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01.
medRxiv (Medicine) 2026-06-22

Disentangling adiposity-related and non-adiposity-related genetic pathways for type 2 diabetes

作者:
Su↗C.-Y↗Lu↗

OBJECTIVE To identify circulating proteins associated with type 2 diabetes (T2D) risk through pathways not fully explained by body mass index (BMI), and to assess therapeutic actionability. RESEARCH DESIGN AND METHODS We applied GWAS-by-subtraction within a genomic structural equation model to European ancestry summary statistics for T2D (74,124 cases, 824,006 controls) and BMI (n = 681,275), partitioning T2D liability into BMI-related and BMI-subtracted components. We then performed proteome-wide Mendelian randomization (MR) using cis-protein quantitative trait loci from four plasma proteomics cohorts: ARIC, deCODE, Fenland, and the UK Biobank Pharma Proteomics Project. Prioritized proteins passed sensitivity analyses with alternative MR methods and were supported by colocalization evidence. Tissue-resolution regulatory support was assessed using cis-eQTL colocalization across GTEx and pancreatic islet, subcutaneous adipose, and whole-blood resources. Actionability was evaluated using the druggable genome and Open Targets. RESULTS GWAS-by-subtraction attenuated the genetic correlation between BMI and BMI-subtracted T2D from 0.54 (SE 0.02) to 0.35 (SE 0.02). Proteome-wide MR prioritized 29 proteins for BMI-subtracted T2D. Thirteen showed eQTL colocalization in at least one tissue, implicating liver and intermediary metabolism (GCDH, NOTCH2), pancreatic islet biology (CTRB2, MANBA), adipose and Wnt signaling (RSPO3, GALNT3), and whole blood regulatory signals (PAM, SNUPN). Sixteen proteins were classified within druggable-genome Tiers 1-3, and five had existing Open Targets compounds. CONCLUSIONS Integrating GWAS-by-subtraction, proteome-wide MR, and colocalization nominated 29 proteins associated with T2D liability not fully explained by BMI. These findings highlight genetically supported targets for follow-up studies of T2D therapies that complement weight-centered approaches.

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02.
bioRxiv (Bioinfo) 2026-06-10

APOSM: Pairwise preference learning improves generative small-molecule design

作者:
Dreisler↗M. W↗Michael↗Hatzakis↗N. S↗Boomsma↗

Small-molecule lead refinement is constrained by the cost of synthesizing and assaying candidates, making the surrogate models that prioritize compounds for experimental testing central to the design process. The reliability of such surrogates is limited by the noise and sparsity of screening measurements. We show that training the surrogate on pairwise comparisons between candidate molecules, rather than on absolute predicted scores, yields a substantially more reliable signal for active candidate selection in this regime. We develop APOSM, an active-learning algorithm that combines a fragment-based generator, a pairwise message-passing graph neural network surrogate, and probabilistic ranking inside a batched acquisition loop. On the Practical Molecular Optimization benchmark and a GPCR ligand rediscovery task, APOSM improves target attainment and sampling efficiency over unguided fragment-based optimization, the Graph-GA genetic algorithm, and a pointwise-regression ablation, with the largest gains on tasks where absolute scores are hardest to calibrate.

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03.
arXiv (CS.CL) 2026-06-18

DSB: Dynamic Sliding Block Scheduling for Diffusion LLMs

作者:
Lizhuo Luo↗Shenggui Li↗Yonggang Wen↗Tianwei Zhang↗

Diffusion large language models (dLLMs) have emerged as a promising alternative for text generation, distinguished by their native support for parallel decoding. In practice, block inference is crucial for avoiding order misalignment in global bidirectional decoding and improving output quality. However, the widely-used fixed, predefined block (naive) schedule is agnostic to semantic difficulty, making it a suboptimal strategy for both quality and efficiency: it can force premature commitments to uncertain positions while delaying easy positions near block boundaries. In this work, we analyze the limitations of naive block scheduling and disclose the importance of dynamically adapting the schedule to semantic difficulty for reliable and efficient inference. Motivated by this, we propose Dynamic Sliding Block (DSB), a training-free block scheduling method that uses a sliding block with a dynamic size to overcome the rigidity of the naive block. To further improve efficiency, we introduce DSB Cache, a training-free KV-cache mechanism tailored to DSB. Extensive experiments across multiple models and benchmarks demonstrate that DSB, together with DSB Cache, consistently improves both generation quality and inference efficiency for dLLMs. Code is released at https://github.com/lizhuo-luo/DSB.

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

Training-Free Metrics for Synthetic Object Detection Data: A Proxy for Detector Performance

作者:
Myeongseok Nam↗Donghoon Yeo↗Seungwook Kim↗

With the recent advent of image generative models, synthetic data are increasingly being used to supplement limited real datasets for training computer vision models. However, not all synthetic datasets improve performance equally, and their effectiveness can only be assessed by training a downstream model, which is computationally expensive and time-consuming. This problem is pronounced in the task of object detection, where the required annotations are much more dense due to bounding boxes. In this paper, we propose a pre-computable metric family, dubbed Conditional-Composition Domain Match (CCDM), which serves as a proxy for the relative utility of candidate synthetic training sets for downstream detection. Experiments on the VisDrone-DET dataset show that the CCDM metric families achieve a Spearman correlation of 1.0 with the downstream performance of YOLOv8, clearly outperforming existing metrics for synthetic image evaluation.

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

Periodic-MAE: Periodic Video Masked Autoencoder for rPPG Estimation

作者:
Jiho Choi↗Sang Jun Lee↗

In this paper, we propose Periodic-MAE, a self-supervised framework for learning generalizable spatio-temporal representations of periodic physiological signals from unlabeled facial videos. The proposed method leverages a masked autoencoder (MAE), which learns high-dimensional facial representations by reconstructing masked video tokens without relying on remote photoplethysmography (rPPG) specific supervision. To explicitly align representation learning with the characteristics of rPPG, we introduce a periodicity-aware frame masking strategy based on video resampling, enabling the encoder to learn representations that capture quasi-periodic temporal patterns relevant to pulse signal estimation. In addition, physiological bandlimit constraints are integrated into the MAE pre-training framework, exploiting the sparsity of pulse signals in the frequency domain to guide the learned representations toward physiologically meaningful patterns. After pre-training, the learned representations are transferred to downstream rPPG estimation, where the encoder serves as a generic feature extractor for recovering pulse-related signals from facial videos. We conduct extensive experiments on four benchmark datasets, including PURE, UBFC-rPPG, MMPD, and V4V. Moreover, we evaluate the proposed approach on a real-world rPPG dataset collected under unconstrained lighting conditions and subject motion. Experimental results demonstrate that Periodic-MAE consistently improves rPPG estimation performance, particularly in challenging cross-dataset and real-world evaluation settings. Our code is available at https://github.com/ziiho08/Periodic-MAE.

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

AudioX-Turbo: A Unified Framework for Efficient Anything-to-Audio Generation

作者:
Zeyue Tian↗Lei Ke↗Zhaoyang Liu↗Ruibin Yuan↗Liumeng Xue↗Yujiu Yang↗Weijia Chen↗Xu Tan↗Qifeng Chen↗Wei Xue↗Yike Guo↗

Audio and music generation based on flexible multimodal control signals is a widely applicable topic, with the following key challenges: 1) a unified multimodal modeling framework, 2) large-scale, high-quality training data, and 3) the prohibitive inference cost of multi-step diffusion sampling. As such, we propose AudioX-Turbo, a unified and efficient framework for anything-to-audio generation that integrates varied multimodal conditions (i.e., text, video, and audio signals) in this work. AudioX-Turbo follows a teacher-student paradigm. The teacher AudioX-Base is built on a Multimodal Diffusion Transformer with a Multimodal Adaptive Fusion module that aligns diverse multimodal inputs for high-fidelity synthesis, and is then distilled into the few-step student AudioX-Turbo via Distribution Matching Distillation adapted to flow matching, complemented by a diffusion-based discriminator for high-quality few-step generation. To support the training of AudioX-Turbo, we construct a large-scale, high-quality dataset, IF-caps-Pro, comprising approximately 9.2M samples curated through a two-stage data collection and annotation pipeline. We benchmark AudioX-Turbo across a wide range of tasks, finding that our model achieves superior performance, especially on text-to-audio and text-to-music generation, while operating at only 4 sampling steps and requiring approximately 25x fewer function evaluations (NFE) than multi-step baselines. These results demonstrate that our method is capable of audio generation under flexible multimodal control, showing efficient and powerful instruction-following capabilities. The code and datasets will be available at https://zeyuet.github.io/AudioX-Turbo/.

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07.
arXiv (CS.CL) 2026-06-16

RASST: Retrieval-Augmented Simultaneous Speech Translation

作者:
Jiaxuan Luo↗Siqi Ouyang↗Jiaxing Xu↗Lei Li↗

Simultaneous speech translation produces target text incrementally from partial speech input. Recent speech large language models have markedly improved SST quality but still struggle with rare and domain-specific terminology. Retrieval augmentation has helped in automatic speech recognition and neural machine translation, but extending it to SST is non-trivial: retrieval must be fast and accurate under partial speech, and the model must decide whether and when to apply retrieved terms during incremental generation. We propose Retrieval-Augmented Simultaneous Speech Translation (RASST), which addresses both challenges. For accurate cross-modal retrieval under partial input, RASST trains a lightweight speech-text retriever that produces chunkwise terminology hints for the Speech LLM via multi-scale retrieval. To use these hints correctly, we synthesize training data that teaches the Speech LLM to decide whether and when to apply each retrieved term. Experiments on ACL 60/60 dev set and the ESO test set show that RASST improves terminology accuracy by nearly 40% and overall translation quality by up to 3 BLEU points, with negligible computational overhead.

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08.
arXiv (CS.LG) 2026-06-17

Robust Local Polynomial Regression with Similarity Kernels

作者:
Yaniv Shulman↗

arXiv:2501.10729v3 Announce Type: replace-cross Abstract: Local Polynomial Regression (LPR) is a widely used nonparametric method for modeling complex relationships due to its flexibility and simplicity. It estimates a regression function by fitting low-degree polynomials to localized subsets of the data, weighted by proximity. However, traditional LPR is sensitive to outliers and high-leverage points, which can significantly affect estimation accuracy. This paper revisits the kernel function used to compute regression weights and proposes a novel framework that incorporates both predictor and response variables in the weighting mechanism. The focus of this work is a conditional density kernel that robustly estimates weights by mitigating the influence of outliers through localized density estimation. The proposed method is implemented in Python and is publicly available at https://github.com/yaniv-shulman/rsklpr. The population analysis quantifies the bias induced by density-based robust weighting, and the reported experiments show lower empirical bias than iterative robust LOWESS while remaining competitive with standard LOWESS. This advancement provides a promising extension to traditional LPR, opening new possibilities for robust regression applications.

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09.
Nature (Science) 2026-06-08

Fifty years since a simple equation described the chaos of biology

作者:
Michael P. H. Stumpf↗

An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics. An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics.

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

Latent Confounded Causal Discovery via Lie Bracket Geometry

作者:
Sridhar Mahadevan↗

arXiv:2606.19610v1 Announce Type: cross Abstract: Recent work on Kan-Do-Calculus (KDC) has established that the boundary between passive observation and active intervention in causal inference is a category-theoretic bi-adjunction, with interventions modeled by left Kan extensions and conditioning by right Kan extensions. This paper introduces two causal discovery algorithms under latent confounding, building on the information-geometric and categorical consequences of KDC. In smooth statistical settings, Radon-Nikodym derivatives between observational and interventional measures induce local causal vector fields; failures of these fields to close under Lie brackets become computable Frobenius residuals, which we interpret as witnesses of failed visible integrability and possible latent or unmodeled structure. Our first algorithm, BRIDGE (Bracket Residuals for Interventional Discovery and Geometric Estimation), combines an interventional density or Radon-Nikodym-ratio engine with a geometric screen that proposes a high-recall family of admissible arrows, identifies non-closing visible pairs as latent-obstruction candidates, and passes the reduced family to downstream score-based or differentiable discovery routines. The second algorithmic contribution, Spectral Kan-Do Flow Matching (SKFM), learns amortized intervention fields and factors latent curvature spectrally, exposing the direct Lie-space endpoint toward which BRIDGE points. A detailed set of experiments show that both algorithms are capable of discovering causal models with latent confounders while collapsing the super-exponential space of possible DAGs by many orders of magnitude. This paper introduces a new paradigm in causal discovery, where latent structure is inferred directly from the geometry of intervention-induced flows.

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

Neural Tree Reconstruction for the Open Forest Observatory

作者:
Marissa Ramirez de Chanlatte↗Arjun Rewari↗Trevor Darrell↗Derek J. N. Young↗

The Open Forest Observatory (OFO) is a collaboration across universities and other partners to make low-cost forest mapping accessible to ecologists, land managers, and the general public. The OFO is building both a database of geospatial forest data as well as open-source methods and tools for forest mapping by uncrewed aerial vehicle. Such data are useful for a variety of climate applications including prioritizing reforestation efforts, informing wildfire hazard reduction, and monitoring carbon sequestration. In the current iteration of the OFO's forest map database, 3D tree maps are created using classical structure-from-motion techniques. This approach is prone to artifacts, lacks detail, and has particular difficulty on the forest floor where the input data (overhead imagery) has limited visibility. These reconstruction errors can potentially propagate to the downstream scientific tasks (e.g. a wildfire simulation.) Advances in 3D reconstruction, including methods like Neural Radiance Fields (NeRF), produce higher quality results that are more robust to sparse views and support data-driven priors. We explore ways to incorporate NeRFs into the OFO dataset, outline future work to support even more state-of-the-art 3D vision models, and describe the importance of high-quality 3D reconstructions for forestry applications.

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

Libra: Efficient Resource Management for Agentic RL Post-Training

作者:
Kaiwen Chen↗Xin Tan↗Jingzong Li↗Hong Xu↗

arXiv:2606.03077v2 Announce Type: replace-cross Abstract: Reinforcement learning (RL) has emerged as a standard post-training paradigm for shaping large language models (LLMs) into capable agents. In agentic RL, the rollout stage generates trajectories while invoking tools, producing long-tailed and non-stationary workloads that expose two fundamental challenges in resource management. First, due to the long-tail distribution, a small fraction of trajectories dominates rollout makespan. Second, rollout and training are subject to cross-stage imbalance, as they exhibit strong asymmetry in compute patterns, memory demands, and sensitivity to sequence length. Compounding this asymmetry, the sequence length distribution drifts continuously as the policy evolves, rendering any static resource split progressively suboptimal. We present Libra, a resource management system to address both challenges via two core mechanisms. The first is a global resource planner that jointly optimizes GPU allocation across rollout and training clusters. It leverages an elastic hybrid pool to enable lightweight, non-blocking worker reallocation between stages. The second is a causality-driven multi-level feedback queue (C-MLFQ) scheduler, which routes requests to heterogeneous rollout buckets based on causal signals derived from tool-return outcomes, rather than relying on fragile length predictions. Evaluated on 48 A800 GPUs, Libra achieves up to 3.0x higher throughput and converges up to 2.5x faster in reward compared to the baselines.

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

SceneCraft: Interactive System for Image Editing via Scene Graph

作者:
Duc-Manh Phan↗Ngoc-Dai Tran↗Duy-Khang Do↗Tam V. Nguyen↗Minh-Triet Tran↗Trung-Nghia Le↗

Recent advances in generative AI have enabled natural language-driven image editing, yet existing systems often fail in complex scenes with multiple interacting objects because they rely heavily on users crafting precise text prompts. To address the absence of structured control, we propose SceneCraft, a novel interactive framework that bridges user intent and model execution by representing images as editable scene graphs. Instead of guessing text prompts through trial and error, users interact directly with a visual graph to perform complex spatial and relational operations. These graph modifications are automatically translated into precise, context-aware editing prompts, effectively eliminating linguistic ambiguity. To ensure robust and diverse results, structured prompts are dispatched to multiple state-of-the-art generative models. Evaluations across diverse editing scenarios show that SceneCraft provides a more intuitive control mechanism, significantly reducing the cognitive burden of manual prompt engineering while generating outputs that users consistently rate as higher in quality and fidelity.

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14.
arXiv (quant-ph) 2026-06-16

Quantifying Coherence-to-Entanglement Conversion Efficiency under Noisy Operations

作者:
Asad Ali↗H. Kuniyil↗M. I. Hussain↗M. T. Rahim↗Abdallah Slaoui↗Saif Al-Kuwari↗

arXiv:2606.16916v1 Announce Type: new Abstract: We investigate the noise-limited conversion of local quantum coherence into bipartite entanglement in a minimal two-qubit protocol comprising a coherent single-qubit input, an incoherent ancilla, an ideal CNOT operation, and subsequent environmental noise. Employing the $l_1$-norm of coherence and the entanglement negativity as resource quantifiers, we establish an exact closed-form correspondence between local single-qubit input coherence and the two-qubit entanglement generated in the noiseless limit, showing that the output negativity is precisely one half of the initial $l_1$-coherence. We then derive analytic expressions for the surviving entanglement and the associated coherence-to-entanglement conversion efficiency under two representative noise mechanisms: independent phase damping and global two-qubit depolarizing noise. The two channels exhibit qualitatively distinct degradation behavior. Phase damping induces a universal multiplicative suppression of the generated entanglement, yielding a coherence-independent conversion efficiency and no finite-noise entanglement sudden death. In contrast, global depolarization introduces an isotropic mixing contribution that shifts the partial-transpose spectrum, producing coherence-dependent degradation and a finite sudden-death threshold. We show that maximally coherent inputs not only maximize the entanglement generated by the CNOT protocol but also optimize its robustness against depolarizing noise. Direct density-matrix simulations validate the analytic results to numerical precision. These findings provide a compact analytic benchmark for assessing how different noise mechanisms constrain coherence-to-entanglement conversion in elementary quantum-information protocols and near-term quantum devices.

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

Anti-causal domain generalization: Leveraging unlabeled data

作者:
Sorawit Saengkyongam↗Juan L. Gamella↗Andrew C. Miller↗Jonas Peters↗Nicolai Meinshausen↗Christina Heinze-Deml↗

arXiv:2602.17187v2 Announce Type: replace-cross Abstract: The problem of domain generalization concerns learning predictive models that are robust to distribution shifts when deployed in new, previously unseen environments. Existing methods typically require labeled data from multiple training environments, limiting their applicability when labeled data are scarce. In this work, we study domain generalization in an anti-causal setting, where the outcome causes the observed covariates. Under this structure, environment perturbations that affect the covariates do not propagate to the outcome, which motivates regularizing the model's sensitivity to these perturbations. Crucially, estimating these perturbation directions does not require labels, enabling us to leverage unlabeled data from multiple environments. We propose two methods that penalize the model's sensitivity to variations in the mean and covariance of the covariates across environments, respectively, and prove that these methods have worst-case optimality guarantees under certain classes of environments. Finally, we demonstrate the empirical performance of our approach on a controlled physical system and a physiological signal dataset.

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16.
arXiv (CS.AI) 2026-06-17

Brep2Shape: Boundary and Shape Representation Alignment via Self-Supervised Transformers

作者:
Yuanxu Sun↗Yuezhou Ma↗Haixu Wu↗Guanyang Zeng↗Muye Chen↗Jianmin Wang↗Mingsheng Long↗

arXiv:2602.07429v2 Announce Type: replace-cross Abstract: Boundary representation (B-rep) is the industry standard for computer-aided design (CAD). While deep learning shows promise in processing B-rep models, existing methods suffer from a representation gap: continuous approaches offer analytical precision but are visually abstract, whereas discrete methods provide intuitive clarity at the expense of geometric precision. To bridge this gap, we introduce Brep2Shape, a novel self-supervised pre-training method designed to align abstract boundary representations with intuitive shape representations. Our method employs a geometry-aware task where the model learns to predict dense spatial points from parametric Bézier control points, enabling the network to better understand physical manifolds derived from abstract coefficients. To enhance this alignment, we propose a Dual Transformer backbone with parallel streams that independently encode surface and curve tokens to capture their distinct geometric properties. Moreover, the topology attention is integrated to model the interdependencies between surfaces and curves, thereby maintaining topological consistency. Experimental results demonstrate that Brep2Shape offers significant scalability, achieving state-of-the-art accuracy and faster convergence across various downstream tasks.Code is available at this repository: https://github.com/thuml/Brep2Shape.

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

ParaScale: Scale-Calibrated Camera-Motion Transfer via a Gauge-Invariant Parallax Number

作者:
Zijie Meng↗

arXiv:2606.19805v1 Announce Type: cross Abstract: Transferring the camera motion of a reference video to a freshly generated one lets creators reuse cinematic moves. Yet reference and target often live at incompatible scales – a sweep across a galaxy versus a nudge across a desk – and naively reusing the recovered trajectory yields either imperceptible or violently exaggerated motion. We trace this to a geometric fact: translation-induced image motion scales as ||T||/Z, so a monocular trajectory is meaningful only up to a depth-scale gauge. We distill this into the Parallax Number Pi = ||Delta T|| / Zbar, a dimensionless, gauge-invariant descriptor of how strongly a camera move is felt, and prove that it – not the raw trajectory – is the quantity that scale-faithful transfer must preserve. ParaScale is a plug-and-play module that reads Pi off any reference video and re-realizes it against the target scene's own depth, per frame, leaving rotation untouched. Sitting between pose extraction and pose injection, it requires no retraining and drops into any pose-conditioned generator. We further introduce the Parallax Consistency Error (PCE), a scale-symmetric metric that – unlike the similarity-aligned TransErr – exposes scene-scale mismatch. Across scale regimes spanning four orders of magnitude and multiple backbones, ParaScale keeps the realized parallax on the identity line and cuts PCE by more than 3x over uncalibrated transfer with no loss of visual fidelity.

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18.
arXiv (CS.AI) 2026-06-17

Towards Leveraging AutoML for Sustainable Deep Learning: A Multi-Objective HPO Approach on Deep Shift Neural Networks

作者:
Leona Hennig↗Tanja Tornede↗Marius Lindauer↗

arXiv:2404.01965v3 Announce Type: replace-cross Abstract: Deep Learning (DL) has advanced various fields by extracting complex patterns from large datasets. However, the computational demands of DL models pose environmental and resource challenges. Deep shift neural networks (DSNNs) offer a solution by leveraging shift operations to reduce computational complexity at inference. Following the insights from standard DNNs, we are interested in leveraging the full potential of DSNNs by means of AutoML techniques. We study the impact of hyperparameter optimization (HPO) to maximize DSNN performance while minimizing resource consumption. Since this combines multi-objective (MO) optimization with accuracy and energy consumption as potentially complementary objectives, we propose to combine state-of-the-art multi-fidelity (MF) HPO with multi-objective optimization. Experimental results demonstrate the effectiveness of our approach, resulting in models with over 80\% in accuracy and low computational cost. Overall, our method accelerates efficient model development while enabling sustainable AI applications.

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19.
Nature (Science) 2026-06-09

Scientists have a bad case of AI FOMO, <i>Nature</i> poll reveals

作者:
Mohana Basu↗

Almost half of the scientists who responded said that they feel broadly negative towards artificial intelligence, but they think that some tools are better than others. Almost half of the scientists who responded said that they feel broadly negative towards artificial intelligence, but they think that some tools are better than others.

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

How far have we gone in Generative Image Restoration? A study on its capability, limitations and evaluation practices

作者:
Xiang Yin↗Jinfan Hu↗Zhiyuan You↗Kainan Yan↗Yu Tang↗Chao Dong↗Jinjin Gu↗

Generative Image Restoration (GIR) has achieved impressive perceptual realism, but how far have its practical capabilities truly advanced compared with previous methods? To answer this, we present a large-scale study grounded in a new multi-dimensional evaluation pipeline that assesses models on detail, sharpness, semantic correctness, and overall quality. Our analysis covers diverse architectures, including diffusion-based, GAN-based, PSNR-oriented, and general-purpose generation models, revealing critical performance disparities. Furthermore, our analysis uncovers a key evolution in failure modes that signifies a paradigm shift for the perception-oriented low-level vision field. The central challenge is evolving from the previous problem of detail scarcity (under-generation) to the new frontier of detail quality and semantic control (preventing over-generation). We also leverage our benchmark to train a new IQA model that better aligns with human perceptual judgments. Ultimately, this work provides a systematic study of modern generative image restoration models, offering crucial insights that redefine our understanding of their true state and chart a course for future development.

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21.
bioRxiv (Bioinfo) 2026-06-10

Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins

作者:
Orr↗A. K↗Bateman↗

Motivation: Spurious protein sequences, resulting from gene prediction errors, theoretically should not yield folded structures. AlphaFold2 was previously shown to predict short spurious sequences with high pLDDT scores and was therefore unlikely to distinguish between real proteins and spurious proteins which are usually short. We evaluate whether newer structure prediction methods (ESMFold and AlphaFold3) similarly predict short sequences with high pLDDT or if they better discriminate between spurious and real proteins. Results: All three structure prediction methods (ESMFold, AlphaFold2, and AlphaFold3) predict short spurious sequences from AntiFam with unexpectedly high pLDDT scores, however the discrimination between spurious and real proteins improves beyond 100 amino acids. By analysing sequences with disparate pTM and pLDDT scores, we identified two likely spurious shadow ORFs in Swiss-Prot and one potentially non-spurious AntiFam entry. Using the structure prediction scores, we developed a Gaussian Process Model and evaluated its performance on AlphaFold DB, identifying potential spurious proteins at scale. While limited on its own, this model can increase confidence in spurious protein identification when combined with other methods.

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

Parameter-Efficient Adaptation of SAM 3 for Automated ITV Generation from 4DCT Images

作者:
Changwoo Song↗

Four-dimensional computed tomography (4DCT) captures the full respiratory cycle of thoracic anatomy, yet current Internal Target Volume contouring workflows process each phase in isolation, discarding temporal coherence and leaving contours vulnerable to phase-specific artifacts. We present a lightweight framework that applies parameter-efficient fine-tuning to the Segment Anything Model 3 (SAM 3) via low-rank adaptation (LoRA) to align its text-prompted segmentation with the medical domain using only seven annotated 3D CT volumes. Furthermore, the framework incorporates a hard negative mining strategy to improve boundary discrimination in low-contrast thoracic regions. At inference, phase-wise predictions are refined through phase-coherent temporal filtering and spatial connectivity analysis. Since respiratory motion is continuous and periodic, genuine anatomy appears in contiguous blocks of phases, whereas transient artifacts appear sporadically and are thus effectively suppressed. Experiments on pulmonary and cardiac structures yield median Dice scores of 0.968 and 0.910 with 95th-percentile Hausdorff distances of 0.998 mm and 2.931 mm, respectively. The proposed framework effectively eliminates the severe false-positive predictions inherent in the zero-shot inference of the unadapted SAM 3. With only seven annotated volumes, the framework retains over 95% of full-data accuracy, and the entire pipeline is trainable on a single consumer-grade GPU, demonstrating a scalable, data-efficient solution for adaptive radiotherapy.

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24.
arXiv (CS.CL) 2026-06-18

RECOM: A Validity Discrimination Tradeoff in Automatic Metrics for Open Ended Reddit Question Answering

作者:
Pushwitha Krishnappa↗Amit Das↗Vinija Jain↗Aman Chadha↗Tathagata Mukherjee↗

Automatic metrics are the default for evaluating LLM-generated text, yet a metric is quietly asked to do two jobs: tell genuine content alignment from surface coincidence (validity), and tell a better system from a worse one (discriminative power). On open-ended, opinion-driven question answering, the two are in tension. We introduce RECOM (Reddit Evaluation for Correspondence of Models), a contamination-free evaluation dataset of 15,000 r/AskReddit questions (September 2025), each paired with its authentic community replies, which postdate every evaluated model's training cutoff. Scoring five open-source LLMs (7–10B) against every reply each metric paired with a random-derangement noise floor we find that no metric does both jobs well. Cosine similarity separates real from random answers (Cohen's $d \approx 2$) but cannot rank the five models ($|d| < 0.1$); BERTScore precision appears to rank the models (raw $|d|$ up to 0.63), but once response length is controlled this collapses to $|d| = 0.09$ and its validity is weak ($d \approx 0.8$, versus cosine's $\approx 2$). Because every metric scores the same outputs, this validity–discrimination tradeoff is a property of the metrics, not the models, and we argue it stems from representation design. Three independent LLM judges reproduce the validity gap and likewise separate the five models only weakly. We recommend reporting metrics on both axes, with an explicit random-baseline floor. RECOM is publicly available at https://anonymous.4open.science/r/recom-D4B0

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25.
arXiv (CS.LG) 2026-06-19

Spectral Retrieval-Augmented Time-Series Forecasting

作者:
Huu Hiep Nguyen↗Minh Hoang Nguyen↗Dung Nguyen↗Hung Le↗

arXiv:2606.19412v1 Announce Type: new Abstract: Time series forecasting leverages historical patterns to predict future values, but traditional methods face challenges when dealing with complex, non-stationary patterns that are difficult to memorize during training. Retrieval-augmented approaches have emerged as promising solutions by retrieving similar historical patterns to enhance predictions. However, existing retrieval methods suffer from two fundamental limitations: spectral blindness, which overlooks critical frequency-domain characteristics that capture underlying periodic structures, and temporal recency, which treats all historical data equally without emphasizing recent, more relevant patterns. In this paper, we propose SpecReTF, a novel retrieval method that addresses these issues by converting time series into windowed frequency representations, measuring similarity with a combined metric that captures both amplitude and phase information. To balance recency and historical context, we apply an exponential moving average weighting scheme that emphasizes recent windows. Extensive experiments on benchmark datasets demonstrate that SpecReTF outperforms time-domain retrieval methods, achieving superior forecasting accuracy across diverse, non-stationary time series.

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