Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

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

Reinforcement Learning for Neural Model Editing

Authors:

Editing pretrained neural networks requires specialized algorithms tailored to specific objectives. Designing such algorithms is often time-consuming and demands significant effort. We present an exploratory framework that formulates neural model editing as a reinforcement learning problem, where agents modify models using reward feedback. We introduce two environments: MaskWorld, where agents scale weights multiplicatively, and ShiftWorld, where agents apply additive weight updates. The reward function combines a utility-preservation objective with a task-specific editing objective, enabling agents to learn targeted modifications while maintaining overall model performance. We evaluate the framework on bias mitigation in text classification and machine unlearning in image classification, both of which traditionally rely on specialized algorithms. Our results show that the learned policies reduce forget set accuracy to nearly 0% while preserving over 90% retain set accuracy on the unlearning task. In the bias mitigation setting, the learned policies improve bias-related performance by more than 5% while maintaining general classification utility. Our findings show that neural model editing can be cast as a reinforcement learning problem, allowing editing policies to be learned from reward feedback rather than manually engineered for each task.

02.
arXiv (CS.CV) 2026-06-11

Semantic search for 100M+ galaxy images using AI-generated captions

Finding scientifically interesting phenomena through slow manual labeling campaigns severely limits our ability to explore the billions of galaxy images produced by telescopes. In this work, we develop a pipeline to create a semantic search engine from completely unlabeled image data. Our method leverages Vision-Language Models (VLMs) to generate descriptions for galaxy images, then contrastively aligns a pre-trained astronomy foundation model with these embedded descriptions to produce searchable embeddings at scale. We find that current VLMs provide descriptions that are sufficiently informative to train a semantic search model that outperforms direct image similarity search. Our model, AION-Search, achieves state-of-the-art zero-shot performance on finding rare phenomena despite training on randomly selected images with no deliberate curation for rare cases. Furthermore, we introduce a VLM-based re-ranking method that nearly doubles the recall for our most challenging targets in the top-100 results. For the first time, AION-Search enables flexible semantic search for over 100 million galaxy images, enabling discovery from previously infeasible searches, including the identification of 36 new extragalactic stellar stream candidates. More broadly, our work provides an approach for making large, unlabeled scientific image archives semantically searchable, expanding data exploration capabilities in fields from Earth observation to microscopy. The code, data, and app are publicly available at https://github.com/NolanKoblischke/AION-Search

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

AdaSR: Adaptive Streaming Reasoning with Hierarchical Relative Policy Optimization

Large reasoning models typically follow a read-then-think paradigm: they observe the complete input, reason over a static context, and then produce the answer. Yet many real-world scenarios are inherently dynamic, such as audio and video stream, where information arrives as a continuous stream and models must reason, update, and respond under partial observations. Recent streaming reasoning methods allow models to think while reading, but they largely rely on supervised imitation of pre-constructed trajectories, which limits their flexibility. In this paper, we propose AdaSR, an adaptive streaming reasoning framework that enables models to reason during input streaming and perform final deliberation once the stream is complete, learning when to think, and how much computation to allocate across different stages. To optimize this hierarchical reasoning process, we introduce Hierarchical Relative Policy Optimization (HRPO), which decomposes policy optimization into streaming reasoning and deep reasoning phases, providing more fine-grained advantage assignment instead of uniformly distributing a single sequence-level advantage over all tokens. HRPO integrates format, accuracy, and adaptive thinking rewards to enforce valid reasoning protocols, preserve final task performance, and encourage latency-aware computation allocation. Experiments show that AdaSR achieves a better balance among reasoning accuracy, computational efficiency, and streaming latency compared with supervised fine-tuning baseline. We release our code at https://github.com/EIT-NLP/StreamingLLM/tree/main/AdaSR.

04.
arXiv (CS.LG) 2026-06-19

Optimal Deterministic Multicalibration and Omniprediction

arXiv:2606.20557v1 Announce Type: new Abstract: A model is multicalibrated on a collection of group weights $G$ if it is calibrated – i.e. unbiased even conditional on its prediction – not just overall, but also after reweighting contexts by each $g \in G$. It is a useful property for many downstream applications and is a basic desideratum of trustworthy machine learning. Before this work, all predictors known to attain the minimax-optimal $\widetilde O(\varepsilon^{-3})$ sample complexity rate for $\varepsilon$-multicalibration were randomized, while deterministic predictors were known only with substantially worse sample complexity. Whether randomization is necessary for optimal sample complexity in multicalibration was explicitly asked by [CLNR26] and implicitly in several prior works. We resolve this open problem by giving a minimax-optimal multicalibration algorithm that outputs a deterministic predictor. We then generalize the algorithm to produce optimal deterministic predictors that satisfy outcome indistinguishability (OI) with respect to finite or finitely covered collections of tests. As an application, this also gives deterministic omnipredictors and panpredictors with optimal sample complexity, resolving open problems posed by [OKK25] and [BHHLZ25].

05.
arXiv (CS.AI) 2026-06-19

GLARE: A Natural Language Interface for Querying Global Explanations

arXiv:2606.19735v1 Announce Type: new Abstract: While global explanations are crucial for understanding vision models across datasets, classes, and decision contexts, their complex and monolithic nature often hinders practical exploration. Because users typically seek targeted answers to specific questions rather than static artifacts, we present an LLM-based interactive interface that provides natural language access to global explanations for black-box image classifiers. The system's core LLM acts as a mediator, translating natural language questions into structured SQL queries over local explanation data. This enables flexible aggregation without exposing users to low-level representations. For each query, the interface outputs statistics-augmented natural language responses, supporting local explanations, and intent-aligned visualizations. We evaluate the system on intent interpretation, query mapping accuracy, generalization to novel queries and datasets, and robustness to linguistic errors. Our results demonstrate that LLM-mediated querying substantially improves the accessibility and usability of global explanations for human-centered XAI.

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

$\mu$VLA: On Recurrent Memory for Partially Observable Manipulation in VLA Models

arXiv:2606.12497v1 Announce Type: new Abstract: Vision-language-action (VLA) models predict chunks of future actions from the current observation, an assumption that fails under partial observability, where decisions depend on information no longer visible. Existing memory-augmented VLAs simultaneously introduce recurrence, retrieval, compression modules, auxiliary objectives, hierarchical memory, or task-specific architectural changes, so the contribution of recurrence itself remains entangled with surrounding machinery. We present a controlled isolation study of recurrence in a strong pretrained VLA backbone. Our formulation augments the transformer with a small set of learnable memory tokens carried across timesteps and updated through self-attention, trained end to end with truncated backpropagation through time, with no auxiliary losses and no architectural changes. We instantiate this as $\mu$VLA, a family of OpenVLA-OFT variants parameterized by memory width m, TBPTT length K, and the memory update rule (cross-step gradients or a detached EMA), so that recurrence is the only varying factor. On MIKASA-Robo, $\mu$VLA improves average success rate on five training tasks from 0.42 to 0.84 at the strongest setting and reaches 0.23 on held-out tasks with the same memory structure versus 0.07 for the memoryless baseline. On tasks requiring different memory structure, performance remains near baseline. On LIBERO, the strongest recurrent variant achieves 96.2% average success, indicating no regression under full observability. We interpret these results as a calibration of the capability envelope of minimal in-backbone recurrence, identifying the regime in which it is sufficient and the regime where additional memory structure is required. Demos and videos can be found in https://avanturist322.github.io/mu-vla/.

07.
Nature (Science) 2026-06-22

Why heritage sites are at risk in a warming world — and how to save them

As rising seas and intensifying disasters threaten historic sites worldwide, new ways to understand, preserve and adapt these places are needed urgently. As rising seas and intensifying disasters threaten historic sites worldwide, new ways to understand, preserve and adapt these places are needed urgently.

08.
arXiv (CS.AI) 2026-06-11

DiffCold: A Diffusion-based Generative Model for Cold-Start Item Recommendation

arXiv:2606.12245v1 Announce Type: cross Abstract: Cold-start item recommendation remains a persistent challenge in real-world systems due to the absence of interaction histories. While prior models attempt to bridge this gap using item content features, they universally suffer from the seesaw dilemma: enhancing performance for cold items inevitably degrades performance for warm items, and vice versa. We identify that this dilemma stems from a fundamental distributional disparity: warm item embeddings occupy a complex ``behavioral manifold" shaped by rich interaction signals, whereas cold item embeddings are constrained to a ``semantic manifold" derived solely from auxiliary content. Existing methods often force a rigid mapping between these inconsistent spaces, causing the model to sacrifice the precision of warm representations to accommodate cold ones. To address this, we propose DiffCold, a diffusion-based generative model that unifies warm and cold representations. Unlike GANs or VAEs, DiffCold leverages conditional diffusion to reconstruct warm item embeddings from content, preserving the underlying manifold structure without degradation. We further tailor this paradigm with two specific designs: a Retrieval-enhanced Aggregator that initializes generation using semantically similar warm items to bypass inefficient noise, and a Simulation-based Representation Alignment module that enforces distribution consistency between generated and real embeddings via contrastive learning. Experiments on three benchmarks confirm that DiffCold resolves the seesaw dilemma, consistently outperforming state-of-the-art methods across all metrics.

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

Towards Global AI-Driven Cervical Cancer Screening

The global elimination of cervical cancer is a key public health goal set by the World Health Organization (WHO), with screening programs reducing mortality by up to 80%. However, access to experts and biopsy services is limited in low- to middle-income countries (LMICs). Deep learning (DL)-based algorithms offer promising support for screening, but most existing approaches have been developed and validated on private datasets from single countries. We present the first DL-based approach to cervical cancer screening validated on data from multiple countries. Technically, we phrase the problem of detecting and classifying lesions in colposcopy images as a multi-task learning problem, in which we simultaneously perform image-level classification and lesion segmentation. Our model was trained on a private data set of acid stain colposcopy images with manually generated lesion segmentation masks and corresponding histopathological results, employing extensive data augmentation to address image variability. In an in-distribution validation with pathology results serving as ground truth, our algorithm outperformed medical experts (Balanced Accuracy: 0.68 vs 0.64) in CIN1- (Cervical intraepithelial neoplasia grade 1 or lower) versus CIN2+ (grade 2 or higher) classification. External validation on four colposcopy data sets from four countries featuring radical differences in prevalence and patient characteristics yielded superior performance of our method compared to baseline methods. Performance variability across countries was high with AUC values ranging from 0.54 - 0.80. Overall, algorithm performance varied with age, transformation zone (cervical area most prone to lesion development), presence of comorbidities and pathognomonic signs, with comorbidities having by far the largest negative effect. Future work should focus on improving model robustness and generalizability.

10.
arXiv (CS.CV) 2026-06-19

3D Scene Graphs: Open Challenges and Future Directions

3D Scene Graphs (3DSGs) have emerged as a powerful representation for spatial AI by combining geometric grounding with semantic and relational abstractions of the environment. Their expressiveness has made them relevant to a broad range of problems in robotics and computer vision, including manipulation, navigation, task planning, scene understanding, and many others. However, the field remains fragmented: different communities adopt distinct formulations, construction pipelines, and evaluation protocols, making it difficult to compare methods, identify common assumptions, and assess remaining challenges for robust real-world deployment. This survey provides a unified and critical review of 3DSGs, with particular emphasis on open challenges and future directions. We first formalize 3DSGs under a common definition and analyze the principal modeling choices that characterize existing formulations, including node and edge attributes, hierarchical structure, dynamic scene representations, and affordance-aware extensions. We then review how 3DSGs are built from raw sensory observations, discussing the most common terminologies, conventions, and techniques. Finally, we examine downstream applications and evaluation strategies, from intrinsic graph quality to task-level performance. To support the community, we also provide a dedicated website that organizes and extends the surveyed content, accessible at https://3dscenegraphs.com/.

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

HAMON: Passive Optical Sequence Mixing for Long-Horizon Forecasting

arXiv:2606.17028v1 Announce Type: cross Abstract: Simple linear and frequency-domain models remain surprisingly competitive in long-horizon time-series forecasting, and recent mechanistic evidence suggests that standard forecasting benchmarks may not require the dense superposed representations that make transformers powerful in other domains. This raises a substrate-level question: if the core forecasting operator is often low-complexity and approximately linear, does it need to be implemented as learned digital temporal mixing? We introduce HAMON, a passive diffractive optical forecasting core in which historical values are encoded onto an optical aperture, future positions are left dark, and cascaded trainable phase masks with free-space diffraction shape the forecast directly in the output field. At inference, prediction is performed by a single passive optical propagation pass with no trainable digital sequence-mixing layer. Across standard benchmarks, HAMON outperforms the strongest digital baselines considered on ETTm2 at all horizons and on ETTh2 at all but the longest horizon, improving MSE by up to 14\% and doing so consistently across horizons rather than at isolated points. It is competitive on Weather and trails the strongest baselines on the remaining ETT settings and on the high-channel-count Traffic and Electricity datasets. Phase encoding, intensity-compatible readout, and phase-scrambling ablations, together with a TorchOptics cross-simulator check, indicate that the forecasts arise from the data-bearing optical field rather than from a digital forecasting head. Because the passive core uses standard Fourier optics, HAMON defines a concrete target for optical hardware and for passive physical sequence mixing.

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

Influence-solvability: a systematic theory of $(1+1)D$ solvability and its application to brickwork circuits

arXiv:2606.12538v1 Announce Type: cross Abstract: `Solvable' circuits, such as dual unitaries and its generalisations, have arisen as paradigmatic examples of tractable chaotic non-equilibrium dynamics, both in classical and quantum systems. However, while increasingly more complicated sufficient conditions have been proposed, a systematic theory classifying and understanding general features of solvable circuits is missing. We develop such a theory by introducing influence-solvable circuits, a class of $(1+1)D$ circuits whose influence matrix, which represents the `bath' generated by its own evolution, is given by a uniform MPS with finite bond-dimension $\chi$. This property allows for efficient computation of subsystem dynamics and essentially contains all known examples of solvable circuits. We derive a set of necessary and sufficient local conditions by using a version of the fundamental theorem of MPS for open boundary conditions. Next we apply our theory to brickwork circuits with $\chi=1$ influence-solvability and perform a systematic classification of classical brickwork circuits with local dimension up to $d=3$ and quantum brickwork circuits with $d=2$. Our search reveals new solvable circuits that are not captured by known solvability conditions.

13.
arXiv (quant-ph) 2026-06-11

The Simplified Stabilizer ZX-Calculus is Minimal

arXiv:2606.12383v1 Announce Type: new Abstract: The stabilizer fragment of the ZX calculus is amongst the most important fragments of the theory. The closely related Clifford+T fragment is approximately universal (arXiv:1705.11151). Additionally, the stabilizer calculus can be described by a small collection of rewrites, most of which have been shown to be necessary (arXiv:1709.08903). However, two rules, describing the red/green compact-structure coincidence and the important bialgebra law, had not been shown to be necessary. We present a countermodel-style argument showing that both of these rules are individually necessary relative to the connectivity meta-rule of Backens–Perdrix–Wang (arXiv:1709.08903), and hence establish that the rule set presented in arXiv:1709.08903 has no redundant rewrite rule.

14.
Nature Medicine 2026-06-12

Efficacy and target engagement of dopamine agonist pramipexole for anhedonic depression: a randomized placebo-controlled trial

Authors:

Anhedonia is a core and disabling symptom of mood disorders with limited treatment options. We evaluated the efficacy and safety of the dopamine agonist pramipexole in patients with mood disorders characterized by clinically significant anhedonia. In this single-center, randomized, double-blind, placebo-controlled trial, adults with major depressive disorder, dysthymia or bipolar depression and elevated Snaith−Hamilton Pleasure Scale (SHAPS) scores were assigned (1:1) to flexible dose, once-daily oral pramipexole as add-on treatment or placebo for 9 weeks. The primary outcome was change in SHAPS score from baseline to week 9. Analyses were conducted in the modified intention-to-treat population. Eighty-five participants were randomized, and 82 were included in the analysis. The primary outcome was met: pramipexole was associated with a greater reduction in SHAPS scores compared to placebo (mean difference: −4.04, 95% confidence interval: −6.89 to −1.18, P = 0.006, Hedges’ g = 0.62). Exploratory analyses indicated that pramipexole was associated with increased light physical activity and relative preservation of reward-related ventral striatal activation. Improvements in anhedonia were sustained during a 6-month open-label extension. Pramipexole was generally well tolerated compared to placebo. Pramipexole significantly improved anhedonia and showed a favorable safety profile, supporting its potential as an augmentation strategy in mood disorders. ClinicalTrials.gov identifiers: NCT05355337 and NCT05825235 . Pramipexole, in patients with major depressive disorder, dysthymia or bipolar depression, reduced Snaith−Hamilton Pleasure Scale scores significantly compared to placebo.

15.
arXiv (CS.CV) 2026-06-16

Faithful Action-unit Causal Reasoning for Counterfactually Faithful Emotion Explanations

Multimodal models can name the action units (AUs) behind a facial emotion, but their AU->emotion rationales are typically plausible rather than faithful: nothing forces the AUs a model invokes to be the AUs that actually drive its prediction. We cast AU->emotion reasoning as a counterfactual-consistency problem between the rationale, the label, and a structural AU->emotion causal graph G, and propose FACR, which grounds the reasoner in an independently induced, polarity-aware G and trains a counterfactual-faithfulness objective: a do-intervention on an AU that G marks causal for a class must move the prediction, while one it marks irrelevant must leave it unchanged. Faithfulness is thereby both trainable and measurable through a matching interventional metric, which we evaluate against a known causal structure, the PSPI pain-AU composition, as no existing affective-reasoning benchmark allows. We are explicit that this metric tests fidelity to the supplied structure rather than its rediscovery: it asks whether the trained reasoner invokes the AUs the structure marks causal, on held-out subjects and a second dataset. Under subject-independent evaluation on UNBC-PAIN, the objective raises the agreement between the invoked AUs and the PSPI composition from a no-objective baseline of 0.08 to 0.57, at a small detection cost; an unfaithfulness control attributes the gain to the objective. On a cross-dataset emotion transfer, the objective likewise raises fidelity to G on a seven-class task (0.50 to 0.84). Finally, we attach a language verbalizer and extend the audit to the generated text: biasing each action unit's emission by its latent activation makes the rationale faithful by construction, so that ablating an AU removes it from the explanation, a property that transfers to a second language-model backbone, whereas a freely generated rationale is unfaithful.

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

A Finite-Volume Scheme for the Continuum Extrapolation of Lattice Step-Scaling in (2+1)D Hamiltonian U(1) Gauge Theory

arXiv:2606.20029v1 Announce Type: cross Abstract: We propose a finite-volume scheme to perform controlled continuum extrapolations of the lattice step-scaling function, a key ingredient for determining the running coupling in a Hamiltonian lattice gauge theory in small volumes. As a testbed, we employ a dual Hamiltonian formulation of pure U(1) gauge theory in (2+1) dimensions and an operator basis that remains efficient toward weak coupling. We describe the implementation of static external charges on the spatial lattice and study, using matrix product states, the resulting confining string, from which we extract the static potential and a force-based renormalized coupling. Using the proposed finite-volume scheme, we demonstrate a stable continuum limit of the step-scaling function on the lattice sizes accessible to present Hamiltonian simulations. The method is readily extendable to other gauge groups and dimensions, providing a pathway toward Hamiltonian step-scaling studies in other theories.

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

From Explicit Elements to Implicit Intent: A Predefined Library for Auditable Behavioral Inference

Authors:

We present SemantiClean, a modular framework for extracting structured semantic signals from e-commerce session data and driving pluggable inference targets including purchase intent, customer segmentation, and product affinity through a shared element library. Unlike conventional end-to-end predictors that optimise solely for accuracy, SemantiClean prioritises auditability, structural governance, and sigma=0 reproducibility, explicitly trading marginal predictive gains for element-level transparency and defensible decision trails. Built upon the Online Shoppers Purchasing Intention (OSPI) dataset, the framework organises twenty-four behavioural elements into a four-layer architecture (Functional, Interaction, Systemic, Contextual) and enforces signal quality through three anti-inflation mechanisms: RedundancyGroup contribution caps, TieredPenaltyCalculator bias penalties, and AdaptiveConstraintMode cold-start protection.This report introduces the LLM-Integrated Semantic Inference Engine, a fully implemented two-phase LLM-driven inference architecture that leverages complete element metadata at inference time. All quantitative results reported herein are produced by this engine. Deterministic engine outputs remain fully reproducible (sigma=0); LLM-dependent results (E8, E10) are subject to controlled output variability under fixed provider/model/temperature settings. The gender inference target remains non-functional in the current implementation and is excluded from all quantitative results.

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

Surflo: Consistent 3D Surface Flow Model with Global State

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

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

Physically Constrained Ensemble Gaussian Process Modelling for Expensive Quantum Systems with Heteroskedastic Noise

arXiv:2606.11240v1 Announce Type: cross Abstract: Accurate modeling of quantum many-body systems often requires computationally expensive simulations such as Density Matrix Renormalization Group (DMRG) or Quantum Monte Carlo (QMC) calculations. These methods, while precise, impose significant time and resource constraints, limiting their use in exhaustive parameter exploration. Moreover, these expensive simulations can contain variable errors over the large unknown parameter space, which needs to be quantified and propagated. Thus, predictive modelling is required to estimate the functional space accurately over scarcely sampled data with heteroskedastic noise, while preserving the physical relevance of the estimation. Therefore, we present a Physically Constrained Ensemble Gaussian Process (pc-EGP) framework designed to efficiently model complex and noisy quantum systems under physical consistency constraints. The proposed method first enforces physical constraints as a user controlled weighted penalty to the data-driven loss function of the Gaussian Process (GP) surrogates. Then an ensemble of such GP models is trained with variable noisy simulations via numerical quadrature method where these multiple GP(s) at different nodes is integrated as a quadrature weighted average. We first demonstrate the framework on synthetically generated data before applying to quantum systems. In the first case study, we leverage DMRG simulations of the Bose-Hubbard Model to predict the critical interaction parameter Uc governing the superfluid-to-Mott-insulator transition. In the second case study, we demonstrate our method on QMC simulations, of a quantum liquid confined inside a nanoporous silicate with the goal of optimizing a chemical environment to realize a one-dimensional superfluid. Compared to conventional GP, pc-EGP achieves a better balance of accuracy and physically meaningful predictions.

20.
arXiv (CS.AI) 2026-06-12

A Minimal Model of Bounded Trade-Off Screening in Multi-Attribute Choice

arXiv:2606.13201v1 Announce Type: new Abstract: Human decision-making often involves choosing between multi-attribute alternatives, yet classical models assume fully compensatory utility aggregation despite evidence that people reject options with poor performance on critical attributes. We propose a bounded trade-off reasoning framework in which decisions are governed by a screening process that evaluates the balance between gains and losses across attributes. The model introduces a trade-off tolerance parameter that controls acceptable imbalance and can vary across contexts. Through simulation, we show that this mechanism produces preference patterns that differ from standard utility-based models and captures context-dependent variation in trade-off behavior. These results establish bounded trade-off screening as a plausible computational mechanism for multi-attribute choice and generate testable predictions for future behavioral studies.

21.
arXiv (CS.CL) 2026-06-16

The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $dark regulome$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically coupled to local sequence predictability, leaving the regulatory interpretation underdetermined. Across three architecturally distinct foundation models (Caduceus-Ph, HyenaDNA, Enformer) and 30,448 dark genome elements at 92 glioma-relevant loci, we introduce a residualization-and-permutation diagnostic that separates predictability-driven from regulation-driven RIS variance. A sharp 10kb proximal-regulatory horizon survives every control we apply, but the LM-derived element-class hierarchy does not: a six-feature linear baseline matches Caduceus top-decile membership at AUC $= 0.985$. Cross-architecture decomposition cleanly separates a sequence-predictability layer (the two language models co-rank long well-predicted transposable elements) from a regulatory-output layer (Enformer alone retains residual cCRE-discriminative signal), with literally zero overlap between the two top-100 lists. Conservation, brain cis-eQTL, and STRING-PPI cross-checks then anchor what biology survives: top-100 elements across all three models are $3.3\times$ enriched per model for matching brain eQTLs ($p_\mathrm{emp} < 5\times 10^{-3}$), while a tempting transposable-element regulatory layer and a striking NRXN1+NLGN1 protein-pair convergence both fail proper permutation tests once those tests are constructed. We deliver the diagnostic as a general methodological tool for any ISM-based regulatory study.

22.
bioRxiv (Bioinfo) 2026-06-16

Infectious Disease Forecasting via Physics-Informed Machine Learning

Infectious disease transmission evolves as a dynamic process shaped by biological mechanisms, population behavior, and intervention policies, yet public health responses are often driven by lagging indicators. Accurate short- and long-term disease forecasting is essential for the timely deployment of intervention strategies, healthcare capacity planning, and uncertainty-aware, risk-informed decision-making. To address this challenge, three broad classes of forecasting models have traditionally been used: statistical, machine learning, and mechanistic approaches. However, each of these modeling paradigms faces fundamental limitations. In particular, traditional statistical models often lack the flexibility needed to capture complex disease dynamics, machine learning approaches require large, high-quality data streams, and mechanistic models are notoriously difficult to calibrate. To overcome these challenges, we propose a novel physics-informed machine learning (PIML) framework for forecasting infectious disease dynamics. Our approach simultaneously forecasts new case and hospitalization counts, along with other key epidemiological quantities such as the time-varying reproduction number. This is achieved through the design of a machine learning model and estimation strategy regularized by a system of differential equations that encode disease dynamics of the SIHR model, thereby bridging the gap between purely data-driven and mechanistic models. We demonstrate the proposed methodology through in-depth numerical studies and an application to COVID-19 data collected in the state of South Carolina.

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

ArtNet: A JEPA-Like Articulatory Predictive Framework for Robust Zero-Shot Phoneme Recognition

arXiv:2606.16595v1 Announce Type: cross Abstract: Zero-shot cross-lingual phoneme recognition is often hindered by the fragility of direct acoustic-to-symbol mapping, which is susceptible to language-specific variations. Echoing joint-embedding predictive architecture (JEPA) work in vision, we propose ArtNet, a framework that explores a structured feature prediction task based on articulatory features to enhance acoustic robustness. Specifically, ArtNet integrates an articulatory predictor, designed to extract universal articulatory representations from self-supervised learning (SSL) features, with a variational information bottleneck (VIB) to suppress language-specific variations. Experiments on seven unseen languages demonstrate that ArtNet, particularly when synergized with the proposed vector-space inventory alignment (VSIA) strategy, significantly outperforms competitive baselines, achieving a 20.56\% relative reduction in phoneme error rate (PER) and 7.01\% in phoneme feature error rate (PFER).

24.
arXiv (CS.LG) 2026-06-11

Coverage Guarantees for Pseudo-Calibrated Conformal Prediction under Distribution Shift

arXiv:2602.14913v2 Announce Type: replace Abstract: Conformal prediction (CP) offers distribution-free marginal coverage guarantees under an exchangeability assumption, but these guarantees can fail if the data distribution shifts. We analyze the use of pseudo-calibration as a tool to counter this performance loss under a bounded label-conditional covariate shift model. Using tools from domain adaptation, we derive a lower bound on target coverage in terms of the source-domain loss of the classifier and a Wasserstein measure of the shift. Using this result, we provide a method to design pseudo-calibrated sets that inflate the conformal threshold by a slack parameter to keep target coverage above a prescribed level. Finally, we propose a source-tuned pseudo-calibration algorithm that interpolates between hard pseudo-labels and randomized labels as a function of classifier uncertainty. Numerical experiments show that our bounds qualitatively track pseudo-calibration behavior and that the source-tuned scheme mitigates coverage degradation under distribution shift while maintaining nontrivial prediction set sizes.

25.
arXiv (quant-ph) 2026-06-17

Frequency-Division Multiplexed CV-QKD System

arXiv:2603.20718v2 Announce Type: replace Abstract: We propose a frequency-division multiplexed (FDM) continuous-variable quantum key distribution (CV-QKD) system with enhanced spectral efficiency through optimized channel spacing of low-symbol-rate signals. A four-channel 10-Mbaud FDM-CV-QKD system was experimentally demonstrated using Gaussian modulation, a transmitted local oscillator, and homodyne detection. Despite the inter-channel interference, under a finite-size scenario (m=1.25x10^6), the system achieved a 3.6-fold back-to-back secret key rate gain and outperformed the single-channel frequency-upconverted signal up to 26.8 km.