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02.
arXiv (CS.CV) 2026-06-17

Universal Image Restoration via Internalized Chain-of-Thought Reasoning

Image restoration seeks to recover high-quality images from degraded inputs but becomes highly ill-posed under complex, mixed degradations. While unified all-in-one models are common, their performance declines as degradation complexity increases. Recent works adopt Chain-of-Thought (CoT) reasoning for multi-round restoration using specialized modules. However, this approach faces two key limitations: (i) increased computational cost due to multi-step processing, and (ii) weak modeling of interactions between degradations during stepwise inference. We introduce CoTIR, a universal image restoration framework that internalizes CoT reasoning within a single model. Concretely, we view image restoration as a specialized subtask of image editing, which implies that a large-scale pre-trained editing model provides a more favorable optimization starting point. Building on this, we fine-tune the model for restoration and further encode structured CoT-style reasoning into the learning objective via a differentiable formulation inspired by Lagrangian optimization, enabling holistic restoration without chaining specialized restorers. To facilitate training and evaluation, we further present CoTIR-Bench, a large-scale benchmark comprising 5.2 million samples with CoT-style reasoning traces. Extensive experiments on CoTIR-Bench and broad real composite degradation scenes show that CoTIR achieves stronger perceptual quality and more competitive fidelity than both all-in-one models and multi-round restoration methods. The source code is available at https://github.com/gy65896/CoTIR.

03.
medRxiv (Medicine) 2026-06-12

Opportunistic CKD Screening in Hospitalized Patients

Background. Chronic kidney disease (CKD) affects 10-13% of adults worldwide but remains largely undiagnosed until advanced stages. Hospitalization provides an opportunity for early detection through opportunistic urine albumin-to-creatinine ratio (UACR) measurement. Methods. We conducted a prospective three-arm study of opportunistic CKD screening in general internal medicine wards at Hadassah Mt. Scopus (MS), Hadassah Ein Kerem (EK), and Shaare Zedek Medical Center (SZMC) in Jerusalem (Protocol HMO-23-0300). Adult inpatients without known CKD or recent UACR were enrolled. Pathological UACR was defined as [≥]30 mg/g. Confirmed CKD required two pathological measurements [≥]90 days apart (KDIGO-compatible). eGFR was computed using the 2021 CKD-EPI race-free equation. Pooled proportions were estimated by fixed-effects logit meta-analysis; odds ratios by DerSimonian-Laird random-effects models. Results. A total of 158 patients were enrolled (MS n=50, EK n=57, SZMC n=51). Pathological first UACR was identified in 43/158 patients (27.2%; 95% CI 21.3-34.1%; I2=0% across centers). Of 24 patients with a second UACR available, 14 (58%) confirmed CKD, yielding a pooled confirmed-CKD rate of 8.9% of all screened patients. In-hospital mortality was significantly higher among patients with pathological UACR (9.3% vs ~2%; Fisher's exact p=0.012). In per-center multivariate logistic regression, three predictors reached pooled significance: BUN (OR 1.10 per mg/dL, 95% CI 1.04-1.17, p=0.002, I2=0%), heart failure (OR 3.21, 95% CI 1.34-7.70, p=0.009, I2=0%), and diabetes mellitus (OR 2.54, 95% CI 1.11-5.82, p=0.028, I2=17%). Cardiac/vascular admissions had the highest pathological UACR rate (~42%); GI/hepatic admissions had 0%. Conclusions. Opportunistic inpatient UACR screening identifies previously unrecognized CKD in approximately 9% of general internal medicine patients, with consistent results across three independent centers. BUN elevation, heart failure, and diabetes are the strongest independent predictors. Pathological UACR carries significant short-term mortality risk, supporting integration of routine screening into inpatient care pathways.

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

Spectro-Temporal Interference Confounds Phase Encoding in Spatial Audio Foundation Models

Recent spatial self supervised audio models achieve high performance on localization tasks, raising questions about their encoding of microsecond interaural phase fine structures. We propose a psychoacoustic benchmark based on the binaural masking level difference to evaluate this. Using an equalization cancellation baseline and a GCC PHAT positive control we evaluate nine frozen audio models spanning binaural SSL, monaural SSL, and neural audio codecs. Four monaural negative controls yield zero BMLD confirming binaural specificity. Two general purpose binaural SSL models exhibit minimal phase sensitivity while dedicated binaural spatial SSL models achieve BMLD comparable to the analytical baseline. Progressive physical ablations show that general purpose binaural SSL models rely on spectro temporal interference textures rather than cross channel phase computation. High detection rates in speech reflect a confounding reliance on broadband envelopes rather than genuine phase encoding.

05.
arXiv (CS.CV) 2026-06-16

The Importance of Phase in Neural Representations: An Internal Oppenheim-Lim Test of Image Classifiers

Oppenheim and Lim (1981) showed that natural images stay recognizable when reconstructed from their Fourier phase alone, while the magnitude carries little of their identity. We ask whether trained image classifiers reproduce this asymmetry inside their hidden layers, and we test it causally: given two images, we transplant the phase of one onto the magnitude of the other at a chosen layer and record which image the prediction follows. In PRISM2D, GFNet, and ViT-B/16 the prediction follows the phase or sign donor, and deleting all image-specific magnitude barely moves accuracy, so identity rides on phase while image-specific magnitude is largely dispensable to the readout. ResNet-50 at first seems to break the pattern, because transplanting sign after its ReLUs does nothing; a fair intervention before the ReLU reveals a strong latent sign code in the late blocks, and a DC-only control shows the readout consumes a channel-wise spatial average. Controls rule out the trivial case in which magnitude simply stops depending on the image. The architectures therefore share a phase/sign identity code but expose it in different bases, set by rectification and readout geometry, which gives a mechanistic account of the texture–shape gap between CNNs and attention models.

06.
medRxiv (Medicine) 2026-06-15

Iron deficiency testing among people with incident heart failure in primary care

Background: Given around 50% of people with heart failure have a degree of iron deficiency, guidelines recommend screening. It is uncertain to what extent this is done in primary care and whether testing is equitable. Aim: To report the proportion of people with incident heart failure who undergo a ferritin test within 12 months. Design and setting: Retrospective primary care cohort study using Clinical Practice Research Datalink Aurum data, between 2016 and 2021. Methods: We report the proportion of adults with an incident diagnosis of heart failure who received a ferritin test within 12 months. Multivariable logistic regression was used to examine the odds of testing based on key demographic covariates and co-morbidities. Results: Among 105,749 individuals with an incident diagnosis of heart failure (mean age 71.6 years, SD 14.3), only 35,688 (33.7%) received a ferritin test within the subsequent year. Increasing age (odds ratio 1.25 per 10-year increase, 95% CI: 1.24-1.27), female sex (male sex OR 0.86, 0.84-0.89) and Asian ethnicity (OR 1.70, 1.59-1.80) were all associated with increased odds of testing as were diagnoses of coeliac disease (OR 1.86, 1.58-2.21), type 1 diabetes (OR 1.82, 1.51-2.19) and cirrhosis (OR 1.64, 1.43-1.87). There was geographic variation in testing, even in adjusted analyses. Conclusion: In a large primary care dataset, two thirds of people with incident heart failure did not receive a ferritin test for iron deficiency within a year of diagnosis demonstrating a gap in current practice and an opportunity for improvements in service delivery.

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

ScholarSum: Student-Teacher Abstractive Summarization via Knowledge Graph Reasoning and Reflective Refinement

Abstractive summarization plays a crucial role in enabling efficient understanding of scientific literature, yet it inherently demands both linguistic fluency and factual faithfulness. Existing approaches often fail to reconcile these two requirements. Extractive methods rely on rigid sentence splicing that disrupts macro-level logical coherence, while large language model (LLM)-based generative approaches, despite mastering linguistic fluency, exhibit limited factual consistency. In this work, we propose ScholarSum, a hierarchical reflective graph-based framework that emulates a student-teacher writing process for fluent and faithful scientific summarization. ScholarSum first organizes the document into a hierarchical knowledge graph by segmenting it into semantically coherent units, whose multi-layered community structure captures global logic and macro-level themes. Guided by this global structure, the student generates an initial draft, which is subsequently refined through fine-grained evidence retrieval. To ensure factual consistency, a teacher-like reviewer then iteratively examines the draft, identifies unsupported content, and prompts targeted re-retrieval and rewriting until the summary meets rigorous quality standards. Extensive experiments demonstrate that ScholarSum significantly outperforms previous baselines in terms of both completeness and faithfulness. Our code is available at https://github.com/Xiaoyu-Tao/ScholarSum.

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

Mutual Distillation of Dual-Foundation Models for Semi-Supervised PET/CT Segmentation

Organ segmentation from PET/CT is critical for quantitative analysis and radiotherapy planning in oncology. To ease the high annotation cost of PET/CT segmentation, semi-supervised learning (SSL) provides a practical and effective solution for developing deep models with limited labeled data. Recent developments in visual foundation models have demonstrated remarkable adaptability with improved efficiency. In this work, we propose a mutual distillation framework that seamlessly exploits both structural and functional foundation models, which act as modality-specific generalists for distilling knowledge from structural CT and metabolic PET imaging. By bridging the gap between the task-specific precision of student models and the segmentation priors of generalist foundation models, we propose MuDuo, a mutual distillation framework that synergistically leverages SAM-Med3D for CT and SegAnyPET for PET to distill their knowledge into a lightweight student network. Our approach eliminates the need for manual prompts while maximizing the utility of unlabeled data for automatic segmentation, achieving state-of-the-art performance on the AutoPET dataset with only 5 labeled cases. Our source code is available at https://github.com/Wu-beining/MuDuo.

09.
arXiv (CS.AI) 2026-06-24

Cycle-Consistent Neural Explanation of Formal Verification Certificates

arXiv:2606.24414v1 Announce Type: new Abstract: Formal verification produces machine-checkable certificates that attest to the satisfaction or violation of temporal properties, yet these certificates remain opaque to non-specialist stakeholders. We propose a cycle-consistent neural architecture that generates faithful natural language explanations of verification certificates. A forward network NN1 maps certificates to explanations, and an inverse network NN2 reconstructs certificates from explanations; a symbolic verifier closes the loop, providing a differentiable faithfulness proxy. A pointer-generator mechanism ensures lexical grounding by copying state names directly from the certificate. We evaluate on 420 test certificates spanning six verification methods (bounded proof, k-induction, inductive invariant, lasso, reachability, witness pair) in both YES and NO verdict variants, drawn from a financial compliance domain with 207 named states. Our trained architecture, combined with a hybrid inference-time routing strategy, achieves 90.0% cycle-verified soundness, surpassing a multi- LLM few-shot baseline (76.1% for the best of 16 LLM combinations across four frontier models) by 13.9 percentage points. The neural model wins on 10 of 12 verdict/kind categories, with three categories reaching 100% soundness. The architecture offers 860x faster inference (185 ms vs. 160 s per certificate for the full multi-LLM baseline), offline operation, deterministic outputs, and zero per-inference cost. These results demonstrate that trained specialization outperforms general-purpose LLM prompting for structured certificate explanation, while eliminating the deployment constraints of cloud-based inference.

10.
arXiv (CS.CL) 2026-06-24

On the Stability of Prompt Ranking in Large Language Model Evaluation

Prompt-based interaction has become a dominant paradigm for using large language models (LLMs), where multiple candidate prompts are evaluated and the top-ranked one is selected for downstream use. This workflow implicitly assumes that prompt rankings are stable under minor variations in evaluation conditions. In this paper, we systematically study prompt ranking stability under common sources of variability, including random seeds and limited evaluation subsets. Across three open-weight LLMs and two benchmark tasks, we find that while overall rank correlations are often moderate to high, the identity of the top-performing prompt frequently changes, leading to unreliable selection decisions. To address this issue, we propose a simple stability-aware selection strategy based on a lower confidence bound, which accounts for both performance and variance. Our results show that this approach improves robustness in unstable settings while remaining competitive in more stable regimes. These findings highlight the importance of accounting for evaluation uncertainty in prompt selection and LLM benchmarking.

11.
medRxiv (Medicine) 2026-06-17

Targeted Proteomic Profiling of Nasal Fluid from the Brain-Nose Interface

The brain-nose interface is an anatomical junction where olfactory neurons from the olfactory bulb traverse the cribriform plate into the nasal mucosa, providing minimally invasive access to the central nervous system (CNS). We hypothesized that nasal fluid from this region could enable detection of neurology-relevant proteins using targeted multiplex assays. Using nosecollect, a targeted nasal sampling device, nasal fluid proximal to brain-nose interface was collected from cognitively impaired patients, alongside matched cerebrospinal fluid (CSF) and plasma. After nasal sample-specific dilution optimization and intra-assay precision evaluation, all matrices were profiled with the Olink Target 96 Neurology and NUcleic acid Linked Immuno-Sandwich Assay CNS disease 120 (NULISAseq CNS Disease 120) panels. Nasal fluid showed technically repeatable detection (intra-assay coefficient of variation

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

Symmetry-Accelerated Classical Simulation of Clifford-Dominated Circuits

arXiv:2510.18977v2 Announce Type: replace Abstract: Classical simulation of quantum circuits plays a crucial role in validating quantum hardware and delineating the boundaries of quantum advantage. Among the most effective simulation techniques are those based on the stabilizer extent, which quantifies the overhead of representing non-Clifford operations as linear combinations of Clifford unitaries. However, finding optimal decompositions rapidly becomes intractable as it constitutes a superexponentially large optimization problem. In this work, we exploit symmetries in the computation of the stabilizer extent, proving that for real, diagonal, and real-diagonal unitaries, the optimization can be restricted to the corresponding subgroups of the Clifford group without loss of optimality. This ``strong symmetry reduction'' drastically reduces computational cost, enabling optimal decompositions of unitaries on up to seven qubits using a standard laptop – far beyond previous two-qubit limits. Additionally, we employ a ``weak symmetry reduction'' method that leverages additional invariances to shrink the search space further. Applying these results, we demonstrate exponential runtime improvements in classical simulations of quantum Fourier transform circuits and measurement-based quantum computations on the Union Jack lattice, as well as new insights into the nonstabilizer properties of multicontrolled phase gates and unitaries generating hypergraph states. Our findings establish symmetry exploitation as a powerful route to scale classical simulation techniques and deepen the resource-theoretic understanding of quantum advantage.

13.
arXiv (CS.CL) 2026-06-11

Breaking Entropy Bounds: Accelerating RL Training via MTP with Rejection Sampling

Reinforcement learning (RL) has become a key component in modern large language models, yet the rollout stage remains the key bottleneck in RL training pipelines. Although Multi-Token Prediction (MTP) offers a natural solution to accelerate rollouts through speculative decoding, many studies have observed that MTP acceptance rates degrade significantly during RL training, leading to limited speedup performance. To address this bottleneck, we present Bebop, a systematic study of MTP in LLM post-training, and offer practical recipes to integrate MTP into large-scale RL pipelines. First, we reveal that the MTP acceptance rate is fundamentally bounded by the fluctuation of model entropy, which demonstrates a clear negative linear relationship with the rise of entropy in the RL stage. Second, we show that probabilistic rejection sampling largely alleviates the disturbance introduced by entropy in RL compared to greedy draft sampling. We further identify that the conventional MTP training objectives (cross-entropy or KL) are suboptimal in such settings, and therefore we propose a novel end-to-end TV loss that directly optimizes multi-step rejection sampling acceptance rate, yielding ~10% acceptance rate improvements, achieving up to 95% acceptance rates and up to 25% extra inference throughput gains across mathematical reasoning, code generation, and agentic tasks. Third, we test various online MTP training strategies during RL and show that pre-RL MTP training with e2e TV loss and rejection sampling achieves a consistent acceptance rate and speedup throughout the entire RL, eliminating the need for costly online MTP updating. We provide extensive experiments and analysis that validate our findings. Experimental results show our method achieves up to 1.8x end-to-end acceleration in async RL training of Qwen3.5, Qwen3.6, and Qwen3.7 models.

14.
arXiv (CS.AI) 2026-06-24

LLM-MINE: Large Language Model based Alzheimer's Disease and Related Dementias Phenotypes Mining from Clinical Notes

arXiv:2603.13673v2 Announce Type: replace Abstract: Accurate extraction of Alzheimer's Disease and Related Dementias (ADRD) phenotypes from electronic health records (EHR) is critical for early-stage detection and disease staging. However, this information is usually embedded in unstructured textual data rather than tabular data, making it difficult to be extracted accurately. We therefore propose LLM-MINE, a Large Language Model-based phenotype mining framework for automatic extraction of ADRD phenotypes from clinical notes. Using two expert-defined phenotype lists, we evaluate the extracted phenotypes by examining their statistical significance across cohorts and their utility for unsupervised disease staging. Chi-square analyses confirm statistically significant phenotype differences across cohorts, with memory impairment being the strongest discriminator. Few-shot prompting with the combined phenotype lists achieves the best clustering performance (ARI=0.290, NMI=0.232), substantially outperforming biomedical NER and dictionary-based baselines. Our results demonstrate that LLM-based phenotype extraction is a promising tool for discovering clinically meaningful ADRD signals from unstructured notes.

15.
arXiv (CS.AI) 2026-06-16

AgenticRec: A Recommendation-Oriented Agentic Framework with Progressive Tool-Integrated Reasoning Optimization

arXiv:2603.21613v2 Announce Type: replace-cross Abstract: Recommender agents built on Large Language Models offer a promising paradigm for personalized recommendation. However, existing agents typically suffer from a misalignment between their tool-integrated reasoning trajectories and recommendation feedback, limiting their ability to distinguish fine-grained user preferences. To address these challenges, we propose AgenticRec, an agentic recommendation framework that formulates recommendation as a tool-integrated reasoning process over a recommendation-oriented tool suite. Built upon this framework, we further develop a dedicated two-stage training paradigm tailored for recommender agents. In the first stage, we introduce Recommendation-Oriented Trajectory Activation, optimize the agentic recommendation ability under implicit feedback. In the second stage, Progressive Preference Refinement further refines the agent through bidirectional preference reasoning over self-bootstrapped hard pairs, progressively sharpening preference boundaries. Theoretical analysis and extensive experiments demonstrate the effectiveness of AgenticRec. Our code is available at https://anonymous.4open.science/r/AgenticRec-FB16.

16.
arXiv (CS.AI) 2026-06-15

Sorries Are Not the Hard Part: An Expert-Review Case Study of a Semi-Autonomous Formalization

arXiv:2606.13925v1 Announce Type: new Abstract: Large language models can often close proof gaps in interactive theorem provers, but a verified theorem is not the same thing as a reusable library contribution. We study this distinction through a detailed case study: a semi-autonomous formalization of Grothendieck's vanishing theorem. The initial version compiles with no sorries, but an expert review found serious problems in definitions, theorem generality, file organization, and the API. We then ran a review-driven refactor and compression process and obtained a second expert review. The before-and-after comparison shows a sharp split: agents adapted well to local, mechanically checkable feedback, but remained weak at choosing definitions and designing APIs. We argue that autoformalization should be evaluated not only by closed sorries, but by whether the resulting formalization survives expert review.

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

Lifecycle-Aware Dynamic Analysis for Secure ML Model Execution

arXiv:2606.19023v1 Announce Type: cross Abstract: The growing reliance on pre-trained Machine Learning (ML) models has introduced new attack surfaces. Recent vulnerabilities demonstrate that malicious behavior can be embedded within model artifacts, often bypassing existing defenses. Current model-scanning solutions primarily rely on static, format-specific rules or known attack signatures, which limit their ability to generalize across frameworks and to detect novel exploitation paths. In contrast, we propose a solution that focuses on the effects an attack has on the host system executing the model and builds on foundational intuitions about ML model execution. In particular, we observe that ML models operate within well-defined lifecycle phases and that, within each phase, interactions with the host system are highly structured and predictable. We translate these intuitions into Moat, a dynamic lifecycle-aware approach for securing ML model execution, and instantiate this design in Re-Moat, our reference implementation. We evaluate Re-Moat across multiple ML frameworks using 77,974 real-world model artifacts from the Hugging Face Hub, 31 Proofs-of-Concept (PoCs) from CVEs, and 334 models from a state-of-the-art dataset, and compare it against state-of-the-art model-scanning solutions. Our results show that our approach detects all evaluated attack classes while maintaining a close-to-zero false-positive rate, validating our intuitions and motivating dynamic analysis for securing ML model execution.

18.
arXiv (CS.LG) 2026-06-12

Understanding Truncated Positional Encodings for Graph Neural Networks

arXiv:2606.13671v1 Announce Type: new Abstract: Positional encodings (PEs) enhance the power of graph neural networks (GNNs), both theoretically and empirically. Two of the most popular families of PEs - spectral (e.g., Laplacian eigenspaces, effective resistance) and walk-based (polynomials of the adjacency matrix) - are theoretically equivalent in expressive power, with expressivity between the 1-WL and 3-WL tests. However, this equivalence assumes the GNN uses the "complete" version of these PEs, which requires $O(n^3)$ time and space complexity. Instead, practitioners commonly use truncated variants of these encodings, such as the first $k$ eigenspaces or powers of the adjacency matrix. However, the theoretical properties of these truncated PEs are unknown. In this work, we initiate the study of these truncated PEs. Theoretically, we show that, under truncation, several families of PEs are fundamentally different in expressive power. As a corollary, we show that truncated spectral PEs are no longer stronger than the 1-WL test. We also study a family of spectral PEs, the $k$-harmonic distances, to highlight the differences in expressive power of even closely related truncated PEs. Finally, we experimentally show that a mix of truncated PEs is preferable to any single family on real-world datasets.

19.
arXiv (CS.CV) 2026-06-11

Image Quality Assessment of Identity Cards Using Measures from Open Face Image Quality

This paper addresses the challenge of assessing image quality in ID cards in remote verification systems by applying capture-related quality measures from the Open Face Image Quality (OFIQ) standard to ID card images. Our preprocessing pipeline includes corner detection, perspective normalization, and comprehensive foreground masking to ensure accurate and unbiased quality measure computation. We evaluate the effectiveness of these measures by analyzing their correlation with the performance of three presentation attack detection (PAD) algorithms across four diverse ID card datasets, where two datasets contain bona fide, i.e. pristine, images and two contain printed mock ID cards. Our results suggest that quality assessment based on some OFIQ measures can significantly improve PAD performance.

20.
PLOS Computational Biology 2026-06-09

Multi-stable oscillations in cortical networks with two classes of inhibition

by Arnab Dey Sarkar, Bard Ermentrout In the classical view of cortical rhythms, interactions between excitatory pyramidal neurons (E) and inhibitory parvalbumin-expressing interneurons (I) are sufficient to generate gamma- and beta-band oscillations. However, it is now well established that multiple inhibitory interneuron subtypes exist and that they play important roles in the generation and modulation of these rhythms. In this paper, we develop a spiking network model consisting of populations of E, I, and an additional interneuron type, somatostatin-expressing neurons (S), which receive excitation from the E cells and inhibit both the E and I populations. The S cells are further modulated by a third inhibitory subtype, vasoactive intestinal peptide (VIP) neurons, which receive inputs from other cortical areas. We reduce the spiking network to a system of nine differential equations that describe the mean membrane potential, firing rate, and synaptic conductance for each population. Using this reduced model, we identify a wide range of parameters that exhibit multiple coexisting rhythms. Employing tools from nonlinear dynamics, we then explore the roles of the two classes of inhibition, as well as VIP modulation, in shaping the properties of these rhythms.

21.
arXiv (CS.CL) 2026-06-16

OBCache: Optimal Brain KV Cache Pruning for Efficient Long-Context LLM Inference

Large language models (LLMs) with extended context windows enable powerful applications but impose significant memory overhead, as caching all key-value (KV) states scales linearly with sequence length and batch size. Existing cache eviction methods address this by exploiting attention sparsity, yet they typically rank tokens heuristically using accumulated attention weights without considering their true impact on attention outputs. We propose Optimal Brain Cache (OBCache), a principled framework that formulates cache eviction as a layer-wise structured pruning problem. Building upon the Optimal Brain Damage (OBD) theory, OBCache quantifies token saliency by measuring the perturbation in attention outputs induced by pruning tokens, with closed-form scores derived for isolated keys, isolated values, and joint key-value pairs. Our scores account not only for attention weights but also for information from value states and attention outputs, thereby enhancing existing eviction strategies with output-aware signals. Experiments on LLaMA and Qwen models demonstrate that replacing the heuristic scores in existing works, which estimate token saliency across different query positions, with OBCache's output-aware scores consistently improves long-context accuracy. Code is available at https://github.com/DreamSoul-AI/OBCache.

22.
arXiv (CS.CL) 2026-06-11

AI Coding Agents Can Reproduce Social Science Findings

Recent anecdotal evidence suggests that AI coding agents can reproduce published findings when provided with original data and code; yet systematic evaluation across social sciences remains limited. Existing evaluation benchmarks are insufficient, either small or conflate agent performance with problems in the reproduction materials themselves, such as code that fails to execute correctly. Here we introduce SocSci-Repro-Bench, a benchmark of 221 tasks spanning four disciplines and 13 substantive domains, constructed from studies whose results are either fully reproducible with available materials or demonstrably non-reproducible due to missing data, allowing us to isolate agents' reproduction capacity. Evaluating two frontier coding agents, Claude Code and Codex, we find that both can reproduce a large share of social science findings, with Claude Code substantially outperforming Codex. These reproduction rates considerably exceed those previously reported for general-purpose LLM-based agents on comparable reproducibility benchmarks. Both agents also perform strongly on a reasoning task requiring identification of underlying research questions, and additional analyses suggest that results are not primarily driven by memorization. Providing the original paper PDF alongside replication materials modestly improves performance but introduces bias on tasks where reproduction is impossible. We also show that agents can be nudged toward confirmatory specification search through subtle prompt framing. Together, these findings suggest that at least some frontier coding agents can serve as reliable executors of computational workflows while underscoring the need for careful benchmarking and prompt design as AI systems assume larger roles in scientific production.

23.
arXiv (CS.LG) 2026-06-19

Computational Methods and Challenges in Cell-Free DNA Analysis for Multi-Cancer Early Detection

arXiv:2606.20174v1 Announce Type: new Abstract: Cell-free DNA (cfDNA) is a promising avenue for non-invasive multicancer early detection (MCED), in that, it can enable multiple cancer detection simultaneously from a single blood draw, with particular sensitivity to cancers that currently lack established screening programs. Here we review the computational methods developed between 2022 and 2025 for cfDNA-based MCED. We focus on how fragmentomics and epigenetic features are extracted and analyzed to detect cancer at early stages. We first briefly outline the biological basis of cfDNA signals, then review classical statistical and machine learning approaches alongside deep learning frameworks including autoencoder-based models. For each method we discuss biological interpretability, validation strategy, and readiness for clinical integration. Furthermore, we categorize the current challenges into technical, computational, and methodological while outlining open problems in the field. This review shows that multimodal ensemble approaches have the strongest promise for clinical integration and the highest readiness. However, for better assessment of future work and side-by-side comparison, standardization of evaluation protocols and reporting results will be crucial.

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

Extensible Fluxonium Architecture Using Tunable Couplers with Low Shunt Capacitance

arXiv:2606.01647v2 Announce Type: replace Abstract: Fluxonium qubits have demonstrated high-fidelity operations and long coherence times in small-scale systems, highlighting their promise for quantum computing. However, large-scale integration into a high-performance two-dimensional (2D) qubit array remains the central challenge for practical applications. In this work, we introduce an extensible architecture for scaling up fluxonium qubits in 2D grids. To address the key challenges, namely achieving controllable strong interaction and high connectivity for qubits featuring small shunting capacitors (footprints), we propose using low-shunt-capacitance couplers to enable tunable interactions between fluxonium qubits. When embedded into 2D square lattices, large couplings can be achieved even with relatively small coupling capacitances, thus enabling multiple connections with sufficient capacitance budget. We further propose coupler realizations based on generalized flux qubit circuits, specifically the quarton and the fluxonium, and demonstrate that both enable fast, high-fidelity gates with low spectator errors, while supporting multiple connections on 2D grids.

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

FlowEdit: Associative Memory for Lifelong Pronunciation Adaptation in Flow-Matching TTS

arXiv:2606.20518v1 Announce Type: new Abstract: Flow-matching text-to-speech systems achieve remarkable zero-shot quality but remain static after deployment: pronunciation errors on out-of-vocabulary proper nouns persist unless the model is retrained. We introduce FlowEdit, a life-long adaptation framework for frozen flow-matching TTS that learns pronunciation corrections as latent conditioning edits rather than weight updates. When corrective feedback is provided, FlowEdit optimizes a token-level perturbation in the text embedding space, then stores the correction in a Modern Hopfield Network serving as content-addressable episodic memory. At inference, corrections are retrieved via soft attention with a similarity gate, enabling fuzzy morphological matching. On our curated benchmark of 312 multilingual proper nouns across 18 language families, FlowEdit reduces target-word Phoneme Error Rate by 92.7% relative to the zero-shot baseline while maintaining identical general-speech quality. Corrections complete in approximately 15 seconds on a single GPU.