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01.
arXiv (CS.CL) 2026-06-17

Reading between the Lines: Leveraging Large Language Models for Global Dementia and Depression Assessment from Clinical Interviews

Dementia and depression are the most prevalent neuropsychiatric disorders in geriatric populations, and their overlapping symptoms pose major challenges for differential diagnosis. In this study, we investigate open-weights Large Language Models (LLMs) for predicting dementia and depression severity from speech samples collected during standardized history taking interviews with 154 German-speaking subjects. We introduce an observer-based Global Depression Scale (GDS-D) aligned with the established Global Deterioration Scale (GDS), enabling parallel global staging of affective and cognitive symptoms. We compare three LLMs (Mistral 3.1, DeepHermes, Qwen3) in two settings: (1) zero-shot prediction and (2) LLM-based feature extraction for Support Vector Regression, using human and pause-enriched transcripts. Results show that LLMs effectively predict depression severity in zero-shot settings (best MAE of 0.60), while dementia assessment benefits substantially from structured feature extraction (best MAE of 0.78), reducing errors by up to 35% over zero-shot baselines. Pause-enriched transcripts achieve competitive performance with human transcriptions, demonstrating the viability of fully automatic screening pipelines for differential neuropsychiatric assessment.

02.
arXiv (math.PR) 2026-06-16

Universality in the target arrival statistics of non-conservative search processes

arXiv:2606.16025v1 Announce Type: cross Abstract: Stochastic search processes in which searchers are continuously introduced to and removed from a target search domain are fundamental to a wide class of physical and artificial systems. The theory of such non-conservative search processes is, however, much less developed than for search processes with a fixed number of particles. Here we exploit a natural mapping between non-conservative stochastic search and queueing theory to derive the full time-dependent distribution of target arrivals under minimal assumptions on the underlying search process. Remarkably, we find that the steady-state inter-arrival time distribution is exactly exponential, regardless of the details of the search process, showing a robust universality that emerges directly from the queueing framework. Thus, counterintuitively, the arrival statistics of a non-conservative search process are much simpler than sequential search-and-capture processes involving a fixed number of searchers. This has major implications for target resource accumulation, where the delivery of resources is counter-balanced by their downstream consumption.

03.
arXiv (CS.CL) 2026-06-17

RepSelect: Robust LLM Unlearning via Representation Selectivity

Making large language models (LLMs) deeply forget specific knowledge and values without sacrificing general capabilities remains a central challenge in unlearning. However, current methods are easily reversed by fine-tuning or few-shot prompting, suggesting their forgetting is only shallow. We identify the root cause. Existing methods target representations shared with both the retain set and the subspace recovered by a fine-tuning attacker, making unlearning both disruptive to general capabilities and easy to reverse. We propose RepSelect (Representation Selectivity), isolates forget-set-specific representations by collapsing top principal components of weight gradients before each update, leaving general capabilities intact while limiting what fine-tuning can recover. We evaluate across two forget categories, biohazardous knowledge and abusive tendencies, and four model families spanning dense and Mixture-of-Experts architectures (Llama 3, Qwen 3.5, Gemma 4 E4B, DeepSeek V2 Lite). Compared to five popular baselines (GradDiff, NPO, SimNPO, RMU, UNDIAL), RepSelect achieves a 4-50x larger reduction in post-relearning answer accuracy than the strongest baseline, and is near-perfectly robust to few-shot prompting attacks. Targeting selective representations is thus an important step towards deep and robust LLM forgetting.

04.
arXiv (CS.LG) 2026-06-18

P-K-GCN: Physics-augmented Koopman-enhanced Graph Convolutional Network for Deep Spatiotemporal Super-resolution

arXiv:2606.19303v1 Announce Type: new Abstract: High-fidelity simulation of spatiotemporal dynamics is computationally prohibitive, necessitating efficient super-resolution techniques to reconstruct high-resolution data from coarse-grained inputs. Traditional data-driven methods often lack physical constraints, and simple physics-informed learning struggles with irregular spatial geometries and intricately evolving temporal dynamics. To tackle these challenges, we propose a Physics-augmented Koopman-enhanced Graph Convolutional Network (P-K-GCN) for spatiotemporal super-resolution on irregular geometries. Specifically, a continuous spline-based GCN is first designed to extract spatial dependencies directly from coarse graph, and Koopman operator theory is incorporated to project the nonlinear dynamics into a compact latent space where temporal progression is linearized. Second, we augment the optimization objective with a physics-based loss to force the data-driven reconstructions to adhere to physical laws for improving predictive fidelity and robustness. Finally, we provide a rigorous theoretical analysis, establishing that the physics augmentation and Koopman regularization mathematically guarantees a reduction in super-resolution error by diminishing Rademacher complexity and tightening generalization bounds. We evaluate our framework on reconstructing spatially high-resolution cardiac electrodynamics across a 3D heart geometry from sparse low-resolution measurements. Numerical experiments demonstrate that our method achieves superior accuracy compared to baseline models.

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

Agent trajectories as programs: fingerprinting and programming coding-agent behavior

arXiv:2606.16988v1 Announce Type: cross Abstract: Benchmark scores tell you what an agent got right; they do not tell you how it got there. In this work, we introduce methods for comparing agents procedurally in different contexts, where the model, tasks, and approaches vary. We compare ten agents and find that they are identifiable by their behavioral habits, which we define as fingerprints: a probe over these procedural signatures attributes an unseen trajectory to the correct agent at 85.7% accuracy, controlling for leakage across tasks. We develop procedural representations for agent problem-solving procedures with an emergent vocabulary induction technique that is meant to be maximally compressive to avoid surface-level variation while being expressive enough to unveil the quirks of the models' patterns. We apply our framework to the software engineering evaluation dataset SWE-Bench to study the structural distinctness of agent trajectories and find that behavior is most similar between models from similar release periods and those that are distilled from one another (e.g., a distilled student model and its teacher have a Jensen-Shannon divergence of 0.25, about half the distance between other model pairs). As more models saturate evaluations, we believe that it will be important to probe model behavior along more holistic dimensions than success rates alone. We introduce ProcGrep, a library for auditing and evaluating agents for how they approach tasks at a procedural level given their traces in a top-down fashion. We believe this work has a range of applications to help developers work with and program coding agents, such as task-aware model routing, agent monitoring, and finer-grained cost analysis.

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

VISA: VLM-Guided Instance Semantic Auditing for 3D Occupancy World Models

Semantic 3D occupancy provides a voxelized world state for autonomous driving and robot decision making, but object and rare-class errors can affect free-space interpretation, collision checking, and temporal state propagation. We show that a common VLM strategy, aligning 3D voxel or object features with crop-caption embeddings, improves text-space similarity without reliably improving closed-set occupancy mIoU. Motivated by this mismatch, we propose VISA, a training-time semantic auditing approach for existing occupancy world models. VISA queries an offline VLM on a representative crop of each physical object instance, obtains a structured audit with class hypotheses, plausible confusions, reliability, attributes, and evidence, and propagates it along the object track. The audit is grounded to matched 3D object voxels and distilled into semantic logits through reliability-weighted taxonomy, attribute-factor, and scene-level audit graph losses, while inference remains unchanged and requires no VLM. On nuScenes, averaged across three runs, VISA improves OccWorld from 19.06 to 20.05 mIoU and GaussianWorld from 21.36 to 21.91 mIoU; on GaussianWorld, object mIoU improves from 18.18 to 19.16 and rare-class mIoU from 15.60 to 16.79. These results suggest that VLMs are better suited to closed-set occupancy as reliability-aware semantic auditors than as generic caption-embedding targets.

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

UST-GNN: A Unified Spatial–Topological Graph Neural Network Framework for Urban Analytics–Demonstrated through a Case Study on Urban Health Prediction

arXiv:2504.04739v3 Announce Type: replace Abstract: Understanding how social, demographic, environmental, and spatial factors jointly shape urban outcomes is essential for sustainable urban development and evidence-based policy. Traditional statistical approaches often struggle to capture complex non-linear relationships, while many machine learning methods overlook the joint roles of spatial autocorrelation and network topology in urban systems. Recent advances in GeoAI have addressed these challenges only partially, often treating spatial effects, graph structure, evaluation, and interpretability separately. We present UST-GNN, a unified spatial–topological graph neural network framework that integrates neighbourhood connectivity, heterogeneous urban features, and positional/locational embeddings into a single representation. Using the MedSAT dataset, which contains over 150 environmental and socio-demographic variables and six prescription outcomes across 4,835 neighbourhoods in Greater London, UST-GNN outperforms strong statistical, geographically enhanced, and graph Machine Learning baselines, improving out-of-sample $R^2$ by 8.4–13.2\% under strict spatial cross-validation. We further introduce a lightweight principal-component module to interpret learned node embeddings geographically and relate them to policy-relevant covariates. The resulting analyses recover established patterns, offer new perspectives on debated associations, and reveal novel predictors warranting further causal investigation. Together, these findings demonstrate the value of graph-based spatial machine learning for urban health analytics, environmental inequality assessment, and evidence-based urban policy. Beyond predictive gains, UST-GNN provides a unified GeoAI analytical pipeline that can be embedded into urban digital twin workflows for scenario testing, monitoring, and data-informed decision-making for healthier, more sustainable cities.

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

Ultra Flash: Scaling Real-Time Streaming Video Generation to High Resolutions

While recent autoregressive video diffusion models achieve remarkable streaming quality, they remain confined to low resolutions (e.g., 480P), leaving efficient, scalable, real-time high-resolution video generation a fundamental open challenge. To bridge this gap, we present Ultra Flash, a cascaded streaming framework capable of real-time high-resolution video generation. Ultra Flash achieves ~30 FPS at 1K resolution and ~18 FPS at 2K resolution on a single GPU through three key contributions: (1) an architecture-preserving T2V-to-TV2V super-resolution training paradigm coupled with an AIGC-oriented data degradation pipeline that effectively preserves the generative capability of the base model, enabling enhanced high-resolution detail when cascaded after mainstream low-resolution generative models; (2) a causal streaming latent upsampler paired with a high-resolution decoder, which enhances spatiotemporal coherence while enabling efficient latent spatial scaling and precise high-resolution decoding with negligible computational overhead; and (3) a cascade high-resolution streaming video generation optimization scheme that first performs hybrid-reward-enhanced sparse causalization and single-step distillation of the super-resolution model, then introduces cascaded streaming self-forcing preference optimization with dynamic cache management, jointly enhancing overall coherence, improving quality, and enabling real-time high-resolution streaming video generation. Extensive experiments demonstrate that Ultra Flash reliably produces ultra-high-resolution streaming video while maintaining state-of-the-art visual quality and superior efficiency. Project Page: https://xin1u.github.io/UltraFlash/

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

ECA: Efficient Continual Alignment for Open-Ended Image-to-Text Generation

Incremental Learning (IL) for Open-ended Image-to-Text Generation (OpenITG) enables models to continuously generate accurate, contextually relevant text for new images while preserving previously acquired knowledge. Unlike prior studies, this paper addresses a more practical scenario in which the predominant category of visual data shifts over time as environments evolve. In this context, we introduce a new notion of continual alignment, which incrementally adapts the alignment module within pre-trained VLMs to preserve high-quality cross-modal representations. Based on this idea, we propose Efficient Continual Alignment (ECA), a novel exemplar-free IL approach for OpenITG. The key challenge is enabling the model to acquire new, task-specific features while minimizing interference with the established alignment without accessing raw data from previous tasks. To address this, ECA employs three core mechanisms: a Mixture of Query (MoQ) module that adapts task-specific query tokens, a Fisher Dynamic Expansion (FeDEx) that dynamically expands model structure based on a Fisher Information Matrix (FIM)-based metric, and an embedding dictionary with Dictionary Replay (DR) to retain past knowledge. To evaluate ECA's performance, we construct four new IL OpenITG benchmarks that better reflect real-world scenarios. Experimental results demonstrate that ECA significantly mitigates catastrophic forgetting and improves IL performance compared to baseline methods. Code and benchmarks are available at https://github.com/Snowball0823/ECA.

10.
arXiv (quant-ph) 2026-06-11

Residual-Squeezing Mechanism of Mismatch in Inverse-Squeezing Kennedy Receivers

arXiv:2601.19093v4 Announce Type: replace Abstract: The discrimination of quantum states is fundamental to quantum information processing. Inverse-squeezing Kennedy (IS-Kennedy) receivers can outperform the coherent-state BPSK Helstrom benchmark at the same energy by converting transmitter-side squeezing into an effective coherent-state separation gain, without violating the Helstrom bound for the squeezed-state alphabet. This work investigates how squeezing mismatch degrades this mechanism. We show that imperfect inverse squeezing transforms the ideally nulled output into a residually squeezed state, thereby altering the photon-number statistics before detection. This residual-squeezing picture reveals a strong physical asymmetry between squeezing-magnitude and squeezing-phase mismatches. Magnitude mismatch produces an energy-independent error floor in the high-signal-energy regime, whereas phase mismatch generates a residual squeezing term that grows with signal energy. In the small-residual-squeezing regime, this leads to a polynomial growth of the leading error contribution and a rapid collapse of the SQL advantage. We also identify a parity-step effect in photon-number-resolving detection: because the nulled residual squeezed vacuum contains only even photon numbers, increasing detector resolution improves the high-energy robustness only when the effective saturation threshold crosses the next even photon number. These results identify phase locking as the dominant bottleneck for IS-Kennedy-type non-Gaussian receivers under unitary squeezing mismatch and provide design guidelines for robust squeezed-state quantum receivers.

11.
arXiv (quant-ph) 2026-06-19

Quantifying Entanglement via Quantum Wasserstein Distances

arXiv:2606.04969v2 Announce Type: replace Abstract: We propose a bipartite entanglement measure defined as the minimal order-1 quantum Wasserstein distance from a state to the set of separable states. Owing to the universal data-processing inequality of the Wasserstein metric, the measure satisfies all fundamental axioms within a single geometric framework. A Lipschitz dual formulation yields explicit lower bounds for pure and mixed states, a sharp constant for two-qubit systems, and an expected value for Haar-random pure states. We further establish a quantitative connection to entanglement witnesses: any negative witness expectation value certifies a lower bound, and the dual variational bound is exactly the maximal violation achievable by a Lipschitz-1 witness. The approach naturally provides subadditivity, trace-distance estimates, and bounds on local observables, while pointing toward large-deviation conjectures. This work introduces a framework at the interface of entanglement theory, optimal transport, and experimental entanglement detection.

12.
bioRxiv (Bioinfo) 2026-06-16

Physics-Driven Zero-Shot Reconstruction of Isotropic 3D Fluorescence Microscopy under Undersampled Acquisition

Three-dimensional (3D) imaging represents the development of next generation of fluorescence microscopy. However, routine axial down-sampling makes isotropic resolution unrealistic. Here, we propose DeepUI, a physical zero-shot framework designed to achieve isotropic 3D fluorescence images from a low axial sampling rate. DeepUI fully leverages the intrinsic characteristics of 3D images through physics-guided degradation, which incorporates spatial-frequency joint learning to generate a scaled optical transfer function, combined with noise degradation and an up-sampling branch. Typically requiring just 5 minutes for training and 0.5 minutes for high-throughput and fast prediction, we demonstrate the superior performance of DeepUI to get isotropic results, and the exclusivity to axial down-sampling conditions, even in more challenging conditions, including defocused background, noise, and resolution blur.

13.
arXiv (CS.CV) 2026-06-17

Beyond Visual Cues: CoT-Enhanced Reasoning for Semi-supervised Medical Image Segmentation

Semi-supervised medical image segmentation has emerged as a dominant research problem in medical image analysis, mitigating annotation scarcity by leveraging consistency regularization on unlabeled data. However, existing approaches operate predominantly via visual pattern matching, relying heavily on pixel-level similarities. This visual-centric dependency often falters in clinical scenarios characterized by the visual-semantic mismatch, where visually similar lesions warrant distinct diagnostic conclusions, thus failing to capture the underlying diagnostic logic used by experts. To address this, we move beyond visual cues and propose CERS (CoT-Enhanced Reasoning Segmentation), a framework that integrates Chain-of-Thought (CoT) reasoning to distinguish pathologically distinct cases. Specifically, we construct a knowledge pool enriched with linguistic reasoning descriptions generated by large language models (LLMs). A semantic-aware reference selection strategy is introduced to identify historical evidence, filtering candidates first by morphology, and then refining them via CoT consistency to eliminate hard negatives. Furthermore, a multi-scale coordinate attention module (MCAM) is designed to effectively fuse this reasoning-derived context into the decoding process. Extensive experiments demonstrate the superiority of CERS against state-of-the-art approaches, particularly in resolving boundary ambiguities and semantic inconsistencies. The code is available at https://github.com/cymasuna/CERS.

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

Minimalist Genetic Programming

arXiv:2606.10237v2 Announce Type: replace Abstract: Genetic programming (GP) is based on two important insights. First, that any learning task can fundamentally be posed as a program induction problem, where the goal is to construct a symbolic hierarchical model that is expressed as a syntax tree. Second, to pose this task as a search problem, and use evolution to locate the desired model. Since it was proposed, GP has produced notable results in a wide range of tasks and problem domains. This work presents an alternative view by modifying the second core insight of GP, posing the problem as a syntactic derivation task instead. In particular, this paper presents Minimalist Genetic Programming (MGP), an algorithm that like GP is biologically inspired, but instead of evolution it takes inspiration from the Minimalist Program to human language, in which syntax is understood as an optimal solution to the problem of linking two other mental systems. In minimalism, the core computational process is a binary set formation operator called $MERGE$, than can be used to incrementally construct complex syntactic structures using a simple Markovian process. MGP is able to discover the core building blocks of the symbolic expressions, and to incrementally combined them using $MERGE$. The proposed system is benchmarked on symbolic regression tasks that are known to be difficult to solve with standard GP systems because of the propensity for bloat. Results show that when a proper lexicon of atomic syntactic objects are chosen, MGP is able to consistently produce the exact ground truth model on a set of symbolic regression tasks where standard GP struggles to do the same. The insights provided by minimalism are shown to be relevant to the problem of program induction, and should be explored further based on the potential exhibited by MGP in this work.

15.
arXiv (quant-ph) 2026-06-12

Quantum-Driven Neuromorphic Computing for Million-Qubit-Scale Workloads

arXiv:2606.12968v1 Announce Type: new Abstract: We introduce Apollo, a 10000 node p-qubit neuromorphic processor fabricated in 16 nm mixed signal CMOS and operating fully at room temperature with a typical analog core power envelope of about 0.5 W. Its fundamental element, the p-qubit, is a bistable stochastic unit whose continuous time state fluctuations are driven by integrated quantum entropy units that inject true quantum derived randomness. This enables ultrafast stochastic transitions at low energy while preserving a classical state representation. Apollo combines these p-qubits with a high degree Hyperion 256 interconnect topology, allowing efficient embedding of dense Ising and QUBO problems with substantially reduced minor embedding overhead compared with sparse annealing platforms. We show that, through the Suzuki Trotter correspondence, the equilibrium statistics and annealing dynamics of the p-qubit network reproduce key properties of transverse field quantum annealing without cryogenic cooling, long lived coherence, or microwave control. Beyond device level validation, Apollo is evaluated on a three dimensional spin glass benchmark previously used to study quantum advantage in superconducting annealers. Across 300 disorder realizations, Apollo reaches substantially lower ground state energies than reported cryogenic quantum annealing hardware, while remaining distinct from classical simulated annealing and simulated quantum annealing. A 350 nm release candidate device experimentally validates the core p-qubit dynamics, thermodynamic sampling correctness, and continuous time annealing behavior. These results establish Apollo as a room temperature, industrially scalable platform for quantum driven energy based optimization, probabilistic inference, generative modeling, and hybrid classical quantum workflows.

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

Stable Menus of Public Goods: AI-Enabled Progress

作者:

arXiv:2606.16989v1 Announce Type: cross Abstract: Using an open problem from the EC 2025 paper "Stable Menus of Public Goods" as a testbed, we conduct experiments to understand the effectiveness of different AI-for-EconCS research workflows. Specifically, we study three questions: Does providing human intuition in the prompt help? Does automated multi-turn interaction help? And, does an LLM outperform a first-year PhD student? Regarding the first two questions, we provide evidence for the following workflow suggestions: (1) prompting with human intuition can encourage the LLM to have better "taste", (2) multi-turn workflows help when the pipeline encourages "ambitious" steps. Regarding the third question, using an unpublished manuscript written by the paper's senior authors prior to collaborating with the first-year PhD student, we compare the effectiveness of the LLM with that of the first-year PhD student, and find that the LLM is slightly less effective.

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

RSRCC: A Remote Sensing Regional Change Comprehension Benchmark Constructed via Retrieval-Augmented Best-of-N Ranking

Traditional change detection identifies where changes occur, but does not explain what changed in natural language. Existing remote sensing change captioning datasets typically describe overall image-level differences, leaving fine-grained localized semantic reasoning largely unexplored. To close this gap, we present RSRCC, a new benchmark for remote sensing change question-answering containing 126k questions, split into 87k training, 17.1k validation, and 22k test instances. Unlike prior datasets, RSRCC is built around localized, change-specific questions that require reasoning about a particular semantic change. To the best of our knowledge, this is the first remote sensing change question-answering benchmark designed explicitly for such fine-grained reasoning-based supervision. To construct RSRCC, we introduce a hierarchical semi-supervised curation pipeline that uses Best-of-N ranking as a critical final ambiguity-resolution stage. First, candidate change regions are extracted from semantic segmentation masks, then initially screened using an image-text embedding model, and finally validated through retrieval-augmented vision-language curation with Best-of-N ranking. This process enables scalable filtering of noisy and ambiguous candidates while preserving semantically meaningful changes. The dataset is available at https://huggingface.co/datasets/google/RSRCC.

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

EnvRL: Learn from Environment Dynamics in Agentic Reinforcement Learning

Reinforcement learning (RL) has emerged as a powerful paradigm for training Large Language Models (LLMs) as agents. However, conventional RL methods for long-horizon agentic tasks often struggle with sparse outcome rewards. Intuitively, this overlooks the rich environment dynamics information contained in rollout interaction trajectories. We argue that the interaction experience inherently serves as an implicit supervision signal, reveals the underlying transition mechanisms of the environment, and enables the agent to construct a more accurate internal model of the environment.. Therefore, in this work, we investigate how to leverage this additional signal to improve policy learning. Specifically, we propose EnvRL, a framework that incorporates environment dynamics learning into agentic RL via two auxiliary objectives: state prediction and inverse dynamics. By jointly optimizing with the primary RL objective, we encourage the agent to internalize environment dynamics from its own interaction experience. Extensive experiments on two long-horizon agentic benchmarks demonstrate that EnvRL achieves significant improvements on success-rates over RL-only baselines, e.g., when trained with GRPO, lifting Qwen-2.5-1.5B-Instruct from 72.8% to 77.4% on ALFWorld, and from 56.8% to 67.0% on WebShop.

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

ComAct: Reframing Professional Software Manipulation via COM-as-Action Paradigm

Existing computer-use agents remain fundamentally limited in professional software manipulation: GUI-based agents suffer from fragile visual grounding and long-horizon error accumulation, while API-basedapproaches struggle with heterogeneous protocols and inaccessible commercial interfaces. In this work,we identify the Component Object Model (COM) as a unified executable abstraction, proposing COM-as-Action: a new paradigm that reframes professional software interaction as deterministic program synthesisrather than sequential visual control. To validate this paradigm in the most demanding environments, weintroduce ComCADBench, the first benchmark for agents operating real industrial CAD software. Ourexperiments reveal a substantial paradigm gap: frontier proprietary models achieve near-zero successunder GUI-based interaction, whereas COM-based execution yields substantial immediate gains. Tobridge the remaining gap between syntactic correctness and geometric accuracy, we develop ComActor, aself-correcting agent trained through a progressive three-stage framework, alongside ComForge, a scalableplatform for large-scale training in Windows containers. Extensive experiments show that ComActorachieves state-of-the-art performance on ComCADBench, with strong resilience in long-horizon taskswhere baselines collapse, and generalizes to external CAD benchmark.

20.
PLOS Computational Biology 2026-06-15

Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

by Daniel S. Berman, Libby M. Lewis, Tom D. Curtis, Olivia N. Tiburzi, Daniel F. Q. Smith, Arturo Casadevall, Laura J. Dunphy Emerging fungal pathogens represent a concerning threat to both global health and food security. In this study, we aimed to address our rising vulnerability to fungal pathogens through the development of the Fung-AI pipeline: an AI/ML-driven approach for antifungal discovery. A generative adversarial network (GAN) was trained to generate novel candidate antifungal peptide sequences. Next, in silico antifungal and hemolytic classifiers were built to further prioritize AI-generated peptides for experimental validation. From a pool of ~10,000 candidates, thirteen peptides were selected for testing over two-stages of experimentation. Five peptides were found to display mild antifungal activity against the wheat pathogen, Fusarium graminearum, with minimal inhibitory concentrations (MICs) ranging from 250 µg/mL to 500 µg/mL. Four of the five peptides also showed activity against the human pathogen, Candida albicans (MIC: 500 µg/mL). Two of our AI-generated antifungal peptides additionally demonstrated low cytotoxicity in HepG2 human liver carcinoma cells (LC50 > 704.2 µg/mL) indicating that they may be useful as scaffolds for future optimization for therapeutic applications. None of our peptides were found to considerably inhibit the emerging pathogen C. auris, suggesting the need for pathogen-specific down-selection of candidate peptides. Overall, we present a proof-of-principle, generative-AI-based approach for the rapid design of de novo antifungal peptides.

21.
arXiv (quant-ph) 2026-06-16

Diagonal-Budgeted Trotterization for Efficient Quantum Hamiltonian Simulation

arXiv:2606.16959v1 Announce Type: new Abstract: Efficient classical simulation of quantum Hamiltonian dynamics is often bottlenecked by exponential state growth and the overhead of generic sparse linear algebra. We introduce diagonal-budgeted Trotterization, a structure-aware strategy that decomposes Hamiltonians into factors preserving diagonal sparsity while tightly controlling fidelity loss. Our implementation, HamSim, utilizes a compact diagonal-sparse data layout and specialized C++/CUDA kernels to bypass the overheads of generic formats like CSR. By leveraging SIMD vectorization, multithreading, and GPU acceleration, HamSim achieves high performance across heterogeneous architectures. Benchmarks on the HamLib suite show that HamSim significantly outperforms Qiskit-Aer. On CPUs, HamSim attains speedups of $182$–$1,269\times$ on optimization instances (TSP, MaxCut) and $4.8$–$841\times$ on physical models (TFIM, Heisenberg). On GPUs, it achieves up to $178\times$ speedup for $12$–$16$ qubit problems. Unlike traditional Trotterization, HamSim maintains near-perfect fidelity without requiring exponential steps. This demonstrates that diagonal-aware numerical kernels provide a scalable foundation for high-fidelity classical Hamiltonian simulation.

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

From Tokens to Regions: CUDA-Sensitive Instruction Tuning for GPU Kernel Generation

arXiv:2606.16231v1 Announce Type: cross Abstract: High-performance CUDA kernels are essential for scalable AI systems, while Large Language Models (LLMs) still struggle to generate correct kernels due to strict and implicit execution constraints. Existing LLM-based approaches either rely on costly agentic or reinforcement-learning (RL) pipelines, or adopt supervised fine-tuning (SFT) objectives that fail to explicitly model CUDA sensitivity, namely code tokens or regions tightly coupled with execution constraints. In this work, we investigate CUDA sensitivity from the perspective of token confidence patterns, showing that CUDA sensitivity appears at both token and region levels, where most CUDA-sensitive tokens are predicted with high confidence, while a smaller low-confidence subset forms regions corresponding to execution-critical structures. These findings suggest that effective CUDA kernel generation should both leverage high-confidence CUDA-sensitive tokens and preserve low-confidence CUDA-sensitive regions. Building on these insights, we propose \underline{CUDA-\underline{Se}nsitive Instruction \underline{T}uning (CuSeT)}, a low-cost post-training method within a simple SFT framework. CuSeT follows the principle of ``from tokens to regions'' by combining adaptive token-level masking with region-aware sample reweighting. Experiments show that CuSeT consistently improves functional correctness across multiple model families and scales, outperforming standard SFT and advanced SFT variants, while achieving competitive performance against frontier CUDA kernel generation models with substantially lower inference cost.

23.
arXiv (quant-ph) 2026-06-15

Quantifying and detecting quantum-state texture

arXiv:2604.07257v2 Announce Type: replace Abstract: Quantum-state texture is a recently proposed quantum resource that characterizes the inhomogeneity of a quantum state's matrix element distribution in the computational basis, enriching our understanding of quantum state structure. To expand its quantification toolkit and establish detection methods, in this article, we investigate the resource theory of texture from both quantitative and detection perspectives. First, we construct a texture measure $\mathcal{T}^{GR}_{\alpha,z}(\rho)$ based on the $\alpha$-$z$ Rényi relative entropy and present some of its inherent properties. Second, we analyze the mathematical relationships between several existing texture measures, revealing connections among different quantifiers. Finally, drawing on the witness concept from other resource theories, we systematically introduce texture witnesses into the texture theory and provide examples of texture witnesses with special properties.

24.
Nature Biotechnology 2026-06-19

Efficient site-specific gene addition using R2 retrotransposons in tobacco and rice

作者:

Precise integration of multikilobase DNA fragments remains a major technical barrier in plants. Here we introduce non-long terminal repeat (non-LTR) R2 retrotransposons as a versatile system for targeted gene integration in plants. We reconstituted R2 activity in Nicotiana benthamiana and benchmarked insertion efficiency and fidelity using a TMV-based episomal reporter system. We demonstrate site-specific integration of GFP (2.2 kb) and recombinase-compatible landing pads (0.6 kb) into 28S rDNA arrays, with intact cassette insertion frequencies up to 75% and 53%, respectively. To temporally constrain donor availability and avoid DNA intermediates, we combined in planta effector expression with recombinant RNA virus-mediated donor delivery. We apply R2 retrotransposons for targeted insertion of resistance cassettes within the rDNA of rice callus, achieving integration efficiencies up to 17%. These results position R2 retrotransposons as a double-strand break-free system for RNA-templated insertion of multikilobase gene cassettes at rDNA loci, for safe-harbor trait stacking in plants with potential applications in crop improvement and synthetic biology. Retrotransposons are applied in plants for safe-harbor transgene integration.

25.
arXiv (CS.CV) 2026-06-18

Quantification of Uncertainty with Adversarial Models in Medical Image Segmentation

Reliable pixel-level uncertainty quantification holds the potential to transform clinical workflows by enabling high-fidelity longitudinal monitoring and distinguishing true pathological changes from artifacts. Ideally, these models provide the stability required for critical treatment planning and surgical intervention. However, standard deep learning models often suffer from miscalibration, yielding overconfident predictions that mask underlying vulnerabilities at subtle pathological boundaries. To address this, we propose QUAM-SM, a post-hoc framework using targeted adversarial search to identify "adversarially fragile" pixels. By actively seeking perturbations that expose predictive instability, our method highlights regions where decisions are most vulnerable to being flipped. Importantly, the framework disentangles epistemic uncertainty from aleatoric uncertainty. Experiments on two public datasets with multiple expert annotations demonstrate that QUAM-SM outperforms both standard and recent uncertainty estimation approaches in terms of reliability and boundary sensitivity. Code is available at https://github.com/HanaJebril/quam_sm