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01.
arXiv (CS.AI) 2026-06-24

ARIA: Adaptive Region-Based Importance Allocation for Conditional Diffusion Distillation

arXiv:2606.23898v1 Announce Type: cross Abstract: Distilling conditional diffusion models aims to transfer the behavior of a large teacher to a smaller student while preserving alignment across conditioning inputs. Unlike recognition tasks, knowledge distillation in conditional diffusion often struggles to transfer knowledge beyond the training distribution, since the predicted noise strongly depends on the conditioning signal. As a result, effective distillation requires exploring a large conditioning space. In practical settings, this creates a major bottleneck. Paired image-condition data may be limited, and generating synthetic images for every available condition is often computationally infeasible, while the pool of conditions, such as text prompts, can be extremely large. Recent work addresses this issue by switching conditions during training, exposing the student to a broader conditioning space without changing the distillation objective. Yet this raises a complementary question: once a large conditioning corpus is available, how should the training effort be allocated? In this work, we introduce ARIA, a framework that adaptively allocates training effort across coarse regions of the conditioning space. By maintaining online estimates of teacher-student discrepancy at the region level, ARIA focuses updates where misalignment persists while preserving the original distillation objective. Empirically, ARIA improves over RC across most architectures and settings, with the clearest gains observed in unseen and underrepresented regimes. We also provide a theoretical analysis showing that the proposed tracking mechanism follows the evolving discrepancy during training under bounded variance and drift assumptions.

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

Operadic consistency: a label-free signal for compositional reasoning failures in LLMs

Detecting LLM reasoning failures at inference time without ground-truth labels has motivated a wide range of confidence baselines, including self-consistency, semantic entropy, and P(True), built on within-question sampling and self-evaluation. Operad theory, the formalism for systems built by iterated substitution, suggests a complementary diagnostic: a model's direct answer to a compositional query should agree with the answer it produces by composing a stated decomposition of the same query. We instantiate this idea as operadic consistency (OC), a per-question signal. Across twelve instruction-tuned LLMs (4B to 671B parameters, open-weights and closed-source) on four multi-hop QA datasets, OC is strongly correlated with accuracy on every dataset (Pearson $r \in [0.86, 0.94]$, all $p \leq 0.0004$), and is the only signal we evaluate with $r \geq 0.85$ uniformly across all four datasets. Chain-of-thought self-consistency (CoT-SC; Wang et al., 2023) matches OC on HotpotQA and DROP ($r = 0.93, 0.87$) but drops to $r \approx 0.45$ on MuSiQue and StrategyQA. At the per-question level, OC contributes information beyond CoT-SC and semantic entropy on every dataset (cluster-robust $p \leq 10^{-16}$ for the OC coefficient), and the conclusion is robust to additionally controlling for constructed decomposition-aware baselines ($p \leq 10^{-13}$). The same signal yields selective-prediction improvements (accuracy at fixed coverage) over a tuned CoT-SC baseline at the equal-cost $K = 3$ budget (AUARC lifts of +0.086 to +0.096 and AUROC lifts of +0.092 to +0.164; 95% CIs exclude zero on every cell). On five frontier thinking models, where the decomposition is extracted from the model's own chain of thought, the same equal-cost comparison gives positive selective-prediction point-estimate lift on all 16 (dataset, budget, metric) cells tested, with 95% CIs excluding zero on 12 of the 16.

03.
arXiv (CS.LG) 2026-06-25

Training Dynamics of Neural Software Defect Predictors under Coupled Data-Quality Issues

arXiv:2606.24968v1 Announce Type: new Abstract: Context: Software defect prediction supports maintenance decisions such as testing prioritization, release-risk assessment, and quality monitoring. However, metric-based SDP datasets often contain coupled data-quality issues, especially class imbalance and class overlap. Prior work has mainly measured their impact through endpoint performance, while recent evidence suggests that such issues may also appear in neural training dynamics (gradients, weights, biases, error trajectories). However, these studies examine issues in isolation, leaving open how internal neural network training patterns manifest when data quality issues are coupled. Objective: We investigate how training-dynamics patterns from class imbalance, overlap, and their coupling can be characterized under interaction-aware conditions in deep learning-based SDP. Method: We conduct a controlled intervention study on class-level UBD datasets, training a fixed MLP under imbalance-only, overlap-only, and joint conditions across five seeds. Training dynamics are logged per epoch; fidelity is monitored via coupling ratios. Patterns are characterized using effect sizes, trajectories, sensitivity analyses, and rule-based classification. Expected contribution: The study will produce an interaction-aware empirical protocol and a candidate taxonomy of training-dynamics patterns for coupled data-quality issues in metric-based SDP.

04.
arXiv (CS.CL) 2026-06-17

ConSA: Controllable Sparsity in Hybrid Attention via Learnable Allocation

Hybrid architectures combining full attention (FA) and sliding-window attention (SWA) are a promising paradigm for efficient LLM inference. However, existing methods typically rely on hand-crafted rules or simple post-hoc heuristics for FA/SWA allocation and offer limited analysis of the attention behaviors underlying these designs. We propose Controllable Sparsity in Hybrid Attention (ConSA), a framework that learns optimal FA/SWA assignment under a user-specified sparsity target. ConSA employs L0 regularization to learn binary masks selecting between FA and SWA for each attention unit, while an augmented Lagrangian constraint enforces the target sparsity at either layer or KV-head granularity. We evaluate ConSA on two LLMs at the 0.6B and 1.7B scales. Learned allocations consistently outperform rule-based baselines, with KV-head-wise allocation yielding clear gains over layer-wise allocation. The learned patterns place SWA in the bottom layers and concentrate FA into contiguous middle-layer blocks, diverging from evenly interleaved patterns in rule-based methods. This structure persists across model scales, sparsity levels, and allocation granularities, revealing a fine-grained spectrum of intrinsic attention behaviors that underlies the learned allocation.

05.
arXiv (CS.AI) 2026-06-19

Can In-Context Learning Support Intrinsic Curiosity?

arXiv:2606.19476v1 Announce Type: cross Abstract: Effective machine learning depends not only on how we model data, but also on what data we choose to collect. While large sequence models have revolutionized data modeling, the problem of automated data selection, or "intrinsic curiosity", remains a significant challenge. Classic approaches incentivize exploration by rewarding an agent based on its "learning progress", which measures how much a newly acquired observation improves a world model's predictive ability. However, evaluating these rewards traditionally requires expensive inner loops of gradient descent updates within each trajectory, rendering them computationally impractical at scale. In this work, we investigate whether the emergent in-context learning (ICL) capabilities of sequence models can eliminate this bottleneck by serving as immediate, update-free world models. Specifically, we evaluate whether an exploration policy can be trained to maximize learning progress, using solely the prediction errors and counterfactual context manipulations of an in-context learner. We first prove that in general Markov decision processes, this is in fact impossible in an unbiased way: the resulting intrinsic rewards either suffer from nuisance terms that bias their estimation of true learning progress, or they cannot be implemented using an in-context learner's prediction errors. Conversely, we prove a positive result for a broad subclass of non-temporal settings, encompassing active learning and Bayesian Experimental Design: here, ICL-derived rewards successfully bound and asymptotically converge to the true learning progress. We corroborate our theory with controlled experiments across continuous and symbolic environments, demonstrating that our ICL-driven framework successfully trains curious data-collection policies that explore optimally.

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

The Market in the Model: Latent Diffusion as Neural Economy

Valuable critique of generative image models within visual culture and the humanities has emphasized the role of datasets in shaping the images they produce. Yet, close studies of the ideological positions embedded into the mechanism of the models have been neglected, leaving them imagined as "black boxes." In a bid to expand, rather than replace, dataset critique, this paper examines the mechanisms of the latent diffusion model in terms of the problems they were brought in to solve on behalf of computer vision engineers, and the decisions each component was tasked with automating. I interpret that ensemble through the histories of its parts and the theory of vision the system inscribes into every generated image. Drawing on Impett and Offert's notion of neural exchange value, I offer this analysis to argue that the model operates as a neural economy: a contained symbolic system that abstracts social communication into commensurable vectors as it transfers the social sphere into parcels for sale. Tracing the training and generation pipelines component by component reveals what each operation displaces, and how it further entrenches the logics of platform and attention economies over social communication. The paper warns that any critique fixated exclusively on copyright and commodity defenses risks reaffirming the very fetishism the model produces, and argues instead for centering social exchange.

07.
bioRxiv (Bioinfo) 2026-06-14

TopoMIL: Topology Improves Multiple Instance Learning in Diagnostic Microscopic Images

Microscopic images of cells and tissues are central to disease diagnosis. In computational pathology, multiple instance learning (MIL) has emerged as a key paradigm for analyzing numerous images within a single patient sample. While the representative distribution of cells in a sample is important for diagnosis, existing MIL frameworks largely overlook it. We introduce TopoMIL, a framework that extracts the representative topological structure of the sample and integrates it into the MIL classifier. Three topological representations are assessed, each with distinct advantages and computational costs. We evaluate TopoMIL on four histopathology and cytomorphology datasets, each presenting unique challenges. Integrating the sample's topological information into MIL enhances classification across average, max, attention-based, and transformer pooling, yielding AUCROC gains of 3.3%, 4.2%, 5.9%, and 0.5%, respectively, with moderate computational cost. Our work underscores the potential of TopoMIL as a scalable extension to existing morphology-based models in computational pathology.

08.
arXiv (quant-ph) 2026-06-11

Exploring Variational Entanglement Hamiltonians

arXiv:2505.10530v3 Announce Type: replace Abstract: Recent advances in analog and digital quantum-simulation platforms have enabled exploration of the spectrum of entanglement Hamiltonians via variational algorithms. In this work we analyze the convergence properties of the variationally obtained solutions and compare them to numerically exact calculations in quantum critical systems. We demonstrate that interpreting the cost functional as an integral permits the deployment of iterative quadrature schemes, thereby reducing the required number of measurements by more than an order of magnitude even in the presence of noise. We further show that a modified ansatz captures deviations from the Bisognano-Wichmann form in lattice models, improves convergence, improves trainability and provides a cost-function-level diagnostic for quantum phase transitions. Finally, we establish that a low cost value does not by itself guarantee convergence in trace distance. Nevertheless, it faithfully reproduces degeneracies and spectral gaps, which are essential for applications to topological phases.

09.
arXiv (CS.CL) 2026-06-25

Diagnosing and Mitigating Compounding Failures in Agentic Persuasion via Taxonomic Strategy Retrieval

Foundation-model agents in multi-step, open-ended environments frequently suffer from compounding errors, where early mistakes contaminate long-horizon trajectories. While Multi-Agent Debate (MAD) succeeds in deterministic domains, agents in subjective tasks like persuasion experience severe problem drift and sycophantic conformity. We identify semantic leakage in standard Retrieval-Augmented Generation (RAG) as a reproducible trigger for these failures, as standard RAG prioritizes vocabulary overlap over logical necessity. To eliminate this leakage, we introduce Taxonomic Strategy RAG (TS-RAG), a systems intervention that routes strategies through a discrete categorical bottleneck to decouple argumentative structure from topical content. Zero-shot, cross-domain evaluations demonstrate that TS-RAG significantly improves the transfer of abstract logic where standard semantic retrieval collapses. Crucially, TS-RAG acts as a "capability bridge" in asymmetric deployments, empowering lightweight persuaders to consistently defeat parametrically superior opponents (improving win rates from 70.5 to 78.5) and accelerating argumentative efficiency. Finally, we introduce trace-level diagnostics via a turn-by-turn Debate State Representation (DSR), demonstrating the necessity of strict constraints to prevent evaluation collapse via default agentic sycophancy.

10.
arXiv (quant-ph) 2026-06-19

Unleashing Emergent Fermions with Rydberg Atom Simulators

arXiv:2606.19444v1 Announce Type: cross Abstract: Rydberg atom simulators, in both analog and digital modes, have attracted significant recent interest due to their versatile geometric reconfigurability. In this work, leveraging this feature, we propose two complementary approaches, one for each mode, to characterize emergent fermions in critical quantum many-body systems. In the analog mode, we assemble the Rydberg atoms in a "developable" (namely, preserving local couplings) Möbius band geometry to realize antiperiodic boundary conditions, where fermionic states reside. Spectroscopic measurement in this sector then reveals universal energy ratios of the bosonic and fermionic states. In the digital mode, we carry out a fermionic version of Kibble-Zurek ramping with a quantum circuit, directly addressing the fermionic scaling form. Reconfigurability allows an exponential speed-up of this task, with an $O(\log L\log\log L)$ circuit-depth overhead. Our work establishes the Rydberg atom simulator as a uniquely powerful platform to attack the notoriously difficult issue of experimentally probing emergent fermions that are nonlocally defined in a bosonic system.

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

User as Engram: Internalizing Per-User Memory as Local Parametric Edits

Authors:

arXiv:2606.19172v1 Announce Type: new Abstract: Personal memory in a language model is two problems: content and reasoning skill. The brain keeps the two apart (a sparse, local engram in the hippocampus for each episode, a slow neocortex for the shared skills that interpret it), so a new fact need not overwrite everything else. Most personalization today keeps a user's facts outside the weights, in a natural-language memory file or a retrieval index. When facts are written into the model instead, the standard recipe is the per-user LoRA adapter, which does the opposite of the brain, folding content and skill into one global weight delta. Writing a user's facts as a LoRA contaminates text unrelated to them; writing the same facts as local Engram rows leaves it mathematically untouched, resulting in a roughly 33,000x smaller memory footprint. We therefore propose User as Engram: store a user's content as surgical edits to the hash-keyed memory table of an Engram model, and carry the reasoning skill in one shared adapter. This layered design matches per-user LoRA's direct recall while delivering 5.6x higher indirect-reasoning accuracy on average, and never makes a single user worse at reasoning than the untouched base. The edit is a glass box: writing a fact switches on its lookup at exactly the trigger, adds the value the answer needs, leaves every other position unchanged to the last bit, and fails if written into the wrong layer. Because different users' facts land in disjoint hash slots, their edits compose: many users live in one shared table at once, stacking additively and losslessly, where a per-user LoRA, a single global weight delta, admits only one. Upon retrieval, a per-user Engram table does not grow with the population the retriever must search, so past ~100 facts it overtakes a retrieval pipeline on a 2.5x larger model.

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

Boundary-Centric Clip-Budgeted Active Learning for Temporal Action Segmentation

Temporal action segmentation (TAS) in untrimmed videos requires dense temporal supervision. However, most of the annotation cost is spent identifying action transitions where segmentation errors concentrate and small temporal shifts can disproportionately degrade segment-level metrics. We introduce B-ACT, a clip-budgeted active learning framework that explicitly allocates supervision to these error-prone boundary regions. B-ACT operates in a hierarchical two-stage loop: (i) it ranks and queries unlabeled videos using predictive uncertainty, and (ii) within each selected video, it detects candidate transitions from the current model predictions and selects the top-$K$ boundaries via a novel boundary score. The boundary score fuses neighborhood uncertainty, class ambiguity, and temporal prediction dynamics to reveal the underlying importance of each frame. Importantly, our annotation protocol requests labels only at the boundary frames while still training on boundary-centered clips to exploit temporal context through the model's receptive field. Extensive experiments on GTEA, 50Salads, and Breakfast demonstrate that boundary-centric supervision delivers strong label efficiency and consistently surpasses representative TAS active learning baselines and prior state of the art under sparse budgets. Gains are largest on datasets where performance is highly sensitive to boundary placement, as measured by edit and overlap-based F1 metrics.

13.
arXiv (CS.AI) 2026-06-16

Honeypot Protocol

Authors:

arXiv:2604.13301v1 Announce Type: cross Abstract: Trusted monitoring, the standard defense in AI control, is vulnerable to adaptive attacks, collusion, and strategic attack selection. All of these exploit the fact that monitoring is passive: it observes model behavior but never probes whether the model would behave differently under different perceived conditions. We introduce the honeypot protocol, which tests for context-dependent behavior by varying only the system prompt across three conditions (evaluation, synthetic deployment, explicit no-monitoring) while holding the task, environment, and scoring identical. We evaluate Claude Opus 4.6 in BashArena across all three conditions in both honest and attack modes. The model achieved 100% main task success and triggered zero side tasks uniformly across conditions, providing a baseline for future comparisons with stronger attack policies and additional models.

14.
arXiv (CS.AI) 2026-06-12

Optimizing Appliance Scheduling for Solar Energy Management Using Metaheuristic Algorithms

arXiv:2606.13407v1 Announce Type: new Abstract: Renewable energy is essential for meeting future energy demands; however, solar energy generation, which occurs only during daylight hours often does not align with household consumption patterns. Appliances such as cookers, washing machines, and dryers are typically operated according to user preferred schedules rather than solar energy availability, creating a scheduling optimization problem. The objective is to determine optimal appliance start times to maximize renewable energy utilization while minimizing user inconvenience and adhering to system constraints. This paper presents a metaheuristic approach using Iterated Local Search (ILS) and Simulated Annealing (SA) to optimize appliance start times, while considering appliance operating durations, power consumption, inverter limit, battery state of charge constraints, and solar generation forecasts. Unlike most existing work, the scheduling is extended beyond a single day to accommodate unfinished tasks from previous days (spillover), ensuring operational continuity and enabling sequential operation across multiple days. Experimental results show that the sequential multi-day scheduling framework effectively manages system constraints while ensuring user convenience under exclusive solar generation. These findings also open opportunities for future research on multi-objective trade-offs between investment in equipment of various sizes, return on that investment, and user satisfaction.

15.
medRxiv (Medicine) 2026-06-15

Natural Language Processing Based Solution for Labeling Brain Metastasis Identified in Radiology Reports

Abstract Purpose: Brain metastases (BM) far exceed primary CNS tumours and constitute the majority workload for neuro-oncology care providers. Currently, the cancer registries only capture synchronous BMs, which is only a small proportion of all BMs. We aim to develop and validate a natural language processing (NLP) algorithm that identifies brain metastases in radiology reports, enabling scalable surveillance of asynchronous BMs. Methods: Using population-based cancer registry data in Alberta, Canada, we identified a cancer cohort diagnosed between 2012–2019 with follow-up to 2022. All brain/head radiology reports at and post-cancer diagnosis were identified. Reports were sampled through a multi-phase approach and manually labeled for BM presence. We trained two Bio_ClinicalBERT models on the "Findings" and "Impressions" sections, respectively, and took the maximum predicted probability as the report-level prediction. Internal and external validation used reports from the Canadian provinces of Alberta, Ontario, and British Columbia. Results: The models were trained on 1,879 samples. For internal validation, 1,833 reports from 357 patients were tested. At a probability threshold of 0.4, the model achieved a sensitivity of 0.888 and precision of 0.499. The ensemble substantially outperformed single-section models, which achieved sensitivities of only 67.8% (Findings) and 74.2% (Impressions). On external validation, sensitivity was 0.918 in Ontario and 0.726 in British Columbia, demonstrating robustness across diverse data distributions. Conclusions: An NLP-based pipeline processing both Findings and Impressions sections has been developed and validated in three Canadian provinces. It meets cancer registry operational requirements and to be implemented into the surveillance workflow in Alberta and British Columbia, providing a foundation for population-level BM surveillance.

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

Hybrid Classical-Quantum (HCQ) Alzheimer's Classification via Supervised $\beta$-VAE and Quantum Kernels

This paper presents a two-stage Hybrid Classical-Quantum (HCQ) pipeline for binary Alzheimer's disease (AD) classification from 3D T1-weighted structural MRI volumes, where the classical and quantum components are designed to complement each other rather than operate independently. A supervised 3D $\beta$-variational autoencoder (VAE) is trained end-to-end under voxel-wise reconstruction, KL-divergence, and focal classification losses that compress each 3D MRI volume (resized from 152 x 184 x 152 to 96 x 96 x 96) into a 64-dimensional latent code. Partial Least Squares (PLS) regression selects the six components in the latent code that best separate Alzheimer's Disease (AD) from cognitively normal (CN) subjects and rescales them into rotation angles, which are encoded onto a six-qubit register using the ZZ quantum feature map to give us the respective quantum states. The input to a precomputed-kernel Support Vector Machine (SVM) is an N x N Gram matrix (N = 308), created by calculating the overlap between every pair of quantum states. The novelty of this work lies in the fact that the quantum kernel operates directly on disease-aware features that are learned end-to-end by a supervised autoencoder, rather than on pre-extracted inputs. On 308 ADNI-1 subjects, consisting of 137 AD and 171 CN subjects, the baseline achieved 67.2% accuracy and 0.759 AUC, while the stability-enhanced variant reached 72.1% accuracy and 0.799 AUC with cross-fold variance halved. 3D Grad-CAM further helped validate our model's focus on brain regions linked to Alzheimer's. The HCQ pipeline could serve as a general-purpose framework for diagnostic classification across biomedical imaging domains that present similar challenges for classical approaches.

17.
arXiv (CS.AI) 2026-06-24

Render-FM: Feedforward Model for Real-time Photorealistic Volumetric Rendering

arXiv:2505.17338v3 Announce Type: replace-cross Abstract: Photorealistic volumetric rendering of CT scans greatly benefits clinical workflows, yet neural approaches such as Neural Radiance Fields (NeRF) and 3D Gaussian Splatting (3DGS) require prohibitive per-scan optimization (hours for NeRF, about 30 minutes for 3DGS), making them impractical in clinical settings. We propose Render-FM, a feedforward model that eliminates this bottleneck by directly regressing 6D Gaussian Splatting (6DGS) parameters from a CT volume in a single 2.8-second forward pass, a 500x speedup over per-scan optimization. To bridge the domain gap between natural scene reconstruction and medical volumetric rendering, we introduce Anatomy-Guided Priming (AGP), which incorporates segmentation masks and transfer functions as structural and appearance priors, information that existing Gaussian splatting methods overlook. Built on an nnU-Net-inspired 3D U-Net trained on diverse CT scans, Render-FM predicts per-voxel 6DGS parameters and supports immediate real-time rendering. Unlike per-scan methods, it generalizes to unseen anatomies, novel transfer functions, and enables compositional organ visualization with zero additional preparation time. Optional 89-second fine-tuning further improves quality, surpassing per-scan optimized baselines. Project page: https://gaozhongpai.github.io/renderfm/.

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

First Proof Second Batch

arXiv:2606.18119v1 Announce Type: new Abstract: To assess the ability of current AI systems to correctly solve research-level mathematics problems, we tested several AI systems on a set of ten problems in a broad range of mathematical fields; these problems arose naturally in the research process of the contributors. This document includes the problems, our methodology, and the results of our testing. We provide links to supplementary documents including the human solutions, the AI-generated solutions, and the referee reports and logs for the AI-generated solutions. The ten problems were contributed by the following mathematicians: (1) Dariusz Kaloci\'nski and Theodore A. Slaman, (2) Richard Schwartz, (3) Aleksa Milojevic and Benny Sudakov, (4) Larry Guth, (5) Oleg Butkovsky, Jonathan Mattingly, and Lorenzo Zambotti, (6) Joshua Evan Greene and Duncan McCoy, (7) Sucharit Sarkar, (8) Sam Payne and Jidong (Jayden) Wang, (9) Sylvie Corteel and John Lentfer, (10) Srivatsav Kunnawalkam Elayavalli.

19.
arXiv (CS.CL) 2026-06-16

Spokes: Optimizing for Diverse Pretraining Data Selection

Diversity plays a critical role in data selection, improving performance under fixed data budgets by reducing redundancy and repetition. However, optimizing for diversity is inherently challenging, as it is a set-level property that depends on interactions between data points rather than individual examples. As a result, existing approaches typically rely on proxies or approximations, which often fail to ensure sufficiently diverse subsets. In this work, we directly optimize diversity by introducing a probabilistic diversification framework based on the G-Vendi score, optimized via exponentiated gradient descent. Our method produces subsets that are substantially more diverse than those obtained via random sampling, achieving a +489 increase in G-Vendi score on a 500k-sample subset. We evaluate our approach on FineWeb and DCLM, where it consistently outperforms existing methods. Notably, SPOKES (diversity-only) improves average downstream performance by +0.4 and +0.5 points over random sampling on DCLM and FineWeb, respectively. More importantly, jointly optimizing for both quality and diversity yields the strongest results: SPOKES achieves gains of +1.5 and +1.4 points on DCLM and FineWeb, outperforming all baselines, including semantic deduplication and quality filtering.

20.
arXiv (CS.LG) 2026-06-18

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning

arXiv:2604.14906v3 Announce Type: replace-cross Abstract: The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through $-$1 programmed ribosomal frameshifting ($-1$ PRF), a mechanism that allows the virus to generate both structural and non-structural proteins from overlapping reading frames. This pseudoknot exhibits both threaded and unthreaded long-lived topologies. The influence of ligand binding on its folding is a process critical for the development of $-$1 PRF small-molecule inhibitors. Understanding this process through unbiased molecular dynamics (MD) simulations can be facilitated by introducing collective variables (CVs) that capture the corresponding slowest dynamical modes. Here, we use spectral map (SM), a thermodynamics-driven machine learning technique, to learn such CVs directly from all-atom MD trajectories of the SARS-CoV-2 RNA pseudoknot in complex with the $-$1 PRF inhibitor merafloxacin and its two structural analogs in neutral and ionized forms. Free-energy landscapes (FELs) derived from the learned CVs indicate that ligand-induced destabilization is topology-selective. In the threaded pseudoknot, the inhibitors destabilize the S2 stem, while in the unthreaded pseudoknot, destabilization occurs in the S1 and S3 stems. Furthermore, the extent to which each ligand reshapes the FEL matches experimentally reported antiviral potency, whereas the protonation state qualitatively alters dynamics within the same RNA topology. Overall, our results show how pseudoknot topology, ligand type, and protonation state collectively influence the slow conformational dynamics of viral RNA and establish physiological protonation as a critical factor for modeling RNA-targeted drug action.

21.
arXiv (CS.AI) 2026-06-25

TopoCast: A Topological Fidelity Framework for Evaluating Transformer-Based Time Series Forecasting

arXiv:2606.25439v1 Announce Type: cross Abstract: Deep learning-based models have achieved state-of-the-art performance in Time Series Forecasting (TSF), yet their evaluation remains dominated by pointwise error metrics such as Mean Squared Error (MSE), which quantify numerical accuracy but overlook structural properties of the forecast signal, including recurrent dynamics, oscillatory behavior, and phase alignment. As a result, forecasts exhibiting over-smoothing, phase shifts, or frequency distortions may achieve favorable error scores despite substantial structural degradation. To address this limitation, we propose TopoCast, a topology-driven framework for evaluating structural fidelity in TSF. TopoCast reconstructs phase-space representations of forecast and ground-truth sequences using Takens delay embedding and applies persistent homology to characterize their intrinsic dynamics. We derive four complementary topological fidelity measures from persistence diagrams and aggregate them into a Topological Fidelity Score (TFS). We further introduce dominant cycle overlap, a novel metric that maps persistent topological features to the temporal domain to assess whether dominant oscillatory patterns occur at the correct time points. Combined with TFS, this yields the Localized Topological Fidelity Score (LTFS), a phase-aware measure that captures temporal localization errors invisible to existing evaluation metrics. Experiments on five Transformer architectures across three real-world benchmark datasets demonstrate that models with similar forecasting errors can exhibit markedly different structural fidelity profiles, revealing failure modes overlooked by conventional evaluation and highlighting the value of topology-aware forecast assessment.

22.
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.

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

CLARITree: Cholesky and Lookahead Accelerations for Regression with Interpretable Piecewise Linear Trees

arXiv:2606.12840v1 Announce Type: new Abstract: Regression trees are among the most interpretable yet expressive model classes in machine learning. Historically, greedy induction has been the dominant approach for constructing well-performing regression trees. While optimal methods based on dynamic programming and branch-and-bound exist, they are computationally prohibitive for general linear regression trees, despite often achieving substantially better performance than greedy approaches. Recent work has shown that specialized lookahead strategies can dramatically improve runtime while maintaining near-optimal performance, primarily in classification settings. In this work, we develop a novel algorithm for near-optimal, sparse, piecewise linear regression trees that combines a lookahead-style search strategy with efficient rank-one Cholesky updates of the Gram matrix. We demonstrate, both theoretically and empirically, that our method achieves a favorable trade-off between computational efficiency, predictive accuracy, and sparsity, and scales significantly better than the current state of the art.

24.
arXiv (CS.CL) 2026-06-12

A Survey on Long-Term Memory Security in LLM Agents: Attacks, Defenses, and Governance Across the Memory Lifecycle

The emergence of writable, cross-session persistent memory in LLM agents introduces a qualitatively different threat landscape from conventional input-centric security concerns, characterized by three properties: persistence, statefulness, and propagation. To systematically characterize this landscape, we propose a Memory Lifecycle Framework that organizes attacks, defenses, and their cross-phase dependencies along two axes: six lifecycle phases (Write, Store, Retrieve, Execute, Share & Propagate, Forget & Rollback) and four security objectives (Integrity, Confidentiality, Availability, Governance). This analysis in turn exposes the need for formal security guarantees at the system level, motivating Verifiable Memory Governance(VMG), a framework of five architectural primitives that specifies what verifiable mechanisms a long-term-memory system must provide to maintain auditable, recoverable control over its memory state. Our analysis indicates that robust Long-Term Memory (LTM) security cannot be retrofitted at retrieval or execution time alone, but must be anchored in storage-time provenance, versioning, and policy-aware retention from the outset.

25.
arXiv (CS.LG) 2026-06-17

Searching Neural Architectures for Sensor Nodes on IoT Gateways

arXiv:2505.23939v2 Announce Type: replace Abstract: This paper presents an automatic method for the design of Neural Networks (NNs) at the edge, enabling Machine Learning (ML) access even in privacy-sensitive Internet of Things (IoT) applications. The proposed method runs on IoT gateways and designs NNs for connected sensor nodes without sharing the collected data outside the local network, keeping the data in the site of collection. This approach has the potential to enable ML for Healthcare Internet of Things (HIoT) and Industrial Internet of Things (IIoT), designing hardware-friendly and custom NNs at the edge for personalized healthcare and advanced industrial services such as quality control, predictive maintenance, or fault diagnosis. By preventing data from being disclosed to cloud services, this method safeguards sensitive information, including industrial secrets and personal data. The outcomes of a thorough experimental session confirm that – on the Visual Wake Words dataset – the proposed approach can achieve state-of-the-art results by exploiting a search procedure that runs in less than 10 hours on the Raspberry Pi Zero 2.