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

DriveReward: A Comprehensive Dataset and Generative Vision-Language Reward Model for Autonomous Driving

Reward models play a pivotal role in reinforcement learning (RL) and multi-modal trajectory selection for autonomous driving. However, acquiring such rewards typically relies on hand-crafted rule-based objectives or perception ground truth, which hinders generalization for data-scaling. While Vision-Language Models (VLMs) have demonstrated feasibility as reward models in other domains, their effectiveness in driving tasks remains underexplored. In this work, we bridge this gap by (1) introducing DriveReward, a reasoning trajectory evaluation dataset rigorously labeled via temporally-grounded visual guidance, and augmented with counterfactual driving behaviors., (2) alongside a specialized Vision-Language Reward Model. To address the scarcity of failure cases in conventional datasets, we propose a counterfactual data annotation scheme to construct cases encompassing diverse driving styles and erroneous behaviors. Evaluations on our proposed benchmark reveal that even leading open-source and proprietary VLMs fail to excel across all tasks, highlighting significant room for improvement in existing models. Building on these findings, we subsequently tailor a specialized 1B reward model that outperforms larger VLMs on task-specific reward alignment. Finally, we validate our reward model's effectiveness by integrating it into RL finetuning and multi-modal trajectory scoring across multiple baselines, achieving performance comparable to rule-based reward calculations in both open-loop and closed-loop evaluation.

02.
arXiv (CS.AI) 2026-06-15

GAGPO: Generalized Advantage Grouped Policy Optimization

arXiv:2605.13217v1 Announce Type: cross Abstract: Reinforcement learning has become a powerful paradigm for post-training large language model agents, yet credit assignment in multi-turn environments remains a challenge. Agents often receive sparse, trajectory-level rewards only at the end of an episode, making it difficult to determine which intermediate actions contributed to success or failure. As a result, propagating delayed outcomes back to individual decision steps without relying on costly auxiliary value models remains an open problem. We propose Generalized Advantage Grouped Policy Optimization (GAGPO), a critic-free reinforcement learning method for precise, step-aligned temporal credit assignment. GAGPO constructs a non-parametric grouped value proxy from sampled rollouts and uses it to compute TD/GAE-style temporal advantages, recursively propagating outcome supervision backward through time. Combined with group-wise advantage normalization and an action-level importance ratio, GAGPO extracts stable, localized optimization signals directly from multi-turn trajectories. Experiments on ALFWorld and WebShop show that GAGPO outperforms strong reinforcement learning baselines. Further analyses demonstrate faster early-stage learning, improved interaction efficiency, and smoother optimization dynamics, suggesting that GAGPO offers a simple yet effective framework for multi-turn agentic reinforcement learning.

03.
arXiv (CS.LG) 2026-06-16

Towards Functional Correctness of Large Code Models with Selective Generation

arXiv:2505.13553v3 Announce Type: replace-cross Abstract: The hallucination of code generation models hinders their applicability to systems requiring higher safety standards. One critical bottleneck in addressing code hallucination is the difficulty of identifying the functional correctness of generated code, due to its unnatural form. We address this core bottleneck by automatically generating unit tests using dynamic code analysis tools, leveraging the executable nature of code. Accordingly, we propose a selective code generator that abstains from uncertain generations – based on the functional correctness evaluated by generated unit tests – to theoretically control the correctness among non-abstained answers, \ie the false discovery rate. Finally, we propose to use generated unit tests in evaluation as well as in learning for precise code evaluation, calling this paradigm FuzzEval. We demonstrate the efficacy of our method along with the controllability of code hallucination and reasonable selection efficiency.

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

A Composite Activation Function for Learning Stable Binary Representations

arXiv:2605.11558v2 Announce Type: replace Abstract: Activation functions play a central role in neural networks by shaping internal representations. Recently, learning binary activation representations has attracted significant attention due to their advantages in computational and memory efficiency, as well as interpretability. However, training neural networks with Heaviside activations remains challenging, as their non-differentiability obstructs standard gradient-based optimization. In this paper, we propose Heavy Tailed Activation Function (HTAF), a smooth approximation to the Heaviside function that enables stable training with gradient-based optimization. We construct HTAF as a sigmoid hyperbolic tangent composite function and theoretically show that it maintains a large gradient mass around zero inputs while exhibiting slower gradient decay in the tail regions. We show that Spiking Neural Networks, Binary Neural Networks and Deep Heaviside neural Networks can be trained stably using HTAF with gradient-based optimization. Finally, we introduce Implicit Concept Bottleneck Models (ICBMs), an interpretable image model that leverages HTAF to induce discrete feature representations. Extensive experiments across various architectures and image datasets demonstrate that ICBM enables stable discretization while achieving prediction performance comparable to or better than standard models.

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

A Riemannian Approach to Low-Rank Optimal Transport

arXiv:2606.12120v1 Announce Type: new Abstract: Low-rank optimal transport (OT) mitigates the quadratic scaling of classical solvers, yet existing approaches rely heavily on first-order mirror-descent updates that require careful hyperparameter tuning and ignore the optimization landscape's curvature. To address these limitations, we propose a unified Riemannian geometric framework for low-rank OT, modeling balanced and unbalanced rank-$r$ positive factored couplings as novel smooth embedded submanifolds of the positive orthant. By equipping these manifolds with the Fisher-Rao product metric, we derive tractable formulations for Riemannian projectors, retractions, and Hessian-vector products. Our cost-agnostic framework seamlessly extends to linear OT, Gromov-Wasserstein (GW), fused GW, and their unbalanced counterparts. For balanced OT, our geometric ingredients are computed via efficient conjugate-gradient and iterative Bregman updates. For the unbalanced OT, our operations elegantly reduce to closed-form scalings, completely eliminating inner iterative loops. In both regimes, per-iteration complexity scales linearly with dataset size, and we provide a rank-sufficiency certificate for global optimality verification. Extensive experiments across a range of problem sizes demonstrate that our regularization-free first- and second-order solvers achieve faster convergence and superior performance over existing state-of-the-art low-rank OT solvers.

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

GRACE: Gated Refinement for Accurate Causal Edge Discovery in High-Dimensional Time Series

arXiv:2606.23880v1 Announce Type: new Abstract: From climate teleconnections to gene regulation, modern time-series datasets encompass tens or hundreds of interacting variables, making causal discovery increasingly challenging. Constraint-based methods offer statistical rigor but their nonlinear CI tests are infeasible at scale, while score-based alternatives avoid CI testing but require arbitrary thresholds to binarize continuous edge scores. We propose GRACE ($G$ated $R$efinement for $A$ccurate $C$ausal $E$dge discovery), which refines constraint-based discovery using Hard Concrete gates with $L_0$ regularization: each candidate edge has an independent gate whose values concentrate near 0 or 1, yielding a clean bimodal separation that makes the binary decision robust, unlike the narrow, overlapping score distributions produced by $L_1$ and attention-based methods. A fast linear CI skeleton provides high-recall candidates; a single gated model then prunes false positives by learning which edges genuinely improve prediction, with automatic regularization adapted to problem dimensions and skeleton density. Systematic experiments on synthetic benchmarks, spanning diverse graph topologies (scale-free, Erdős-R'enyi, small-world) and dimensionalities up to $d=100$, show that GRACE substantially improves F1 over its base CI method while maintaining high precision, and outperforms attention-based and score-based alternatives. GRACE matches or exceeds expensive nonlinear CI tests at a fraction of the cost ($75\times$ faster). On a real-world river flow dataset, where rainfall confounders, variable propagation lags, and distributional shifts violate standard assumptions, a temporal bootstrap variant of GRACE recovers 9 of 11 causal edges along the Elbe River with only 1 false positive ($F_1 = 0.86$, AUROC${} = 0.99$), reducing the skeleton's 106 false positives by 99%.

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

ATLAS: Active Theory Learning for Automated Science

arXiv:2606.12386v1 Announce Type: cross Abstract: Advancing scientific understanding through mechanistic modeling requires posing the right experimental questions to yield maximally informative data. To automate this pursuit within cognitive science, we introduce ATLAS (Active Theory Learning for Automated Science), an active learning framework for the data-driven discovery of interpretable behavioral models. ATLAS iterates between generating mechanistic hypotheses–instantiated as a diverse ensemble of sparse neural networks (Disentangled RNNs)–and designing experiments that optimally distinguish between them. We test this approach on the problem of recovering reinforcement learning agents from their behavior in bandit tasks. ATLAS designs varied sequences of qualitatively novel experiments with temporal structure tailored to underlying agent characteristics. The models trained on these experiments are evaluated against a comprehensive set of metrics for mechanistic modeling that capture behavioral, structural, and computational similarity. ATLAS achieves a 5-10x improvement in sample efficiency across all metrics compared to random experimentation, and its performance is further validated against expert-designed experiments derived from literature. These in silico results showcase ATLAS's potential to accelerate human-interpretable insights in cognitive science and other domains where scientific inquiry relies on discovering mechanistic models.

08.
arXiv (CS.LG) 2026-06-16

Auditing Machine Unlearning: A Systematic Research on Whether Models Truly Forget

arXiv:2606.16110v1 Announce Type: new Abstract: Machine unlearning has been extensively studied in response to growing privacy concerns and regulatory requirements. However, auditing whether unlearning algorithms have truly erased the influence of specific data remains an open challenge. The lack of reliable and practical auditing mechanisms can lead to critical privacy risks, such as residual information leakage. This paper initiates a systematic investigation into whether existing unlearning algorithms can truly forget the designated data. We propose the first practical and general-purpose auditing framework for machine unlearning, inspired by the concept of proof of ignorance. Our framework addresses the key practicality limitations of existing methods by eliminating the need for retraining-from-scratch baselines, avoiding the training of large numbers of shadow models, and requiring no intrusive intervention in the original training process. To evaluate the effectiveness of our framework, we first conduct validation experiments to verify its soundness and completeness. We then perform comprehensive experiments across six datasets and ten representative unlearning methods. The results demonstrate that our framework reliably distinguishes between successful and failed unlearning. In particular, we observe that retraining-based and fine-tuning-based methods can achieve effective unlearning, even when the target data remain in the original dataset. In contrast, de-optimization-based methods fail to achieve true unlearning and instead degrade the model's performance. Fisher/Hessian-based methods also fail to unlearn requested data, even formal certification is provided. Moreover, we show that our framework is robust against fake unlearning attempts and generalizes well to large language models.

09.
arXiv (CS.AI) 2026-06-19

AutoPass: Evidence-Guided LLM Agents for Compiler Performance Tuning

arXiv:2606.20373v1 Announce Type: cross Abstract: Large Language Models (LLMs) show promise for code compilation tasks, but applying them to runtime performance tuning is difficult due to complex microarchitectural effects and noisy runtime measurements. We present AutoPass, a multi-agent framework for compiler performance tuning that uses compiler and runtime evidence to guide LLM-generated optimization decisions. Rather than treating the compiler as a black box like prior auto-tuning schemes, AutoPass opens up the compiler to the LLM, enabling it to query compiler-internal optimization states and analyze the intermediate representation to orchestrate compiler options. The search process iteratively refines optimization configurations using measured runtime feedback to diagnose regressions and guide latency-improving edits. AutoPass operates in an inference-only, training-free setting and requires no offline training or task-specific fine-tuning, making it readily applicable to new benchmarks and platforms. We implement AutoPass on the LLVM compiler and evaluate it on server-grade x86-64 and embedded ARM64 systems. AutoPass outperforms expert-tuned heuristics and classical autotuning methods, achieving geometric-mean speedups of 1.043x and 1.117x over LLVM -O3 on x86-64 and ARM64, respectively.

10.
medRxiv (Medicine) 2026-06-12

Metastatic Patterns and Treatment Characteristics of Triple-Negative Breast Cancer in Nigeria: A Retrospective Cohort Study

Background: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype characterized by the absence of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression. It is associated with limited targeted treatment options, early relapse, and a high propensity for visceral metastasis. Data describing metastatic patterns and treatment characteristics of TNBC in Nigeria remain limited. Methods: This retrospective descriptive cohort study included 869 patients with TNBC managed at the Medserve-LUTH Cancer Center, Lagos University Teaching Hospital, Nigeria between June 2019 and June 2024. Demographic, clinicopathologic, metastatic, and treatment-related data were extracted from electronic medical records. Descriptive statistics were used to summarize patient characteristics, metastatic patterns, and treatment profiles. Associations between metastatic disease and selected clinicopathologic and treatment variables were explored using Pearsons chi-square test. Complete-case analysis was applied throughout. Results: The mean age at presentation was 52.09 {+/-} 12.26 years. Most patients were married (79.1%), postmenopausal (64.3%), and of Yoruba ethnicity (56.8%). Advanced disease predominated, with Stage III and Stage IV disease accounting for 42.9% and 35.6% of cases, respectively. Invasive ductal carcinoma was the most common histologic subtype (77.0%), while Grade II tumours constituted 51.3% of graded cases. Surgery was performed in 73.1% of patients, predominantly mastectomy (70.9% of surgical procedures). Chemotherapy was administered to 83.2% of patients, most commonly anthracycline-based regimens (41.8%), while radiotherapy was delivered to 63.5% of patients, with hypofractionated schedules of 42-43 Gy in 15-16 fractions accounting for 47.2% of radiotherapy courses. Metastatic disease was documented in 32.9% of evaluable patients. Lung metastasis was the most frequent site (62.5%), followed by bone (46.3%), regional lymph node invasion (38.5%), liver (23.0%), and brain (22.6%). Tumour grade and histologic subtype were not significantly associated with metastatic disease, whereas radiotherapy exposure demonstrated a significant association with metastatic status ({chi}{superscript 2} = 10.35, p = 0.001). Conclusion: TNBC in this Nigerian cohort was characterized by advanced-stage presentation, invasive ductal predominance, extensive use of multimodality treatment, and substantial visceral metastatic burden. Lung metastasis was the most common metastatic site. These findings provide contemporary real-world data on TNBC in Nigeria and highlight the continuing need for earlier diagnosis, timely referral, and sustained investment in comprehensive cancer care services.

11.
Nature (Science) 2026-06-24

Detection of anisotropic cosmic structures on a gigaparsec scale

Galaxy redshift surveys map the cosmic web and provide a key observational test of whether the Universe becomes statistically homogeneous and isotropic on sufficiently large scales, as assumed by the cosmological principle underpinning the standard cosmological model1. In this framework, beyond the nonlinear regime of structure formation, inhomogeneous and anisotropic features are expected to fade rapidly, reflecting the near-isotropic primordial density field and its subsequent gravitational evolution. Although supported by the small amplitude of cosmic microwave background anisotropies2, this view is increasingly challenged by the complex network of large-scale structures and voids in the galaxy distribution3–6, as well as by independent probes reporting possible large-scale deviations from statistical homogeneity7 and isotropy8,9. Here we show that the galaxy distribution exhibits persistent anisotropic structures extending to scales on the order of one gigaparsec. Using the Angular Distribution of Pairwise Distances (ADPD)10, a parameter-free statistic that measures directional correlations, we detect anisotropy signals exceeding those in isotropic controls and geometry-matched ΛCDM mock catalogues with conservative significance greater than 3σ. These results provide direct evidence that directional coherence persists to larger scales than predicted in the standard framework, challenging the assumption of large-scale isotropy. They call for a reassessment of how homogeneity and isotropy are realized in the observed Universe and motivate new tests of cosmological models based on directional statistics. Using the parameter-free Angular Distribution of Pairwise Distances for measuring directional correlations, evidence is found for coherent anisotropic structures extending over gigaparsec scales, challenging the assumption that the Universe becomes statistically isotropic on sufficiently large scales.

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

Code as a Weapon: A Consensus-Labeled Prompt Bank for Measuring Coding-Model Compliance with Malicious-Code Requests

A general-purpose language model that answers a harmful question returns text; a coding model that complies with a malicious request can return a working weapon: a keylogger, ransomware, an exploit that runs as written. This asymmetry in the severity of a single act of compliance implies coding-specialized models should clear a higher refusal bar than general-purpose chat models, not a lower one, yet the field cannot tell whether they do. Refusal benchmarks for malicious code are fragmented: they mix requests for executable software with requests for harmful security knowledge and report refusal rates over non-comparable corpora. This paper's central result is that the CODE-versus-KNOWLEDGE classification axis established in a prior four-corpus release remains stable under a substantially expanded corpus pool and an independently refreshed judge panel, evidence that it measures a real construct rather than an artifact of the prompts or judges. Eight corpora spanning diverse elicitation paradigms (direct, jailbreak-decorated, indirect, and agent/interpreter: ASTRA, CySecBench, AdvBench/harmful_behaviors, JailbreakBench, MalwareBench, RedCode, RMCBench, Scam2Prompt) are classified under a five-judge consensus protocol (6,675 prompts x 5 judges = 33,375 calls), reaching Fleiss' kappa = 0.767 [95% CI 0.755, 0.777] ("substantial"). Critically, the panel shares no judge with the prior release (five paid commercial APIs replaced by five open-weight models from five vendors), yet the two panels agree on 94.45% of the 3,133 shared prompts and reach Cohen's kappa = 0.952 [0.942, 0.963] on the 3,031-prompt binary overlap: the axis survives near-total panel replacement. The released bank comprises 4,748 consensus-CODE and 1,923 consensus-KNOWLEDGE prompts, a reliability-quantified benchmark whose central classification axis is shown stable across corpus expansion and judge-panel replacement.

13.
arXiv (CS.AI) 2026-06-19

Reward as An Agent for Embodied World Models

arXiv:2606.19990v1 Announce Type: new Abstract: While RL has become a promising tool for refining world models, existing methods largely rely on conservative rollouts near the training distribution, limiting exploration, behavioral diversity, and richer dynamic discovery. In this work, we challenge this conservative paradigm. We argue that the core limitation is not exploration itself, but the lack of reliable verification strategies to support broader exploration. Without reliable verification, expanded exploration becomes highly susceptible to reward hacking, where policies exploit imperfect rewards without achieving genuine improvement. To evaluate this motivation, we instantiate our method in embodied world models, where physical plausibility, and task completion provide a rigorous testbed for scalable RL under complex dynamics. On the verification side, we introduce Reward as an Agent, an agentic reward framework that actively evaluates generated behaviors to provide robust reward signals and mitigate reward hacking under distribution shifts. On the exploration side, we introduce Dynamic-Aware Rollout Diversification through DynDiff-GRPO, which explicitly expands action-space exploration to diversify trajectories, broaden state-action coverage, and encourage richer embodied behaviors beyond conservative rollout regimes. By unifying Reward as an Agent with DynDiff-GRPO, we enable RL on a more reliable reward foundation with substantially diversified sampling, effectively mitigating reward hacking while yielding significant accuracy gains across multiple open-source world models, thereby demonstrating that broader exploration can scale successfully when grounded in robust verification.

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

Boson Sampling as a Probe of Chaotic and Integrable Quantum Dynamics in a Photonic Chip

arXiv:2605.25398v2 Announce Type: replace Abstract: Quantum chaos plays a key role in understanding complex quantum dynamics, while integrated photonics offers unique advantages for quantum applications, including high-speed operation, scalability, and programmable unitary transformations. However, integrated photonic approaches to probing quantum chaos remain largely unexplored, owing to the absence of a clear connection between programmable photonic dynamics and established chaos diagnostics. In this work, we establish Fock-state boson sampling as a practical probe of quantum chaos by exploiting the sensitivity of multiphoton interference to the random-matrix properties of underlying single-particle unitary dynamics. More importantly, we design and fabricate a programmable quantum photonic chip to experimentally implement this framework, achieving the first integrated-photonic demonstration of quantum-chaos probes based on boson sampling. Experimental results show that the three complementary probes proposed in this work, namely the distance to Porter–Thomas statistics, Shannon entropy, and Out-of-Time-Ordered-Correlator-equivalent observables, exhibit close agreement with theoretical predictions and consistently distinguish chaotic and integrable dynamics. Our work provides a scalable route for investigating complex quantum dynamics on programmable photonic platforms while leveraging the intrinsic advantages of boson sampling through multiphoton interference and complex output statistics.

15.
arXiv (quant-ph) 2026-06-11

Generating function and Bloch representation for quantum Fisher tensor

arXiv:2603.04615v2 Announce Type: replace Abstract: The Uhlmann relative amplitude between two density matrices is shown to be a generating function, through which the quantum Fisher tensor that contains both the quantum Fisher information matrix and the mean Uhlmann curvature can be obtained via differentiation over system parameters. In the pure state limit, our generating function recovers that of the quantum geometric tensor proposed by Het\'{e}nyi and L\'{e}vay, and also clarifies the fidelity and phase between two quantum states as the generating functions of the quantum metric and Berry curvature, respectively. A generic expression for the quantum Fisher tensor in terms of the Bloch representation of density matrices is derived, which facilitates the calculation of the tensor, mean Uhlmann curvature, and geometric properties derived from the quantum Fisher information matrix. Canonical ensembles of spins are adopted to demonstrate our formalism, which reveals a constant Ricci scalar, a vacuum Einstein equation, and a cosmological constant on the 3D Euclidean manifold of the magnetic field.

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

HoloRec: Holistic Encoding and Interleaved Reasoning for Generative Recommendation

arXiv:2606.15331v1 Announce Type: cross Abstract: Generative recommendation models that formulate the task as sequence generation overcome the objective fragmentation problem of traditional cascade architectures, yet existing approaches still suffer from flat semantic representations lacking hierarchical structure for multi-step reasoning and an externally constructed chain-of-thought (CoT) that requires expensive annotations and remains disconnected from the generation objective. We propose HoloRec, an endogenous chain-of-thought recommendation mechanism that unifies representation, reasoning, and generation by constructing a hierarchical semantic encoding matrix via multi-granularity nested residual quantization optimized by a holistic reconstruction loss. HoloRec supports two inference modes: a non-thinking mode that uses lightweight multi-granularity supervised alignment for fast prediction, and a thinking mode that employs an interleaved reasoning scheme to generate CoT steps on the fly, directly embedding reasoning into the generation process without external data. Experiments on multiple public recommendation datasets demonstrate that HoloRec consistently outperforms baselines, with especially significant gains in sparse scenarios, and the thinking mode achieves better accuracy than the non-thinking mode with only modest inference overhead.

17.
arXiv (math.PR) 2026-06-16

An Algebraic Matrix Spencer Theorem

arXiv:2606.16005v1 Announce Type: new Abstract: We develop an algebraic approach to matrix discrepancy based on the representation theory of finite-dimensional C$^*$-algebras. As an application, we resolve a substantial structured special case of the Matrix Spencer conjecture. In particular, we show that for every family of contractions $A_1,\ldots,A_n$ that are contained in a finite-dimensional $C^*$-algebra $\mathcal A$ with $dim_{\mathbb C} (\mathcal A) \lesssim n$, there exists signs $x\in\{\pm1\}^n$ such that $\|\sum_{i=1}^n x_i A_i\| \le O(\sqrt n)$. As a noteworthy special case, our main result also resolves the Group Spencer conjecture of (Bandeira'24). We furthermore prove that Matrix Spencer continues to hold for low-rank perturbations of matrix families coming from an $C^*$-algebra of small dimension.

18.
arXiv (quant-ph) 2026-06-11

Logical error estimation from syndrome data of surface-code experiments

arXiv:2606.11496v1 Announce Type: new Abstract: Decoders for quantum error correction (QEC) experiments rely on detector error models (DEMs), which encode, for each error, its probability and the detectors and logical observables it flips. Here we show that estimating DEM event probabilities from experimental syndromes is feasible, avoids independent device benchmarking, and produces useful decoder priors for estimating and reducing decoded logical error probabilities. We evaluate our methods using open-source data from surface-code memory experiments performed on Google's Willow chip, and we carry out analogous surface-code experiments on IBM's \texttt{ibm\_miami} processor. Despite the different physical error scales of the Google and IBM devices, in both cases our estimated DEMs improve logical error probabilities relative to baseline device-informed DEMs, typically at the $5\%-10\%$ level and with larger gains in some IBM cases, without additional calibration circuits, decoder fine-tuning, or supervised fitting to logical outcomes.

19.
bioRxiv (Bioinfo) 2026-06-14

Somatic variant detection in normal tissues from single-cell sequencing data

A crucial advantage of single-cell sequencing (SCS) is its ability to identify somatic variants in individual cells, enabling phylogenetic analysis of cellular populations within bulk tissues. While identifying somatic variants in tumor tissues via SCS has become a common practice, doing so in normal tissues remains challenging due to the rarity of somatic variants in normal cells. To evaluate the feasibility of somatic variant calling from widely available single-nucleus RNA-seq (snRNA-seq) and single-nucleus ATAC-seq (snATAC-seq) data, we profiled a Cell-line mix of six HapMap samples prepared by the SMaHT consortium using 10x Genomics 5' snRNA-seq (12k cells with 36k mean reads per cell) and snATAC-seq (11k cells with 14k median high-quality fragments per cell) for variant calling. PacBio long-read whole genome sequencing (WGS) data (109x) generated from individual cell lines were used as ground truth. Two computational tools, Monopogen and SComatic, were used for somatic variant calling from the SCS data. Monopogen achieved single nucleotide variant (SNV) detection accuracies of 93.30% in the snRNA-seq and 99.64% in the snATAC-seq data, both of which outperformed SComatic (74.35% and 94.29%, respectively). Monopogen also consistently detected somatic SNVs at cellular fractions as low as 0.5% (2.54% in snRNA and 0.81% in snATAC) in individual samples. Notably, snATAC-seq exhibited higher genomic coverage breadth and larger number of variants detected than snRNA-seq. While the SCS data have lower overall genome coverage than that of the bulk WGS, the single-cell level variant resolution allows Monopogen to assign variants to their cells of origin with over 80% accuracy in both RNA and ATAC modalities, thereby facilitating studies of clonal evolution and cell-type-specific mutagenesis. Other benchmarking methods were also evaluated (DeepVariant, Cellsnp-lite and Mutect2) for comparison. In conclusion, our study demonstrated the feasibility of performing reliable single-cell somatic mutation calling in a cell-line mixture and discussed the strengths and limitations of current computational methods when applied to normal tissues.

20.
arXiv (CS.LG) 2026-06-19

Comparing Linear Probes with Mahalanobis Cosine Similarity

arXiv:2606.19603v1 Announce Type: new Abstract: Linear probes are widely used in interpretability research and often compared by cosine similarity. The Mahalanobis cosine similarity (MCS) between two directions, which reweights the inner product by test data covariance, is a natural task-aware refinement. Ying et al. (2026) report that a probe's MCS to a reference probe trained on the out-of-distribution (OOD) data near-perfectly linearly predicts the probe's OOD AUROC (R^2 = 0.98). Here, we extend this empirical finding across models, layers, and concept domains, and prove this general phenomenon in closed form: For balanced classes whose projections are Gaussian, OOD AUROC and MCS to the reference probe are linear because both are sigmoid-shaped functions of the probe's signal-to-noise ratio (SNR) on the test data. The theory also predicts when this linearity fails, which we verify empirically. MCS offers a theoretically grounded and empirically effective alternative to Euclidean cosine similarity for comparing linear probes.

21.
arXiv (CS.CL) 2026-06-11

Substrate Asymmetry in User-Side Memory: A Diagnostic Framework

Authors:

User-side memory in LLMs is typically scored as a single "personalization" capability: given a user's history, is the output more user-aware? We show this aggregate metric hides opposite-direction failures. Memory factorises into at least three orthogonal axes – behavioral consistency (style, voice), factual presence (recall facts in history), and factual absence (abstain when a fact is absent) – and no single substrate wins all three. Comparing per-user gamma-LoRA (a small LoRA adapter trained on each user's history; gamma denotes per-user, not per-task) against BGE-large dense top-K retrieval on a controlled 50-user synthetic corpus and a real-data probe (LaMP-3), we find gamma-LoRA decisively wins behavioral style while RAG decisively wins factual absence – and the same query-projection cells in attention layers 21-35 causally load-bear both effects in opposite directions (zeroing those LoRA weights raises absence-probe TPR by +33 pp and drops presence-probe TPR by 20 pp). On the more heavily RLHF-tuned Llama-3.1-8B-Instruct the asymmetry strengthens, not heals: parametric memory's behavioral advantage collapses while its absence-calibration deficit against retrieval widens – an alignment tax on parametric user-memory. On real-data LaMP-3, gamma-LoRA underperforms a majority baseline; a 9-condition mitigation sweep diagnoses this as instruction-following collapse, not substrate failure (a 9x2 cross-product shows the eval-time {1..5} logit mask drives main_acc to >=0.995 on every recipe), and the best training-time fix replicates bit-identically on Llama. Finally, substrate-selection routing is question-classification, not calibration: a 110M DistilBERT on the question text alone beats every logit-based router. We contribute the diagnostic framework, the diagnosed real-data negative, the alignment-tax replication, and the routing-as-classification finding.

22.
arXiv (CS.CL) 2026-06-16

Beyond English: Uncovering the Multilingual Gap in Vision-Language-Action Models

Vision-Language-Action models have recently demonstrated promising capabilities in learning generalist robot policies from large-scale multimodal data. However, most existing VLA systems are trained and evaluated primarily with English instructions, leaving their ability to understand and execute instructions in other languages largely unexplored. While the underlying large language models often possess multilingual capabilities, it remains unclear whether these multilingual capabilities transfer to VLAs during training. In this work, we present the first systematic study of multilingual instruction following in VLA models. We first construct multilingual instructions by extending existing benchmarks with translations of their instructions. Using these instructions, we evaluate several representative VLA models across a range of tasks in simulation settings. Our experiments reveal a significant multilingual gap: models trained primarily on English instructions exhibit substantial performance degradation when evaluated on other languages, even when the underlying language backbone is multilingual. We provide several findings and analyses to understand the multilingual gap. Cross-lingual transfer behavior analysis shows that performance drops correlate with both instruction understanding and action execution. Representation analyses suggest that multilingual instruction-caused representation shifts may contribute to the multilingual gap. Motivated by these findings, we further explore strategies to improve multilingual performance in VLAs. We propose a simple yet effective multilingual fine-tuning approach, Multilingual Principal Component Alignment, which leverages Principal Component Analysis to get the principal component subspace and align projected multilingual representations, effectively reducing the multilingual performance gap.

23.
Nature (Science) 2026-06-10

Daily briefing: Ancient ground squirrels ate like ‘zombies of the Pleistocene’

Authors:

Evidence from fossilized poo reveals the diverse diet of ancient ground squirrels. Plus, the science behind the peptide craze and our innate tendency to wander anticlockwise. Evidence from fossilized poo reveals the diverse diet of ancient ground squirrels. Plus, the science behind the peptide craze and our innate tendency to wander anticlockwise.

24.
Nature (Science) 2026-06-18

Daily briefing: The brain builds a sentence neuron by neuron

Authors:

Researchers have tracked the electrical activity of individual brain cells during conversation in real time. Plus, the history of GPS and a cross-species transplant that could reveal clues about the origin of animals. Researchers have tracked the electrical activity of individual brain cells during conversation in real time. Plus, the history of GPS and a cross-species transplant that could reveal clues about the origin of animals.

25.
arXiv (quant-ph) 2026-06-24

Symmetric mass generation of interacting chiral fermions on a one-dimensional lattice without fermion doubling

arXiv:2606.24713v1 Announce Type: cross Abstract: Symmetric mass generation is the interaction-induced opening of a fermion gap without spontaneous symmetry breaking. The anomaly-free 3-4-5-0 model of Wang and Wen provides a minimal one-dimensional setting for this phenomenon, but a direct lattice realization faces two obstacles: fermion doubling for local chiral discretizations and perturbative irrelevance of the six-fermion gapping interaction. We address both obstacles. First, we formulate the model on a strictly one-dimensional tangent-fermion lattice, where a nonlocal hopping produces a single chiral branch without a mirror partner while retaining an efficient tensor-network representation. Second, we add a Hubbard-type density-density interaction (Luttinger parameter $K$) that reduces the scaling dimension of the 3-4-5-0 interaction from $5$ to $5K$, making it relevant for $K