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01.
arXiv (CS.AI) 2026-06-15

Actionable Interpretability Must Be Defined in Terms of Symmetries

arXiv:2601.12913v4 Announce Type: replace Abstract: This paper argues that interpretability research in Artificial Intelligence (AI) is fundamentally ill-posed as existing definitions of interpretability fail to describe how interpretability can be formally tested or designed for. We posit that actionable definitions of interpretability must be formulated in terms of *symmetries* that inform model design and lead to testable conditions. Under a probabilistic view, we hypothesise that four symmetries (inference equivariance, information invariance, concept-closure invariance, and structural invariance) suffice to (i) formalise interpretable models as a subclass of probabilistic models, (ii) yield a unified formulation of interpretable inference (e.g., alignment, interventions, and counterfactuals) as a form of Bayesian inversion, and (iii) provide a formal framework to verify compliance with safety standards and regulations.

02.
arXiv (CS.AI) 2026-06-18

ARIADNE: Agnostic Routing for Inference-time Adapter DyNamic sElection

arXiv:2606.19079v1 Announce Type: new Abstract: The increasing deployment of parameter-efficient fine-tuning (PEFT) has led to model ecosystems in which a single backbone is paired with many task-specialized adapters. In this setting, inference-time queries often arrive without task labels, requiring the system to automatically select the most appropriate adapter from a growing and heterogeneous adapter pool. Existing routing methods either depend on access to adapter internals, such as weight decompositions or gradient-based statistics, or require additional router training, which limits scalability and portability as new adapters are added. We introduce ARIADNE, a training-free, adapter-agnostic routing framework for dynamic adapter selection at inference time. ARIADNE represents each adapter through a set of centroids computed from embeddings of its training set, capturing the data distribution associated with that adapter. Given an unlabeled input, it selects an adapter by measuring proximity to these centroids in latent space. Because routing is performed entirely in the input embedding space, ARIADNE is compatible with arbitrary PEFT methods and requires no modification to the adapters or training procedures. Primarily evaluated with Llama 3.2 1B Instruct on 23 diverse NLP tasks, ARIADNE recovers 97.44% of the upper bound performance. Scaling to 44 tasks, it achieves 89.7% average selection accuracy, without additional training or access to adapter internals.

03.
arXiv (CS.LG) 2026-06-15

More with LESS – Local Scene Representations for Tactile Imaging

arXiv:2606.14344v1 Announce Type: new Abstract: Tactile imaging seeks to reconstruct the internal structure of soft objects through touch sensing, with applications in medical diagnosis and robotic manipulation. Recent self-supervised learning approaches have shown promising results, but rely on global, unstructured representations and robot-controlled sensing, limiting generalization and practical use. We propose Local Encoder for Spatial Sensing (LESS), an object-centric tactile representation that exploits the local nature of touch. The tactile scene is modeled as a grid of recurrent encoders with local receptive fields, whose states are fused to reconstruct 2D or 3D images of internal structure. This compositional design enables strong generalization: models trained on single-inclusion phantoms accurately image objects with multiple inclusions and varying sizes. The local structure further supports spatial uncertainty estimation. In addition, we enable hand-held tactile imaging via external pose tracking and human-like palpation data, and extend tactile imaging to full 3D reconstruction.

04.
arXiv (CS.LG) 2026-06-12

A2D2: Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding

arXiv:2606.13565v1 Announce Type: new Abstract: Discrete diffusion models offer a simple and stable likelihood-based framework for sequence generation, recently extended to any-length settings via token insertion. Principled reward-guided fine-tuning for any-length discrete diffusion, however, remains largely unexplored. We introduce Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding (A2D2), a unified framework for reward-guided fine-tuning of any-length discrete diffusion models via joint optimization of the insertion and unmasking policies together with a quality-based inference schedule. We derive the Radon-Nikodym derivative for the joint insertion-unmasking path measures, enabling theoretically guaranteed convergence to the intractable reward-tilted sequence distribution without requiring target samples. Building on this, we establish unmasking and insertion quality as tractable approaches for minimizing decoding error and introduce the Adaptive Joint Decoding (AJD) loss, which provably yields the optimal path measure that generates the reward-tilted distribution. Empirically, A2D2 improves reward optimization while enhancing generation flexibility and accuracy over prior fixed-length fine-tuning and inference-time guidance methods.

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

Dr-DCI: Scaling Direct Corpus Interaction via Dynamic Workspace Expansion

Agentic search over large corpora relies on retriever-mediated interfaces (e.g., BM25 or ColBERT) for scalable candidate discovery. While effective at ranking relevant documents, these interfaces expose evidence only as ranked results or bounded document views, limiting agents' ability to reorganize material and verify constraints across documents. Direct Corpus Interaction (DCI) addresses this limitation by exposing shell-executable corpus operations for flexible search, filtering, comparison, and verification. However, full-corpus terminal commands become slow and unstable as the corpus grows, degrading performance and efficiency. We introduce DR-DCI, a retriever-steered DCI framework that treats retrieval as an agent-callable action for expanding a local workspace. Rather than operating directly over the full corpus, the agent dynamically pulls relevant documents into an evolving workspace and conducts DCI operations within it. This design combines retriever-level recall with DCI-style precision: retrieval keeps exploration scalable, while DCI preserves the local operations needed for effective evidence resolution. Experiments show that DR-DCI is both effective and efficient across scales. On Browsecomp-Plus, DR-DCI reaches 71.2\% accuracy, improving over raw DCI and ablated variants by up to 8.3 points while reducing tool usage, wall time, and estimated cost. With workspace-preserving context reset, accuracy further improves to 73.3\%. In corpus-scaling experiments, DR-DCI remains effective from 100K to 10M documents, whereas raw DCI becomes unstable and BM25 performs substantially worse. DR-DCI also scales to a 20M-scale file-per-document Wiki-18 QA setting, achieving an average score of 63.0 across six benchmarks and outperforming retrieval-based and trained search-agent baselines. Ablation analysis further shows that ranked previews and inter-document DCI are key to performance.

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

Exact Entanglement Dynamics Beyond Nearest-Neighbor Dual-Unitary Floquet Systems

Authors:

arXiv:2606.11311v1 Announce Type: new Abstract: Exact results using dual-unitarity largely rely on nearest-neighbor structures, while finite-range interactions typically lead to complications. Going beyond the usual nearest-neighbor setting, we introduce an analytically tractable family of finite-range kicked Ising models that admit exact closed-form entanglement dynamics. The construction is based on a staggered structure in which dual-unitarity is present on sublattices that are then coupled to each other. The central observation is that these inter-sublattice couplings do not obstruct the dual-unitarity of the resulting model. For the minimal interaction range of $r= 2$, we derive exact expressions for all the $n-$Rényi entanglement entropies at all times and show that the result is the sum of the two coupled sublattice contributions. Our framework extends naturally to larger finite interaction ranges and to systems with heterogeneous local Hilbert spaces, without additional assumptions. It thus provides a controlled setting for studying exact entanglement growth beyond strictly nearest-neighbor dual-unitary models.

07.
arXiv (CS.LG) 2026-06-11

Few-Shot Resampling for Scalable Statistically-Sound Data Mining

arXiv:2606.11235v1 Announce Type: new Abstract: A key step in knowledge discovery is the evaluation of data mining results. In several applications, including pattern mining, graph analysis, and others, this step includes the evaluation of the statistical significance of the results, to avoid spurious discoveries due only to noise or random fluctuations in the data. While specialized procedures have been developed for some specific applications, resampling-based approaches are widely used, in particular for complex analyses where analytical results cannot be derived. However, current resampling-based approaches require the generation and analysis of thousands of resampled datasets, and are therefore impractical for large datasets or computationally intensive analyses. In this paper, we introduce FewRS, a simple and effective resampling-based approach to assess the statistical significance of data mining results with rigorous guarantees on the probability of false discoveries. Our approach can be used in every situation where resampling-based approaches are applied. FewRS builds on our derivation of a novel bound to the supremum deviation of test statistics representing the quality of data mining results. We prove that FewRS needs to generate and analyze an extremely small number of resampled datasets, leading to a highly scalable approach with wide applicability. We test our approach on common tasks such as pattern mining and network analysis. In all cases, our approach results in a reduction of up to two orders of magnitude in running time compared to the state of the art, while preserving high statistical power, enabling the statistical validation of data mining results on large-scale real-world datasets.

08.
arXiv (CS.CL) 2026-06-17

When English Isn't the Best Teacher: Source Language Effects in Cross-Lingual In-Context Learning

Cross-lingual transfer in multilingual NLP has been widely explored in supervised fine-tuning contexts, where factors like data availability and linguistic similarity largely determine transfer quality. As the field shifts toward few-shot In-Context Learning (ICL), it is often presumed that insights from fine-tuning carry over unchanged. Yet this assumption has not been rigorously evaluated, leaving open the question of how to choose source languages for cross-lingual ICL. We conduct a broad empirical study of cross-lingual transfer in ICL spanning seven tasks, six models, and a typologically diverse set of languages. We further analyze language confusion, a key obstacle for generative tasks in cross-lingual ICL. Our results show that conventional fine-tuning-based expectations do not consistently apply in the ICL regime and point to alternative heuristics for selecting source languages effectively.

09.
arXiv (quant-ph) 2026-06-12

Squeezing Enhancement in Lossy Multi-Path Atom Interferometers

arXiv:2409.04091v3 Announce Type: replace Abstract: This paper explores the sensitivity gains afforded by spin-squeezed states in atom interferometry, in particular using Bragg diffraction. We introduce a generalised input-output formalism that accurately describes realistic, non-unitary interferometers, including losses due to velocity selectivity and scattering into undesired momentum states. This formalism is applied to evaluate the performance of one-axis twisted spin-squeezed states in improving phase sensitivity. Our results show that by carefully optimising the parameters of the Bragg beam splitters and controlling the degree of squeezing, it is possible to improve the sensitivity of the interferometer by several dB with respect to the standard quantum limit despite realistic levels of losses in light pulse operations. However, the analysis also highlights the challenges associated with achieving these improvements in practice, most notably the impact of finite temperature on the benefits of entanglement. The results suggest ways of optimising interferometric setups to exploit quantum entanglement under realistic conditions, thereby contributing to advances in precision metrology with atom interferometers.

10.
arXiv (quant-ph) 2026-06-15

Quantitative and Optimal Device-Independent Lower Bounds on Detection Efficiency

arXiv:2511.19302v2 Announce Type: replace Abstract: This paper examines a quantitative and optimal lower bound on the detector efficiency in a (2,2,2) Bell experiment within a fully device-independent framework, whereby the detectors used in the experiment are uncharacterized. We provide a tight lower bound on the minimum efficiency required to observe a desired Bell-CHSH violation using the Navascués-Pironio-Acín (NPA) hierarchy, confirming tightness up to four decimal places with numerical optimization over explicit quantum realizations. We then introduce the effect of dark counts and demonstrate how to quantify the minimum required efficiency to observe a desired CHSH violation with an increasing dark count error. Finally, to obtain an analytical closed-form expression of the minimum efficiency, we consider the set of no-signaling behaviors that satisfy the Tsirelson bound, which are easier to characterize than the quantum set. Using such behaviors, we find a simple closed-form expression for a lower bound on the minimum efficiency which is monotonically increasing with the CHSH violation, though the analytically obtained lower bounds are meaningfully below the numerically tight lower bound.

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

A fast direct solver based neural network for solving PDEs

arXiv:2606.19895v1 Announce Type: cross Abstract: The matrices arising from large scale $N$-body problems can be efficiently represented using hierarchical matrices, whose key idea is that the admissible off-diagonal sub-matrices can be well approximated by low-rank matrices across a hierarchy of matrix partitions. HODLR (Hierarchical Off-Diagonal Low-Rank) matrices are a subclass of hierarchical matrices in which all off-diagonal submatrices at every level of a recursive binary partition are low-rank. In this article, we present a neural network that learns the inverse operation of HODLR matrices based on the fast direct solver for HODLR matrices developed by Ambikasaran and Darve (2013). We further extend the architecture to learn nonlinear solution operators associated with PDEs by replacing some of the linear layers with deep sub-networks. We demonstrate the performance of the proposed architecture by performing a comprehensive set of experiments that include (i) solving a linear problem such as the Fredholm integral equation of the second kind, (ii) solving PDEs such as the nonlinear Schrödinger equation, Burgers' equation, and the steady-state Darcy's flow equation, (iii) generalization study across varying parameter values, (iv) comparing the inference time of the proposed network with the run time of a classical numerical solver, and (v) comparing the proposed network with some of the existing neural operator learning networks.

12.
arXiv (CS.CL) 2026-06-15

AgentSpec: Understanding Embodied Agent Scaffolds Through Controlled Composition

LLM agents are increasingly built not as single model calls, but as scaffolded systems that combine reasoning, memory, reflection, action execution, and learning. While such scaffolds often improve performance, they are often embedded in tightly coupled pipelines, making it difficult to isolate component contributions, compare alternative designs, or understand how module interactions shape agent behavior. We introduce AgentSpec, a modular specification framework that represents embodied agents as typed compositions of reusable policy components with standardized interfaces. AgentSpec standardizes the interfaces among perception, memory, reasoning, reflection, action, and optional learning, enabling components to be swapped and recombined under controlled conditions. We instantiate this framework across DeliveryBench, ALFRED, MiniGrid, and RoboTHOR, and analyze reasoning, memory, reflection, and reinforcement-learning modules across model backbones. Our results show that agent performance is governed by scaffold compatibility and interaction effects rather than isolated module strength. In particular, structured multi-granularity memory improves long-horizon state tracking, reasoning and memory interact non-uniformly across environments, reflection trades off correction and cost, and RL-trained policies compose best when optimized with deployment-time scaffold structure. AgentSpec provides a controlled foundation for studying, comparing, and designing composable LLM agents. Our code, baselines and interactive playground are publicly available at https://agentspec-embodied.github.io.

13.
arXiv (CS.AI) 2026-06-15

VISTA: View-Consistent Self-Verified Training for GUI Grounding

arXiv:2606.14579v1 Announce Type: new Abstract: When applying Group Relative Policy Optimization (GRPO) for GUI Grounding, rollouts are sampled from a single screenshot view; groups often become either all failures on difficult instances or all successes on easy ones, yielding no useful relative advantage. We propose VISTA (View-Consistent Self-Verified Training), a GRPO-based training framework that constructs each comparison group from multiple target-preserving views of the same GUI instance.Each view is generated by a crop that keeps the target element visible and remaps its box exactly, so model rollouts are compared across semantically equivalent but geometrically different inputs. To stabilize short coordinate generation without turning reinforcement learning into unconditional imitation, VISTA further adds a self-verified cross-view anchor: an oracle answer optimized with an advantage-weighted loss, excluded from the group baseline and activated only when the model has produced a maximum-reward rollout. Across five GUI-grounding benchmarks and multiple Qwen backbones, VISTA consistently improves grounding accuracy.On ScreenSpot-Pro, it raises Qwen3-VL 4B/8B/30B-A3B from 55.5/52.7/53.7 to 63.4/65.8/67.0. Robustness analyses further show higher worst-view accuracy and lower prediction flip rates.

14.
arXiv (CS.CV) 2026-06-18

Beyond Nearest Neighbor Interpolation in Data Augmentation

Avoiding the risk of undefined categorical labels using nearest neighbor interpolation overlooks the risk of exacerbating pixel level annotation errors in augmented training data. Additionally, the inherent low pass filtering effects of interpolation algorithms exacerbate the risk of degrading high frequency structural details within annotated regions of interest. To avoid these risks, the author modified convolutional neural networks data transformation functions by incorporating a modified geometric transformation function, removing reliance on nearest neighbor interpolation, and integrating a mean-based class filtering mechanism to handle undefined categorical labels with alternative interpolation algorithms. The author also implemented an offline data augmentation pipeline to generate interpolation specific augmented training data, enabling quantitative assessment of interpolation specific low pass filtering effects on augmented training data. Experimental evaluation on three medical image segmentation datasets and the XBAT+ datasets demonstrated performance gains across multiple quantitative metrics.

15.
arXiv (quant-ph) 2026-06-16

Optimal Toffoli-Depth Multi-Controlled Toffoli Decomposition in 2D Qubit Layout

arXiv:2606.15113v1 Announce Type: new Abstract: The multi-controlled Toffoli (MCT) gate is a key primitive in quantum arithmetic, oracle construction, and quantum cryptanalysis. Although recent work has established optimal Toffoli-depth MCT decompositions under all-to-all qubit connectivity, their realization on near-term quantum hardware with restricted qubit connectivity remains largely unexplored. While general-purpose quantum mappers can route arbitrary circuits, they do not explicitly exploit the repeated interaction patterns inherent in MCT decompositions. In our present paper, we study architecture-aware mappings of optimal Toffoli-depth MCT decompositions onto restricted two-dimensional qubit layouts. We begin with a structured geometric placements that preserve the parallelism of state-of-the-art Toffoli and MCT decompositions with no additional depth overhead. We further introduce a motif-based packing framework in which decomposition layers are represented by interaction motifs derived from basic Toffoli gates. By embedding these motifs vertex-disjointly into hardware graphs, we characterize the minimum-size topologies supporting the required qubit resources and derive explicit bounds on the resulting depth overhead under tight qubit budgets. Finally, we compare these bounds with routing-aware placement heuristics and empirically evaluate the effectiveness of embedding different motifs across a range of hardware topologies.

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

Million-scale multimodal pollen microscopy with expert-guided foundation models

Automated pollen identification from microscopy remains a bottleneck in aerobiology, palaeoecology and biodiversity monitoring, because scalable systems must generalise across specimen preparation, scanner settings and geographic origins while retaining palynological interpretability. To address this gap, we present a million-scale multimodal pollen microscopy resource, Pollen AI Atlas, assembled from pure-species whole-slide bright-field images spanning four geographic origins, four scanner settings and 46 taxon labels across 31 botanical families. Seeded by one manually selected exemplar per source slide, token-level mining and filtering produced 1,511,390 released grain detections with 99.6\% proposal precision in expert-curated test regions. Each detection was paired with machine-generated grain-level morphological captions from five open-weight vision-language models, guided by expert-verified palynological anchors, yielding structured descriptions of aperture systems, wall ornamentation, shape and size. Among the evaluated models, Gemma4 provided the most controlled primary caption set, combining tight length control, no leakage and the strongest text-retrieval performance. Baseline benchmarks with frozen visual features reached 88.16\% top-1 accuracy, while cross-regional retrieval showed that caption-derived text embeddings remained robust when image similarity degraded (mAP@20 0.811 versus 0.262). Released data, annotations, captions, splits, code, and weights provide a benchmark for pollen recognition, cross-regional domain adaptation and domain-specific multimodal microscopy learning.

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

MedAI: Evaluating TxAgent's Therapeutic Agentic Reasoning in the NeurIPS CURE-Bench Competition

arXiv:2512.11682v2 Announce Type: replace Abstract: Therapeutic decision-making in clinical medicine constitutes a high-stakes domain in which AI guidance interacts with complex interactions among patient characteristics, disease processes, and pharmacological agents. Tasks such as drug recommendation, treatment planning, and adverse-effect prediction demand robust, multi-step reasoning grounded in reliable biomedical knowledge. Agentic AI methods, exemplified by TxAgent, address these challenges through iterative retrieval-augmented generation (RAG). TxAgent employs a fine-tuned Llama-3.1-8B model that dynamically generates and executes function calls to a unified biomedical tool suite (ToolUniverse), integrating FDA Drug API, OpenTargets, and Monarch resources to ensure access to current therapeutic information. In contrast to general-purpose RAG systems, medical applications impose stringent safety constraints, rendering the accuracy of both the reasoning trace and the sequence of tool invocations critical. These considerations motivate evaluation protocols treating token-level reasoning and tool-usage behaviors as explicit supervision signals. This work presents insights derived from our participation in the CURE-Bench NeurIPS 2025 Challenge, which benchmarks therapeutic-reasoning systems using metrics that assess correctness, tool utilization, and reasoning quality. We analyze how retrieval quality for function (tool) calls influences overall model performance and demonstrate performance gains achieved through improved tool-retrieval strategies. Our work was awarded the Excellence Award in Open Science. Complete information can be found at https://curebench.ai/.

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.LG) 2026-06-15

FreshRetailNet-LT: A Stockout-Annotated Censored Demand Dataset for Latent Demand Recovery and Forecasting in Fresh Retail

arXiv:2505.16319v4 Announce Type: replace Abstract: Accurate demand estimation is critical for the retail business in guiding the inventory and pricing policies of perishable products. However, it faces fundamental challenges from censored sales data during stockouts, where unobserved demand creates systemic policy biases. Existing datasets lack the temporal resolution and annotations needed to address this censoring effect. To fill this gap, we present FreshRetailNet-50K, the first large-scale benchmark for censored demand estimation. It comprises 50,000 store-product time series of detailed hourly sales data from 898 stores in 18 major cities, encompassing 863 perishable SKUs meticulously annotated for stockout events. The hourly stock status records unique to this dataset, combined with rich contextual covariates, including promotional discounts, precipitation, and temporal features, enable innovative research beyond existing solutions. We demonstrate one such use case of two-stage demand modeling: first, we reconstruct the latent demand during stockouts using precise hourly annotations. We then leverage the recovered demand to train robust demand forecasting models in the second stage. Experimental results show that this approach achieves a 2.73% improvement in prediction accuracy while reducing the systematic demand underestimation from 7.37% to near-zero bias. With unprecedented temporal granularity and comprehensive real-world information, FreshRetailNet-50K opens new research directions in demand imputation, perishable inventory optimization, and causal retail analytics. The unique annotation quality and scale of the dataset address long-standing limitations in retail AI, providing immediate solutions and a platform for future methodological innovation. The data (https://huggingface.co/datasets/Dingdong-Inc/FreshRetailNet-50K) and code (https://github.com/Dingdong-Inc/frn-50k-baseline}) are openly released.

20.
bioRxiv (Bioinfo) 2026-06-12

From Proteome Mining to Structural Validation: Phosphopyruvate Hydratase as a Structurally Tractable Drug Target in Kinetoplastid Parasites

Chagas disease, caused by Trypanosoma cruzi, demands novel therapeutic strategies that overcome the toxicity and limited efficacy of current treatments. To address this need, herein we report an integrative, target-centric strategy that combines parasite proteome mining, structural modeling, and experimental validation. Functional enrichment and druggability analyses identified phosphopyruvate hydratase (PPH) as a promising candidate due to its essential metabolic role and limited similarity to human homologs. Notably, proteome mining revealed the presence and conservation of PPH across kinetoplastid parasites, including Leishmania donovani, supporting its evaluation beyond T. cruzi. For the selected PPH sequences, AlphaFold-derived three-dimensional models underwent extensive molecular dynamics refinement, yielding stable conformational ensembles suitable for structure-based studies. Using this validated model, virtual screening of the Latin American Natural Products Database - LANaPDB - identified aptosimon as a top-ranked compound candidate. Molecular dynamics simulations further showed ligand-dependent binding behavior, suggesting alternative binding modes distinct from the canonical substrate configuration. In vitro assays demonstrated consistent antiparasitic activity against intracellular T. cruzi amastigotes (IC50 = 3.52 ug/mL) and Leishmania donovani promastigotes (IC50 = 13.06 ug/mL), supporting the biological relevance of the aptosimon-related lignan chemotype, hinokinin, across two kinetoplastid parasite models. Together, these results support PPH as a structurally tractable and biologically relevant candidate target, while identifying an aptosimon-related lignan chemotype, represented experimentally by hinokinin, as a cross-species antiparasitic scaffold that warrants further biochemical target-validation studies.

21.
arXiv (CS.LG) 2026-06-19

DisjunctiveNet: Neural Symbolic Learning via Differentiable Convexified Optimization Layers

arXiv:2605.30456v2 Announce Type: replace Abstract: Many learning tasks in science and engineering are characterized by sparse datasets, which limits the effectiveness of purely data-driven approaches. At the same time, these problems are often accompanied by rich domain knowledge derived from physical laws, operational requirements, and expert heuristics. Such knowledge is frequently expressed as rules involving logical propositions and linear inequalities. Existing neuro-symbolic methods typically enforce these rules approximately through soft penalties, assume input-independent rules when designing specialized architectures, or rely on non-differentiable post-processing at inference time to achieve hard constraint satisfaction. While recent advances in differentiable optimization layers enable end-to-end feasibility enforcement within neural networks, extending these approaches to logical or mixed-integer rules remains challenging due to inherent nonconvexity. In this work, we propose a unified end-to-end framework for enforcing hard, input-dependent mixed integer linear constraints within neural networks. Our approach represents rules as disjunctive constraints and applies hierarchical convex relaxations to obtain convex hull formulations. These relaxations yield tractable linear constraints that can be embedded as differentiable optimization layers while enabling exact rule satisfaction. We demonstrate the effectiveness of the proposed framework on real-world datasets, achieving perfect rule satisfaction and strong predictive performance.

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

Latent Geometric Chords for Query-Efficient Decision-Based Adversarial Attacks

While decision-based black-box adversarial attacks present a severe security threat, current methodologies suffer from fundamental limitations. Pixel-wise attacks frequently introduce unnatural, high-frequency visual artifacts, while latent-space frameworks are confined by the limited search space of low-dimensional manifolds and inherent reconstruction flaws. To resolve these limitations, we propose Latent Geometric Chords (LGC) for Query-Efficient Decision-Based Adversarial Attacks alongside a variant, LGC-H. At its core, LGC navigates decision boundaries by executing a curvature-aware geometric search within a compressed semantic manifold. To guarantee high visual fidelity and circumvent dimensionality bottlenecks, we introduce a Residual-based Adversarial Generation (RAG) mechanism. RAG isolates semantic perturbations as geometric chords and superimposes them directly onto the original source image. RAG substantially resolves baseline reconstruction flaws and effectively doubles the permissible search space dimensions. Experimental results demonstrate that LGC achieves robust cross-dataset transferability and substantially outperforms state-of-the-art baselines. Notably, our method, LGC, minimizes perturbation magnitudes while achieving state-of-the-art visual fidelity–with a Structural Similarity Index Measure (SSIM) exceeding 0.99 and a Learned Perceptual Image Patch Similarity (LPIPS) below 0.01 at 5000 queries–and sustaining high attack success rates under stringent perceptual constraints, successfully compromising adversarially trained robust models. The source code is available at: https://github.com/eihmuekhine/Latent-Geometric-Chords.

24.
arXiv (CS.LG) 2026-06-19

Execution-State Capsules: Graph-Bound Execution-State Checkpoint and Restore for Low-Latency, Small-Batch, On-Device Physical-AI Serving

Authors:

arXiv:2606.20537v1 Announce Type: new Abstract: Mainstream LLM serving systems reuse prefix work mainly through paged or radix key-value (KV) caches. This is highly effective for high-throughput, high-concurrency serving, but it manages only one positional fragment of execution state: the KV cache. We study the opposite regime: low-latency, small-batch, on-device physical-AI serving, where interactive LLM agents, speech systems, and robot policies repeatedly branch, reset, interrupt, and re-enter under tight responsiveness budgets. We introduce execution-state capsules, a graph-bound checkpoint and restore mechanism for the complete restorable state at a committed boundary. FlashRT is a white-box, backend-facing kernel runtime whose evaluated NVIDIA CUDA backend runs captured graph plans over contiguous static buffers with no block-table indirection. Because the live state is a closed set of named buffers, a capsule can snapshot, restore, fork, or roll back the whole execution boundary, including KV, recurrent state, convolution state, MTP state, and metadata. This moves reuse from token-addressed KV fragments to graph-bound execution-state boundaries. On an RTX 5090, capsule restore is byte-exact at the stored-state level and token-identical under greedy decode. A KV-only ablation diverges, showing that recurrent state is load-bearing. GPU-resident snapshot and restore are sub-millisecond, and TTFT speedup over cold prefill grows from 3.9x at 2k tokens to 27x at 16k tokens. On Jetson AGX Thor and DGX Spark, the same correctness and structural properties hold. Capsules are not a replacement for high-throughput KV-cache serving; they define a complementary latency-first serving point for explicit execution-state reuse.

25.
bioRxiv (Bioinfo) 2026-06-14

Somatic variant detection in normal tissues from single-cell sequencing data

A crucial advantage of single-cell sequencing (SCS) is its ability to identify somatic variants in individual cells, enabling phylogenetic analysis of cellular populations within bulk tissues. While identifying somatic variants in tumor tissues via SCS has become a common practice, doing so in normal tissues remains challenging due to the rarity of somatic variants in normal cells. To evaluate the feasibility of somatic variant calling from widely available single-nucleus RNA-seq (snRNA-seq) and single-nucleus ATAC-seq (snATAC-seq) data, we profiled a Cell-line mix of six HapMap samples prepared by the SMaHT consortium using 10x Genomics 5' snRNA-seq (12k cells with 36k mean reads per cell) and snATAC-seq (11k cells with 14k median high-quality fragments per cell) for variant calling. PacBio long-read whole genome sequencing (WGS) data (109x) generated from individual cell lines were used as ground truth. Two computational tools, Monopogen and SComatic, were used for somatic variant calling from the SCS data. Monopogen achieved single nucleotide variant (SNV) detection accuracies of 93.30% in the snRNA-seq and 99.64% in the snATAC-seq data, both of which outperformed SComatic (74.35% and 94.29%, respectively). Monopogen also consistently detected somatic SNVs at cellular fractions as low as 0.5% (2.54% in snRNA and 0.81% in snATAC) in individual samples. Notably, snATAC-seq exhibited higher genomic coverage breadth and larger number of variants detected than snRNA-seq. While the SCS data have lower overall genome coverage than that of the bulk WGS, the single-cell level variant resolution allows Monopogen to assign variants to their cells of origin with over 80% accuracy in both RNA and ATAC modalities, thereby facilitating studies of clonal evolution and cell-type-specific mutagenesis. Other benchmarking methods were also evaluated (DeepVariant, Cellsnp-lite and Mutect2) for comparison. In conclusion, our study demonstrated the feasibility of performing reliable single-cell somatic mutation calling in a cell-line mixture and discussed the strengths and limitations of current computational methods when applied to normal tissues.