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01.
bioRxiv (Bioinfo) 2026-06-10

HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues

Cellular heterogeneity is a major confounder in bulk DNA methylation data for epigenome-wide association studies. Existing reference-based DNAm deconvolution methods often ignore hierarchies among related cell types and may generalize poorly across datasets due to limited variability in reference profiles. We developed HOMED (Hierarchically Optimized Methylation Deconvolution), a framework that integrates cell-lineage hierarchies, single-cell RNA sequencing-guided deconvolution, and paired bulk RNA-seq/DNAm data for CpG signature optimization. Across simulated and real peripheral blood mononuclear cell, lung, and placental datasets, HOMED consistently yielded the highest PCCs and lowest RMSEs, outperforming existing scRNA-seq-guided DNAm deconvolution methods, improving accuracy, resolution, and cross-tissue generalizability.

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

InfoPO: Information-Driven Policy Optimization for User-Centric Agents

arXiv:2603.00656v2 Announce Type: replace Abstract: Real-world user requests to LLM agents are often underspecified. Agents must interact to acquire missing information and make correct downstream decisions. However, current multi-turn GRPO-based methods often rely on trajectory-level reward computation, which leads to credit assignment problems and insufficient advantage signals within rollout groups. A feasible approach is to identify valuable interaction turns at a fine granularity to drive more targeted learning. To address this, we introduce InfoPO (Information-Driven Policy Optimization), which frames multi-turn interaction as a process of active uncertainty reduction and computes an information-gain reward that credits turns whose feedback measurably changes the agent's subsequent action distribution compared to a masked-feedback counterfactual. It then combines this signal with task outcomes via an adaptive variance-gated fusion to identify information importance while maintaining task-oriented goal direction. Across diverse tasks, including intent clarification, collaborative coding, and tool-augmented decision making, InfoPO consistently outperforms prompting and multi-turn RL baselines. It also demonstrates robustness under user simulator shifts and generalizes effectively to environment-interactive tasks. Overall, InfoPO provides a principled and scalable mechanism for optimizing complex agent-user collaboration. Code is available at https://github.com/kfq20/InfoPO.

03.
arXiv (CS.CV) 2026-06-17

Do We Really Need Diffusion? A Fast U-Net for Paired Medical Image Translation

Magnetic resonance imaging-signal fat fraction (MRI-SFF) quantifies tissue fat and serves as an established biomarker for metabolic and musculoskeletal disorders. The acquisition requires, however, specialized MRI sequences, which are not available routinely. We investigate whether SFF can be estimated from widely available T2-weighted (T2w) MRI via image-to-image translation (I2I). We further compare a lightweight 4-level U-Net to a state-of-the-art Denoising Diffusion Probabilistic Model (DDPM) using a dataset of 230 048 paired 2D images (183 517 train, 23 621 val, 22 910 test) from the German National Cohort (NAKO). Both models clearly outperform the identity baseline (Pearson correlation r = 0.769, mean absolute error MAE = 0.070 +/- 0.054), which confirms that the models learn a non-trivial cross-modal mapping. Interestingly, the lightweight U-Net outperforms the DDPM in both correlation (r = 0.975 vs. 0.962) and error (MAE = 0.014 +/- 0.015 vs. 0.019 +/- 0.019), while reducing inference time by a factor of 208 (25.2 ms vs. 5 227.2 ms per image using 50 Denoising Diffusion Implicit Model (DDIM) steps). The strong clinical performance at substantially reduced computational cost enables real-time clinical use.

04.
arXiv (CS.LG) 2026-06-12

Disentangling Dynamical Systems: Causal Representation Learning Meets Local Sparse Attention

arXiv:2603.14483v2 Announce Type: replace Abstract: Parametric system identification methods estimate the parameters of explicitly defined physical systems from data. Yet, they remain constrained by the need to provide an explicit function space, typically through a predefined library of candidate functions chosen via available domain knowledge. In contrast, deep learning can demonstrably model systems of broad complexity with high fidelity, but black-box function approximation typically fails to yield explicit descriptive or disentangled representations revealing the structure of a system. We develop a novel identifiability theorem, leveraging causal representation learning, to uncover disentangled representations of system parameters without structural assumptions. We derive a graphical criterion specifying when system parameters can be uniquely disentangled from raw trajectory data, up to permutation and diffeomorphism. Crucially, our analysis demonstrates that global causal structures provide a lower bound on the disentanglement guarantees achievable when considering local state-dependent causal structures. We instantiate system parameter identification as a variational inference problem, leveraging a sparsity-regularised transformer to uncover state-dependent causal structures. We empirically validate our approach across four synthetic domains, demonstrating its ability to recover highly disentangled representations that baselines fail to recover. Corroborating our theoretical analysis, our results confirm that enforcing local causal structure is often necessary for full identifiability.

05.
arXiv (math.PR) 2026-06-24

A Pathwise Approach to the Strong Feller Property and Irreducibility of Nonlinear Branching Processes

arXiv:2606.24821v1 Announce Type: new Abstract: We study the strong Feller property and irreducibility for continuous-state nonlinear branching processes defined as solutions to stochastic differential equations with jumps. Due to boundary degeneracy and discontinuous jump coefficients, classical methods do not apply. We develop a pathwise approach combining state-dependent time change, truncated auxiliary processes, and localized coupling to establish these two properties. As applications, we obtain exponential convergence to a unique quasi-stationary distribution in the absorbing case, and uniform exponential ergodicity in the non-absorbing case. This pathwise approach is flexible and can be adapted to a broader class of jump-diffusions without relying on specific coefficient structures.

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

Variational Inference via Entropic Transport Descent

arXiv:2606.25265v1 Announce Type: new Abstract: Particle-based variational inference (ParVI) methods approximate an intractable target distribution by evolving an ensemble of interacting samples. Existing approaches rely predominantly on kernel-based repulsion (e.g., SVGD), which suffers from variance collapse in high dimensions and mode collapse on multimodal targets – pathologies caused by the absence of global transport structure. We introduce entropic transport descent (ETD), a ParVI family that frames each particle update as an entropy-regularized optimal transport problem. Derived from the JKO proximal scheme by lifting to the space of couplings and relaxing via the KL chain rule, each ETD iteration reduces to a Sinkhorn computation. The resulting transport plan provides global coordination, guiding each particle to nearby high-density proposals and naturally preserving multimodal structure. ETD can operate entirely score-free, requiring only pointwise evaluations of the unnormalized target density. Experiments on variance-collapse diagnostics, Bayesian logistic regression, neural networks, and molecular Boltzmann distributions show that ETD matches or outperforms SVGD, AGF-SVGD, and SGLD, with the largest gains in high-dimensional and multimodal settings.

07.
arXiv (CS.AI) 2026-06-18

Beyond Safe Data: Pretraining-Stage Alignment with Regular Safety Reflection

arXiv:2606.19168v1 Announce Type: new Abstract: To achieve deeper safety alignment for large language models (LLMs), recent efforts have studied how to push safety interventions earlier into the pretraining stage, primarily by filtering unsafe data or rewriting it into safer forms. We argue that pretraining-stage alignment should go beyond making the data safe: LLMs may compose seemingly benign knowledge and capabilities into unsafe behaviors. To this end, we propose Safety Reflection Pretraining, a pretraining-stage alignment method which regularly inserts short safety reflections into pretraining corpora to integrate self-monitoring directly into language modeling, establishing a foundational capability that is subsequently reinforced by compatible post-training. Our experiments with 1.7B models pretrained on FineWeb-Edu show that Safety Reflection Pretraining improves safety classification accuracy and substantially reduces the success rates of inference-stage and finetuning attacks. Complementary to our real-world experiments, we also introduce a fully controlled synthetic environment, MedSafetyWorld, with a clear definition of safety and a reasoning structure under which models can easily generalize unsafe behaviors from safe data. Ablations in MedSafetyWorld further demonstrate a clear advantage of Safety Reflection Pretraining in preventing models from acting on unsafe behaviors generalized from safe data, compared with data filtering and rewriting. Taken together, our findings suggest that pretraining alignment should not only make the training data safe, but also shape the behaviors that models are likely to acquire from safe data.

08.
arXiv (CS.LG) 2026-06-25

The Gentle Collapse: Distributional Metrics for Continual Learning

arXiv:2606.25165v1 Announce Type: new Abstract: Accuracy degradation is the standard metric for Catastrophic Forgetting (CF), however, it records only whether forgetting occurred or not. It saturates at the extremes and collapses discretely at task boundaries, hiding the internal structure of what is being forgotten. We introduce six softmax-derived metrics spanning true-label rank (TLR), predictive confidence, and distributional divergence that characterize forgetting continuously, each normalized to [0, 1] with no modification to training. On CIFAR-100, these metrics carry information where accuracy does not: at 0% accuracy, the Confusion Margin spans an IQR of [0.32, 0.50] across classes that accuracy treats identically. We demonstrate that this richer signal is actionable in mitigating catastrophic forgetting. Per-sample metric scores used as loss weights reduce forgetting by 1.3 percentage points over uniform experience replay (ER) on CIFAR-100. Furthermore, the slope of a metric over a small window provides a stable sampling criterion: at a small-window size (e.g. 3 epochs), accuracy-trend degrades to 34.79% (std. = 2.32) while log-TLR achieves 41.07% (std. = 0.57). This gap is structural since reliable small-window trend estimation requires a continuous signal. On TinyImageNet, log-TLR trend sampling reduces forgetting by 7.7 percentage points over the ER baseline.

09.
arXiv (CS.LG) 2026-06-18

How fast can you find a good hypothesis?

arXiv:2509.03734v3 Announce Type: replace-cross Abstract: In the hypothesis selection problem, we are given sample and query access to finite set of candidate distributions (hypotheses), $\mathcal{H} = \{H_1, \ldots, H_n\}$, and samples from an unknown distribution $P$, both over a domain $\mathcal{X}$. The goal is to output a distribution $Q$ whose distance to $P$ is comparable to that of the nearest hypothesis in $\mathcal{H}$. Specifically, if the minimum distance is $\mathsf{OPT}$, we aim to output $Q$ such that, with probability at least $1-\delta$, its total variation distance to $P$ is at most $C \cdot \mathsf{OPT} + \varepsilon$. The optimal approximation for proper algorithms (where $Q \in \mathcal{H}$) is $C=3$ using $\Theta(\log(n/\delta)/\varepsilon^2)$ samples from $P$ and for improper algorithms (where $Q$ is not necessarily in $\mathcal{H}$) is $C=2$ using $\tilde{\Theta}(\log(n/\delta)/\varepsilon^2)$ samples from $P$. In the improper setting, the algorithm achieving $C=2$ [Bousquet, Braverman, Kol, Efremenko, Moran, FOCS 2021] runs in time which grows polynomially with $|\mathcal{X}|$ – it does not run in finite time for real-valued distributions. A promising path towards improved runtime is to consider improper algorithms which output a mixture $Q$ of the hypotheses as such a distribution can be represented in $n$ words of memory. We show (1) a lower bound that no algorithm which outputs a mixture can achieve approximation better than $C = 3-2/n$ unless the number of samples is polynomial in $|\mathcal{X}|$, as well as (2) an algorithm which runs in time $poly(n)$ and achieves the same approximation guarantee. In the proper setting, [Aliakbarpour, Bun, Smith, NeurIPS 2024] provided an algorithm with $C=3$ running in $\tilde{O}(n/(\delta^3\varepsilon^3))$ time. We improve this time complexity to $\tilde{O}(n/(\delta \varepsilon^2))$, significantly reducing the dependence on the confidence and error parameters.

10.
arXiv (CS.CL) 2026-06-12

Examining the Cognitive Gap Between Authors and Peer Reviewers on Academic Paper Novelty

Novelty is a crucial metric for assessing the quality of academic papers. Scholars strive to highlight the novel aspects of their work, particularly in the title, abstract, and introduction. Peer review, serving as the gatekeeper of scientific rigor, rigorously evaluates the novelty of papers, yet a cognitive gap may exist between author self-promotion and reviewer evaluation. To investigate this, we analyzed 15,328 academic papers published in Nature Communications from 2016 to 2021, along with their peer-review comments. We found that both reviewers and authors emphasize result-oriented innovation, with reviewers adopting a more comprehensive evaluation perspective. Furthermore, by examining promotional intensity against inherent paper novelty, we found that its effect depends on the paper's actual innovation level. Highly innovative papers benefit from stronger promotional language, receiving more positive evaluations. We also found that promotional language significantly correlates with reviewer disagreement on novelty specifically for papers of moderate innovativeness, whereas it has negligible impact for papers with either very high or very low novelty. This reveals how promotional language operates most prominently in the gray area of academic evaluation.

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

Dual-Uncertainty Guided Policy Learning for Multimodal Reasoning

Reinforcement learning with verifiable rewards (RLVR) has advanced reasoning capabilities in multimodal large language models. However, existing methods typically treat visual inputs as deterministic, overlooking the perceptual ambiguity inherent to the visual modality. Consequently, they fail to distinguish whether a model's uncertainty stems from complex reasoning or ambiguous perception, preventing the targeted allocation of exploration or learning signals. To address this gap, we introduce DUPL, a dual-uncertainty guided policy learning approach for multimodal RLVR that quantifies and leverages both perceptual uncertainty (via symmetric KL divergence) and output uncertainty (via policy entropy) to guide policy updates. By establishing an uncertainty-driven feedback loop and employing a dynamic branch prioritization mechanism, DUPL recalibrates the policy advantage to focus learning on states with high perceptual or decisional ambiguity, enabling effective targeted exploration beyond passive data augmentation. Evaluated on diverse multimodal reasoning benchmarks spanning mathematical and general domains, DUPL achieves solid gains. It improves Qwen2.5-VL accuracy by up to $12.3%$ (3B) and $7.9%$ (7B), and Qwen3-VL-Instruct by up to $10.7%$ (4B) and $12.4%$ (8B), consistently outperforming GRPO, while seamlessly generalizing to alternative algorithms (DAPO, $+6.5%$ avg) and architectures (LLaVA-OneVision-1.5, $+4.7%$ avg). These results demonstrate that DUPL is an effective and generalizable approach for multimodal RLVR.

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

Prior over Evidence: Stereotype-Driven Diagnosis in LLM-Based L2 Pronunciation Feedback

Large language models are increasingly deployed for written pronunciation feedback in second-language (L2) English learning, under the assumption that their diagnoses are grounded in the supplied speech evidence rather than in priors from pretraining. This assumption is tested on 1,800 L2-Arctic utterances spanning six L1 backgrounds, three audio-capable LLMs, four pronunciation dimensions, and five evidence conditions ranging from a text-only baseline to numeric acoustic features and raw audio. Each (utterance x model x condition x dimension) cell is scored on three metrics: Rating Accuracy (RA) against gold labels, Evidence Coherence (EC) assessing internal consistency without ground truth, and Grounded Correctness (GC) evaluated against gold evidence. Results show three findings across models. First, rating accuracy and grounded reasoning decouple: 39.6% of judged cells contain internally coherent reasoning that supports a wrong rating, against only 15.8% where the reasoning supports a correct rating. Second, phoneme-level feedback converges to a fixed inventory of L2-English difficulty phones that recurs across all six L1 backgrounds and all evidence conditions. Third, acoustic evidence improves the rating only when the supplied feature directly probes the target dimension: textualised F0 range raises pitch-variation grounding from (0.18-0.19) to (0.45-0.62) across all three models, while stress and phoneme correctness, which require target-to-realisation alignment, remain ungrounded. The same audio waveform without textualised F0 values does not reproduce this improvement. These findings indicate that current general-purpose LLMs are more reliable as verbalisers of externally computed pronunciation evidence than as standalone diagnostic engines.

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

From Tokens to Policy: Causal and Interpretable Heterogeneous Treatment Effects Identification

arXiv:2606.17010v1 Announce Type: new Abstract: Heterogeneous Treatment Effect (HTE) identification is crucial to explain the impact of an intervention and optimize our policies accordingly. Existing approaches trade expressivity for interpretability, but, if some active heterogeneity drivers are unmeasured, methods at both ends of this spectrum allow for spurious HTE characterization with no causal reading. In this work, we focus on controlled experiments and argue that an oracle HTE causal characterization via the latent interactors is now within reach, thanks to (i) more extensive pre-treatment measurements, i.e., multi-modal and multi-view, and (ii) scalable representations with minimal human supervision. We then re-frame HTE identification as a Markov-blanket discovery problem on a sufficient and aligned pre-treatment representation, and introduce Neural EXposure Interaction Search (NEXIS), an iterative procedure with provable and empirically validated consistent selection. We deploy NEXIS on two anti-poverty programs in Africa, augmenting each with satellite imagery capturing previously unmeasured environmental effect modifiers, leading to novel, interpretable and prescriptive guidelines to optimize the programs' next iterations.

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

Fast-dLLM++: Fr\'{e}chet Profile Decoding for Faster Diffusion LLM Inference

Diffusion large language models promise parallel token generation, yet inference remains bottlenecked by deciding which masked tokens can be safely committed together. Fast-dLLM addressed this with KV caching and confidence-guided parallel decoding, but its decoding theory uses a homogeneous high-confidence assumption that effectively reduces each candidate set to its weakest selected token. We argue that this leaves speed on the table because real decoding steps exhibit heterogeneous confidence profiles. We propose Fast-dLLM++, a training-free extension that introduces Fr\'{echet profile decoding}: selecting parallel commit sets from the full sorted confidence profile rather than a single worst-case confidence. The resulting rule is a heterogeneous-confidence generalization of Fast-dLLM's factor selector and it recovers the previous rule exactly in the equal-confidence case and adds a provable heterogeneity bonus when the selected tokens have uneven confidences. Fast-dLLM++ leaves the model, diffusion process, and cache implementation entirely unchanged, making it a drop-in replacement for existing Fast-dLLM decoding. Experiments on GSM8K, MATH, HumanEval, and MBPP with the LLaDA-8B model show that the theoretical improvement translates directly into empirical gains: profile-aware selection improves the accuracy–throughput frontier by exploiting safe parallelism that weakest-token rules miss, achieving up to 37\% higher throughput at comparable accuracy. Our code release is at https://github.com/Ringo-Star/FastdLLM_plusplus.

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

Behavioral Audit of Machine Unlearning Has a Privacy Cost

arXiv:2606.14518v1 Announce Type: new Abstract: The removal of learned data from Machine Learning models through Machine Unlearning (MU) has been widely studied; however, there has yet to be an agreed-upon scheme for auditing MU. Existing work has shown that a dishonest model owner can falsify evidence to avoid executing MU, while curious auditors (and adversaries) can infer the privacy-sensitive properties of the model and its training data even with limited access. Yet auditing of MU under mutual distrust between the model owner and the auditor remains unexplored. We provide an information-theoretic proof for this scenario: for convex ML models, a generic audit scheme that relies solely on querying the model for behavioral signals cannot identify insufficiently unlearned models without revealing membership information of the retained set. Therefore, auditing MU under the assumption of a dishonest model owner and an honest-but-curious auditor faces an inherent privacy-audit tradeoff. Our empirical results on convex models strongly supports this result, while further experiments demonstrate that this privacy-audit tension persists in non-convex models. Our results call for a more careful consideration of the privacy-audit tension under a realistic auditor threat model, and serve as a foundation for more scrutiny of designs of privacy-preserving audit schemes for the MU pipeline. We also release our code implementation at https://github.com/LiouTang/Behavioral-Unlearn-Audit.

16.
arXiv (CS.CL) 2026-06-24

Posterior Refinement: Fast Language Generation via Any-Order Flow Maps

Non-autoregressive generation offers a powerful paradigm for iterative refinement, allowing models to recursively critique, erase and regenerate arbitrary subsets of tokens. However, existing non-autoregressive models fail to realize this potential. Masked Diffusion Models (MDMs) suffer from factorization error, causing sample quality to collapse when generating multiple tokens simultaneously. Flow Map Language Models (FMLMs) circumvent this bottleneck via joint sequence transport for excellent few-step generation, but sacrifice the inference-time flexibility of MDMs. We introduce FMLM+, a framework that bridges this gap by equipping FMLM with masking-style noise schedules. While generating the full sequence in a single step, FMLM+ simultaneously scores the global consistency of each token a posteriori. We leverage this to introduce Posterior Refinement, a novel inference-time refinement strategy that enables the model to adaptively self-correct its outputs, matching the performance of discrete baselines with 32x fewer NFEs. Across diverse benchmarks, we demonstrate that FMLM+ with Posterior Refinement improves the speed–quality tradeoff over both MDM and FMLM families, providing a scalable foundation for high-fidelity language modeling.

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

PT-WNO: Point Transformer with Wavelet Neural Operator for 3D Point Cloud Semantic Segmentation

Point cloud semantic segmentation requires architectures that capture both fine-grained local geometry and broad global scene structure. Transformer-based networks have demonstrated strong performance by focusing on detailed local feature aggregation; however, global context is conveyed primarily through skip connections across encoder-decoder stages, which we argue is insufficient for full scene understanding. We hypothesize that augmenting skip connections with a learnable global feature extraction module allows the network to acquire scene-level knowledge before descending into local detail, leading to richer and more contextually grounded representations. To this end, we propose Point Transformer with Wavelet Neural Operato (PT-WNO), which integrates a shared Wavelet Neural Operator (WNO) branch alongside the skip connections of a point cloud transformer backbone. At each encoder-decoder transition, point features are projected onto a dense 3D volumetric grid where the WNO captures multi-scale global spectral context through learnable wavelet decomposition and reconstruction. These global features are fused back into the network via lightweight adapters, complementing rather than replacing the existing skip connections. Experiments on four large-scale 3D point cloud benchmarks demonstrate the effectiveness of PT-WNO. On S3DIS (Area 5), PT-WNO achieves 71.59% mIoU, outperforming the Point Transformer v3 (PTv3) baseline by +1.03 points. On DALES it achieves 81.05% mIoU (+1.47 over the baseline). On ScanNet~v2, PT-WNO obtains 76.19% mIoU, remaining competitive with the baseline (76.36%).

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

MooMIns – Monocular 3D Reconstruction and Object Pose Estimation from Multiple Instances

Simultaneous 3D reconstruction and 6D object pose estimation from a single monocular image is an inherently ill-posed problem. In industrial settings, however, multiple instances of an object are often randomly arranged in bins, implicitly providing several views of the same object within a single image. We show that this implicit multi-view geometry can be exploited to simultaneously reconstruct the object in 3D and estimate the 6D pose of each visible object instance. We present MooMIns, a new Gaussian-splatting-based approach that inverts the original Gaussian splatting formulation: instead of rendering a single scene from multiple cameras, we render multiple object instances from a single camera. Our method is initialized with SAM3 instance segmentation masks and a modified Structure from Motion (SfM) pipeline. In contrast to learned monocular depth estimation, we perform true geometry-based reconstruction from image evidence, avoiding hallucinations caused by training data priors. We evaluate MooMIns on synthetic and real bin-picking scenarios, and demonstrate accurate reconstruction of previously unseen objects as well as reliable pose estimation of individual instance

19.
PLOS Computational Biology 2026-05-29

Structural and dynamic basis of NOD2 tandem CARD association and NOD1/2–RIP2 signaling complexes

by Jitendra Maharana, Aritra Bej, Debasish Biswal, Debashis Panda, Arjun Sharma NOD1 and NOD2, founding members of the NOD-like receptor (NLR) family, play a crucial role in host defense against bacterial infections. Recognition of peptidoglycan-derived ligands triggers ATP-dependent oligomerization of the NACHT domain, exposing the CARD domains that recruit the adaptor protein RIP2 via CARD–CARD interactions to activate the NF-κB signaling cascade. Although NOD1/2-RIP2 interactions and RIP2CARD filament assembly are established, the precise interfaces that stabilize hetero–CARD filaments remain poorly defined. Here, we integrate in silico structural modeling with molecular dynamics (MD) simulations to elucidate structurally compatible arrangements of NOD1–RIP2 and NOD2–RIP2 hetero–CARD filaments. Our results reveal that NOD1CARD subunits form a structurally compatible homomeric scaffold via canonical (type-I–III) interfaces, accommodating multiple tiers of RIP2CARD rings at both filament termini. Meanwhile, the NOD2 tandem CARDs adopt multiple discrete conformations, reflecting a more intricate structural mechanism. In stable filament conformations, tandem CARDs converge at the type-II interface, with RIP2CARD rings stacking onto CARDa (top-down) and CARDb (bottom-up) interfaces, highlighting the structural role of NOD2CARDb in RIP2-mediated CARD–CARD interaction. In silico mutagenesis, involving charge-reversal and alanine scanning of key interfacial residues, disrupts NOD1–RIP2 and NOD2–RIP2 interactions at both top-down and bottom-up interfaces, leading to rapid interface destabilization within 0.1–0.4 μs of simulation. Together, these results reveal conserved and receptor-specific mechanisms governing NOD1/2–RIP2 CARD–CARD interactions and provide deeper structural and dynamic insights into the complex structural mechanisms for NLR-mediated inflammatory signaling.

20.
arXiv (CS.LG) 2026-06-25

Don't Go Breaking My LLM: The Impact of Pruning Attention Layers on Explanation Faithfulness and Confidence Calibration

arXiv:2606.24970v1 Announce Type: new Abstract: Pruning Large Language Models (LLMs) reduces memory and inference costs by removing parts of the network, producing smaller models that retain most of their accuracy. As attention layers are the most resource-intensive parts of LLMs, pruning them is a promising compression strategy. Prior work shows that up to 33% of attention layers can be pruned with minimal accuracy loss. Nevertheless, the impact of attention pruning on model interpretability, specifically faithfulness and confidence calibration, remains unstudied. To address this gap, we study how pruning attention layers affects explanation faithfulness and confidence calibration across five LLMs and eight datasets. While the pruned models often maintain high accuracy, we find that their faithfulness and calibration often degrade. Notably, faithfulness and calibration can fluctuate significantly, even when accuracy remains stable, highlighting a misalignment between model confidence, interpretability, and accuracy. Our findings suggest that layer pruning can affect LLMs' interpretability and reliability in ways not captured by accuracy and efficiency measures alone. We recommend including explainability and calibration metrics when evaluating pruned models.

21.
arXiv (CS.CV) 2026-06-24

CrossFusion: A Multi-Scale Cross-Attention Convolutional Fusion Model for Cancer Survival Prediction

Cancer survival prediction from whole slide images (WSIs) is a challenging task in computational pathology due to the large size, irregular shape, and high granularity of the WSIs. These characteristics make it difficult to capture the full spectrum of patterns, from subtle cellular abnormalities to complex tissue interactions, which are crucial for accurate prognosis. To address this, we propose CrossFusion, a novel multi-scale feature integration framework that extracts and fuses information from patches across different magnification levels. By effectively modeling both scale-specific patterns and their interactions, CrossFusion generates a rich feature set that enhances survival prediction accuracy. We validate our approach across six cancer types from public datasets, demonstrating significant improvements over existing state-of-the-art methods. Moreover, when coupled with domain-specific feature extraction backbones, our method shows further gains in prognostic performance compared to general-purpose backbones. The source code is available at: https://github.com/RustinS/CrossFusion

22.
arXiv (CS.CL) 2026-06-12

SupraBench: A Benchmark for Supramolecular Chemistry

Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications. However, designing host-guest systems remains time-consuming, requiring days of dry-lab verification per candidate pair. Although LLMs have emerged as a fast alternative with strong performance on molecular binding tasks, no benchmark currently systematically evaluates LLMs for host-guest reasoning across fundamental supramolecular chemistry tasks, e.g., binding affinity prediction. To this end, we collaborate with domain experts to release the first Supramolecular Benchmark, called SupraBench, to evaluate LLMs in chemistry reasoning. Specifically, we design four fundamental tasks, i.e., binding affinity prediction, top-binder selection, solvent identification, and host-guest description, plus an auxiliary vision-based task for molecular identification. We also release SupraPMC, a curated 16M-token corpus of Supramolecular chemistry articles distilled from Europe PMC, to support the adaptation to the supramolecular domain. We benchmark a broad range of open and proprietary LLMs and find that LLMs leave substantial headroom across all tasks. Domain adaptation pretraining over SupraPMC transfers cleanly to in-distribution regression but trades off against strict letter-format output. Moreover, the difficulty profile differs sharply across task families, revealing distinct failure modes that indicate specific gaps in current supramolecular chemistry reasoning. Our source codes and benchmark datasets are available at https://github.com/Tianyi-Billy-Ma/SupraBench.

24.
arXiv (quant-ph) 2026-06-15

Improved delta-kick cooling with multiple nonideal kicks

arXiv:2505.08413v2 Announce Type: replace Abstract: Delta-kick cooling is a technique employed to achieve low kinetic temperatures by decreasing momentum width at the cost of increased position width. In an ideal implementation, this method uses a harmonic potential to deliver a single near-instantaneous momentum kick. In practice, potentials that are approximately harmonic near their center are commonly used. As a result, the breakdown of the harmonic approximation far from the center limits the cooling performance. Inspired by aberration cancellation in optics, we propose to use compound matter-wave lens systems for $\delta-$kick cooling with Gaussian potentials. By strategically combining attractive and repulsive kicks, we show that it is possible to mimic the effect of a harmonic potential. For a test case with reasonable experimental parameters, our method suggests a reduction in kinetic temperature by a factor of $2.5$ using a 2-pulse sequence and by a factor of $3.2$ using a 3-pulse sequence.

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

Efficient Quantum Circuits for Coherent Conversion Between General First- and Second-Quantized Many-Body Representations

arXiv:2606.25029v1 Announce Type: new Abstract: Quantum simulation at fixed particle number admits two equivalent descriptions, a first-quantized (particle) representation and a second-quantized (occupation-number) representation. Their quantum resource costs differ sharply across computational tasks, so the ability to convert coherently between them is valuable. We construct an explicit unitary $Q$, with inverse $Q^\dagger$, that maps a first-quantized state to its fixed-$N$ occupation-number form while diagnosing the input's particle-exchange symmetry. The conversion is therefore symmetry-agnostic at the input yet fully resolved at the output, and it applies uniformly to bosonic, fermionic, and parastatistical sectors. At its foundation lies a structural identification that we place at the center of this work: the quantum Schur transform supplied by Schur-Weyl duality is the non-abelian Fourier transform of the commuting pair $(S_N,U(d))$, and the occupation-number representation is its weight basis, retaining only the labels shared by both factors, the irrep $\lambda$ and the $\mathfrak{u}(d)$ weight. This reduction is lossless for bosons and fermions, while a canonical Gelfand-Tsetlin promise renders it one-to-one for the remaining sectors. Algorithmically, $Q$ composes the strong Schur transform with reversible arithmetic that computes occupations as successive row-sum differences of the Gelfand-Tsetlin pattern, yielding gate complexity $\mathrm{poly}(N,d,\log(1/\epsilon))$. The converted state is prepared efficiently in quantum memory. Any classical algorithm that outputs it explicitly, however, pays a cost set by the sector dimension, which is polynomial of degree $N$ in $d$ at fixed $N$ and exponential in $N$ when $d=\Theta(N)$. Finally, an efficient classical sampler for the induced occupation-number distribution would yield one for arbitrary quantum circuits, contrary to standard complexity assumptions.