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

Mask-Proof: An LLM-based Automated Data Curation Pipeline on Mathematical Proofs

arXiv:2606.15258v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly capable of mathematical problem solving and can even assist with research-level proofs, yet we still lack a scalable and reproducible way to measure step-level reasoning in long proofs across diverse sources. This evaluation gap limits trustworthy AI assistance in proof-certified scientific progress. Existing evaluations often emphasize final answers or rely on costly expert grading, while end-to-end proof generation remains open-ended and hard to verify automatically. We introduce Mask-Proof, a pipeline that turns real proofs into automatically checkable masked-step tasks. It masks key formula steps, provides the necessary surrounding context, and evaluates model reconstructions with an LLM-based equivalence judge using repeated votes for stability. The resulting Mask-ProofBench contains 292 curated problems across diverse research areas. Experiments with 17 models show that reasoning-enhanced models outperform standard models by 12% to 27%. Our evaluator achieves 96.8% agreement with expert annotators, enabling faithful, reproducible, and comparable measurement of step-level mathematical reasoning. Benchmark, annotations, and code are available at https://github.com/weating/Mask-Proof.

02.
arXiv (CS.AI) 2026-06-18

Mechanism-Guided Selective Unlearning for RLVR-Induced Reasoning

arXiv:2606.19222v1 Announce Type: cross Abstract: We propose MAST (Mechanism-Aligned Selective Targeting), a mechanism-guided method for unlearning RLVR-induced reasoning with substantially lower collateral damage than standard full-parameter updates. In matched SFT/RLVR checkpoints on Qwen2.5-Math-1.5B and Qwen3-1.7B-Base, the SFT-to-RLVR increment differs sharply from the SFT update in token-level delta-log-probability, and full-parameter gradient ascent forgets only by damaging retain MATH and GSM8K. MAST ranks attention-projection tensors by off-principal energy, update magnitude, and forget-gradient coupling magnitude, then updates only the top-ranked subset. On the primary model, MAST induces statistically significant target forgetting (MATH forget 45/150 to 37/150; McNemar p=0.0078) while preserving GSM8K (+0.8 pp) and MATH retain (-0.5 pp). The advantage reproduces across seeds, NPO/SimNPO objectives, and Qwen3, where MAST preserves GSM8K while full-parameter unlearning collapses it.

03.
arXiv (CS.CV) 2026-06-12

OccAny: Generalized Unconstrained Urban 3D Occupancy

Relying on in-domain annotations and precise sensor-rig priors, existing 3D occupancy prediction methods are limited in both scalability and out-of-domain generalization. While recent visual geometry foundation models exhibit strong generalization capabilities, they were mainly designed for general purposes and lack one or more key ingredients required for urban occupancy prediction, namely metric prediction, geometry completion in cluttered scenes and adaptation to urban scenarios. We address this gap and present OccAny, the first unconstrained urban 3D occupancy model capable of operating on out-of-domain uncalibrated scenes to predict and complete metric occupancy coupled with segmentation features. OccAny is versatile and can predict occupancy from sequential, monocular, or surround-view images. Our contributions are three-fold: (i) we propose the first generalized 3D occupancy framework with (ii) Segmentation Forcing that improves occupancy quality while enabling mask-level prediction, and (iii) a Novel View Rendering pipeline that infers novel-view geometry to enable test-time view augmentation for geometry completion. Extensive experiments demonstrate that OccAny outperforms all visual geometry baselines on 3D occupancy prediction task, while remaining competitive with in-domain self-supervised methods across three input settings on two established urban occupancy prediction datasets. Our code is available at https://github.com/valeoai/OccAny .

04.
arXiv (CS.LG) 2026-06-15

Hybrid Uncertainty Sensitivity Analysis Based on the HSIC for High-Dimensional Responses with Aleatory–Epistemic Separation

arXiv:2606.14053v1 Announce Type: cross Abstract: Quantifying the influence of hybrid aleatory and epistemic uncertainties on high-dimensional system responses remains a major challenge in global sensitivity analysis (GSA). Existing Hilbert–Schmidt Independence Criterion (HSIC)-based approaches are primarily restricted to single-output settings and lack a rigorous decomposition of heterogeneous uncertainty sources and their interactions. To address this limitation, a novel double-space tensor-product RKHS framework is proposed for sensitivity analysis under hybrid uncertainty. By constructing factorized kernels over both the latent input space and the multidimensional output space, a concurrent double Möbius inversion is derived to orthogonally decompose the global dependence measure into pure aleatory effects, pure epistemic effects, and their interaction contributions. The resulting dimension-wise sensitivity indices preserve the uncertainty attribution structure across all output dimensions. To satisfy the independence assumptions required by the decomposition, an auxiliary-variable representation based on the inverse probability integral transform is introduced, enabling the treatment of hierarchical uncertainties and Copula-induced correlations within a unified latent space. A fully vectorized single-loop implementation is further developed to avoid the computational burden of nested Monte Carlo simulation. Statistical significance and estimation uncertainty are quantified through permutation testing and Bootstrap confidence intervals. Numerical studies on a modified multi-output Ishigami function and an aerodynamic pressure-field problem demonstrate the accuracy, scalability, and practical applicability of the proposed framework.

05.
arXiv (CS.AI) 2026-06-11

Steering Where to Listen: Instruction-Based Activation Steering Redirects Temporal Attention in Large Audio-Language Models

arXiv:2606.11400v1 Announce Type: cross Abstract: Large Audio-Language Models (LALMs) excel at audio understanding but expose little about where in an audio signal they attend. We introduce instruction-based vector steering, which constructs a steering vector by contrasting activations from differently instructed prompts while keeping the audio fixed. Through a systematic probe of LALM attention, we find that - unlike standard prompting or audio-based steering - this intervention significantly redistributes the temporal attention allocated to audio tokens, concentrating it on acoustically relevant regions. We then show that this attention shift is behaviorally meaningful: in a controlled three-event setting, reading out the temporal position of maximal steering-induced attention change recovers the location of a queried sound event without any training, attaining 60.87% and 68.72% overlap with ground-truth intervals on Qwen2-Audio and Audio Flamingo 3, far above direct prompting (31.84%, 46.75%) and random baselines (27.74%). Our results characterize a mechanistic property of instruction-based steering in LALMs and provide a training-free probe for the latent temporal structure these models encode.

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

DiagFlowBench: Evaluating How Language Models Handle Off-Procedure Inputs in Grounded Diagnostic Dialogue

arXiv:2606.17904v1 Announce Type: new Abstract: Language models increasingly serve as advisory systems in maintenance operations. To prevent hallucination, recent systems ground these models in procedural documentation to constrain them to approved steps. In practice, however, operator queries frequently stray from this path, requiring models to recognise out-of-scope inputs mid-conversation, a dynamic that current benchmarks rarely prioritise. We introduce DiagFlowBench, a dataset of 50 industrial diagnostic flowcharts from a consumer manufacturer converted into 1,676 multi-turn conversations that contrast compliant with out-of-scope utterances. Evaluating a panel of ten commercial and open-weight models reveals high variability in abstention rates, with models commonly selecting a real but contextually inadequate step rather than fabricating facts. The inherent plausibility and authority of this mapped but wrong advice exposes a challenging vulnerability for grounding systems.

07.
arXiv (CS.LG) 2026-06-12

Self-Guidance: Enhancing Neural Codecs via Decoder Manifold Alignment

arXiv:2606.12940v1 Announce Type: cross Abstract: Neural speech codecs based on Vector-Quantized VAEs (VQ-VAEs) are core audio tokenizers for speech LLMs, yet their reconstruction fidelity is bottlenecked by quantization error. Modifying the quantizer or increasing model capacity are common fixes, but they complicate downstream language modeling. Our core idea is to align the decoder's internal feature manifolds when processing both the quantized tokens and their original continuous embeddings, using a lightweight feature-mapping loss. This requires minimal training overhead and no inference-time changes. Applied to XCodec2, self-guidance improves all reconstruction metrics, achieving state-of-the-art low-bitrate performance. Notably, it enables a 4x codebook reduction without fidelity loss, which downstream TTS experiments show significantly improves LLM-based synthesis by simplifying the token modeling space. Multiple statistical observations and visualizations corroborate the enhanced internal manifold alignment in the decoder. Extensive experiments confirm its generality across various inductive biases. Self-guidance thus establishes an efficient, broadly applicable method for high-fidelity neural audio coding.

08.
arXiv (CS.LG) 2026-06-12

Uncertainty Estimation for Molecular Diffusion Models

arXiv:2606.13451v1 Announce Type: new Abstract: Diffusion models have seen wide adoption for 3D molecular generation, yet they offer no principled signal of when a generated molecule is likely to be of low quality. We propose a post-hoc method for estimating per-sample uncertainty in pretrained molecular diffusion models. Building on a Laplace approximation of the denoising network, we measure the variability of the noise prediction across the generation trajectory. Empirically, we show that the resulting uncertainty score is informative of sample quality, exhibiting a negative correlation with established sample-level quality metrics. We further study how the proposed uncertainty score can be used to filter generated samples, improving model performance via test-time scaling.

09.
bioRxiv (Bioinfo) 2026-06-22

Drug-Prot: A query system for statistical inference of drug effects and interactions in dynamic proteomic networks

Understanding drug effects and drug-drug interactions is essential for developing combination therapies. We present Drug-Prot, a computational framework that leverages large-scale perturbation proteomics to quantify causal drug effects, drug-drug interactions, and dynamic protein relationships. Using data from 63 single drugs and 59 drug combinations applied to 18 breast cancer cell lines at 6, 24, and 48 hours, Drug-Prot estimates drug effects on protein expression and reconstructs directed temporal protein dependency networks. The publicly available software enables targeted analyses of user-defined protein sets, substantially reducing the multiple-testing burden. Through an interactive web application, users obtain corrected p-values for single-drug and combination effects, directed temporal dependency networks, and downloadable results without requiring access to the underlying proteomic dataset. As a use case, we apply invariance-regularized Random Forests to triple-negative breast cancer cell lines to identify proteins associated with drug response. Querying these proteins in Drug-Prot reveals drug-specific and interaction effects at the protein-network level, illustrating how the framework links candidate causal protein features to actionable drug combinations.

10.
arXiv (CS.CV) 2026-06-18

SuperCarver: Texture-Consistent 3D Geometry Super-Resolution for High-Fidelity Surface Detail Generation

Conventional production workflow of high-precision mesh assets necessitates a cumbersome and laborious process of manual sculpting by specialized 3D artists/modelers. The recent years have witnessed remarkable advances in AI-empowered 3D content creation for generating plausible structures and intricate appearances from images or text prompts. However, synthesizing realistic surface details still poses great challenges, and enhancing the geometry fidelity of existing lower-quality 3D meshes (instead of image/text-to-3D generation) remains an open problem. In this paper, we introduce SuperCarver, a 3D geometry super-resolution pipeline for supplementing texture-consistent surface details onto a given coarse mesh. We start by rendering the original textured mesh into the image domain from multiple viewpoints. To achieve detail boosting, we construct a deterministic prior-guided normal diffusion model, which is fine-tuned on a carefully curated dataset of paired detail-lacking and detail-rich normal map renderings. To update mesh surfaces from potentially imperfect normal map predictions, we design a noise-resistant inverse rendering scheme through deformable distance field. Experiments demonstrate that our SuperCarver is capable of generating realistic and expressive surface details depicted by the actual texture appearance, making it a powerful tool to both upgrade historical low-quality 3D assets and reduce the workload of sculpting high-poly meshes.

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

On the Addressability Problem on CSS Codes

arXiv:2502.13889v4 Announce Type: replace Abstract: Recent discoveries in asymptotically good quantum codes have intensified research on their application in quantum computation and fault-tolerant operations. This study focuses on the addressability problem within CSS codes: we ask what circuits might implement logical gates on strict subsets of logical qubits. With some notion of fault-tolerance, we prove several impossibility results: for CSS codes with non-zero rate, one cannot address a logical $H$, $HS$, $SH$, or $\mathsf{CNOT}$ to any non-empty strict subset of logical qubits using a circuit made only from 1-local Clifford gates. Furthermore, we show that one cannot permute the logical qubits in a code purely by permuting the physical qubits, if the rate of the code is (asymptotically) greater than 1/3 and the distance is at least 3. We can show a similar no-go result for $\mathsf{CNOT}$s and $\mathsf{CZ}$s between two such high-rate codes, albeit under a more restrictive assumption on the circuit, which we call "global" (though recent addressable CCZ gates use global circuits). This work pioneers the study of distance-preserving addressability in quantum codes, mainly by considering automorphisms of the code. This perspective offers new insights and potential directions for future research. We argue that studying this trade off between addressability and efficiency of the codes is essential to understand better how to do efficient quantum computation.

12.
arXiv (CS.CV) 2026-06-11

ReMoT: Reinforcement Learning with Motion Contrast Triplets

We present ReMoT, a unified training paradigm to systematically address the fundamental shortcomings of VLMs in spatio-temporal consistency – a critical failure point in navigation, robotics, and autonomous driving. ReMoT integrates two core components: (1) A rule-based automatic framework that generates ReMoT-16K, a large-scale (16.5K triplets) motion-contrast dataset derived from video meta-annotations, surpassing costly manual or model-based generation. (2) Group Relative Policy Optimization, which we empirically validate yields optimal performance and data efficiency for learning this contrastive reasoning, far exceeding standard Supervised Fine-Tuning. We also construct the first benchmark for fine-grained motion contrast triplets to measure a VLM's discrimination of subtle motion attributes (e.g., opposing directions). The resulting model achieves state-of-the-art performance on our new benchmark and multiple standard VLM benchmarks, culminating in a remarkable 25.1% performance leap on spatio-temporal reasoning tasks.

13.
arXiv (math.PR) 2026-06-19

Critical parameters of germ-monotone families of branching random walks

arXiv:2602.21062v2 Announce Type: replace Abstract: We introduce a broad class of families of branching random walks on a countable set $X$, which we refer to as germ-monotone branching random walks (GMBRWs). The processes in each family are parametrized by a positive parameter $\lambda>0$, which controls the overall reproductive speed, and they are monotonically increasing in $\lambda$ with respect to the germ order, a notion that extends classical stochastic domination. This framework encompasses a wide range of models, including classical continuous-time branching random walks, as well as discrete-time counterparts of certain non-Markovian processes such as ageing branching random walks. We define a general notion of critical parameter $\lambda(A)$ associated with each subset $A \subseteq X$, which serves as a threshold separating almost sure extinction in $A$ from positive probability of survival in $A$. This unifies and extends the classical global and local critical parameters $\lambda_w$ and $\lambda_s$, which can be recovered as special cases. We then investigate how modifications of the reproduction laws, either on a finite set or on a more general subset of $X$, affect these critical parameters. Our results extend earlier contributions in the literature.

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

Meta-Learning Transformers to Improve In-Context Generalization

arXiv:2507.05019v2 Announce Type: replace-cross Abstract: In-context learning enables transformer models to generalize to new tasks based solely on input prompts, without any need for weight updates. However, existing training paradigms typically rely on large, unstructured datasets that are costly to store, difficult to evaluate for quality and balance, and pose privacy and ethical concerns due to the inclusion of sensitive information. Motivated by these limitations and risks, we propose an alternative training strategy where we leverage a collection of multiple, small-scale, and domain-specific datasets. We empirically demonstrate that the increased quality and diversity of such data improve the generalization abilities of in-context learners beyond their training domain, while achieving comparable performance with models trained on a single large-scale dataset. We investigate this paradigm by leveraging meta-learning to train an in-context learner on the Meta-Album collection under several settings. Firstly, we show the performance in a controlled environment, where the test domain is completely excluded from the training knowledge. Secondly, we explore the robustness of these models to forgetting in a continual scenario where the information is accessible for a limited time. Finally, we explore the more challenging unsupervised scenario. Our findings demonstrate that transformers still generalize for in-context prediction when trained on a curated dataset collection while offering advantages in modularity and replaceability.

15.
arXiv (CS.LG) 2026-06-18

Toward Simultaneously Optimal Regret in U-Calibration

arXiv:2606.18527v1 Announce Type: cross Abstract: U-calibration studies online forecasting algorithms whose predictions can be consumed by any unknown downstream agent, guaranteeing sublinear regret simultaneously for all proper loss functions. Existing U-calibration algorithms achieve worst-case optimal $O(\sqrt{T})$ regret for every bounded proper loss, but they fail to adapt to easier losses: as we show, even for smooth losses such as squared loss, they incur $\Omega(\sqrt{T})$ regret instead of the optimal $O(\log T)$ regret. In this work, we show that this limitation is not inherent. Specifically, we design a single forecast algorithm that simultaneously achieves $\tilde O(\sqrt{T})$ regret for every bounded proper loss and $O(\log T)$ regret for every bounded smooth proper loss. More generally, our algorithm also attains logarithmic regret for losses that are smooth relative to the log-barrier, which include several non-Lipschitz examples. Our approach is based on a novel variant of Follow-the-Perturbed-Leader (FTPL) in which perturbations are applied directly in the prediction space using self-concordant noise. The resulting analysis also departs substantially from prior FTPL analyses due to the complex nature of this noise and may be of independent interest.

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

Learning to Share: Selective Memory for Efficient Parallel Agentic Systems

arXiv:2602.05965v2 Announce Type: replace-cross Abstract: Agentic systems solve complex tasks by coordinating multiple agents that iteratively reason, invoke tools, and exchange intermediate results. To improve robustness and solution quality, recent approaches deploy multiple agent teams running in parallel to explore diverse reasoning trajectories. However, parallel execution comes at a significant computational cost: when different teams independently reason about similar sub-problems or execute analogous steps, they repeatedly perform substantial overlapping computation. To address these limitations, in this paper, we propose Learning to Share (LTS), a learned shared-memory mechanism for parallel agentic frameworks that enables selective cross-team information reuse while controlling context growth. LTS introduces a global memory bank accessible to all teams and a lightweight controller that decides whether intermediate agent steps should be added to memory or not. The controller is trained using stepwise reinforcement learning with usage-aware credit assignment, allowing it to identify information that is globally useful across parallel executions. Experiments on the AssistantBench and GAIA benchmarks show that LTS significantly reduces overall runtime while matching or improving task performance compared to memory-free parallel baselines, demonstrating that learned memory admission is an effective strategy for improving the efficiency of parallel agentic systems. Project page: https://joefioresi718.github.io/LTS_webpage/

17.
arXiv (quant-ph) 2026-06-12

Symmetry and Topology of Monitored Quantum Dynamics

arXiv:2412.06133v4 Announce Type: replace-cross Abstract: The interplay between unitary dynamics and quantum measurements induces diverse phenomena in open quantum systems with no counterparts in closed quantum systems at equilibrium. Here, we generally classify Kraus operators and their effective non-Hermitian dynamical generators, thereby establishing the tenfold classification for symmetry and topology of monitored free fermions. Our classification elucidates the role of topology in measurement-induced phase transitions and identifies potential topological terms in the corresponding nonlinear sigma models. Furthermore, we establish the bulk-boundary correspondence in monitored quantum dynamics: nontrivial topology in spacetime manifests itself as topologically nontrivial steady states and gapless boundary states in Lyapunov spectra, such as Lyapunov zero modes and chiral edge modes, leading to the topologically protected slowdown of dynamical purification.

18.
arXiv (quant-ph) 2026-06-15

Efficient Simulation of Szegedy Quantum Walk Formulations and Algorithms

arXiv:2606.14226v1 Announce Type: new Abstract: Quantum walks provide a versatile framework for quantum algorithms across a wide range of applications. We develop efficient classical simulation methods for Szegedy quantum walks that avoid explicit construction of the full unitary evolution operator. Unlike previous approaches restricted to a particular walk formulation, our framework is built from fundamental update and reflection operators, enabling the simulation of a broader class of Szegedy walk formulations. We further extend these methods to phase-estimation-based algorithms coupled to the walk, including implementations suitable for large sparse graphs. The resulting methods achieve optimal $O(N^2)$ complexity for dense graphs with $N$ nodes. For sparse graphs, the computational cost scales linearly with the number of edges, which is $O(N)$ in many cases. We implement the framework in the Python package SQWLib and illustrate its capabilities through simulations of representative algorithms, including quantum simulated annealing and quantum search on graphs. These results provide a practical tool for studying Szegedy-walk-based algorithms numerically beyond purely analytical treatments.

19.
medRxiv (Medicine) 2026-06-15

VarEx: A Large Language Model Pipeline for Automated Extraction of Exposures, Outcomes, and Covariates from Epidemiologic Studies

Objective: Observational studies are essential for investigating risk factors for Alzheimer's disease and related dementias (ADRD), but inconsistent reporting and selection of covariates can contribute to residual confounding, omitted-variable bias, and reduced reproducibility. We developed and evaluated VAREX (Variable Extraction), a large language model (LLM)-based information extraction framework designed to automatically identify exposures, outcomes, and covariates from epidemiologic studies and populate structured evidence repositories. Materials and Methods: VAREX combines retrieval-augmented generation, biomedical language-model embeddings, semantic chunking, cross-encoder reranking, and prompt-engineered LLM workflows to extract epidemiologic variables from full-text biomedical articles. The framework was evaluated using a reference-standard corpus of observational studies examining blood pressure variability (BPV) and Alzheimer's disease-related dementias (ADRD), together with external validation datasets involving other exposure-outcome relationships. Extracted variables were compared with independently curated human reference standards using semantic matching and one-to-one assignment procedures. Covariates were additionally classified into ten epidemiologically relevant semantic categories. Results: In the primary BPV[->]ADRD corpus (10 studies), VAREX achieved a precision of 0.91, recall of 0.84, and F1-score of 0.87 for variable extraction. Covariate classification accuracy was 0.90, yielding a strict extraction-and-classification F1-score of 0.78. External validation datasets demonstrated comparable performance across diverse epidemiologic domains, with extraction F1-scores ranging from 0.73 to 0.85. Category-level performance was strongest for health behaviors (F1=0.96), sociodemographic variables (F1=0.90), and medication exposures (F1=0.89). Compared with published estimates of manual systematic-review effort, VAREX reduced processing time from approximately 61 minutes to 9 minutes per article, representing an 85.7% reduction in review time. Discussion: These findings demonstrate that LLM-based information extraction can accurately identify and classify epidemiologic variables across heterogeneous observational-study designs. Automated extraction enables scalable construction of structured repositories of exposures, outcomes, and covariates while substantially reducing the labor required for evidence synthesis and systematic reviews. Conclusion: VAREX provides an effective framework for automated extraction and classification of epidemiologic variables from the biomedical literature. By supporting large-scale evidence synthesis and structured knowledge resource development, VAREX may facilitate more rigorous observational research, improved confounder identification, and enhanced reproducibility in epidemiology.

20.
arXiv (CS.LG) 2026-06-16

Robust Transformer-Based One-Step Stock Index Forecasting via Shifted Data Augmentation

arXiv:2606.15701v1 Announce Type: new Abstract: Transformers have shown remarkable success in sequence modeling, yet their direct application to financial time series remains challenging due to noisy signals, short-memory dynamics, and distributional shifts. This paper proposes a modified Transformer architecture for one-step stock index forecasting, combined with advanced learning-rate scheduling and a novel Shifted Data Augmentation (SDA) technique. We evaluate the proposed framework on two benchmark stock index datasets, VN30 and S&P 500. Experimental results demonstrate that cosine annealing with warmup consistently improves forecasting accuracy over the generalized inverse-power scheduler. Furthermore, SDA substantially reduces forecasting errors and run-to-run variability while improving robustness to hyperparameter selection. The combination of cosine annealing scheduling and SDA achieved the best performance on both datasets, indicating that data augmentation can play a more important role than increasing model complexity in Transformer-based financial forecasting. These findings provide a practical and computationally efficient approach for robust stock index forecasting in noisy financial environments.

21.
PLOS Medicine 2026-05-14

Antibody fine specificity correlates with protection from malaria for the RTS,S vaccine in young African children: A post hoc analysis of a phase IIb randomised controlled trial

作者:

by Alessia Hysa, D. Herbert Opi, Joshua Waterhouse, Sandra Chishimba, Jessica L. Horton, Natalie Kingston, Hans J. Netter, David Wetzel, Michael Piontek, Gaoqian Feng, Jahit Sacarlal, Carlota Dobaño, Liriye Kurtovic, James G. Beeson Background The RTS,S/AS01 malaria vaccine was recently approved for implementation in children, but only provides modest and short-lived efficacy against malaria. RTS,S targets a portion of the Plasmodium falciparum (Pf) circumsporozoite protein (CSP), comprising the central NANP-repeat region and C-terminal domain. Mechanisms of immunity and correlates of protection for the RTS,S vaccine are not well defined, hindering progress towards generating highly effective CSP-based vaccines. Methods and findings We investigated epitope specificity and cross-reactivity of vaccine-induced antibodies to six peptides representing CSP epitopes in the N-terminal and central NANP-repeat region. We evaluated antibody reactivity in preclinical mouse vaccine studies, among CSP-specific monoclonal antibodies (mAbs), and in a large RTS,S phase IIb clinical trial in young children 1–4 years old (n = 735).The preclinical mouse vaccine studies and CSP-specific mAbs were used to initially evaluate IgG responses to the six peptides. Mice immunised with the central NANP-repeat region had IgG with cross-reactivity to an epitope in the N-terminal region. Additionally, we demonstrated that a single CSP-specific mAb could display cross-reactivity to several CSP epitopes. Through post hoc quantification and analysis of antibody responses in the RTS,S phase IIb clinical trial, we found that a subset of children generated IgG with specificity for a short NANP-repeat epitope (NANP2; amino acid sequence: NANPNANP) and cross-reactivity to an N-terminal epitope (J1; amino acid sequence: KQPADGNPDPNANPN). Notably, children with high IgG responses to NANP2 and J1 had a significantly reduced risk of clinical malaria, compared to children with low responses (IgG to NANP2 (aHR: 0.838 (95% CI [0.716, 0.981]; p = 0.028)) and J1 (aHR: 0.718 (95% CI [0.611, 0.844]; p 

22.
arXiv (CS.AI) 2026-06-11

Improving Generalization and Data Efficiency with Diffusion in Offline Multi-agent RL

arXiv:2307.01472v2 Announce Type: replace Abstract: We present a novel Diffusion Offline Multi-agent Model (DOM2) for offline Multi-Agent Reinforcement Learning (MARL). Different from existing algorithms that rely mainly on conservatism in policy design, DOM2 enhances policy expressiveness and diversity based on diffusion model. Specifically, we incorporate a diffusion model into the policy network and propose a trajectory-based data-reweighting scheme in training. These key ingredients significantly improve algorithm robustness against environment changes and achieve significant improvements in performance, generalization and data-efficiency. Our extensive experimental results demonstrate that DOM2 outperforms existing state-of-the-art methods in all multi-agent particle and multi-agent MuJoCo environments, and generalizes significantly better to shifted environments {(in $28$ out of $30$ settings evaluated)} thanks to its high expressiveness and diversity. Moreover, DOM2 is ultra data efficient and requires no more than $5\%$ data for achieving the same performance compared to existing algorithms (a $20\times$ improvement in data efficiency).

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

ResidualPlanner+: a scalable matrix mechanism for marginals and beyond

arXiv:2305.08175v5 Announce Type: replace-cross Abstract: Noisy marginals are a common form of confidentiality protecting data release and are useful for many downstream tasks such as contingency table analysis, construction of Bayesian networks, and even synthetic data generation. Privacy mechanisms that provide unbiased noisy answers to linear queries (such as marginals) are known as matrix mechanisms. We propose ResidualPlanner and ResidualPlanner+, two highly scalable matrix mechanisms. ResidualPlanner is both optimal and scalable for answering marginal queries with Gaussian noise, while ResidualPlanner+ provides support for more general workloads, such as combinations of marginals and range queries or prefix-sum queries. ResidualPlanner can optimize for many loss functions that can be written as a convex function of marginal variances (prior work was restricted to just one predefined objective function). ResidualPlanner can optimize the accuracy of marginals in large scale settings in seconds, even when the previous state of the art (HDMM) runs out of memory. It even runs on datasets with 100 attributes in a couple of minutes. Furthermore, ResidualPlanner can efficiently compute variance/covariance values for each marginal (prior methods quickly run out of memory, even for relatively small datasets). ResidualPlanner+ provides support for more complex workloads that combine marginal and range/prefix-sum queries (e.g., a marginal on race, a range query on age, and a combined race/age tabulation that answers age range queries for each race). It even supports custom user-defined workloads on different attributes. With this added flexibility, ResidualPlanner+ is not necessarily optimal, however it is still extremely scalable and outperforms the prior state-of-the-art (HDMM) on prefix-sum queries both in terms of accuracy and speed.

24.
bioRxiv (Bioinfo) 2026-06-23

biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes

Genomic epidemiology workflows typically require expert curation of multiple specialized tools, extensive manual parameter tuning, and access to heterogeneous compute infrastructure. While standard generative AI models often hallucinate in complex biological domains, we introduce biomeStat: an autonomous AI agent that functions as a strict deterministic orchestrator. By automatically writing code to execute established bioinformatics tools in sandboxed environments, biomeStat dynamically provisions compute resources (CPU and GPU) and guarantees reproducibility, making it immediately useful for scientists without requiring command-line expertise. To demonstrate the platform, we performed a fully autonomous genomic epidemiology and structural analysis of 1,000 Dengue virus (DENV) genomes sampled from 16 Asian countries between 2000 and 2025. The agent seamlessly orchestrated phylogenetic reconstruction (IQ-TREE, TreeTime), Bayesian phylodynamics (BEAST2 via NVIDIA H200 GPU), selection pressure analysis (HyPhy), and structural mapping (PyMOL). The analysis was completed in under 24 hours of wall-clock time, revealing endemic stability (R_e ~1.0) and identifying 1,869 candidate immune escape sites structurally colocalized with B-cell and T-cell epitopes. Furthermore, the agent validated 176 highly conserved drug target residues across the viral replication complex, confirming that resistance-associated positions for emerging antivirals JNJ-1802 and NITD-688 remain absolutely conserved across all four serotypes. By bridging the gap between natural language intent and deterministic computational execution, biomeStat reduces weeks of expert effort into a single-session analysis with full methodological transparency.

25.
arXiv (CS.CV) 2026-06-16

Self-Supervised Learning as Discrete Communication

Most self-supervised learning (SSL) methods learn continuous visual representations by aligning different views of the same input, offering limited control over how information is structured across representation dimensions. In this work, we frame visual self-supervised learning as a discrete communication process between a teacher and a student network, where semantic information is transmitted through a fixed-capacity binary channel. Rather than aligning continuous features, the student predicts multi-label binary messages produced by the teacher. Discrete agreement is enforced through an element-wise binary cross-entropy objective, while a coding-rate regularization term encourages effective utilization of the constrained channel, promoting structured representations. We further show that periodically reinitializing the projection head strengthens this effect by encouraging embeddings that remain predictive across multiple discrete encodings. Extensive experiments demonstrate consistent improvements over continuous agreement baselines on image classification, retrieval, and dense visual prediction tasks, as well as under domain shift through self-supervised adaptation. Beyond backbone representations, we analyze the learned binary codes and show that they form a compact and informative discrete language, capturing semantic factors reusable across classes.