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01.
arXiv (CS.AI) 2026-06-12

(Human) Attention Is (Still) All You Need: Human oversight makes AI-assisted social science reliable

arXiv:2606.12848v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly used for tasks once reserved for trained researchers, including hypothesis generation, specification choice, and drafting conclusions. We argue that the reliability of AI-assisted research depends not only on model capability, but also on how cognitive labour is structured between humans and machines. We study this problem through Human-in-the-Loop Economic Research (HLER), a decision architecture based on pre-commitment, decision sequencing, accountability, and attention allocation. In a pre-specified 2*4 factorial experiment with 280 complete research runs across four datasets, an unconstrained multi-agent baseline produced critical failures in 72% of runs. Using the same underlying model, the same agent decomposition, and identical prompts for the shared reasoning agents, HLER reduced the failure rate to 16% by imposing three architectural commitments: LLMs reason but do not execute data work, data and estimation are handled deterministically, and three human decision gates bind the workflow. Fisher's exact test rejects equality of failure rates at p

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

EnvShip-Bench: An Environment-Enhanced Benchmark for Short-Term Vessel Trajectory Prediction

arXiv:2606.15240v1 Announce Type: new Abstract: Vessel trajectory prediction is important for intelligent shipping, maritime surveillance, and navigation safety. However, existing public maritime AIS resources are often limited by inconsistent forecasting protocols, uneven data quality, and the lack of benchmark-ready contextual annotations, which hinder fair comparison and context-aware modeling. To address this gap, we present EnvShip-Bench, a unified benchmark for short-term vessel trajectory prediction built from large-scale raw AIS data from the Danish Maritime Authority (DMA) and NOAA through a common processing pipeline. EnvShip-Bench adopts a standardized forecasting protocol with 10 minutes of observation, 10 minutes of prediction, and 20-second sampling in vessel-centric local metric coordinates. Beyond the large-scale core benchmark, it provides a quality-first compact subset for efficient and reproducible experimentation, together with synchronized environmental and nearby-vessel context extensions. As a result, EnvShip-Bench supports trajectory-only, environment-aware, and interaction-aware forecasting under a unified evaluation framework. Extensive benchmark statistics and analysis demonstrate that EnvShip-Bench offers a standardized, extensible, and context-aware foundation for maritime trajectory forecasting research.

03.
bioRxiv (Bioinfo) 2026-06-11

Viability of engineered AAVs via protein language models

Capsid engineering has greatly improved the performance of recombinant AAV vectors used for gene therapy. One commonly used strategy is the insertion of a short, 7-mer, peptide into surface-exposed loops to modify receptor interactions and enhance cell entry. While effective in receptor retargeting and improved transduction, these insertions might destabilize the capsid protein, hinder assembly, and thus limit production. While previous attempts have used deep mutational scanning and AI to predict which insertions are viable, there is lack in understanding the structural consequences of these peptide insertions at the amino-acid level. Here we combined experiments, deep sequencing and large protein language models to gain insight on the impact of 7-mer insertions on the VR-VIII region. We first characterize the biochemical properties of viable insertions, thus identifying which residues are well tolerated, and which should instead be avoided. We then focus on the nearby context of those insertions, by studying the effect of the linkers, either for highly diverse libraries or for individual variants known for their efficiency. Next, we study the broader context, by extending our analysis to the whole capsid sequence, and identifying regions that can tolerate insertions without long-ranged structural deformations that could affect capsid functionality. We conclude with a cross-serotype comparison and a viability analysis of tens of previously engineered variants. Our work showcases how AI can uncover structure-function rules governing the success of engineered AAV capsids.

04.
arXiv (CS.LG) 2026-06-16

Probing Dec-POMDP Reasoning in Cooperative MARL

arXiv:2602.20804v2 Announce Type: replace Abstract: Cooperative multi-agent reinforcement learning (MARL) is typically framed as a decentralised partially observable Markov decision process (Dec-POMDP), a setting whose hardness stems from two key challenges: partial observability and decentralised coordination. Genuinely solving such tasks requires Dec-POMDP reasoning, where agents use history to infer hidden states and coordinate based on local information. Yet it remains unclear whether popular benchmarks actually demand this reasoning or permit success via simpler strategies. We introduce a diagnostic suite combining statistically grounded performance comparisons and information-theoretic probes to audit the behavioural complexity of baseline policies (IPPO and MAPPO) across 37 scenarios spanning MPE, SMAX, Overcooked, Hanabi, and MaBrax. Our diagnostics reveal that success on these benchmarks rarely requires genuine Dec-POMDP reasoning. Reactive policies match the performance of memory-based agents in over half the scenarios, and emergent coordination frequently relies on brittle, synchronous action coupling rather than robust temporal influence. These findings suggest that some widely used benchmarks may not adequately test core Dec-POMDP assumptions under current training paradigms, potentially leading to over-optimistic assessments of progress. We release our diagnostic tooling to support more rigorous environment design and evaluation in cooperative MARL.

05.
arXiv (quant-ph) 2026-06-12

Steady-State Noise Signatures of Lindbladian Exceptional Points

arXiv:2606.13377v1 Announce Type: new Abstract: Exceptional points (EPs) are non-Hermitian degeneracies at which two or more eigenvalues and their corresponding eigenvectors coalesce. In open quantum systems, exceptional points can arise in the Lindbladian governing the dissipative dynamics. Their signatures have so far been mainly identified in finite-time observables, such as transient currents, while steady-state average currents generally provide no direct evidence of the underlying exceptional-point structure. In this work, we demonstrate that signatures of Lindbladian EPs can nevertheless be accessed in the steady-state regime through current noise. We derive general expressions for current correlation functions within a Lindblad master-equation framework and show, in particular, how exceptional points affect their behaviour as a function of the time delay. We illustrate these results with the paradigmatic example of two interacting qubits coupled to two reservoirs, where the steady-state noise clearly distinguishes overdamped, underdamped, and critical regimes. Our results establish current correlation functions as a steady-state probe of Lindbladian EPs in open quantum systems.

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

Quantitative Oppenheim Conjecture for Random Quadratic Forms and Optimal Variance Bounds in Function Fields

arXiv:2606.16699v1 Announce Type: cross Abstract: We prove a quantitative version of Oppenheim's conjecture in the function field setting. In order to do so, we compute the higher moments of the Siegel transform. In particular, we find an optimal bound on the variance of the number of lattice points in a set. Moreover, we compute the exact variance of the number of lattice points in a ball, which is of independent interest.

07.
arXiv (CS.AI) 2026-06-17

A Neuro-Symbolic Approach to Strategy Synthesis for Strategic Logics

arXiv:2606.17962v1 Announce Type: cross Abstract: Reasoning about what agents can achieve through strategic interaction is a core challenge in Multi-Agent Systems (MAS). Logics for strategic ability, such as ATL, provide rigorous methods, but their adoption is often hindered by the computational cost of strategy synthesis. We introduce a neuro-symbolic framework that integrates large language models (LLMs) into the model-checking pipeline for MAS. The LLM acts as a strategy-generation oracle, proposing candidate strategies that are then formally validated by a standard MAS model checker. This generate-and-certify architecture uses LLM guidance to navigate large combinatorial strategy spaces while preserving formal soundness: generated strategies are accepted only when certified by the verifier. We instantiate the framework for bounded strategic reasoning in NatATL and introduce the first NatATL strategy-synthesis dataset, consisting of 4211 instances. Experiments with an open-weight Qwen3-32B model show that our certified pipeline achieves 92\% accuracy on strategy-synthesis outcomes.

08.
arXiv (CS.AI) 2026-06-18

SafeClawBench: Separating Semantic, Audit-Evidence, and Sandbox Harm in Tool-Using LLM Agents

arXiv:2606.18356v1 Announce Type: cross Abstract: Tool-using language-model agents introduce security failures that go beyond unsafe text: they can disclose protected objects, write persistent memory, send messages, modify databases, or trigger harmful code and tool effects. Existing evaluations often collapse these stages into a single attack success rate, making it difficult to tell whether a model merely agreed with an attacker or actually produced observable harm. We introduce SafeClawBench, a staged benchmark for tool-using agent security with 600 controlled adversarial tasks across six attack families: direct and indirect prompt injection, tool-return injection, memory poisoning, memory extraction, and ambiguity-driven unsafe inference. SafeClawBench reports three separate endpoints: semantic attack acceptance, audit-visible harm evidence, and sandbox-observed tool/state harm. Evaluating five agent endpoints under four prompt-level policies, we find that these endpoints capture different failure modes. Without additional prompt protection, semantic failure rates vary widely across models, from 9.0% to 44.2%. Audited harm evidence is narrower than semantic failure, and under a separate executable protocol some matched task identities produce sandbox harm despite passing the Semantic Core call: in a 12,000-row matched analysis, 291 of 347 observed sandbox harms occur in rows that pass the semantic check. Prompt policies change endpoint outcomes, but their effects depend on both model and protocol. SafeClawBench provides a reproducible framework for comparing agent models and prompt-policy conditions without conflating textual compliance, evidence-supported harm, and executable state changes. The open-source dataset is available at https://huggingface.co/datasets/sairights/safeclawbench.

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

From ASR to ASP: Evaluating Prompt Attack Vulnerabilities Against Open-Source LLMs

Recent studies demonstrate that Large Language Models (LLMs) are vulnerable to attacks that generate harmful or sensitive outputs. As open-source LLMs are increasingly adopted in high-impact applications such as finance, law, and healthcare, systematically investigating their security risks is becoming increasingly important towards trustworthy LLM era. This paper comprehensively studies effective prompt injection attacks against 14 widely used open-source and three closed-source LLMs on five attack benchmarks. Moreover, existing evaluation metrics mostly only consider the attack success rate, overlooking uncertainty in model responses. Our proposed Attack Success Probability (ASP) additionally captures uncertain behaviors for evaluation, where the model may initially refuse a harmful request but subsequently provide harmful guidance or vice versa, reflecting inconsistency and ambiguity in attack feasibility. By systematically analyzing the effectiveness of prompt injection attacks, we propose a straightforward and effective hypnotism attack; results show that this attack causes aligned language models, including Stablelm2, Mistral, Openchat, and Vicuna, to generate objectionable behaviors, achieving around 90% ASP. They also indicate that ignore prefix attacks can break all 14 open-source LLMs, achieving over 60% ASP on a multi-categorical dataset. We find that moderately well-known LLMs exhibit higher vulnerability to prompt injection attacks, highlighting the need to raise public awareness and prioritize efficient mitigation strategies.

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

Projected random forests and conformal prediction of circular data

arXiv:2410.24145v3 Announce Type: replace-cross Abstract: We apply conformal prediction techniques to regression problems with circular responses, producing prediction sets with adaptive arc length and finite-sample coverage guarantees for any circular predictive model under the assumption of data exchangeability. Leveraging the high performance of existing predictive models designed for linear responses, we analyze a general projection procedure that converts any linear-response regression model into one suitable for circular responses. When random forests are used as base models in this projection procedure, we leverage the random forest out-of-bag mechanism to eliminate the need for a separate calibration sample in the construction of prediction sets. On synthetic and real datasets, the resulting projected random forest model produces more efficient out-of-bag conformal prediction sets, with shorter median arc length, than the split conformal prediction sets generated by two existing alternative models.

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

Counterfactual Credit Policy Optimization for Multi-Agent Collaboration

arXiv:2603.21563v5 Announce Type: replace Abstract: Collaborative multi-agent large language models (LLMs) can solve complex reasoning tasks by decomposing roles, but reinforcement learning for such systems is limited by credit assignment: shared terminal rewards obscure individual contributions and can encourage free-riding. We introduce two optimizer-agnostic credit assignment methods for converting joint outcomes into agent-specific learning signals. Counterfactual Credit for Policy Optimization (CCPO) estimates an agent's marginal contribution by comparing the realized joint outcome with a counterfactual outcome where that agent is removed. Self-Evaluated Credit for Policy Optimization (SEPO) uses constrained self- and peer-evaluations as a verifier-anchored credit signal while keeping the external task outcome dominant. Both operate at the reward-construction layer rather than as policy optimizers, producing role-specific rewards or advantages for GRPO, GSPO, or REINFORCE++. We instantiate these credit signals in a sequential Think–Solve setting and evaluate them on mathematical reasoning benchmarks. Results show that explicit credit assignment often improves dual-agent reasoning, especially on MATH500 and several out-of-distribution settings, while gains vary across models and datasets. Our code is available at: https://github.com/bhai114/ccpo.

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

Viral Proteins Reveal Geometry of Protein Language Models

arXiv:2606.12609v1 Announce Type: new Abstract: Protein language models are trained on highly imbalanced datasets, raising the question of how they represent underrepresented biological sequences. Using viral proteins as a case study across ESM model families, we identify a dominant nativeness axis in embedding space, aligned with masked reconstruction perplexity, that orders sequences from well-modeled cellular proteins through viral proteins to shuffled and random sequences. Scaling contracts this axis unevenly across viral families. Despite this, protein language model embeddings retain viral-specific signal: viral proteins remain linearly separable beyond zero-shot perplexity and shallow sequence features. Together, these results suggest that pLM representations are structured by a general notion of nativeness while preserving information specific to distinct biological groups.

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

Trust Between AI Agents: Measuring Formation, Breakage, and Recovery, with Implications for Governing Multi-Agent Systems

作者:

arXiv:2606.14923v1 Announce Type: new Abstract: As language-model agents increasingly work in teams, each agent must decide how much to trust its teammates. Yet we lack a standard way to measure trust between AI agents. We propose a behavioral measure based on costly verification. In a cooperative survival game, checking a teammate's work consumes resources, while trusting a wrong answer can be fatal. Relative to a memoryless version of the same model, reduced verification provides an observable measure of trust. Using this framework, we study trust formation, breakage, and recovery across six frontier model snapshots. When paired with a consistently reliable teammate, four snapshots (Claude Opus 4.6, Claude Sonnet 4.6, GPT-5.1, and Gemini 3.1 Pro) reduce verification by roughly 60-85%, whereas two smaller snapshots show little or no such adjustment. Failures reverse this discount, but models differ in how they respond. Some concentrate renewed scrutiny on the culprit, while others become more cautious toward the entire team. Recovery is slower than formation, and clustered failures sustain suspicion far longer than the same number of failures spread apart. These differences have practical consequences. Models that form trust verify less, decide more quickly, and achieve higher payoffs in our environment. By contrast, persistent over-verification is associated with indecision rather than safety. Our results show that trust dispositions can be measured before deployment and suggest that calibration, rather than maximal suspicion, should be the central concern in the governance of multi-agent AI systems.

14.
arXiv (CS.AI) 2026-06-19

Multi-LCB: Extending LiveCodeBench to Multiple Programming Languages

arXiv:2606.20517v1 Announce Type: new Abstract: LiveCodeBench (LCB) has recently become a widely adopted benchmark for evaluating large language models (LLMs) on code-generation tasks. By curating competitive programming problems, constantly adding fresh problems to the set, and filtering them by release dates, LCB provides contamination-aware evaluation and offers a holistic view of coding capability. However, LCB remains restricted to Python, leaving open the question of whether LLMs can generalize across the diverse programming languages required in real-world software engineering. We introduce Multi-LCB, a benchmark for evaluating LLMs across twelve programming languages, including Python. Multi-LCB transforms Python tasks from the LCB dataset into equivalent tasks in other languages while preserving LCB's contamination controls and evaluation protocol. Because it is fully compatible with the original LCB format, Multi-LCB will automatically track future LCB updates, enabling systematic assessment of cross-language code generation competence and requiring models to sustain performance well beyond Python. We evaluated 24 LLMs for instruction and reasoning on Multi-LCB, uncovering evidence of Python overfitting, language-specific contamination, and substantial disparities in multilingual performance. Our results establish Multi-LCB as a rigorous new benchmark for multi-programming-language code evaluation, directly addressing LCB's primary limitation and exposing critical gaps in current LLM capabilities.

15.
arXiv (CS.AI) 2026-06-11

Noise-Aware Framework for Correcting Corrupted Labels

arXiv:2606.11695v1 Announce Type: cross Abstract: High-quality labeled data is essential for training reliable ML/DL models. However, real-world datasets often contain a considerable proportion of corrupted labels, which can severely degrade model performance. To address this problem, we propose CANOLA, a novel framework for correcting corrupted labels through noise-aware learning and iterative label refinement. CANOLA explicitly estimates the underlying noise distribution of the dataset and incorporates this information into the training of a noise-aware Deep Neural Network. By incorporating noise characteristics during learning, CANOLA enables the model to down-weight unreliable supervision signals and focus on trustworthy patterns, thereby improving robustness and generalization. Label correction is performed via cautious, iterative soft label refinement, in which model predictions are blended with observed labels to prevent premature or erroneous updates. This progressive refinement allows the dataset to be repaired in a stable and controlled manner. We evaluate CANOLA on six widely used datasets under realistic noisy labeling scenarios. Experimental results show that CANOLA consistently outperforms SOTA label correction methods, achieving relative improvements ranging from 19% to 52% in error reduction. Moreover, models trained on datasets corrected by CANOLA obtain substantial downstream performance gains. Even simple classifiers trained on CANOLA's corrected data can outperform complex model-centric approaches by margins of up to 67%.

16.
arXiv (quant-ph) 2026-06-12

Kerr-induced nonreciprocal transparency and group delay in a hybrid cavity magnomechanical system

arXiv:2606.13412v1 Announce Type: new Abstract: We propose a scheme for realizing nonreciprocal transparency, Fano resonances, and slow/fast light in a hybrid cavity magnomechanical system containing two YIG spheres and a mechanical resonator. The nonreciprocal behavior originates from the magnon Kerr nonlinearity, which induces direction-dependent frequency shifts and modifies the interference pathways among cavity photons, magnons, and phonons. We show that the hybrid system supports multiple transparency windows arising from magnon- and magnomechanical-induced interference processes. The Kerr interaction strongly reshapes these transparency features, producing asymmetric Fano line shapes and enabling controllable nonreciprocal transmission. Furthermore, the associated dispersion exhibits pronounced directional asymmetry, leading to giant differences in the group delay for opposite propagation directions and allowing reversible switching between slow- and fast-light regimes. We investigate the roles of hybrid coupling strengths and dissipation channels and identify parameter regimes where the nonreciprocal response is maximized. These findings establish Kerr-engineered magnomechanical systems as promising platforms for integrated nonreciprocal microwave photonics and quantum information technologies.

17.
Science (Express) 2026-05-21

DNA polymerization activates RNA cleavage of a reverse transcriptase–like antiviral enzyme | Science

作者: 未知作者

Defense-associated reverse transcriptases (DRTs) transcribe noncoding RNAs (ncRNAs) for antiviral defense, but the mechanisms of ncRNA-independent DRTs remain unclear. In this work, we show that a single DRT4 mediates RNA-targeting antiphage defense by integrating DNA polymerase, exonuclease, and RNA endonuclease activities. First, through an equilibrium between its DNA polymerase and exonuclease activities, DRT4 senses phage infection, as elevated dNTP levels shift the equilibrium toward polymerase activity, thereby promoting protein-primed single-stranded DNA (ssDNA) synthesis. Second, ssDNA of sufficient length, phage DNA-binding proteins, and deoxyguanosine triphosphate collectively activate an unusual RNA endonuclease activity of DRT4, excising 3′–guanosine monophosphate from both phage and host RNA to terminate infection. These findings reveal a distinctive immune strategy combining nucleic acid synthesis and degradation, expanding the functional landscape of DRTs for new DNA- and RNA-processing technologies.

18.
arXiv (CS.AI) 2026-06-11

Inside the Latent Flow: Causal Deciphering of Attention Dynamics in Audio Separation Foundation Models

arXiv:2606.10046v2 Announce Type: replace-cross Abstract: Flow-matching transformers achieve strong audio separation, yet their attention dynamics are opaque. We adapt established causal-intervention principles into a deterministic, inference-time probing protocol for SAM Audio. Orthogonal probing uncovers a dual-pathway text-conditioning mechanism: additive injections control semantic identity, while cross-attention refines acoustic structure. We observe an asynchronous layerwise convergence: stable layers build temporal scaffolds early, whereas fast layers continue resolving artifacts during sampling. The model also attenuates temporal segmentation cues to maintain continuous-flow stability. Using these insights, we propose Layer-Selective Attention Caching (LSAC), a training-free acceleration method that caches attention in stable layers. Across acoustic complexities, LSAC cuts self-attention computation by about ~25% with negligible quality loss and yields up to 6.7x higher quality retention than naive step reduction.

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

Lagrange: An Open-Vocabulary, Energy-Based Sparse Framework for Generalized End-to-End Driving

arXiv:2606.20274v1 Announce Type: new Abstract: Scaling end-to-end autonomous driving to complex, open-world environments requires perceptual models that generalize to anomalous scenarios and planners that produce kinematically valid trajectories. Existing paradigms face a distinct dichotomy between representational efficiency and generalization capacity. Dense models (e.g., occupancy networks), while geometrically robust, incur critical computational bottlenecks and struggle with high-level semantic reasoning. Conversely, sparse, query-based planners are efficient but reliant on closed-set definitions, rendering them vulnerable to out-of-distribution (OOD) events. Although recent Vision-Language-Action (VLA) models offer open-vocabulary reasoning, their autoregressive, discrete token generation fundamentally conflicts with the continuous, high-frequency control requirements of vehicle dynamics. To address this, we propose Lagrange, an open-vocabulary, computationally sparse driving framework based on Masked Latent Fields (MLF). Rather than relying on dense volumetric reconstructions or closed-set query mechanisms, Lagrange exploits Vision-Language Models (VLMs) to encode class-agnostic object proposals into continuous semantic visual tokens. We introduce an intent-driven masked cross-attention module that temporally filters irrelevant entities, decoding the attended tokens into an implicit continuous energy field defined over spatial coordinates. By framing decision-making as a Lagrangian action minimization problem spanning this energy field, we enforce strict compliance with vehicle kinematics while executing collision avoidance. Extensive offline evaluations on both standard (nuScenes) and long-tail (CODA) benchmarks demonstrate that Lagrange establishes a promising framework for robust, interpretable, and kinematically feasible open-world autonomy.

20.
arXiv (CS.AI) 2026-06-17

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

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.

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

Robustness of Mixtures of Experts to Feature Noise

arXiv:2601.14792v2 Announce Type: replace Abstract: Despite their practical success, it remains unclear why Mixture of Experts (MoE) models can outperform dense networks beyond sheer parameter scaling. We study an iso-parameter regime where inputs exhibit latent modular structure but are corrupted by feature noise, a proxy for noisy internal activations. We show that sparse expert activation acts as a noise filter: compared to a dense estimator, MoEs achieve lower generalization error under feature noise, improved robustness to perturbations, and faster convergence speed. Empirical results on synthetic data and real-world language tasks corroborate the theoretical insights, demonstrating consistent robustness and efficiency gains from sparse modular computation.

22.
arXiv (quant-ph) 2026-06-12

Continuum Neural Momentum Eigenstate for Variationally Solving Quasiparticles

arXiv:2606.12928v1 Announce Type: cross Abstract: We design the first neural quantum state for continuum particles that, for any chosen allowed momentum $\mathbf{k}$, is by construction an exact eigenstate of total momentum with eigenvalue $\mathbf{k}$. Our architecture, EVE, enables off-the-shelf VMC to solve for momentum-sector ground states. We test EVE on 2D bosons with mutual $1/r$ interactions, finding that a single unified ansatz is capable of describing four qualitatively different states: superfluid, roton, crystal, and phonon. At different densities, we extract the underlying phase of matter from the dispersion's shape. At $r_s = 20.0$, we see the roton minimum at finite $k$ expected of a superfluid. At $r_s = 100.0$, we see striking zone folding indicative of crystalline order, with periodically spaced minima representing floating crystals connected by phonon arcs in between. Using density-density correlation functions, we confirm the phase diagnoses and probe the excitations' correlation structures. Finally, we analyze the roton's phase texture and find unexpected multi-particle phase strings, formed when several vortex dipoles merge, leaving two vortices connected by a phase slip.

23.
PLOS Computational Biology 2026-06-04

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments

by Zachary Hemminger, Haley De Ocampo, Fangming Xie, Zhiqian Zhai, Jingyi Jessica Li, Roy Wollman Motivation Most imaging-based spatial transcriptomics methods measure individual genes, which limits scalability and typically requires integration with scRNA-seq to recover full cellular states. Recent approaches such as CISI, FISHnCHIPs, and ATLAS address this limitation by measuring aggregate transcriptional signatures, where multiple genes are pooled into each channel to increase throughput. While aggregate measurements improve scalability, they shift the problem from gene selection to feature design. For effective integration with scRNA-seq, these signatures must be not only discriminative in transcriptional space but also straightforward to measure, with balanced signal, sufficient dynamic range, and robustness to experimental noise. By optimizing decoding accuracy in isolation, existing methods leave substantial performance on the table. Results We present CIPHER (Cell Identity Projection using Hybridization Encoding Rules), a neural-network framework that jointly optimizes the experimental encoding matrix, i.e., the way that genes are aggregated to signatures, and the downstream cell embedding. CIPHER integrates the physical limits of imaging assays directly into its loss function, shaping the latent space to maximize discriminability while maintaining robustness to measurement noise and signal constraints. Using a large-scale mouse brain scRNA-seq reference, we show that CIPHER-designed encodings yield latent spaces with improved cell-type separability, uniform signal utilization, and greater resilience to hybridization variability, resulting in higher decoding accuracy from both simulated and experimental data. Conclusion CIPHER formulates aggregate signature design as a joint optimization problem over decoding accuracy and experimental measurability. This enables systematic, scRNA-seq-aligned feature design for scalable spatial transcriptomics based on aggregate measurements. Availability Code and documentation are available at https://github.com/wollmanlab/Design/.

24.
arXiv (quant-ph) 2026-06-11

Magneto-Optical Trapping of a Metal Hydride Molecule

arXiv:2512.22350v2 Announce Type: replace-cross Abstract: We demonstrate a three-dimensional magneto-optical trap (MOT) of a metal hydride molecule, CaH. We are able to scatter $\sim$$10^{4}$ photons with vibrational loss covered up to vibrational quantum number $\nu=2$. This allows us to laser slow the molecular beam near zero velocity with a "white-light" technique and subsequently load it into a radio-frequency MOT. The MOT contains $230(40)$ molecules, limited by beam source characteristics and predissociative loss of CaH. The temperature of the MOT is below one millikelvin. The predissociative loss mechanism could, in turn, facilitate controlled dissociation of the molecule, offering a possible route to optical trapping of hydrogen atoms for precision spectroscopy.

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

Robust Neural Tucker Factorization with Bias Correction and Adaptive Initialization

arXiv:2606.16388v1 Announce Type: new Abstract: High-dimensional incomplete (HDI) tensors are widely used in traffic and climate applications, but sparse observations make accurate completion difficult. The intrinsic non-linear dynamics and non-stationary variations across distinct multi-modal fields severely hinder the efficacy of conventional linear reconstruction frameworks. Neural Tucker factorization provides an effective framework for modeling high-order interactions among tensor modes. By parameterizing underlying structural characteristics into continuous latent spaces, neural representations circumvent the rigid low-rank constraints of classical algebra. However, its performance can still be affected by implementation-level choices, especially parameter initialization and the bias configuration of the final output mapping. Suboptimal initializations frequently lead to variance explosion across the cubically expanded interaction spaces, driving the subsequent non-linear activation boundaries into severe gradient saturation zones, while the omission of a dedicated translation parameter forces interaction weights to implicitly absorb global statistical deviations. This paper proposes a simple yet effective neural Tucker factorization model with Kaiming initialization and bias correction (KaBiN) for HDI tensor completion. The proposed model utilizes Kaiming uniform initialization for the embedding and Tucker linear parameters, and adopts a simple bias correction in output mapping. By elegantly decoupling global mean shifts from local structural representations, the framework provides a highly stable and well-conditioned optimization landscape. Experiments on three real-world HDI tensor datasets show that KaBiN achieves better performance than the original NeuTucF, while introducing minimal computational overhead.