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01.
arXiv (CS.LG) 2026-06-16

Conformal Candidate Certification for Offline Model-Based Optimization

Authors:

arXiv:2606.15217v1 Announce Type: cross Abstract: Offline model-based optimization (MBO) proposes candidates by optimizing a surrogate trained on a fixed historical dataset. Because candidates are deliberately out-of-distribution, surrogate rankings are least reliable exactly where the optimizer is most aggressive, yet existing methods provide no per-candidate statistical certificate that a design meets a target threshold. We propose Conformal Candidate Certification (CCC), a post-hoc wrapper that attaches a calibrated one-sided lower bound to each candidate and advances only those whose bound exceeds the target. We show that entropy-regularized surrogate maximization induces a Gibbs-tilted proposal, so the same surrogate supplies importance weights for weighted conformal prediction without a separate density-ratio estimation step. In a controlled synthetic study, CCC certifies $16.7\%$ of an aggressive proposal pool with empirical coverage 0.990 at nominal 0.90, while standard conformal prediction ignoring the covariate shift collapses to 0.416 coverage.

02.
arXiv (CS.AI) 2026-06-16

AI Contagion in Social Networks

arXiv:2606.15206v1 Announce Type: cross Abstract: We study how artificial intelligence (AI) interacts with social communication networks to shape the stability of collective knowledge. Agents exchange information through a network while receiving AI-generated content, and AI systems retrain on the aggregate social information they influence. This interaction generates two feedback forces: an AI contagion channel, through which distortions diffuse across the network, and an AI social distortion multiplier, through which retraining amplifies past errors. Despite the high dimensionality of the environment, we show that the long-run behavior of the system admits a two-dimensional representation whose spectral radius determines whether AI-mediated information systems are dynamically stable or unstable. We characterize a sharp regulatory frontier identifying the minimum filtering required for stability and show how network topology shapes systemic informational risk.

03.
arXiv (CS.LG) 2026-06-11

Hybrid Iterative Neural Low-Regularity Integrator for Nonlinear Dispersive Equations

arXiv:2605.04853v2 Announce Type: replace Abstract: We propose HIN-LRI, a hybrid framework that augments a classical numerical solver with a neural operator trained to correct the solver's structured truncation error. A base low-regularity integrator provides a consistent first-order approximation to nonlinear dispersive PDEs, while a lightweight neural network, operating on a low-dimensional latent manifold, learns the residual defect that analytical methods cannot close. An explicit time-step scaling on the neural correction ensures that its Lipschitz contribution remains $\mathcal{O}(\tau)$, yielding a Gronwall stability factor bounded uniformly in the step size and independent of the spatial resolution. The network is trained end-to-end through a solver-in-the-loop objective that unrolls the full iteration and penalises trajectory error in a Bourgain-type norm, aligning learning with multi-step solver dynamics rather than isolated one-step targets. Under stated assumptions, the global error satisfies $C(\varepsilon_{net}+\delta)\,\tau^\gamma\ln(1/\tau)$, where $\varepsilon_{net}$ measures the network approximation quality and $\delta$ the training shortfall. Experiments on three dispersive benchmarks with rough data show that HIN-LRI improves accuracy over analytical integrators, splitting methods, and neural PDE surrogates, with stable spatial refinement, effective out-of-distribution transfer, and modest online overhead.

04.
arXiv (quant-ph) 2026-06-16

Long-range nonstabilizerness of topologically encoded states from mutual information

arXiv:2605.22424v2 Announce Type: replace Abstract: We study long-range nonstabilizerness (LRN), namely the obstruction to remove nonstabilizerness with shallow-depth local quantum circuits. In one-dimensional settings, the mutual information between disconnected spatial regions has proven to be a powerful tool to diagnose LRN. In this work, we focus on encoded states of two-dimensional topologically-ordered systems, and explore the ability of the mutual information to serve as a diagnostic of LRN. Focusing on the concrete setting of lattice models defined on a torus, we show that information about LRN can be gained from the analysis of the mutual information between non-overlapping regions containing non-contractible loops, and of the change of such mutual information under modular real-space transformations. We exemplify this idea in the toric code and the non-abelian string-net model with doubled Fibonacci topological order. In the former case, we show that the mutual information provides a full classification, certifying LRN for all encoded non-stabilizer states. In the latter case, instead, our approach does not lead to a full classification, as it detects LRN for all states except from a finite subset with special transformation properties under the modular group. Finally, we discuss how our results on LRN constrain the logical gates that can be implemented fault-tolerantly on the torus.

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

On the Benefits of Weight Normalization for Overparameterized Matrix Sensing

arXiv:2510.01175v2 Announce Type: replace Abstract: While normalization techniques are widely used in deep learning, their theoretical understanding remains relatively limited. In this work, we establish the benefits of (generalized) weight normalization (WN) applied to the overparameterized matrix sensing problem. We prove that WN with Riemannian optimization achieves linear convergence, yielding an exponential speedup over standard methods that do not use WN. Our analysis further demonstrates that both iteration and sample complexity improve polynomially as the level of overparameterization increases. To the best of our knowledge, this work provides the first characterization of how WN leverages overparameterization for faster convergence in matrix sensing.

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

Graph Learning Should Move Beyond Restrictive Views of Spectral and Message-Passing GNNs

arXiv:2602.10031v2 Announce Type: replace Abstract: Graph neural networks (GNNs) are commonly divided into message-passing neural networks (MPNNs) and spectral GNNs, reflecting two largely separate research traditions in machine learning and signal processing. While MPNNs have a precise definition, there is no widely accepted criterion for what makes a mapping a spectral GNN. Most existing work restricts spectral GNNs to layered architectures based on linear spectral filters. Under this restriction, we show that spectral and spatial GNNs have largely equivalent expressive power. To promote progress in the field, we propose a precise definition of spectral GNNs based on eigenbasis symmetries, in contrast to the definition of MPNNs via neighborhood permutation symmetries. We further argue that the two perspectives offer complementary strengths. MPNNs provide a natural language for discrete structure and expressivity analysis through tools from logic and graph isomorphism, while the spectral perspective offers principled tools for understanding smoothing, bottlenecks, stability, and community structure. Overall, we argue that progress in graph learning will be accelerated by clarifying the similarities and differences between these perspectives and by moving toward a unified theoretical framework.

07.
arXiv (CS.LG) 2026-06-11

HAMNO: A Hierarchical Adaptive Multi-scale Neural Operator with Physics-Informed Learning for Dynamical Systems

arXiv:2606.11963v1 Announce Type: new Abstract: Neural operators provide a powerful framework for learning solution mappings of partial differential equations directly in function space. However, many existing architectures still struggle to represent nonlinear time-dependent systems that involve multi-scale structures, long-range interactions, and stable long-time evolution. In this work, we introduce the Hierarchical Adaptive Multi-scale Neural Operator (HAMNO), a neural-operator architecture that combines local convolutional representations, global spectral operators, and hierarchical encoder-decoder processing. The central component of HAMNO is a data-dependent gating mechanism that adaptively balances local and global information at each spatial location, allowing the model to resolve fine-scale features while preserving long-range dependencies. We further develop a physics-informed extension, PI-HAMNO, based on a multi-objective loss strategy that combines data fitting with strong- and weak-form physics constraints. The strong-form term penalizes the domain-integrated squared PDE residual in physical coordinates, while the weak-form term is constructed by multiplying the governing residual by finite-element test functions and evaluating the resulting element integrals using centroid-based tetrahedral quadrature. The framework is evaluated on non-periodic Allen-Cahn (AC), Cahn-Hilliard (CH), and Swift-Hohenberg (SH) equations defined on cubic domains. Across long-horizon rollout, data-limited training, out-of-distribution initial-condition shifts, and random-seed variations, HAMNO improves predictive accuracy over standard neural-operator baselines, while PI-HAMNO further enhances stability, physical consistency, and data efficiency. The implementation is publicly available at https://github.com/MBamdad/HAMNO .

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

When Roleplaying, Do Models Believe What They Say?

Language models can state that "the Earth orbits the Sun" and, when role-playing Aristotle, assert the opposite. Recent work argues that persona adoption is fundamental to how language models operate, with models constantly selecting the most appropriate persona for a given context. Does such role-playing merely change the model's outputs, or does it also affect what the model internally represents as truthful? We study this question with linear truth probes, applying them to LLMs role-playing historical personas whose likely beliefs differ from modern consensus. For each persona, we compare false claims the persona would likely have endorsed (*era-believed*) with topic-matched false claims they would not have endorsed (*era-false*). Across prompting, in-context learning, and supervised fine-tuning, persona induction suppresses era-believed statements less than equally false alternatives, yet they remain classified as false overall. Role-play therefore shifts what these models say more than what they internally represent as true. We contrast this with models trained on harmful advice that exhibit Emergent Misalignment (EM). Across three model families (Qwen 2.5 14B, Qwen 3 8B, and Llama 3.3 70B), their false claims move substantially toward the true region of probe space, are defended under challenge roughly half the time versus about a sixth for role-play, and are used in downstream reasoning. Role-play and Emergent Misalignment thus are points on a spectrum of belief internalization, where role-play changes what a model says with little representational change, while Emergent Misalignment shifts the internal representation of false claims without fully marking them as true.

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

Look Again Before You Abstain:Budgeted Conformal Evidence Acquisition for Reliable Vision-Language Model

Large vision-language models (LVLMs) hallucinate: they assert visual details that the image does not support. A principled remedy is selective prediction with a distribution-free guarantee-verify each claim and abstain when the claim is not grounded, so that the hallucination rate among asserted claims is provably bounded. We show, however, that this guarantee is bought at a brutal price: to keep the hallucination rate below $5\%$ on a balanced object-existence benchmark, a state-of-the-art conformal filter must abstain on more than $80\%$ of claims. We argue that abstention is wasteful when more visual evidence is cheaply available, and introduce Budgeted Conformal Evidence Acquisition (BCEA), which replaces the binary answer/abstain decision with a three-way choice: answer, abstain, or acquire additional visual evidence by re-examining the image (zooming, cropping, or applying a claim-specific intervention) under a bounded compute budget. We make two observations. First, acquisition that is plugged naively into a calibrated filter breaks the statistical guarantee – realized risk overshoots the target by up to $17$ points – because the acquisition step destroys the exchangeability that conformal calibration relies on. Second, folding the entire acquisition policy into the score function and re-calibrating on post-acquisition scores restores the finite-sample guarantee while still recovering coverage. BCEA further uses structured, claim-type-specific interventions. Across the POPE benchmark and COCO-constructed existence and spatial-relation claims, on four open VLMs, BCEA controls the hallucination rate at the target level and consistently improves coverage over a guaranteed-abstention baseline.

10.
arXiv (CS.CV) 2026-06-11

RSTR: Reducing SpatioTemporal Redundancy in Diffusion Transformers

Diffusion Transformers (DiTs) have achieved remarkable success in image generation, yet their deployment is hindered by high computational costs. We identify two sources of redundancy. First, temporal redundancy: Classifier-Free Guidance (CFG) applies costly dual forward passes at every timestep, yet guidance matters only at specific steps, and variable scales at critical steps can compensate for skipping others. Second, spatial redundancy: under variable guidance, different transformer blocks exhibit heterogeneous sensitivity, yet uniform calibration across all blocks wastes computation while failing to address their varying requirements. We present RSTR, the first framework to jointly reduce spatiotemporal redundancy in diffusion transformers. Stage-1 addresses temporal redundancy through evolutionary search, discovering sparse guidance schedules with variable scales. Stage-2 addresses spatial redundancy through adaptive rank allocation, assigning calibration capacities to transformer regions based on their sensitivity. Experiments on DiT-XL/2, PixArt-$\alpha$, FLUX, and state-of-the-art Qwen-Image demonstrate 50%-70% compute savings while maintaining or improving quality. On DiT-XL/2, RSTR achieves 57% savings with 15% FID improvement; on Qwen-Image, 3.43$\times$ speedup with preserved quality.

11.
medRxiv (Medicine) 2026-06-18

From Paper Letters to an Integrated Digital Workflow: Improving Efficiency, Reliability, and Engagement in Health Guidance

Background: Post-checkup health guidance in Japan has traditionally relied on paper-based communication and manual administrative processes. These workflows are time-consuming, prone to transcription errors, and can delay timely engagement with health guidance recipients. Objective: To assess whether replacing a paper-based workflow with an integrated digital system using Microsoft Access, robotic process automation (RPA), and web-based responses could improve administrative efficiency, operational reliability, and engagement among health guidance recipients. Methods: This single-site quality improvement initiative redesigned the existing letter-based workflow. Access served as a central interface for managing recipients and generating guidance letters. RPA (EzRobot) automated repetitive clerical and billing-related tasks. A web form accessed via a QR code enabled recipients to respond digitally. Outcomes included manual administrative handling time per case, occurrence of transcription-related errors, health guidance completion rate, and guidance duration distribution. Results: Following implementation, staff active handling time per case decreased from approximately 10 minutes to less than 1 minute (approximately 30 seconds), while automated RPA execution typically required about 4-5 minutes per case without staff input. No transcription-related errors were detected during the post-implementation observation period. Health guidance completion rates improved from 28.3% to 39.2% (chi-square test, P=200 days decreased from 30.5% to 20.9% and cases with >=240 days decreased from 13.6% to 8.9% (R4 n=59, R5 n=158). Conclusion: An integrated Access-RPA-Web workflow was associated with improvements in administrative efficiency and operational reliability in post-checkup health guidance while retaining human verification and exception handling. This pragmatic, non-AI-dependent approach may offer a useful model for process-level improvement in preventive care settings.

12.
arXiv (CS.LG) 2026-06-16

Dynestyx: A Probabilistic Programming Library for Dynamical Systems

arXiv:2606.16985v1 Announce Type: cross Abstract: State-space models (SSMs) are the standard formalism for Bayesian treatment of dynamical systems, with natural applications in statistics, signal processing, and machine learning. Despite their importance in both theory and application, dynamical systems have proven difficult to incorporate in modern probabilistic programming languages (PPLs), making state-of-the-art methods less accessible to practitioners and introducing friction in following the "Bayesian workflow." We introduce dynestyx, a probabilistic programming library with first-class support for SSMs, including state-of-the-art methods in the estimation of both states and parameters. Through a single, unified interface, users may specify arbitrary priors for discrete-time or continuous-time dynamical systems, perform inference over mixed-effect data, and make state and parameter estimates with principled uncertainty quantification.

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

Who Should Lead Decoding Now? Tracking Reliable Trajectories for Ensembling Masked Diffusion Language Models

Masked Diffusion Language Models (MDLMs) have emerged as a distinct paradigm for sequence generation. As MDLMs become diverse in capabilities and knowledge coverage, an important question is how to combine their knowledge. Toward this, we first investigate the unique decoding dynamics of MDLMs. We find that successful generations exhibit stable confidence dynamics over answer-relevant positions, while unreliable trajectories can often be corrected by injecting promising intermediate states from other models. Guided by this observation, we propose $TIE$ ($T$rajectory-based $I$terative $E$nsembling), a knowledge fusion framework in which MDLMs iteratively identify reliable decoding trajectories and relay them across models. TIE tracks confidence dynamics over answer-relevant positions to determine which model currently follows a more reliable trajectory and selectively transfers partially denoised sequences across models. As the model on the more promising trajectory often changes across denoising steps, TIE allows different models to contribute complementary strengths at different stages of generation. Strong performance across diverse reasoning tasks, along with our analyses, suggests that TIE offers a practical approach to the underexplored problem of MDLM ensembling.

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

Topological Flow Matching

arXiv:2606.15897v1 Announce Type: cross Abstract: Flow matching is a powerful generative modeling framework, valued for its simplicity and strong empirical performance. However, its standard formulation treats signals on structured spaces, such as fMRI data on brain graphs, as points in Euclidean space, overlooking the rich topological features of their domains. To address this, we introduce topological flow matching, a topology-aware generalization of flow matching. We interpret flow matching as a framework for solving a degenerate Schrödinger bridge problem and inject topological information by augmenting the reference process with a Laplacian-derived drift. This principled modification captures the structure of the underlying domain while preserving the desirable properties of flow matching: a stable, simulation-free objective and deterministic sample paths. As a result, our framework serves as a drop-in replacement for standard flow matching. We demonstrate its effectiveness on diverse structured datasets, including brain fMRIs, ocean currents, seismic events, and traffic flows.

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

Connecting Speech to Words through Images

How can we learn the mapping between written words and their spoken counterparts in the absence of explicit textual supervision? We present a visually grounded method for building a vocabulary of spoken words using only images and their spoken descriptions. First, image captioning systems are used to build a vocabulary of written words representing salient visual concepts in the images. For each word, we then find utterances whose image captions contain that word. Then we use an unsupervised word discovery technique to align these utterances to locate instances of the target word. The result is spoken word segments that are linked to written words – all accomplished without any text supervision. In spoken word retrieval and keyword spotting experiments, the proposed approach outperforms a strong neural baseline while being more interpretable. These results demonstrate the feasibility of the approach in English and motivate future work on low-resource languages without transcripts.

17.
arXiv (quant-ph) 2026-06-19

Matrix-product state skeletons in Onsager-integrable quantum chains

arXiv:2511.07212v2 Announce Type: replace Abstract: Matrix-product state (MPS) skeletons are connected networks of Hamiltonians with exact MPS ground states that underlie a phase diagram. Such skeletons have previously been found in classes of free-fermion models. For the translation-invariant BDI and AIII free-fermion classes, it has been shown that the underlying skeleton is dense, giving an analytic approach to MPS approximation of ground states anywhere in the class. In this paper, we partially expose the skeleton in certain interacting spin chains: the $N$-state Onsager-integrable chiral clock families. We construct MPS that form a dense MPS skeleton in the gapped regions surrounding a sequence of fixed-point Hamiltonians (the generators of the Onsager algebra). Outside these gapped regions, these MPS remain eigenstates, but no longer give the many-body ground state. Rather, they are ground states in particular sectors of the spectrum. Our methods also allow us to find further MPS eigenstates; these correspond to low-lying excited states within the aforementioned gapped regions. This set of MPS excited states goes beyond the previous analysis of ground states on the $N=2$ free-fermion MPS skeleton. As an application of our results, we find a closed form for the disorder parameter in a family of interacting models. Finally, we remark that many of our results use only the Onsager algebra and are not specific to the chiral clock model representation.

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

Rethinking the Pointer Loss in Table Structure Recognition: Geometry-Aware Pointer Loss for Spatial Locality

Table Structure Recognition (TSR) using a pointer network achieves impressive results by predicting HTML sequences while aligning tags to detected text (or cell) regions. However, our analysis reveals that when pointer networks fail, 79.6% of errors occur between spatially adjacent cells (Manhattan distance

19.
arXiv (CS.LG) 2026-06-17

Differential Privacy of Gaussian Process Posterior Sampling

arXiv:2606.17995v1 Announce Type: cross Abstract: We study the privacy of releasing posterior sample paths from a Gaussian process (GP) when the entire training set including covariates and responses is private. Unlike standard differential-privacy (DP) mechanisms that add external noise, posterior sampling is random by construction. We show that this intrinsic randomness yields DP guarantees by deriving explicit Rényi-DP bounds for GP posterior sample-path release. The bounds separate posterior-mean leakage from data-dependent posterior-covariance leakage showing that meaningful privacy depends sharply on effective ridge regularisation. We apply membership-inference attacks to show that empirical leakage follows the predicted dependence on regularisation, posterior variance and the number of released posterior sample-paths. Utility experiments on downstream posterior-sampling tasks identify noisy-observation regimes where privacy-compatible regularisation preserves useful decisions with modest utility loss. When stronger privacy is needed, the intrinsic guarantee can be sharpened by adding calibrated GP noise, providing an explicit additional privacy knob.

20.
bioRxiv (Bioinfo) 2026-06-11

Hyper3D-lite: count-preserving representation auditing for long-read multi-contact genome data

Authors:

Long-read and single-molecule sequencing technologies are rapidly increasing molecule-level data, with platforms such as Oxford Nanopore, PacBio HiFi, and Roche sequencing-by-expansion advancing at different technology readiness levels. In the specific context of Pore-C and HiPore-C multi-contact chromatin-conformation assays, long-read multi-contact 3D genome assays preserve molecule-level contact context, but common downstream pairwise projections can expand one multi-contact molecule into many pair records. This creates a representation problem: apparent contact evidence can increase through the counting frame before biological interpretation begins. Hyper3D-lite addresses this problem as a representation-first audit tool for read-to-fragment-style long-read multi-contact inputs. It compares all-pair projection with CPB, a count-preserving statistical accounting reference point, and separates broad software outputs from conservative higher-order candidate calls.

21.
bioRxiv (Bioinfo) 2026-06-16

Super Learner Ensemble Modeling of CPTAC Proteomic Data for Survival Prediction in Head and Neck Squamous Cell Carcinoma

Survival analysis in head and neck squamous cell carcinoma (HNSCC) is traditionally performed using Cox proportional hazards models, alongside some exploration into black-box machine learning methods. The Super Learner (SL) algorithm addresses this model selection dilemma by combining diverse candidate algorithms into a weighted ensemble to perform comparably to the best candidate method. This study evaluates the performance of SL in HNSCC. Proteomic features as well as clinical covariates from 96 CPTAC HNSCC samples were modeled with three candidate algorithms (Cox LASSO, Cox Ridge, and Random Survival Forest) as well as the ensemble SL method. Models were optimized via Uno's time-dependent Concordance Index (C-index) and tested at 1- and 3-year time horizons using 2000 bootstrap resamples. The Cox Ridge regression model achieved the highest predictive accuracy among the four total methods. However, the SL demonstrated stable performance over both time horizons (1-year C-index: 0.985; 3-year C-index: 0.960). Variable importance analysis of the Cox Ridge model successfully identified malignant proteins (ATR, MAML1, MIEN1) alongside novel potential prognostic indicators (ZNF800, KERA). This analysis emphasizes the statistical necessity for larger cohorts for ensemble learning, while providing a benchmark of proteomic indicators in HNSCC.

22.
arXiv (CS.CV) 2026-06-17

Attention Sinks in Diffusion Transformers: A Causal Analysis

Attention sinks – tokens that receive disproportionate attention mass – are assumed to be functionally important in autoregressive language models, but their role in diffusion transformers remains unclear. We present a causal analysis in text-to-image diffusion, dynamically identifying dominant attention recipients per timestep and suppressing them via paired, training-free interventions on the score and value paths. Across 553 GenEval prompts on Stable Diffusion~3 (with SDXL corroboration), removing these sinks does not degrade text-image alignment (CLIP-T) or preference proxies (ImageReward, HPS-v2) at $k{=}1$; only under stronger interventions ($k\!\geq\!10$) does HPS-v2 exhibit a metric-dependent boundary, while CLIP-T remains robust throughout. The perceptual shifts induced by suppression are nonetheless sink-specific – $\sim\!6\times$ larger than equal-budget random masking – revealing an empirical dissociation between trajectory-level perturbation and semantic alignment in diffusion transformers. \footnote{Code available at https://github.com/wfz666/ICML26-attention-sink.}

23.
arXiv (CS.CV) 2026-06-17

Universal Image Restoration via Internalized Chain-of-Thought Reasoning

Image restoration seeks to recover high-quality images from degraded inputs but becomes highly ill-posed under complex, mixed degradations. While unified all-in-one models are common, their performance declines as degradation complexity increases. Recent works adopt Chain-of-Thought (CoT) reasoning for multi-round restoration using specialized modules. However, this approach faces two key limitations: (i) increased computational cost due to multi-step processing, and (ii) weak modeling of interactions between degradations during stepwise inference. We introduce CoTIR, a universal image restoration framework that internalizes CoT reasoning within a single model. Concretely, we view image restoration as a specialized subtask of image editing, which implies that a large-scale pre-trained editing model provides a more favorable optimization starting point. Building on this, we fine-tune the model for restoration and further encode structured CoT-style reasoning into the learning objective via a differentiable formulation inspired by Lagrangian optimization, enabling holistic restoration without chaining specialized restorers. To facilitate training and evaluation, we further present CoTIR-Bench, a large-scale benchmark comprising 5.2 million samples with CoT-style reasoning traces. Extensive experiments on CoTIR-Bench and broad real composite degradation scenes show that CoTIR achieves stronger perceptual quality and more competitive fidelity than both all-in-one models and multi-round restoration methods. The source code is available at https://github.com/gy65896/CoTIR.

24.
arXiv (CS.LG) 2026-06-19

Multi-Task Bayesian In-Context Learning

arXiv:2606.20538v1 Announce Type: new Abstract: Bayesian predictive inference provides a principled framework for uncertainty quantification, data efficiency, and robust generalization. However, exact inference is often intractable, and scalable approximations may remain computationally expensive or require restrictive modeling assumptions that degrade predictive performance. Prior-Data Fitted and in-context models have recently emerged as an amortized alternative by learning to map datasets directly to predictive distributions, but existing approaches are tightly coupled to the support of the training prior and lack explicit mechanisms for adapting to new priors at test time, resulting in limited robustness under distribution shift. We introduce a multi-task in-context learning framework for amortized hierarchical Bayesian predictive inference that explicitly represents prior information as a prefix of in-context datasets. A transformer trained on sequences of prior and target tasks learns to adapt its predictions across families of priors. On a suite of evaluations with increasing difficulty, including out-of-meta-distribution priors and priors with high-dimensional latent structures, our method matches oracle Bayesian predictors while being orders of magnitude faster. We further demonstrate its practical relevance on a real-world spatiotemporal temperature prediction benchmark. Code is available at https://github.com/martianmartina/multi-task-bayesian-icl/.

25.
Science (Express) 2026-04-16

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science

Authors: Unknown Author

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.