverse events, such as leukopenia and acute kidney injury, were rare, occurring in less than 5% of patients. Over the course of treatment, gastrointestinal adverse events such as vomiting and nausea showed a significant decline, indicating possible patient adaptation or improved clinical management. Results from the multivariate Poisson regression analysis revealed that age and comorbidities were significant predictors of adverse events. Patients aged 65 years and above had a 56% lower risk of developing adverse events compared to younger patients (Adjusted Risk Ratio [aRR] = 0.44, 95% CI: 0.25-0.79, p = 0.005). Conversely, patients with comorbid conditions such as diabetes or hypertension were approximately 2.6 times more likely to experience adverse events compared to those without comorbidities (aRR = 2.65, 95% CI: 1.58-4.43, p < 0.001). The effect of sex was not statistically significant after adjustment (aRR = 1.03, 95% CI: 0.70-1.50, p = 0.86). At the end of the treatment period, 74.9% of patients achieved successful outcomes, including both those who were cured and those who completed treatment without being classified as cured. However, 25.1% had unsuccessful outcomes, which included treatment failure, relapse, or death. Conclusion: In conclusion, adverse events are common in the treatment of MDR-TB with second-line All-Oral drugs, with gastrointestinal adverse events being the most prevalent. These findings highlight the importance of monitoring and managing adverse events to optimize treatment outcomes for MDR-TB patients in Ghana.

18.
medRxiv (Medicine) 2026-06-24

ADVISE: A Machine Learning Framework for Early Recognition of a Surrogate Marker for Ventilator-Associated Pneumonia Using Routinely Collected Critical Care Data

Background Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critical care, affecting 20-36% of mechanically ventilated patients. Early prediction is hampered by the absence of a reliable, objective diagnostic standard. We developed ADVISE (Automated Dudley Ventilation Infection Series Evaluation), a machine learning model to predict physiological deterioration consistent with developing VAP using routinely collected electronic health record data from a UK NHS intensive care unit. Methods Retrospective observational study of admissions at Russell's Hall Hospital ICU (2008-2026). Following National Data Opt-Out exclusion (158 admissions, 4.2%), 3,566 admissions generated 33,208 candidate 48-hour observation blocks. Six temporal variables - FiO2, ventilator mode, P:F ratio, procalcitonin (PCT), secretion amount, and secretion description - were extracted across the baseline window (hours 1-24). A composite VAP-surrogate outcome required concurrent P:F ratio decline (>=5%) and PCT rise (>=0.5 ng/mL) across the outcome window (hours 25-48). After sequential quality filters, 2,134 blocks (18 positive, 0.84% prevalence) were retained. An XGBoost classifier was trained using nested 5-fold cross-validation with scale_pos_weight=114.0 and ROC-based hyperparameter optimisation on 1,495 training blocks, evaluated on 639 held-out test blocks. Performance was assessed via AUROC, AUPRC, and calibration (Brier score). Bootstrap resampling (1,000 iterations) generated 95% confidence intervals. Results On the held-out test set (n=639, 5 positive outcomes), ADVISE achieved AUROC 0.874 [95% CI: 0.771-0.939] and AUPRC 0.031 [0.008-0.069], representing a 4.0-fold improvement over the no-skill baseline. Nested cross-validation mean AUROC was 0.844 +/- 0.078 (range 0.716-0.915). At the Youden-optimal threshold, sensitivity was 0% with specificity 97.8%, reflecting extreme class imbalance (0.78% test prevalence). A threshold targeting 80% sensitivity achieved sensitivity 80.0% [33.3-100.0%], specificity 87.4% [84.8-89.9%], positive predictive value 4.8% [1.1-9.9%], and negative predictive value 99.8% [99.4-100.0%], detecting 4 of 5 VAP cases with approximately 80 false alarms (12.6% false positive rate). Brier score was 0.0078. Feature importance identified baseline P:F ratio as the dominant predictor (41.3% total gain), followed by ventilator mode (26.1%), secretion amount (13.2%), secretion description (9.1%), procalcitonin (5.9%), and FiO2; (4.5%). Conclusions ADVISE demonstrates that baseline oxygenation trajectory and ventilatory support patterns - derived exclusively from routinely charted ICCA variables - can identify admissions at risk of VAP-related physiological deterioration with meaningful discrimination (AUROC 0.874) despite severe class imbalance. The 80% sensitivity operating point offers a clinically actionable alert rate (12.6% FPR), supporting integration into existing ICU workflows. This proof-of-concept study establishes feasibility; multi-site prospective validation is required before clinical deployment.

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

Why Sampling Is Not Choosing: Intentionality, Agency, and Moral Responsibility in Large Language Models

Recent advances in large language models (LLMs) have prompted claims that such systems exhibit agency or qualify as moral agents. This paper argues that these attributions are misguided. We maintain that moral responsibility requires commitment-bearing agency grounded in intrinsic intentionality and self-attributed action, and that such agency constitutes the form of free will relevant to responsibility. Although LLMs generate coherent and normatively evaluable outputs, their operation is fully characterized by probabilistic input-output mappings learned from data. Their apparent intentionality is derived rather than intrinsic, and their outputs are neither owned as commitments nor guided by reasons. Variability introduced by stochastic sampling does not amount to choice or authorship. We address objections from the intentional stance, functionalism, compatibilism, and the presence of moral reasoning in model outputs, arguing that none suffice to establish genuine agency.

20.
bioRxiv (Bioinfo) 2026-06-18

Trajectory inference of epithelial-centered neighborhood profiles reconstructs a pseudo-temporal continuum in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by complex lung architecture and spatially heterogeneous remodeling, which have hindered integrated analysis of cell-intrinsic activity and intercellular communication during disease progression. Here we profiled six IPF lung specimens comprising more than 630,000 cells using the Xenium 5k panel and developed an epithelial-centered neighborhood profiling framework based on the local cellular composition around each epithelial cell. This approach captured fibrosis-associated variation in epithelial niches without requiring predefined histological regions. Pseudo-temporal continuum inference of these profiles reconstructed a continuous axis that reflected the spatial progression of fibrotic remodeling from relatively preserved alveolar regions to fibrotic and airway-like remodeled regions. Within this spatial dataset, we mapped coordinated changes in epithelial states, local microenvironments, epithelial intracellular pathway activities, and directional interactions with neighboring cell types along the same axis. Our findings provide a spatial framework that generates testable hypotheses for progressive epithelial niche remodeling in IPF.

21.
arXiv (CS.CL) 2026-06-15

UP-NRPA: User Portrait based Nested Rollout Policy Adaptation for Planning with Large Language Models in Goal-oriented Dialogue Systems

To address the challenge that current dialogue policy planning methods struggle to dynamically adapt to diverse user characteristics, this paper proposes a User Portrait based Nested Rollout Policy Adaptation (UP-NRPA) online framework with Large Language Models. In contrast to conventional approaches dependent on model training and require offline reinforcement learning policy models for user groups, UP-NRPA enables dynamic customization of dialogue strategies through an adaptive mechanism. This is achieved by leveraging real-time user feedback alongside personality, preferences, and objectives mapped from the current user portrait, thereby adapting to user characteristics without offline reinforcement learning. In collaborative and non-collaborative dialogue benchmarks, UP-NRPA demonstrated considerable benefits, achieving an impressive 100% success rate in multiple dialogue tasks. Particularly in negotiation tasks, the sale-to-list ratio (SL) increased by 56.41%. This demonstrates that UP-NRPA can adapt to diverse user needs without requiring a training mechanism, enabling the dialogue system to adapt to user characteristics.

22.
bioRxiv (Bioinfo) 2026-06-18

segSHAPE: RNA secondary structure prediction from nanopore direct RNA sequencing

RNAs adopt complex structures that regulate key biological processes, making accurate structure prediction essential. Chemical probing coupled with Nanopore direct RNA sequencing (DRS) offers a route to single-molecule structural inference, but current tools are limited by inaccurate signal-to-sequence alignment, which degrades modification-rate estimation and downstream structure prediction. Here we introduce segSHAPE for RNA secondary structure prediction from Nanopore DRS data (both RNA002 and RNA004 chemistries), a probe-agnostic framework that improves signal alignment using prior information of basecalling and per-read signal baseline shift correction, learns position-specific k-mer raw signal parameters, and estimates per-nucleotide modification rates with an unsupervised anomaly detector. On three public RNA002 DRS datasets spanning different chemical probes (AcIm, NAI-N3) and RNAs from 421 to 1552 nt, segSHAPE achieves the highest F1 score and Matthews correlation coefficient (MCC) on all RNAs, exceeding the strongest baseline by 3.4 to 5.8 percentage points in MCC. It additionally captures the ligand-induced conformational change of the thiamine pyrophosphate (TPP) riboswitch RNA directly from RNA002 DRS data using the DEPC probe. On a public RNA004 DRS dataset, segSHAPE improves over the sm-PORE-cupine baseline by 17 ROC-AUC points in modification rate estimation and by 6.7 MCC points in structure prediction. These results establish segSHAPE as a unified, probe-agnostic pipeline for RNA structure prediction from Nanopore DRS data.

23.
arXiv (CS.CL) 2026-06-15

Token-Level LLM Collaboration via FusionRoute

Large language models (LLMs) exhibit strengths across diverse domains. However, achieving strong performance across these domains with a single general-purpose model typically requires scaling to sizes that are prohibitively expensive to train and deploy. On the other hand, while smaller domain-specialized models are much more efficient, they struggle to generalize beyond their training distributions. To address this dilemma, we propose FusionRoute, a robust and effective token-level multi-LLM collaboration framework in which a lightweight router simultaneously (i) selects the most suitable expert at each decoding step and (ii) contributes a complementary logit that refines or corrects the selected expert's next-token distribution via logit addition. Unlike existing token-level collaboration methods that rely solely on fixed expert outputs, we provide a theoretical analysis showing that pure expert-only routing is fundamentally limited: unless strong global coverage assumptions hold, it cannot in general realize the optimal decoding policy. By augmenting expert selection with a trainable complementary generator, FusionRoute expands the effective policy class and enables recovery of optimal value functions under mild conditions. Empirically, across both Llama-3 and Gemma-2 families and diverse benchmarks spanning mathematical reasoning, code generation, and instruction following, FusionRoute outperforms both sequence- and token-level collaboration, model merging, and direct fine-tuning, while remaining competitive with domain experts on their respective tasks.

24.
bioRxiv (Bioinfo) 2026-06-24

V3Cell: A Vision-Guided Virtual 3D Cell Framework for Phenotypic Modeling and Perturbation Prediction

Predicting how organoids respond to chemical perturbations is central to disease modeling and drug discovery. Existing virtual cell models operate at the single-cell level, producing static endpoint predictions from destructive assays. This leaves a critical gap at the organoid scale, where biological identity is defined by tissue-level architecture and continuous developmental dynamics rather than single-cell features. Here we introduce V3Cell, a vision-guided framework that constructs in silico surrogates of organoids directly from non-invasive brightfield microscopy. A foreground-aware model constructs static virtual 3D cells across colon, stomach, and lung organoid lineages. These virtual 3D cells closely match real samples across distributional metrics, micro-texture, and lineage-specific morphometrics, with small effect sizes for most descriptors. A temporal module further predicts developmental fate from as few as six early-frame observations and models fate-conditioned spatiotemporal trajectories that closely recapitulate real perturbation responses. V3Cell requires no omics profiling or fluorescent labeling, establishing a non-invasive brightfield-based paradigm for organoid-scale perturbation prediction. Our code and data are publicly available at https://github.com/Laineyoulu/V3Cell.

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

LegalHalluLens: Typed Hallucination Auditing and Calibrated Multi-Agent Debate for Trustworthy Legal AI

AI systems deployed in legal workflows hallucinate at rates that aggregate metrics report at ~52%, but this average conceals where errors concentrate and in which direction they run, leaving compliance officers without an actionable signal for trustworthy deployment. We present LegalHalluLens, an auditing framework with three components: typed hallucination profiles across four legally-motivated claim categories (numeric, temporal, obligation/entitlement, factual) over CUAD (Hendrycks et al., 2021); a Risk Direction Index (RDI) that reduces omission-versus-invention bias to a single deployment-comparable scalar; and a typed debate pipeline calibrated to both magnitudes and directions. Across 510 contracts and 249,252 clause-level instances we measure a within-model gap of approximately 38-40 pp between obligation/numeric and temporal claims that aggregate reporting hides, and show that two systems with matched 52% rates can carry opposite RDIs. The debate pipeline reduces fabricated detections by 45% with per-category gains tracking the diagnosis, matching commercial APIs with a substantially smaller backbone (4B active parameters). Typed profiles and RDI surface failure modes that aggregate metrics hide; we further show these diagnostics serve as calibration inputs for multi-agent debate pipelines, where Skeptic challenges and asymmetric gates targeted at measured failure modes outperform generically-tuned debate. The framework supports direction-aware procurement, accountability, and agent design for legal AI deployed in the wild.