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

EurekAgent: Agent Environment Engineering is All You Need For Autonomous Scientific Discovery

LLM-based agents have shown increasing potential in automating scientific discovery. Given an optimizable metric and an execution environment, they can propose, validate, and iterate scientific solutions, and have produced results that outperform human-designed approaches. As model capabilities continue to improve, we argue that the bottleneck for autonomous scientific discovery is shifting from prescribing agent workflows to designing agent environments: the resources, constraints, and interfaces that shape agent behavior. We frame this as environment engineering: building environments that amplify productive behaviors, such as open-ended exploration, systematic artifact management, and inter-agent collaboration, while suppressing harmful behaviors, such as reward hacking and high-friction human oversight. We present EurekAgent, an environment-engineered agent system for metric-driven autonomous scientific discovery. EurekAgent engineers the environment along four dimensions: permissions engineering for bounded agent execution and isolated evaluation; artifact engineering for filesystem and Git-based collaboration; budget engineering for budget-aware exploration; and human-in-the-loop engineering for easy human supervision and intervention. EurekAgent sets new state-of-the-art results on multiple mathematics, kernel engineering, and machine learning tasks, including new state-of-the-art 26-circle packing results discovered with less than $11 in total API cost. We open-source our code and results, and call for environment engineering as a core research direction for developing reliable autonomous research agents.

02.
arXiv (math.PR) 2026-06-11

An Information-Theoretic Analysis of Threshold Group Testing

arXiv:2606.11353v1 Announce Type: cross Abstract: We study the Threshold Group Testing (TGT) problem in the noiseless and non-adaptive setting, where the objective is to exactly recover a sparse binary vector from pooled tests, using as few tests as possible. In TGT, each test applied to a subset of items returns a positive outcome if the number of 1's (defective items) in that subset meets or exceeds a specified threshold, and has a negative outcome otherwise. We investigate how the complexity of TGT compares to that of Classical Group Testing (CGT), corresponding to the special case of the threshold equal to one, and analyse the impact of increasing the threshold on the required number of tests. Our main contribution is the derivation of a sharp information-theoretic phase transition at $c_{\mathrm{inf}}^{\mathrm{TGT}}k\log(n/k)$ (non-adaptive) tests for TGT within the constant-column test design. The threshold constant $c_{\mathrm{inf}}^{\mathrm{TGT}}$ is expressed as a function of the prevalence of defectives and the threshold value. Our upper bound is derived under an analytic assumption, and we verify that this assumption is satisfied for a threshold value of 2. The value of $c_{\mathrm{inf}}^{\mathrm{TGT}}$ reveals that TGT on the constant-column design has the same information-theoretic behaviour as CGT in the low-prevalence regime. Yet, strikingly, at higher prevalences, the threshold leads to a significant reduction in the number of tests. On the other hand, we provide evidence that when the asymptotic proportion of defective items is positive, TGT actually becomes strictly harder than CGT (excluding trivial reductions).

03.
arXiv (quant-ph) 2026-06-16

Inflationary branch decoherence and the cosmological arrow of time

作者:

arXiv:2602.21263v3 Announce Type: cross Abstract: We analyze branch decoherence in inflationary quantum cosmology by computing reduced density matrices and branch-overlap factors for long-wavelength perturbations. The Hartle-Hawking no-boundary state is real in the semiclassical regime and contains both expanding and contracting WKB components, whereas the tunneling state is selected as an outgoing complex WKB branch; expanding-contracting decoherence is therefore central for the former and mainly diagnostic for the latter. Using the influence-functional formalism, we derive the noise kernel for a light spectator environment and evaluate decoherence under horizon-based and EFT-motivated coarse grainings. We then compute the single-mode branch overlap directly from the Bunch-Davies mode functions, obtaining $|\mathcal{D}_k(z)|=[z^2/(z^2+1)]^{1/4}$ in the massless limit and $|\mathcal{D}_k(z)|\sim z^\nu$ on superhorizon scales for massive fields, where $z=-k\eta$ is the dimensionless wavenumber with $\eta$ the conformal time. In the massless case, the accumulated geometric branch functional is evaluated in closed form, with a leading cutoff-sensitive phase-space term and a universal subleading contribution. The calculation provides an explicit quantitative bridge between quantum-cosmological boundary conditions, inflationary squeezing, and the emergence of effectively classical cosmological histories.

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

Compressed Computation is (probably) not Computation in Superposition

arXiv:2606.14673v1 Announce Type: new Abstract: We study whether the Compressed Computation (CC) toy model (Braun et al., 2025) is an instance of computation in superposition. The CC model appears to compute 100 ReLU functions with just 50 neurons, achieving a better loss than expected from only representing 50 ReLU functions. We show that the model mixes inputs via its noisy residual stream, corresponding to an unintended mixing matrix in the labels. Splitting the training objective into the ReLU term and the mixing term, we find that performance gains scale with the magnitude of the mixing matrix and vanish when the matrix is removed. The learned neuron directions concentrate in the subspace associated with the top 50 eigenvalues of the mixing matrix, suggesting that the mixing term governs the solution. Finally, a semi-non-negative matrix factorization (SNMF) baseline derived solely from the mixing matrix reproduces the qualitative loss profile and improves on prior baselines, though it does not match the trained model. These results suggest CC is not a suitable toy model of computation in superposition.

05.
arXiv (CS.CV) 2026-06-12

Revisiting Vehicle Color Recognition in Long-Tailed Surveillance Scenarios

Vehicle color recognition is an important cue for vehicle identification in surveillance systems, especially when license plates are illegible due to low resolution, occlusion, motion blur, or poor illumination. However, real-world vehicle color distributions are highly imbalanced, making overall accuracy insufficient to assess performance on rare but operationally relevant colors. This paper presents a comprehensive study of vehicle color recognition under severe class imbalance using UFPR-VeSV, a challenging real-world surveillance dataset. We investigate synthetic minority-class augmentation through two off-the-shelf generative strategies: text-conditioned image generation with RunDiffusion/JuggernautXL and image-conditioned color editing with Gemini 2.0 Flash. The curated synthetic data are combined with modern visual representations, loss reweighting, learning-rate scheduling, color-safe augmentation, foreground-aware preprocessing, and ensemble fusion. The bestperforming approach achieves 94.6% micro accuracy and 79.7% macro accuracy, improving macro accuracy by 8.2 percentage points over recent literature. A manual error analysis further shows that many remaining failures are visually ambiguous even for human annotators, highlighting the practical limits of color-based vehicle identification in unconstrained surveillance imagery. The generated images and source code are publicly available at https://github.com/viniciusorru/vcr-synthetic

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

The Optimal Rate Function in Covariant Quantum State Tomography

arXiv:2606.16948v1 Announce Type: new Abstract: The problem of quantum tomography is to estimate an unknown quantum state $\rho$ from a measurement of $n$ copies of $\rho$. One can ask which tomography protocol, i.e.\ which choice of multi-copy measurement, gives the best possible estimate of $\rho$. To do so, we characterize tomography protocols by their rate function, which governs the exponential rate at which a protocol assigns probability to a particular estimate $\sigma$ of the true state $\rho$. This rate function is a quantum mechanical generalization of the classical relative entropy between the true state and its estimate, and depends on the choice of protocol. It is bounded by the quantum relative entropy, and we show that this bound is sharp: for any $\rho$ and $\sigma$ we construct a family of protocols whose rate functions converge to the quantum relative entropy $D(\sigma\|\rho)$. We consider the family of covariant tomography protocols; these are the basis independent state estimation schemes that assume no prior information about $\rho$ and $\sigma$. Keyl described a specific tomography protocol based on Schur sampling, and conjectured that among all covariant tomography protocols it has the largest possible rate function for all $\sigma$ and $\rho$. We prove this conjecture. The resulting rate function is an annealed version of quantum relative entropy, due to the cost of learning the eigenbasis in covariant quantum state tomography.

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

Contextual Invertible World Models: A Neuro-Symbolic Agentic Framework for Colorectal Cancer Drug Response

arXiv:2603.02274v3 Announce Type: replace-cross Abstract: Precision oncology is currently limited by the small-N, large-P paradox, where high-dimensional genomic data is abundant but pharmacological response samples are sparse. While deep learning achieves predictive accuracy, it frequently fails to provide the mechanistic clarity required for clinical adoption. We present the Contextual Invertible World Model (CIWM), a Neuro-Symbolic Agentic Framework that bridges this gap by integrating a quantitative machine learning emulator with a Large Language Model reasoning layer. Utilising a stringently curated, high-fidelity data engineering pipeline on the Sanger GDSC dataset (\( N=83 \)), we isolate true biological signals from in vitro artifacts to establish a rigorous baseline predictive correlation for complex transcriptomics (\( r=0.268 \)). Through Inverse Reasoning, we perform in silico CRISPR perturbations across the colorectal landscape. The framework autonomously overturns classical mechanistic assumptions, identifying a hierarchical dominance of mutant KRAS over the APC/Wnt-axis in driving 5-fluorouracil resistance (\( \Delta=-0.0469 \)) via a "KRAS Shield" mapped to MAPK/PI3K networks. Furthermore, the agentic layer identified a "PIK3CA Paradox", revealing that repairing PIK3CA inadvertently increases chemoresistance (\( \Delta=+0.0085 \)) by triggering a compensatory feedback loop that hyperactivates the dominant MAPK survival pathway.

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

Gated QKAN-FWP: Scalable Quantum-inspired Sequence Learning

arXiv:2605.06734v2 Announce Type: replace-cross Abstract: Fast Weight Programmers (FWPs) encode temporal dependencies through dynamically updated parameters rather than recurrent hidden states. Quantum FWPs (QFWPs) extend this idea with variational quantum circuits (VQCs), but existing implementations rely on multi-qubit architectures that are difficult to scale on noisy intermediate-scale quantum (NISQ) devices and expensive to simulate classically. We propose gated QKAN-FWP, a fast-weight framework that integrates FWP with Quantum-inspired Kolmogorov-Arnold Network (QKAN) using single-qubit data re-uploading circuits as learnable nonlinear activation, known as DatA Re-Uploading ActivatioN (DARUAN). We further introduce a scalar-gated fast-weight update rule that stabilizes parameter evolution, supported by a theoretical analysis of its adaptive memory kernel, geometric boundedness, and parallelizable gradient paths. We evaluate the framework across time-series benchmarks, MiniGrid reinforcement learning, and highlight real-world solar cycle forecasting as our main practical result. In the long-horizon setting with 528-month input window and 132-month forecast horizon, our 12.5k-parameter model achieves lower scaled Mean Square Error (MSE), peak amplitude error, and peak timing error than a suite of classical recurrent baselines with up to 13x more parameters, including Long Short-Term Memory (LSTM) networks (25.9k-89.1k parameters), WaveNet-LSTM (167k), Vanilla recurrent neural network (11.5k), and a Modified Echo State Network (132k). To validate NISQ compatibility, we further deploy the trained fast programmer on IonQ and IBM Quantum processors, recovering forecasting accuracy within 0.1% relative MSE of the noiseless simulator at 1024 shots. These results position gated QKAN-FWP as a scalable, parameter-efficient, and NISQ-compatible approach to quantum-inspired sequence modeling.

09.
arXiv (CS.AI) 2026-06-12

Reasoning as Pattern Matching: Shared Mechanisms in Human and LLM Everyday Reasoning

arXiv:2606.13607v1 Announce Type: new Abstract: When large language models (LLMs) fail to generalize or make haphazard errors in reasoning, it is often taken as evidence that LLMs are not truly reasoning, but rather performing a kind of pattern matching. The implication is that people's behavior does not exhibit the same types of failures because human reasoning uses principled and abstract world models. We evaluate human participants and 25 LLMs on their ability to engage in common-sense reasoning about a variety of everyday situations and observe similar patterns of errors in both people and models. We then identify the set of attention heads driving LLM responses and find that these heads implement a form of pattern-matching. These attention heads allow us to predict seemingly inexplicable reasoning errors in people caused by ostensibly irrelevant prompt details. Taken together, our results suggest that everyday causal reasoning in people and LLMs is more consistent with a form of pattern-matching than with abstract world models.

10.
arXiv (CS.CL) 2026-06-15

OLaPh: Optimal Language Phonemizer

Phonemization is a critical component in text-to-speech synthesis. Traditional approaches rely on deterministic transformations and lexica, while neural methods offer potential for higher generalization on out-of-vocabulary (OOV) terms. We introduce OLaPh (Optimal Language Phonemizer), a hybrid framework that integrates extensive multilingual lexica with advanced NLP techniques and a statistical subword segmentation function. Evaluations on the WikiPron benchmark show OLaPh significantly outperforms established baselines in overall accuracy and maintains robustness on OOV data through advanced fallback mechanisms. To further explore neural generalization, we utilize the framework to synthesize a high-consistency training corpus for an instruction-tuned Large Language Model (LLM). While the deterministic framework remains more accurate overall, the LLM demonstrates strong generalization, matching or partly exceeding the framework's performance. This suggests that the LLM successfully internalized phonetic intuitions from the synthetic data that transcend the framework's capabilities. Together, these tools provide a comprehensive, open-source resource for multilingual grapheme-to-phoneme conversion (G2P) research.

11.
arXiv (math.PR) 2026-06-16

Hua-Chen New Theory of Economic Optimization

arXiv:2504.19134v4 Announce Type: replace-cross Abstract: Between 1957-1985, Chinese mathematician Loo-Keng Hua pioneered economic optimization theory through three key contributions: establishing economic stability's fundamental theorem, proving the uniqueness of equilibrium solutions in economic systems, and developing a consumption-integrated model 50 days before his death. Since 1988, Mu-Fa Chen has been working on Hua's theory. He introduced stochastics, namely Markov chains, to economic optimization theory. He updated and developed Hua's model and came up with a new model (Chen's model) which has become the starting point of a new economic optimization theory. Chen's theory can be applied to economic stability test, bankruptcy prediction, product ranking and classification, economic prediction and adjustment, economic structure optimization. Chen's theory can also provide efficient algorithms that are programmable and intelligent. {Stochastics} is the cornerstone of Chen's theory. There is no overlap between Chen's theory, and the existing mathematical economy theory and the economics developments that were awarded Nobel Prizes in Economics between 1969 and 2024. The distinguished features of Chen's theory from the existing theories are quantitative, calculable, predictable, optimizable, programmable and can be intelligent. This survey provides a theoretical overview of the newly published monograph [5rw24]. Specifically, the invariant of the economic structure matrix, also known as the Chen's invariant, was first published in this survey.

12.
arXiv (CS.LG) 2026-06-19

Optimal Ansatz-free Hamiltonian Learning In Situ

arXiv:2606.19486v1 Announce Type: cross Abstract: Characterizing the features of a Hamiltonian that governs a quantum system serves as a fundamental subroutine of quantum device calibration, signal sensing, and error correction. Recent works proposed protocols have achieved the optimal Heisenberg-limited scaling learning ansatz-free Hamiltonians from their real-time evolutions without fully specifying interaction structures. However, these protocols rely on both deep circuits with interleaving probes and control, and extremely short time resolution, making them difficult to implement on near- and intermediate-term in situ quantum experiments. In this work, we propose a computationally efficient, control-free, and ancilla-free algorithm that uses only Pauli product state preparation and measurement, and learns an ansatz-free Hamiltonian $H$ with $||H||\leq\Lambda$ in total evolution time of $\Theta(\frac{\Lambda}{\epsilon^2}\log(\frac{\Lambda}{\epsilon}))$. The evolution time cost of our algorithm is optimal for any control-free protocols as we further prove a lower bound of $\Omega(\frac{\Lambda}{\epsilon^2}\log(\frac{\Lambda}{\epsilon}))$. Technically, our method introduces a randomized-sampling framework that combines band-limited kernel-based time sampling with a displacement sieve for Hamiltonian structure learning. The characteristic probe time resolution depends only on $\Lambda$ instead of $\varepsilon$, which makes our protocol especially appealing in the high-precision regime for sensing and calibration applications. We also show that the algorithm maintains the same asymptotic total evolution time in the presence of state-preparation-and-measurement (SPAM) noise when the Hamiltonian is local after calibration. Our results demonstrate the fundamental cost of experimentally friendly Hamiltonian learning and provide a practical route to rigorous in situ characterization of near-term quantum platforms.

13.
arXiv (quant-ph) 2026-06-12

Optimal classical shadow estimation of unitary channels at Heisenberg limit

arXiv:2606.13638v1 Announce Type: new Abstract: Full tomography of an unknown quantum evolution is resource-intensive and often unnecessary when the goal is only to predict selected properties. This motivates the study of classical shadow estimation of unitary channels (CSEU), a task in which one queries an unknown $d$-dimensional unitary $U$ and stores classical data that can later be used to predict expectation values $\mathrm{tr}[O \cdot U\rho U^\dagger]$ up to additive error $\varepsilon$ for arbitrary input states $\rho$ and observables $O$. We propose a parallel, non-adaptive CSEU protocol using $\mathcal{O}(d\varepsilon^{-1})$ queries when the input states or observables have constant rank. This achieves Heisenberg scaling with respect to $\varepsilon$ and is query-optimal, as we prove a matching $\Omega(d\varepsilon^{-1})$ lower bound that remains valid even with stronger access to the unknown unitary. Our query-optimal CSEU protocol provides a versatile and powerful tool for quantum learning theory, pushing the performance limits of several fundamental learning tasks, including unitary channel tomography, Hamiltonian learning, boundary-regime quantum channel tomography, Pauli transfer matrix learning, inverse-free amplitude estimation, pure-state property estimation, and shallow-circuit learning. Remarkably, we show that optimal unitary channel tomography can be achieved using only parallel queries, closing the gap between the best achievable efficiency of parallel and sequential tomography protocols. Together, these applications establish our framework as a fundamental tool for learning properties of quantum processes, particularly for certain key tasks that require high precision.

14.
arXiv (CS.CL) 2026-06-15

Indirect Computing Model with Indirect Formal Method

作者:

This paper,from the perspective of a collaborative intelligent computing system formed by combining human-computer interface and collaborative computing programs, discusses the principles of optimized cloud computing technology supported by the combination of an indirect computing model and an indirect formal method. On the basis of systematically reviewing the influence of previous theoretical achievements Turing's computability theory,Kleene's formal theory of small strings,von Neumann's digital computer architecture and Turing's hypothesis on AI judgment on the mainstream general-purpose digital computer paradigm,the author focuses on introducing an indirect computing model and an indirect formal theory compatible with both large and small strings. Using Chinese information data as an example,the design concept of a collaborative intelligent computing system prototype is presented. The significance is that this achievement facilitates optimization of cloud computing from data centers to knowledge centers.

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

CacheRL:Multi-Turn Tool-Calling Agents via Cached Rollouts and Hybrid Reward

We present CacheRL, a system for training small agent foundation models that achieves 92 percent process accuracy on multi-step tool-calling tasks, approaching GPT-5's 94 percent while requiring 100 times less compute. Our approach addresses three challenges in practical agent training: transferring tool-calling knowledge from large models at scale, enabling reinforcement learning without costly live tool execution, and learning robustly from noisy cached environments. CacheRL introduces three key innovations. First, a hybrid thinking trajectory pipeline augments agent trajectories with LLM-generated reasoning traces, producing training examples that teach models not only what tools to call but also why. Second, the CacheAgentLoop eliminates live execution costs through a three-tier fuzzy cache while preserving trajectory fidelity using token-level masking. Third, a cache-tier-aware reward dynamically adjusts answer-quality weights to avoid penalizing models for cache-induced limitations. Through iterative supervised fine-tuning (SFT) and Group Relative Policy Optimization (GRPO), CacheRL improves Qwen3-4B-Thinking's validation reward from 0.43 to 0.78. On public agentic tool-calling benchmarks, our model achieves competitive performance against frontier models such as GPT-5. Ablation studies show that removing knowledge transfer reduces performance by 41 percent, while cache-aware rewards contribute a 17 percent improvement. Interestingly, reinforcement learning improves training stability but yields limited gains beyond strong supervised fine-tuning, suggesting that data quality and reward design play a more important role than complex optimization methods in building practical small agent models.

16.
arXiv (quant-ph) 2026-06-19

Anomalous magneto-optical response at $\mathrm{RuO_2 / WSe_2}$ van der Waals interface

arXiv:2606.20262v1 Announce Type: cross Abstract: Ruthenium dioxide ($\mathrm{RuO_2}$) has been proposed as an altermagnetic candidate, although its magnetic ground state remains controversial. Here, we probe weak interfacial magnetic states at the surface of (001)-oriented $\mathrm{RuO_2}$ films using the magnetic proximity effect (MPE) in a van der Waals heterostructure consisting of monolayer tungsten diselenide ($\mathrm{WSe_2}$) atop $\mathrm{RuO_2}$. Temperature-dependent magneto-optical spectroscopy reveals an anomalous excitonic energy shift and a deviation from conventional Varshni behavior below 55 K that are absent in an encapsulated $\mathrm{WSe_2}$ control sample. The anomalous shift reverses sign upon field cooling with opposite magnetic field polarity, indicating a magnetic origin. Polarization-resolved measurements further show a nearly field-independent and fluctuating valley splitting in $\mathrm{WSe_2 / RuO_2}$ in strong contrast to the conventional linear Zeeman splitting observed in the control bare $\mathrm{WSe_2}$ sample. These results suggest that the valley states are governed predominantly by interfacial exchange fields associated with weak surface magnetic states in $\mathrm{RuO_2}$, which do not produce a conventional linear Zeeman response within the applied magnetic field range. Importantly, this approach enables direct optical probing of emergent surface magnetism without introducing an additional ferromagnetic layer, positioning MPE-based optical probing as a tool for investigating weak surface magnetism and offering new possibilities for studying magnetic materials with controversial magnetic states.

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

Bayesian Inference and Decision Audits for Public Archives of Frontier AI Evaluations

作者:

arXiv:2606.17005v1 Announce Type: new Abstract: Public AI evaluations are often read as terminal leaderboards, yet the underlying evidence is a selective time series shaped by reporting rules, benchmark revisions, and missingness. Repeated public archives for LiveBench and Open LLM Leaderboard v2 serve as the primary longitudinal record; LMArena provides a preference stress test; and GAIA and tau-bench contribute limited agentic pilots. Together, these archives instantiate a Bayesian inference problem: under a fixed reporting convention, one constructed terminal-only example over $1{,}000$ systems is compatible with two pre-terminal histories, yielding times of $23.03$ or $75.13$ to reach within $0.05$ of the ceiling under the same terminal-tail model. In synthetic posterior comparisons, action-facing diagnostics differ across observation regimes. The candidate selection-aware frontier model fails synthetic recovery, objective-archive prediction, preference transfer, and uncertainty calibration; correspondingly, fixed audit gates reject its stronger claims. An archive-and-adjudication protocol reconstructs public evaluation histories, isolates a verified timing boundary, and falsifies unsupported frontier claims.

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

Benchmarking Web Agent Safety under E-commerce Deceptive Interfaces

As autonomous web agents are increasingly deployed to perform real-world tasks, ensuring their safety has become a critical concern. In this work, we study web agent behavior under realistic deceptive interfaces in the e-commerce domain. We introduce WebDecept, a lightweight and configurable plugin framework that enables controlled injection of deceptive interface patterns into existing web environments. Using WebDecept, we instantiate seven deceptive patterns commonly observed on the open web, including targeted advertisements, domain redirection, and shopping manipulation. By injecting these patterns into the frontend during task execution, we perform controlled evaluation of multiple multimodal web agents. Our results show that current web agents are highly susceptible to multiple classes of deceptive interfaces, and that prompt-based constraints are often insufficient to mitigate these failures. We further analyze how the design choices of deceptive patterns influence the success of such manipulations. These findings highlight safety challenges that should be addressed as web agents are scaled toward real-world deployment.

19.
bioRxiv (Bioinfo) 2026-06-21

DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads

Accurate coding sequence prediction in short prokaryotic metagenomic reads remains challenging due to sequence fragmentation, unknown sequence origins, and sequencing errors. Here we introduce DeepCDS, a deep learning-based ab initio coding sequence predictor trained on short prokaryotic sequences with and without simulated Illumina-like sequencing errors. DeepCDS integrates ESM-2 protein language model embeddings with nucleotide-level information to predict complete and fragmented coding sequence regions. Benchmarking on 215 phylogenetically diverse prokaryotic organisms demonstrates that DeepCDS consistently outperforms current state-of-the-art methods in coding sequence detection, start and stop codon localization, and robustness to different sequencing error profiles, while remaining operational at shorter sequence lengths than existing tools support. These findings demonstrate that protein language models capture distinct signals relevant for nucleotide-level coding sequence detection, especially at very short lengths. Ultimately, DeepCDS may help uncover the functional potential of the vast microbial diversity that remains genomically uncharacterized.

20.
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.

21.
arXiv (math.PR) 2026-06-15

Sectional Curvature for Kantorovich-Wasserstein and Hellinger-Kantorovich Geometries

arXiv:2606.14318v1 Announce Type: cross Abstract: We derive an explicit formula for the sectional curvature of the space ${\cal M}(M)$ of finite measures on a Riemannian manifold M. The space ${\cal M}(M)$ is equipped with the Hellinger-Kantorovich metric $HK$. Even in the case M=R^n, the curvature is comprised of two parts: the `lifted part' is negative, and the `twisted part' is positive. It will be analyzed in detail for the multidimensional torus. Our general approach to sectional curvature in geodesic spaces also leads to new insights into the curvature of the space $P_2(M)$ of probability measures on M equipped with the Kantorovich-Wasserstein metric $W_2$.

22.
arXiv (CS.CL) 2026-06-18

ScholaWrite: A Dataset of End-to-End Scholarly Writing Process

Writing is a cognitively demanding activity that requires constant decision-making, heavy reliance on working memory, and frequent shifts between tasks of different goals. To build writing assistants that truly align with writers' cognition, we must capture and decode the complete thought process behind how writers transform ideas into final texts. We present ScholaWrite, the first dataset of end-to-end scholarly writing, tracing the multi-month journey from initial drafts to final manuscripts. We contribute three key advances: (1) a Chrome extension that unobtrusively records keystrokes on Overleaf, enabling the collection of realistic, in-situ writing data; (2) a novel corpus of full scholarly manuscripts, enriched with fine-grained annotations of cognitive writing intentions. The dataset includes \LaTeX-based edits from five computer science preprints, capturing nearly 62K text changes over four months; and (3) analyses and insights into the micro-dynamics of scholarly writing, highlighting gaps between human writing processes and the current capabilities of large language models (LLMs) in providing meaningful assistance. ScholaWrite underscores the value of capturing end-to-end writing data to develop future writing assistants that support, not replace, the cognitive work of scientists.

23.
arXiv (CS.AI) 2026-06-11

Mind the Perspective: Let's Reason Recursively for Theory of Mind

arXiv:2606.11724v1 Announce Type: new Abstract: Theory of Mind (ToM) reasoning requires inferring agents' beliefs from partial and asymmetric observations, which remains an open challenge for LLMs. Existing prompting-based approaches improve ToM reasoning through observable-event filtering or temporal belief chains, without explicitly modeling nested beliefs. We introduce RecToM, an inference-time framework for ToM reasoning that models nested beliefs via recursive perspective construction. RecToM constructs each character perspective from the preceding character perspective along the character chain specified by the question, reducing higher-order belief questions to actual-world questions within the final constructed perspective. We further provide a KD45 analysis showing that RecToM's perspective construction induces a well-formed belief modality beyond simple event filtering. Experiments on ToM benchmarks, including Hi-ToM, Big-ToM, and FanToM, across multiple LLM backbones show that RecToM consistently outperforms recent advanced approaches, achieving state-of-the-art performance. Notably, RecToM reaches 100\% accuracy on Hi-ToM with GPT-5.4 and Qwen3.5, a benchmark requiring higher-order ToM reasoning.

24.
arXiv (CS.CV) 2026-06-11

Cross-Modal Benchmarking for Robotic Perception in Natural Environments

Natural environments present a complex challenge to robotics perception systems. Current models, particularly vision foundation models, are largely trained on structured, urban environments leading to weaknesses in their perception for field robotics tasks. We showcase the limitations of current models using our recently released WildCross benchmark, a new cross-modal benchmark for place recognition and metric depth estimation in large-scale natural environments. WildCross comprises over 476K sequential RGB frames with semi-dense depth and surface normal annotations, each aligned with accurate 6DoF pose and synchronized dense lidar submaps. In this work, we provide an expanded analysis of the benchmark results from the recent WildCross benchmark, with particular emphasis on expanded metric depth estimation experiments. Access to the code repository and dataset for this work can be found at https://csiro-robotics.github.io/WildCross.

25.
arXiv (CS.LG) 2026-06-15

EM-NeSy: Expectation Maximization for Neurosymbolic Learning

arXiv:2606.14463v1 Announce Type: new Abstract: Neurosymbolic (NeSy) models integrate neural networks and symbolic reasoning for robust and interpretable AI. State-of-the-art NeSy models require that the symbolic component is expressed in a differentiable way, often complicating the use of approximate inference. We propose EM-NeSy which casts probabilistic NeSy learning as an instance of the Expectation-Maximization (EM) algorithm. In the expectation step, we compute the posterior over the neurally predicted symbols conditioned on the label via probabilistic inference. In the maximization step, we update the neural parameters based on this posterior using gradient descent only through the neural component. This formulation unlocks the full potential of the EM algorithm for NeSy learning. It allows NeSy to extend naturally to approximate reasoning without any additional modifications or differentiability requirements of the symbolic component. Furthermore, it recovers the standard end-to-end gradient-based NeSy setting under exact inference. Our experimental results demonstrate the scalability and computational efficiency of EM-NeSy.