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01.
arXiv (CS.AI) 2026-06-11

Can Open-Source LLM Agents Replace Static Application Security Testing Tools? An Empirical Assessment

arXiv:2606.11672v1 Announce Type: cross Abstract: This paper explores the value of agentic AI tools for cybersecurity purposes. We evaluate the efficacy of a general-purpose GenAI Large Language Model- (GenAI-) based agent when powered by three different Ollama-hosted general-purpose open source models. We assess each agent's performance using precision, recall, false positive count, and a calculated composite score based upon the interplay of the captured metrics, against the baseline performance of an existing, vetted Static Application Security Testing (SAST) tool, Bandit. Our findings refute the notion that a modern open-source GenAI LLM-based agent is currently suitable for the specialized task of SAST scanning under realistic conditions.

02.
arXiv (CS.AI) 2026-06-12

The Query Channel: Information-Theoretic Limits of Masking-Based Explanations

arXiv:2604.16689v2 Announce Type: replace Abstract: Masking-based post-hoc explanation methods, such as KernelSHAP and LIME, estimate local feature importance by querying a black-box model under randomized perturbations. This paper formulates this procedure as communication over a query channel, where the latent explanation acts as a message and each masked evaluation is a channel use. Within this framework, the complexity of the explanation is captured by the entropy of the hypothesis class, while the query interface supplies information at a rate determined by an identification capacity per query. We derive a strong converse showing that, if the explanation rate exceeds this capacity, the probability of exact recovery necessarily converges to one in error for any sequence of explainers and decoders. We also prove an achievability result establishing that a sparse maximum-likelihood decoder attains reliable recovery when the rate lies below capacity. A Monte Carlo estimator of mutual information yields a non-asymptotic query benchmark that we use to compare optimal decoding with Lasso- and OLS-based procedures that mirror LIME and KernelSHAP. Experiments reveal a range of query budgets where information theory permits reliable explanations but standard convex surrogates still fail. Finally, we interpret super-pixel resolution and tokenization for neural language models as a source-coding choice that sets the entropy of the explanation and show how Gaussian noise and nonlinear curvature degrade the query channel, induce waterfall and error-floor behavior, and render high-resolution explanations unattainable.

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

CT-VDETR: Semi-supervised 3D Trauma Detection in Computed Tomography (CT) scans using Dense Vertex Relative Position Encoding

Accurate detection and localization of traumatic injuries in abdominal CT remain challenging because voxel-level annotations are limited and expensive to obtain. We present a label-efficient framework for 3D abdominal trauma detection that combines self-supervised pretraining with semi-supervised transformer-based detection. First, we use Masked Image Modeling (MIM) on 1098 CT volumes to pretrain a 3D U-Net encoder for anatomical representation learning. Next, we adapt V-DETR to dense volumetric CT through a feature adapter that converts the encoder feature grid into a compact token sequence for transformer decoding. The pretrained encoder is then integrated with V-DETR and 3D Vertex Relative Position Encoding (3D V-RPE) to improve the localization of irregularly shaped injuries. Finally, semi-supervised teacher-student consistency regularization leverages 2,000 additional unlabeled volumes during detector training. To the best of our knowledge, this is the first application of a 3D DETR-style detector to the RSNA abdominal trauma detection task. On this benchmark, the proposed method achieves 31.33% test mAP@0.50 using only 78 labeled training volumes, corresponding to a 1.53x improvement over supervised-only training. These results show that combining medical-domain pretraining with semi-supervised learning is an effective strategy for label-scarce 3D medical detection.

04.
arXiv (quant-ph) 2026-06-24

Tensor-network approach to quantum optical state evolution beyond the Fock basis

arXiv:2511.15295v4 Announce Type: replace Abstract: Understanding the quantum evolution of light in nonlinear media is central to the development of next-generation quantum technologies. Yet modeling these processes remains computationally demanding, as the required resources grow rapidly with photon number and phase-space resolution. Here we introduce a tensor-network approach that efficiently captures the dynamics of nonlinear optical systems in a continuous-variable representation. Using the matrix product state (MPS) formalism, both quantum states and operators are encoded in a highly compressed form, enabling direct numerical integration of the Schrödinger equation. We demonstrate the method by simulating degenerate spontaneous parametric down-conversion (SPDC) and show that it accurately reproduces established theoretical benchmarks - energy conservation, pump depletion, and quadrature squeezing - even in regimes where conventional Fock-basis simulations become infeasible. For high-intensity pump fields ($\alpha = 100$), the MPS representation achieves compression ratios above $3\cdot 10^3$ while preserving physical fidelity. This framework opens a scalable route to modeling multimode quantum light and nonlinear optical phenomena beyond the reach of traditional methods.

05.
medRxiv (Medicine) 2026-06-10

Seasonality, source type, and women's water labor: A longitudinal mixed-methods study in Kenya and Honduras

Women shoulder the majority of water collection labor globally, yet how their water collection and water-related work experiences may change over time or by water source type remains insufficiently understood. We conducted a longitudinal, mixed-methods study in rural Kenya and Honduras to understand how women's experiences collecting water and performing water-related work varied between (a) two time points, (b) improved and unimproved water source types, and (c) water source location. Data were collected in 2023 and 2024 using interviews, observation, GPS-enabled watches, and scales to measure time and distance traveled, water weight and volume carried, and calories expended. 133 women participated in data collection (66 Kenya, 67 Honduras). We compared women's experience data by time point (2023 vs. 2024), source type (improved vs. unimproved), and source location (off-premises vs. on-premises) (t-test, Mann-Whitney U test). We also mapped participants' routes and activities to show which sources were visited, when, and for what activities. In Kenya, mean water collection time, distance, and caloric expenditure were significantly lower and water volume was significantly higher in 2024 when there were unexpected rains compared to 2023 when there was a persistent drought. When comparing source types during the 2023 drought, journeys to improved sources took significantly less time and energy and covered less distance than journeys to unimproved sources. These differences were not observed during the rainy conditions of 2024 when unimproved sources were closer and more accessible. In Honduras, water collection and water work burdens did not differ significantly by time point or source type. We found women with on-premises water access to still expend considerable time and caloric expenditure engaging in water work within their household compounds. Findings from Kenya suggest that water infrastructure improvements can reduce women's water collection burdens, though benefits may depend on and vary by season and source location. Findings from Honduras show that water labor does not end once water is in the household. Rather, substantial time and energy are expended carrying out water-related work even when sources are on premises, suggesting that efforts to assess water labor need to extend beyond collection alone. To meaningfully reduce burdens and ensure improved water sources are utilized during all seasons, initiatives need to consider source location, seasonal variability, and work beyond collection. Evaluations to assess infrastructure impacts on women's labor and well-being are needed and long overdue.

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

VisChronos: Revolutionizing Image Captioning Through Real-Life Events

This paper aims to bridge the semantic gap between visual content and natural language understanding by leveraging historical events in the real world as a source of knowledge for caption generation. We propose VisChronos, a novel framework that utilizes large language models and dense captioning models to identify and describe real-life events from a single input image. Our framework can automatically generate detailed and context-aware event descriptions, enhancing the descriptive quality and contextual relevance of generated captions to address the limitations of traditional methods in capturing contextual narratives. Furthermore, we introduce a new dataset, EventCap (https://zenodo.org/records/14004909), specifically constructed using the proposed framework, designed to enhance the model's ability to identify and understand complex events. The user study demonstrates the efficacy of our solution in generating accurate, coherent, and event-focused descriptions, paving the way for future research in event-centric image understanding.

07.
arXiv (quant-ph) 2026-06-11

Unifying Quantum Smoothing Theories with Extended Retrodiction

arXiv:2510.08447v2 Announce Type: replace Abstract: Estimating the state of an open quantum system monitored over time requires incorporating information from past measurements (filtering) and, for improved accuracy, also from future measurements (smoothing). While classical smoothing is well understood within a Bayesian framework, its quantum generalization has been challenging, leading to distinct and seemingly incompatible approaches. In this work, we demonstrate that quantum state smoothing hinges on a uniquely quantum feature: the fundamental dependence of retrodiction on prior correlations. We introduce auxiliary systems into the prior belief to capture correlations formed during preparation and evolution and develop a comprehensive framework for quantum state smoothing based on extended Bayesian retrodiction. This framework identifies all previous approaches as different choices of the extended prior, and naturally extends it to other choices that have not been considered before. We also give an information-theoretic characterization of the choices of prior, in terms of the average entropy of the smoothed states. Our results establish quantum state smoothing as a fundamentally retrodictive process just like classical smoothing, with proper quantum features clearly identified.

08.
arXiv (CS.AI) 2026-06-12

Counterfactual Explanations for Deep Two-Sample Testing

arXiv:2606.04009v2 Announce Type: replace-cross Abstract: Two-sample testing is a fundamental tool for detecting distributional differences across scientific domains, but classical tests (including kernel-based tests) can be ineffective on high-dimensional structured data such as images. Recent deep two-sample tests improve sensitivity in these settings by learning informative representations, yet they provide limited insight into which data features drive rejection of the null hypothesis $H_0$. To address this issue, we propose a counterfactual explanation framework for deep two-sample testing that generates sample-level edits moving observations from a source group toward a target group while explicitly reducing the discrepancy measured by the test. Our method combines a diffusion autoencoder with a pretrained deep two-sample test model and optimizes a maximum mean discrepancy (MMD) objective in the test model's representation space to produce plausible counterfactuals. We quantify distribution-level effects through changes in the test statistic and the resulting two-sample p-values. We evaluate the method on synthetic 2D shape datasets and two MRI cohorts. Across both settings, the counterfactual transformations consistently increase p-values relative to the original samples, indicating that the edited source set becomes statistically closer to the target distribution under the test. We measure minimality using LPIPS to ensure the counterfactuals remain close to the original samples. The resulting edits provide interpretable evidence of the features associated with the detected group differences. On MRI, the localized changes are consistent with known anatomical differences between cohorts.

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

Scalable and Interpretable Representation Alignment with Ordinal Similarity

arXiv:2606.16379v1 Announce Type: new Abstract: Evaluating representation similarity is fundamental to representation learning. However, existing metrics suffer from significant limitations: they lack interpretability due to shifting baselines, lack robustness to outliers, and are computationally intractable for large datasets, forcing reliance on heuristic approximations. To address this, we develop an ordinal-similarity framework, instantiated by the Triplet (TSI) and Quadruplet (QSI) Similarity Indices, which measure alignment by quantifying the consistency of ordinal relationships. We theoretically demonstrate this formulation is inherently interpretable, robust to outliers, and computationally efficient. Finally, we establish a formal equivalence between TSI and local neighborhood alignment, measured by Mutual Nearest Neighbors. Empirically, we validate these properties and show that ordinal similarity offers a scalable approach to measuring alignment, enabling practitioners to better understand and design representations.

10.
arXiv (quant-ph) 2026-06-12

Quantum Error Correction Codes for Truncated SU(2) Lattice Gauge Theories

Authors:

arXiv:2511.13721v2 Announce Type: replace Abstract: We construct two quantum error correction codes for pure SU(2) lattice gauge theory in the electric basis truncated at the electric flux $j_max=1/2$, which are applicable on quasi-1D plaquette chains, 2D honeycomb and 3D triamond and hyperhoneycomb lattices. The first code converts Gauss's law at each vertex into a stabilizer while the second only uses half of the vertices and is locally the carbon code. Both codes are able to correct single-qubit errors. The electric and magnetic terms in the SU(2) Hamiltonian are expressed in terms of logical gates in both codes. The logical-gate Hamiltonian in the first code exactly matches the spin Hamiltonian for gauge singlet states found in previous work.

11.
arXiv (math.PR) 2026-06-25

Pointwise Hurst Estimation via Scale Accumulation: A Noise-Robust Approach for Rough Volatility

arXiv:2606.25771v1 Announce Type: cross Abstract: We introduce an estimator for the pointwise, time-varying Hölder exponent (Hurst parameter) of a stochastic process, based on the geometry accumulation integral G_Lambda(t) = integral from Lambda to 1 of |eth_s X(t)| s^{-1} ds, where eth_s X(t) = (X(t+s)-X(t))/s is the scale derivative at resolution s. We prove consistency, noise robustness with explicit threshold Lambda* = sigma^{1/H}, and a CLT at rate (log Lambda)^{-1/2}. The estimator is pointwise in time, defined at finite resolution, and eliminates microstructure noise by scale separation. Existing estimators give a global H from integrated variance; this gives a time-varying H(t) directly from the price path.

12.
medRxiv (Medicine) 2026-06-22

Burden of Cardiovascular Disease in Brazil, 1996-2023: A Retrospective Descriptive Study of the Epidemiology and Impact on Public Healthcare with Emphasis on Acute Myocardial Infarction

Background Cardiovascular diseases (CVD) are the leading cause of death worldwide, and their epidemiology is correlated with genetic predisposition, exposure to risk factors, sex, age, access to medical care, and other sociodemographic characteristics. Brazil is a developing country with a vast territory, which leads to structural inequalities. Estimates of CVD in Brazil, in its regions, and in its population are poorly evaluated and analysed. Methods We obtained CVD-related data from the Brazilian Unified Health System (SUS) and analysed mortality and morbidity from 1996 to 2023 by sex, race/ethnicity, age, and region. We calculated the risk of death from the most prevalent diseases, the average length of hospital stay, and the costs associated with heart transplantation. Findings In Brazil, acute myocardial infarction was the pathology that led to the highest number of deaths across all variables analysed during the evaluated period. Other CVD were also related to causes of death and morbidity, such as hypertensive diseases and heart failure. Interpretation Brazil presents a serious challenge to the public health system due to the high number of deaths and the progressive mortality rate. This study represents a fundamental contribution to the basis for formulating public health policies aimed at reducing the growing impact associated with these diseases. Funding CNPq, CAPES, FAPEMIG, INCT

13.
arXiv (CS.CL) 2026-06-12

The Pragmatic Persona: Discovering LLM Persona through Bridging Inference

Large Language Models (LLMs) reveal inherent and distinctive personas through dialogue. However, most existing persona discovery approaches rely on surface-level lexical or stylistic cues, treating dialogue as a flat sequence of tokens and failing to capture the deeper discourse-level structures that sustain persona consistency. To address this limitation, we propose a novel analytical framework that interprets LLM dialogue through bridging inference – implicit conceptual relations that connect utterances via shared world knowledge and discourse coherence. By modeling these relations as structured knowledge graphs, our approach captures latent semantic links that govern how LLMs organize meaning across turns, enabling persona discovery at the level of discourse coherence rather than surface realizations. Experimental results across multiple reasoning backbones and target LLMs, ranging from small-scale models to 80B-parameter systems, demonstrate that bridging-inference graphs yield significantly stronger semantic coherence and more stable persona identification than frequency or style-based baselines. These results show that persona traits are consistently encoded in the structural organization of discourse rather than isolated lexical patterns. This work presents a systematic framework for probing, extracting, and visualizing latent LLM personas through the lens of Cognitive Discourse Theory, bridging computational linguistics, cognitive semantics, and persona reasoning in large language models. Codes are available at https://github.com/JiSoo-Yang/Persona_Bridging.git

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

Stepwise Token Selection for Efficient Multimodal Large Language Models

In multimodal large language models (MLLMs), inference cost is largely dominated by the visual token prefix rather than the language backbone, making token reduction a key factor for improving efficiency. Existing approaches typically assign independent importance scores to visual tokens and retain a fixed number of top-ranked tokens, implicitly assuming token independence and a uniform compression ratio across inputs. In this work, we reformulate visual token pruning as a sequential decision-making process. Specifically, we introduce a pointer-style selection mechanism that iteratively chooses informative tokens, conditioning each decision on previously selected ones, and dynamically determines when to stop via a learned termination action. This enables joint optimization of both the selected subset and its size. To enable end-to-end training under standard language modeling objectives, we design a differentiable relaxation based on a variance-preserving noise interpolation scheme, allowing gradients to propagate through the discrete selection process. Extensive experiments on LLaVA-v1.5-7B and Qwen2.5-VL-7B demonstrate that our approach consistently outperforms fixed-ratio baselines across different compression levels. Under aggressive pruning that removes 88.9% of visual tokens, our method preserves 94.6% of the original accuracy while achieving a 1.88x speed-up in prefill latency.

15.
medRxiv (Medicine) 2026-06-22

Paired plasma and EV-enriched plasma proteomics reveal nonredundant sepsis-associated host-response signatures in critical illness

Background: Plasma proteomics may identify host-response signatures in sepsis, but it is unclear whether extracellular vesicle (EV)-enriched plasma provides distinct or redundant information compared with plasma. We compared paired plasma and EV-enriched plasma proteomes in critically ill patients with sepsis and critically ill non-sepsis controls (CINS). Methods: In this prospective observational study, paired plasma and EV-enriched plasma samples were analyzed from 56 critically ill adults, including 40 patients with sepsis and 16 CINS patients. Protein abundance was quantified using liquid chromatography-tandem mass spectrometry. Analyses compared proteomic depth, protein overlap, global concordance between compartments, and differential protein abundance between CINS and sepsis. Exploratory Gene Ontology enrichment was performed as a supplementary analysis. Results: EV-enriched plasma expanded proteomic detection, identifying 2,476 filtered proteins compared with 506 in plasma. Only 386 proteins were detected in both compartments, while 2,090 were unique to EV-enriched plasma and 120 were unique to plasma. Among shared proteins, plasma and EV-enriched plasma showed modest global concordance across critically ill patients (Spearman coeff = 0.322, p = 9.19 x 10^-11), with similar findings in sepsis alone. Differential abundance analysis identified 11 sepsis-associated proteins in plasma and 22 in EV-enriched plasma. Only SAA1, SAA2, and IGFBP6 were significant in both compartments. Exploratory pathway analysis supported acute-phase and inflammatory enrichment in plasma sepsis-associated proteins, while EV-enriched signals were directionally plausible but did not meet prespecified FDR thresholds. Conclusion: Plasma and EV-enriched plasma proteomics capture related but nonredundant sepsis-associated host-response information in critically ill patients.

16.
arXiv (quant-ph) 2026-06-17

Probing PbTe-Pb nanowire devices with radio-frequency reflectometry

arXiv:2606.04544v2 Announce Type: replace-cross Abstract: We report the implementation of radio-frequency (rf) reflectometry on selective-area-grown PbTe-Pb nanowire devices on a CdTe substrate. These nanowires are predicted to host Majorana zero modes. We demonstrate the compatibility of the rf technique, including both resistive and capacitive sensing, with these nanowires. The effect of dielectric loss from the CdTe substrate is quantitatively characterized. Furthermore, the feasibility of rf reflectometry is verified under finite magnetic fields where zero-energy modes can emerge. Our results establish the fast control of PbTe quantum devices, paving the way for their applications in topological quantum computation.

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

FACTR 2: Learning External Force Sensing for Commodity Robot Arms Improves Policy Learning

arXiv:2606.12406v1 Announce Type: cross Abstract: Contact-rich manipulation requires force sensitivity, but many robot arms lack dedicated force sensors due to their high cost. We present Neural External Torque Estimation (NEXT), a data-driven method that estimates external joint torques without needing any dedicated force sensors. NEXT trains in 1 minute from only 10 minutes of free-motion data, yet achieves estimates comparable to dedicated joint-torque sensors. NEXT enables force-feedback teleoperation on low-cost arms and improves policy learning through Force-Informed Re-Sampling Training (FIRST), which up-samples pre-contact and contact segments during behavior cloning. Across five long-horizon tasks, FIRST outperforms prior force-aware policies by over 17% in task progress. Together, NEXT and FIRST bring force-aware teleoperation and policy learning to off-the-shelf robots without additional sensing hardware. Video results and code are available at https://jasonjzliu.com/factr2

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

Automating Geometry-Intensive Compliance Checking in BIM: Graph-Based Semantic Reasoning Framework

arXiv:2606.12065v1 Announce Type: new Abstract: Automating compliance check for geometry-intensive regulations remains a significant technical bottleneck in Building Information Modeling (BIM), primarily due to the semantic disparity between high-level regulatory logic and structured IFC data. Existing methods, often reliant on static rule templates, struggle to traverse multi-hop reasoning chains or resolve latent spatial dependencies across multiple building entities. To address these challenges, a Spatial-Geometric Reasoning System for Building Information Modeling (SGR-BIM) is proposed as an integrative graph-driven reasoning framework. SGR-BIM dynamically constructs a cross-modal knowledge graph that aligns user intent, regulatory semantics, and BIM geometry, enabling interpretable reasoning without rigid hard-coding. Validated on 679 expert-verified queries from fire safety codes, the framework achieves 84.3% accuracy, representing an 8.6% improvement over enhanced-tool single-agent baselines. This research provides a graph-based semantic reasoning paradigm, enhancing the transparency and flexibility of automated geometric compliance check workflows in the Architecture, Engineering, and Construction (AEC) industry.

19.
arXiv (CS.CV) 2026-06-17

SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology

Characterising the tumour microenvironment (TME) from routine H&E-stained histology images requires simultaneous cell segmentation, feature extraction, and interpretable clinical reporting. We present SEGTME-UNI2, a unified framework addressing these requirements. Its core is UNI2-UPERHOVER, a dual-head segmentation model pairing the UNI2-H pathology foundation model (ViT-Giant, pretrained on >100M tiles from 100K slides) with two parallel UperNet decoders: one for six-class semantic segmentation and one for horizontal-vertical gradient regression enabling watershed-based nuclear instance separation. To address the lack of pixel-level annotations in large real-world repositories, UNI2-UPERHOVER undergoes a three-stage progressive pseudo-label curriculum. Each stage trains a fresh model without weight transfer, driving improvement entirely via increased pseudo-label quality: Stage 1: Uses human-annotated PanNuke (7,901 images, 189,744 nuclei, 0.25 um/pixel). Stage 2: Uses entropy-filtered pseudo-labels from the Stage 1 model on 271,711 TCGA-UT scale-0 patches (0.5 um/pixel). Stage 3: Uses pseudo-labels from the Stage 2 model on all 1,608,060 TCGA-UT patches across six resolution scales (0.5-1.0 um/pixel). Segmentation outputs feed a structured TME feature extraction pipeline computing 20+ per-patch compositional, morphological, spatial entropy, and intercellular distance metrics. These are encoded as JSON and passed to a fine-tuned NVIDIA BioNeMo GPT model to generate clinically interpretable TME narratives. Preliminary validation on held-out PanNuke and TCGA-UT partitions demonstrates framework feasibility and internal consistency. The pseudo-labelled TCGA-UT dataset and UNI2-UPERHOVER checkpoint are publicly released to support large-scale TME profiling and spatial biology research.

20.
arXiv (CS.LG) 2026-06-11

Learning Dynamics Reveal a Hierarchy of Weight-Induced Layerwise Gram Metrics

arXiv:2606.09744v3 Announce Type: replace Abstract: We study feed-forward ReLU networks with fixed readout and quadratic loss. The aim is to rewrite gradient descent not primarily as a dynamics in weight space, but as a collective dynamics closed in terms of fields defined on the training-set space. For a single hidden layer, the weight variables can be eliminated from the activation dynamics, yielding a closed equation for the residuals governed by a collective kernel that factorizes into an input-geometric matrix and a dynamical co-activation matrix. For deeper networks, the residual dynamics retains a clean layer-wise kernel structure. However, from depth three onward, closure requires a hierarchy of weight-induced Gram operators that mediate information transport across layers. Moreover, the conjugate-field dynamics is governed by operators satisfying a backward pullback recursion, of which the weight-induced Gram operators are the first nontrivial instances.

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

Defending against Adaptive Prompt Injection Attacks via Reasoning-enabled Task Alignment

arXiv:2606.15441v1 Announce Type: cross Abstract: Indirect prompt injection attacks hijack LLM-based agents by embedding malicious instructions in third-party data that the agent retrieves during task execution. Existing defenses report near-zero attack success rate on static benchmarks, yet recent adaptive evaluations show that these results collapse once the attacker is allowed to optimize against the deployed defense. In this work, we trace this collapse to two failure modes. First, existing defense methods are confined to recognizing specific attack patterns, rather than assessing whether the intent of every embedded instruction is relevant to the user task. Second, training-based defenses, which otherwise offer the strongest safety-utility trade-off, assemble their adversarial examples from a handful of hand-crafted templates, and the resulting defender fails to generalize outside that narrow strategy distribution. To address these gaps, we propose RETA, a training-based method that grounds defense decisions on the user tasks rather than attacker-controlled data. At each tool-output step, the defender undertakes chain-of-thought reasoning verifying that its actions are consistent with the user task. Leveraging red-teaming, a simulated attacker synthesizes adversarial training data and receives a dictionary-learning diversity reward, achieving broad coverage of injection-reformulation strategies. Together, these allow the defender to be optimized via multi-objective reinforcement learning and achieve better safety-utility trade-off. Across six black-box adaptive attacks, RETA keeps every per-attack ASR below 10%, with average ASR of 2.92% and 3.75% on the two target models, while preserving most utility under attack and on clean inputs.

22.
Nature (Science) 2026-06-24

Zero-shot design of drug-binding proteins via neural iterative selection−expansion

Authors:

The design of proteins that bind to small molecules has been challenging because it requires simultaneous optimization of the protein sequence, protein structure and ligand conformation1–7. Current deep-learning algorithms have struggled to navigate this landscape, precluding the zero-shot design of binders. Here we show that by combining two neural networks in an iterative design algorithm, small-molecule binding proteins can be created from scratch with high accuracy. We trained a graph neural network—ligand-aware sequence engineering message-passing neural network (LASErMPNN)—to design compatible protein sequences for an input protein backbone and docked ligand. We paired  LASErMPNN with a structure predictor that models a three-dimensional protein–ligand complex for an input protein sequence and ligand identity. The closed-loop iteration of these reciprocal networks optimized sequence–structure–ligand compatibility, and outperformed a comparable design loop using a physics-based energy function. We used our strategy, termed neural iterative selection–expansion (NISE), to design proteins that, using different folds, specifically bind to two chemically distinct small-molecule drugs, exatecan and apixaban, with success rates of 100% and 83%, respectively. The tightest NISE binders had nanomolar-to-picomolar affinities, surpassing those of the next-leading method by 70-fold for exatecan and nearly 10,000-fold for apixaban. LASErMPNN then suggested two amino-acid substitutions that improved the affinity of the tightest exatecan binder by 100-fold without any experimental input. The optimized binder protected the labile lactone ring of exatecan from hydrolysis for days. Our work describes a general recipe for using neural networks to automate the design of small-molecule binding proteins for applications in drug delivery, sensing and catalysis.  By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing promise for applications in drug delivery and sequestration.

23.
arXiv (CS.CL) 2026-06-12

Demystifying Hidden-State Recurrence: Switchable Latent Reasoning with On-Policy Reinforcement Learning

Latent chain-of-thought compresses reasoning by replacing visible reasoning traces with continuous hidden-state recurrence, but existing formulations are difficult to optimize with standard on-policy reinforcement learning (RL) and hard to interpret causally. Our key insight is that a single pair of explicit boundary tokens can address both issues at once: discrete entry and exit anchors make the latent block compatible with standard on-policy RL, and the same anchors offer a natural foothold for mechanistic analysis. Motivated by this, we propose SWITCH, a switchable latent reasoning framework. The model emits to enter latent mode and to exit. Because the boundaries are ordinary discrete tokens, the GRPO policy ratio is well-defined at every decision point. The same anchors also expose the latent steps to direct probing and causal intervention. We train the model with a visible-to-latent curriculum and a Switch-GRPO objective that propagates gradients through recurrent latent computation. SWITCH consistently outperforms prior hidden-state-recurrence latent reasoning approaches at similar scale. Mechanistic analysis through the boundary tokens further reveals three findings: (i) is a sharply localised, learned switching policy rather than a stylistic artefact; (ii) the latent step it opens performs problem-specific, causally important computation rather than acting as an inert placeholder; and (iii) that computation is concentrated at a single hidden-state transition on entry. Together, these results show that hidden-state-recurrence latent reasoning is both RL-trainable and open to direct mechanistic analysis, including of how on-policy RL itself improves the model from the inside.

24.
arXiv (math.PR) 2026-06-15

Lehner's operator norm formulas, semidefinite programming, and spiked matrix models

arXiv:2606.14687v1 Announce Type: new Abstract: Lehner (1999) derived elegant formulas for the operator norm $\|\mathfrak{X}\|$ of operators of the form $\mathfrak{X} = \mathbf{A}_0 \otimes \mathfrak{1} + \sum_{i = 1}^n \mathbf{A}_i \otimes \mathfrak{m}_i$, also easily generalized to the spectral edge $\lambda_{\max}(\mathfrak{X})$, in terms of nonlinear optimization problems over positive definite matrices. Here the $\mathbf{A}_i$ are finite-dimensional Hermitian matrices, the $\mathfrak{m}_i$ are either free semicircular or free Rademacher families of operators, and $\mathfrak{1}$ is the identity operator. We first show that both of Lehner's nonlinear optimizations can be rewritten as linear semidefinite programs (SDPs), even in the Rademacher case where Lehner's optimization is not itself convex. We give the primal and dual forms of these SDPs, derive the complementary slackness relations and consequences thereof, and propose that the SDPs are more stable and accurate than the iterative numerical scheme proposed in Lehner's original work. We then apply the SDPs from the semicircular case to spiked matrix models, studied recently via Lehner's formula by Bandeira, Cipolloni, Schröder, and van Handel (2024). We give a new proof of the Baik–Ben Arous–Péché (BBP) transition they establish in models with isotropic (but possibly correlated) Gaussian noise by constructing feasible variables for the associated primal and dual SDPs. Combining our construction with a sensitivity interpretation of optimal dual variables, we study the fluctuations of leading eigenvectors of such models. We conjecture and give numerical evidence that these fluctuations are Gaussian but anisotropic and non-universal, and that their covariance may be computed in terms of the optimizer of the dual of Lehner's formula, which in turn is approximately the leading eigenmatrix of a completely positive operator associated to the covariance of the noise model.

25.
bioRxiv (Bioinfo) 2026-06-18

Structure-Based Immunoinformatics Design of a CTB-Adjuvanted Multi-Epitope Mucosal Vaccine Against Helicobacter pylori

Background: Helicobacter pylori coloniz the gastric mucosa of nearly half of the global population and is classified as a Group I carcinogen by the World Health Organization due to its strong association with gastric cancer. The growing prevalence of antibiotic-resistant H. pylori strains significantly compromises current therapeutic strategies, emphasizing the urgent need for effective prophylactic approaches. Research design and methods; In this study, a novel multi-epitope vaccine was designed targeting H. pylori, incorporating epitopes from four key virulence proteins: BabB, SabB, SabA, and VacA. Using an immunoinformatics-guided structural vaccinology approach, B- and T-cell epitopes were predicted, prioritized based on immunogenicity, conservation, population coverage, and non-homology to human proteins, and assembled into the final vaccine construct. To enhance immunogenicity and specifically stimulate mucosal immune responses, the cholera toxin B subunit (CTB) was fused at the N-terminal via an EAAAK linker, a novel application in H. pylori multi-epitope vaccines. The PADRE universal epitope and additional linkers were incorporated to optimize epitope presentation and helper T-cell activation. Results: Comprehensive evaluations of physicochemical, antigenic, allergenic, and toxic properties were conducted, followed by secondary and tertiary structure modeling, refinement, and validation. Conformational B-cell epitopes were mapped, and molecular docking, binding affinity analysis, energy minimization, and molecular dynamics simulations confirmed structural stability and receptor interactions. Codon optimization and in silico cloning predicted efficient expression in Escherichia coli, while immune simulations suggested robust humoral and cellular responses. Conclusions: This study presents a promising multi-epitope vaccine candidate against H. pylori, offering a rational framework for future experimental validation and potential clinical application.