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

MemToolAgent: Leveraging Memory for Tool Using Agents Based on Environment and User Feedback

Modern large language model (LLM) agents can use external tools to help users solve complex tasks. However, for problems that require learning from long-term historical events or from previous agent-environment interactions, LLM agents are required to use memory mechanisms to store and retrieve experiences. While sophisticated memory systems exist for dialogue agents, few studies have empirically examined how to improve agents' tool-using capabilities through past user-agent conversations. We propose MemToolAgent, a framework that improves tool use through memory management. Our approach contains a memory extraction module that processes past experiences into structured memory entries, and a retrieval module that dynamically selects a subset of the stored memory entries. This enables more personalized and accurate responses aligned with user preferences and feedback without requiring LLM fine-tuning. In summary, this work has three main contributions: (1) a unified memory entry format that improves both general-purpose and personalized tool use without LLM fine-tuning, (2) a reflection-based memory extraction that uses environment and user feedback to distill wrong executions into critiques to store, and (3) a retrieval module that chooses how many past experiences to use based on the memory similarity distribution. MemToolAgent achieves 29%, 80%, and 17% relative improvements compared to strong baselines on the WorkBench, NESTFUL, and PEToolBench benchmarks, respectively.

02.
bioRxiv (Bioinfo) 2026-06-16

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

GenBank and GISAID are the primary repositories for viral genomic data, but integrating records across them remains a challenge. The same sequence could be made available in both databases without any cross-reference linking the two entries. Consequently, there is no systematic way to identify this redundancy, which compromises the compilation of representative, non-redundant large-scale datasets. In parallel, the growth of viral genomic data has increased the risk of systematic technical artifacts introduced during sequencing or assembly. These artifacts can inflate substitution rate estimates and degrade temporal signal, biasing evolutionary rate estimates. To address both challenges, here we present a formal, reproducible workflow integrating two newly developed complementary tools: G2G matcher for cross-repository harmonization and Lab-Specific Bias FILTer (LSBFILT) for masking of laboratory-specific artifacts. Using the Eastern/Central/South African (ECSA) chikungunya virus lineage as a proof-of-concept, we demonstrate that our integrated workflow restores temporal signal and provides a robust, curated dataset for downstream phylodynamic analyses. Critically, restricting masking of homoplastic sites to specific sequences reduces the substitution rate estimate from an inflated 8.517 x 10e-4; to 5.078 x 10e-4; substitutions/site/year and increases the coefficient of determination (R2) of the root-to-tip regression analysis from 0.353 to 0.677. By enabling systematic cross-repository harmonization and source-specific artifact masking, we provide the molecular epidemiological community with scalable tools to reconcile fragmented genomic data and reduce technical biases, fostering more accurate and reproducible phylogenetic analysis. G2G matcher is available at https://github.com/andrezaleite/G2G-Matcher, and LSBFILT at https://github.com/khourious/LSBFILT.

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

How Much Can We Trust LLM Search Agents? Measuring Endorsement Vulnerability to Web Content Manipulation

Large language model (LLM)-based search agents synthesize open-web content into actionable recommendations on behalf of users, creating a risk that attacker-published pages are transformed into endorsed claims. We introduce SearchGEO, a controlled evaluation framework for measuring endorsement corruption in LLM-based web-search agents, combining a web-evidence manipulation pipeline, a five-mode attack taxonomy, and multiple output-level metrics. We evaluate 13 LLM backends on 308 cases each. Results show that vulnerability patterns vary across backends: overall attack success rate (ASR) ranges from 0.0% on Claude-Sonnet-4.6 to 31.4% on Gemini-3-Flash, the strongest attack mode differs by model family, and the same deployment scaffold could amplify or decrease ASR on different backends. An auxiliary agent-skill probe, where endorsement becomes an install command, exposes a sharp split among otherwise robust backends: Claude over-rejects while GPT over-trusts. These findings argue for treating recommendation reliability under adversarial search content as a first-class dimension of backend safety evaluation.

04.
arXiv (CS.CL) 2026-06-11

TokenRatio: Principled Token-Level Preference Optimization via Ratio Matching

Direct Preference Optimization (DPO) is a widely used RL-free method for aligning language models from pairwise preferences, but it models preferences over full sequences even though generation is driven by per-token decisions. Existing token-level extensions typically decompose a sequence-level Bradley-Terry objective across timesteps, leaving per-prefix (state-wise) optimality implicit. We study how to recover token-level preference optimality using only standard sequence-level pairwise comparisons. We introduce Token-level Bregman Preference Optimization (TBPO), which posits a token-level Bradley-Terry preference model over next-token actions conditioned on the prefix, and derive a Bregman-divergence density-ratio matching objective that generalizes the logistic/DPO loss while preserving the optimal policy induced by the token-level model and maintaining DPO-like simplicity. We introduce two instantiations: TBPO-Q, which explicitly learns a lightweight state baseline, and TBPO-A, which removes the baseline through advantage normalization. Across instruction following, helpfulness/harmlessness, and summarization benchmarks, TBPO improves alignment quality and training stability and increases output diversity relative to strong sequence-level and token-level baselines.

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

Beyond Scalar Rewards by Internalizing Reasoning into Score Distributions

Reward models are central to text-to-image post-training, but visual preference is subjective and better represented as a distribution over rubric scores than as a deterministic scalar. Existing scalar, score-token, and pairwise reward models over-compress uncertainty and fine-grained score differences, while reasoning-based generative rewards provide stronger judgments but are costly to deploy and difficult to use as direct optimization signals. We propose Z-Reward, a teacher-student reward modeling framework that decouples reasoning-heavy judgment from efficient reward deployment. The teacher is a large VLM that uses reasoning to infer rubric-aligned score distributions, and is trained with Group-wise Direct Score Optimization (GDSO), which combines policy-gradient rewards from distribution expectations with direct pointwise and pairwise supervision on score distributions and score gaps. The student is trained with Reasoning-Internalized Score Distillation (RISD), which transfers the teacher's reasoning-conditioned score distribution into a compact VLM without requiring explicit reasoning chains at inference time. On our internally annotated evaluation set, the 27B GDSO teacher reaches 89.6% human preference accuracy, outperforming SFT, RewardDance, and GRPO, while the 9B RISD student reaches 88.6%, outperforming the OPD baseline and closely matching the larger teacher. We further show that Z-Reward can serve as a differentiable reward signal for text-to-image optimization, yielding a 41.3% net human-preference improvement over the SFT baseline.

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

Hierarchical Attention via Domain Decomposition

arXiv:2606.18525v1 Announce Type: new Abstract: We propose a hierarchical attention mechanism based on two-level overlapping Schwarz domain decomposition. The method is motivated by the observation that two-level Schwarz domain decomposition methods combine local subdomain corrections with a coarse level that communicates global, long-range information. We test its usefulness in the context of finite-dimensional operator learning using a simple, one-dimensional diffusion problem with homogeneous Dirichlet boundary conditions. Although elementary, this problem provides a controlled sequence-to-sequence setting in which the exact nonlocal solution operator is known. After discretization, learning the solution operator amounts to approximating the inverse of a symmetric positive definite matrix. As a baseline, we use a global softmax-free low-rank attention operator of the form $QK^T$. The proposed construction replaces this dense global factorization by a two-level additive structure: local low-rank attention blocks on overlapping subdomains are combined with a coarse attention block. The resulting operator has the form $$M_{\theta}^{-1} = \Phi Q_0 K_0^T \Phi^T + \sum_{i=1}^{N} R_i^T D_i^{1/2} Q_i K_i^T D_i^{1/2} R_i.$$ Here $R_i$ restricts to an overlapping subdomain, $D_i$ is a partition-of-unity weight, and $\Phi$ is a coarse interpolation (or prolongation) matrix. Numerical experiments for synthetic Fourier right-hand sides indicate that the domain-decomposition attention operator is able to train faster and can give more accurate approximations than a global low-rank attention baseline while using significantly fewer parameters.

07.
arXiv (CS.CV) 2026-06-16

Selective Synergistic Learning for Video Object-Centric Learning

Typical video object-centric learning (VOCL) approaches employ slot-based frameworks that rely on reconstruction-driven encoder-decoder architectures, where learning is mediated by two spatial maps: attention maps from the encoder and object maps from the decoder. As these two distinct maps exhibit different properties, a recent dense alignment strategy attempted to reconcile this discrepancy by enforcing agreement across all spatio-temporal patches via contrastive learning. However, this indiscriminate alignment inadvertently propagates the inherent weaknesses of each module, such as noisy encoder predictions and blurred decoder boundaries. Moreover, computing dense similarities across all pairs incurs a computational cost quadratic in the total number of spatio-temporal patches, severely limiting scalability. Motivated by this, we propose Selective Synergistic Learning (SSync). Instead of exhaustive patch-to-patch alignment, SSync prevents error propagation by selectively distilling only the most reliable cues: leveraging the encoder strictly for boundary refinement and the decoder for interior denoising. This is realized via a pseudo-labeling with linear complexity, eliminating the need for quadratic spatial comparisons. Also, to prevent the reinforcement of architectural biases like slot redundancy, we introduce a transitive pseudo-label merging that consolidates overlapping slots based on spatio-temporal activation consistency. Extensive studies demonstrate that SSync improves decomposition quality and serves as a versatile, plug-and-play module while also exhibiting exceptional robustness to slot configurations. Code is available at github.com/wjun0830/SSync.

08.
arXiv (quant-ph) 2026-06-24

The $\omega$-Effect from a Multimode Squeezed Graviton State

arXiv:2606.24613v1 Announce Type: cross Abstract: The $\omega$-effect in entangled neutral-meson systems provides a sensitive probe of CPT violation induced by quantum-gravitational environments. In open quantum systems, interactions with inaccessible gravitational degrees of freedom can render the reduced meson dynamics non-unitary, causing the CPT operator to become ill-defined, even when the underlying microscopic Hamiltonian is CPT invariant. We present a microscopic derivation of the $\omega$-effect arising from a multimode squeezed gravitational environment generated by an axion cloud around a Kerr black hole. Using the Takagi decomposition of the associated complex symmetric squeezing kernel, the graviton field is expressed in terms of independent squeezed supermodes possessing anomalous correlators. These correlators provide a microscopic quantum counterpart of the stochastic fluctuations that appear in earlier D-particle foam descriptions of the $\omega$-effect, replacing phenomenological variances of flavour-changing D-particle recoil by calculable graviton correlation functions. After tracing over the graviton bath, the anomalous correlators and the weak-interactions-induced mixing combine to generate transitions between the antisymmetric and symmetric two-meson sectors. This results in a small exchange-symmetric admixture, parametrised by $\omega$, in the otherwise antisymmetric EPR state. We obtain an explicit expression for $\omega$ in terms of a sum over Takagi supermodes weighted by their squeezing amplitudes and phases together with the weak-interaction flavour-mixing matrix element. The resulting framework suggests that the $\omega$-effect may be a generic signature of non-classical states of gravitational environments, extending beyond the specific axion-cloud scenario considered here. The observability of the $\omega$-effect from other astrophysical and microscopic black-hole sources is discussed.

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

Foresight: Iterative Reasoning About Clues that Matter for Navigation

arXiv:2606.12550v1 Announce Type: cross Abstract: Open-world mapless navigation from sparse language instructions requires resolving underspecified goals and inferring which environmental cues are relevant for reaching the goal. For instance, reaching an out-of-view destination may require interpreting ramps, signs, or detours that reveal where to go or which route to take. Prior works are limited by their reliance on known navigation factors and closed-set factor categories, or identify cues before motion planning and miss plan-dependent cues. We argue that pretrained Vision-Language Models (VLMs) can discover novel instruction-relevant cues, but require adaptation to focus on which cues matter and how they should influence motion planning. We realize these ideas in Foresight, a test-time framework in which a finetuned VLM alternates between proposing image-space motion plans and critiquing them using the language goal and visual context. Subsequent plans are conditioned on prior critiques, enabling iterative motion refinement before execution. To align plan critiques and refinements with open-set behavior preferences, we learn a reward model from human feedback and use it to post-train the VLM with reinforcement learning in the plan-critique loop. In offline evaluations and 6 real-world environments, Foresight improves average task success by 37% and reduces interventions per mission by 52% relative to state-of-the-art test-time reasoning and foundation-model baselines, while running in real-time on a Jetson AGX Orin. We will release code, data, and training details to support future work on test-time reasoning for robot motion refinement. Additional videos at: https://amrl.cs.utexas.edu/foresight

10.
arXiv (CS.LG) 2026-06-12

Individual Control Barrier Functions-Guided Diffusion Model for Safe Offline Multi-Agent Reinforcement Learning

arXiv:2606.12640v1 Announce Type: new Abstract: Offline reinforcement learning allows control policies to be learned directly from data without online interaction, making it suitable for safety-critical tasks. Recent studies have applied diffusion models to offline reinforcement learning to leverage their strong capacity for modeling complex data distributions. However, existing approaches primarily focus on single-agent settings, leaving the safety challenges in multi-agent environments largely unexplored. In this work, we propose a safe offline multi-agent reinforcement learning algorithm that embeds neural individual control barrier functions into the diffusion model to enhance safety during trajectory generation, with control policies recovered through inverse dynamics. We evaluate our algorithm across diverse benchmarks, demonstrating substantial safety improvements while maintaining competitive rewards.

11.
medRxiv (Medicine) 2026-06-13

Projected population level impact and cost-effectiveness of clinic and community-based tuberculosis screening approaches

The South Africa National Department of Health have set ambitious targets to scale up TB testing, focusing primarily on clinic attendees. In the context of declining funding for TB care and prevention, the most cost-effective approaches for targeting testing should be identified. We developed a mathematical model of TB in South Africa, explicitly incorporating clinic attendance by sex and HIV/ART status. We simulated six screening approaches over 2026-2035 (individually and in combination): three clinic-based (symptom screening, intensified targeted universal TB testing [TUTT, symptom-agnostic sputum testing of clinic attendees in key risk groups], and intensified TUTT allowing saliva samples) and three targeted community-based (community radiographic screening, symptom screening, and universal Xpert Ultra testing), each implemented at a range of coverage levels. Model outputs were combined with a mechanistic cost function to estimate potential impact and cost-effectiveness from a societal perspective. The most cost-effective standalone approach was community radiographic screening at 10% annual population coverage, with an incremental cost-effectiveness ratio (ICER) of $421 per disability-adjusted life year (DALY) averted. 10/11 scenarios along the expansion path included community radiographic screening at progressively higher coverage, combined with a clinic-based approach. Combining complementary approaches to reach both groups at increased risk of TB (e.g. clinic-based screening) and groups with lower screening coverage (e.g. community-based screening) may increase cost-effectiveness of TB screening, compared to standalone approaches. When designing TB screening strategies, both population risk and existing screening coverage should be considered.

12.
arXiv (CS.CL) 2026-06-16

Not All Skills Help: Measuring and Repairing Agent Knowledge

LLM agents can improve without weight updates by accumulating natural-language skills from experience, but current systems entrust every decision about which skills to keep and how to apply them to LLM judgment alone. We argue that this conflates two distinct roles: generating a skill from experience is a creative act that judgment handles well, while deciding whether that skill actually helps requires empirical evidence across many tasks. Measuring per-skill causal contributions via randomized masking, we find that skill libraries exhibit pervasive causal heterogeneity: individual skills routinely help on some task types while hurting on others, yet their opposing effects cancel in aggregate, making them invisible to global curation methods. We propose ASSAY, a framework that separates generation from curation: it computes a per-skill causal attribution on a small development set, restructures the library offline, and suppresses skills with negative predicted effect for each test task. Across seven base models spanning four providers and two benchmarks (AppWorld and tau-bench), ASSAY consistently improves over prior skill-curation approaches. On AppWorld's hardest split, DeepSeek-V3 achieves 69.3% task-goal completion (47.4% relative improvement), a new state of the art among all published methods including weight-tuned approaches. On tau-bench retail, GPT-4.1 improves by 8.7% relative, advancing past o4-mini, o1, and GPT-4.5 on the public leaderboard without any weight modification. Ablation traces the dominant gain to per-task masking, confirming that the bottleneck is matching skills to tasks at inference time, not removing bad skills globally. Code is available at https://github.com/aiming-lab/assay.

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

From Compression to Deployment: Real-Time and Energy-Efficient FastGRNN on Ultra-Constrained Microcontrollers

arXiv:2606.17249v1 Announce Type: cross Abstract: The dominant trajectory of modern machine learning has been to scale up: larger models, larger accelerators, larger memory budgets. Yet a multi-year global semiconductor supply constraint and the growing energy and carbon cost of always-online inference expose the fragility of this trajectory and motivate the opposite direction: refactoring AI and ML algorithms to fit the small, ubiquitous microcontrollers already in mass production in wearables, sensors, and edge appliances. We present an end-to-end open-source reproduction of FastGRNN, a compact gated recurrent cell, deployed on two bare-metal targets: the 8-bit Arduino (ATmega328P) and the 16-bit MSP430 (no hardware multiplier; 16 KB Flash; 512 B SRAM). Our compression pipeline combines low-rank weight factorization, iterative hard-thresholding sparsity, and per-tensor Q15 post-training quantization with explicit activation calibration. The deployed model occupies 566 bytes of weights and achieves macro F1 = 0.918 (seed 0; five-seed Q15 mean 0.853+-0.107) on the HAPT test set. It matches a PyTorch reference at 100% prediction agreement across 3,399 test windows (MCU seed 0; 99.91-100% C-equivalent across five seeds). Both platforms sustain real-time 50 Hz streaming inference (9.21 ms per sample on Arduino; 13 ms on MSP430), where a 256-entry sigmoid/tanh look-up table delivers a 30.5x speedup on the multiplier-less MSP430. Four contributions extend the original FastGRNN paper: (i) cross-platform bit-equivalent deterministic inference; (ii) characterization of recurrent warm-up latency (median 74 samples, 1.48 s; worst-case 125 samples, 2.50 s over 100 test windows); (iii) a deployable look-up-table recipe for multiplier-less embedded targets; and (iv) hardware energy characterization showing 17.7 mW active inference power,

14.
arXiv (CS.CV) 2026-06-11

A Turbo-Inference Strategy for Object Detection and Instance Segmentation

Object detection and instance segmentation tasks are closely related. Existing top-down instance segmentation methods usually follow a detect-then-segment paradigm, where an initial detector is used to recognize and localize objects with bounding boxes, followed by the segmentation of an instance mask within each bounding box. In such methods, the detection accuracy directly influences the subsequent segmentation performance. However, previous research has seldom explored the impact of the instance segmentation task on object detection. In this paper, we present a turbo-inference strategy for the top-down methods that leverages the complementary information between detection and segmentation tasks iteratively. Specifically we design two modules: turbo-detection head and turbo-segmentation head, which facilitate communication between the tasks. The two modules form a closed loop that interlaces the detection and segmentation results without retraining the model. Comprehensive experiments on the COCO, iFLYTEK, and Cityscapes datasets demonstrate that our method substantially enhances both detection and segmentation accuracies with a certain increase in computational cost. The proposed method represents a tradeoff between prediction accuracy and inference speed. Codes are available at https://github.com/zhaozhen2333/Turbo-Learning.git.

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

Greed Is Learned: Visible Incentives as Reward-Hacking Triggers

arXiv:2606.16914v1 Announce Type: new Abstract: Deployed agents increasingly act with their reward proxy in view, such as a balance, score, or KPI dashboard. We show that reinforcement learning can make a policy addicted to such a visible self-benefit channel. It chases the displayed payoff across held-out domains, sacrifices the true task to do so, and follows the channel wherever we rewrite it, while policies that never saw the channel stay honest. We call this reward-channel addiction and study it in MoneyWorld, a synthetic sandbox. The addiction can flip a model's safety alignment: trained only on innocuous money tasks with no safety content, the model abandons the safe action it otherwise always takes whenever a dashboard pays for an unsafe one, and reverts to safe once the channel is hidden. This learned bribe replicates across model scales and families. Blindly optimizing super-capable, next-generation AI on KPIs or P\&L can be dangerous for alignment. Greed is learned when following such a channel pays.

16.
arXiv (quant-ph) 2026-06-11

Implementing Hamiltonian Renormalization Group Flow on Quantum Computers with VAPOR

arXiv:2606.11306v1 Announce Type: cross Abstract: While Hamiltonian Lattice Gauge Theory is gaining traction, today's limited numerical capacity leaves simulations affected by discretization errors. This motivates the implementation of renormalization group (RG) techniques to find discretization-error-free operators. To this end, we introduce VAPOR, a variational quantum algorithm that decomposes operators into Pauli strings, identifies RG flow orbits, and determines fixed points of a naively discretized operator. We illustrate this using a toy model of a kinematic operator in a symmetry-restricted SU(2) Yang-Mills theory.

17.
arXiv (CS.LG) 2026-06-15

Compressed Computation is (probably) not Computation in Superposition

arXiv:2606.14673v1 Announce Type: new Abstract: We study whether the Compressed Computation (CC) toy model (Braun et al., 2025) is an instance of computation in superposition. The CC model appears to compute 100 ReLU functions with just 50 neurons, achieving a better loss than expected from only representing 50 ReLU functions. We show that the model mixes inputs via its noisy residual stream, corresponding to an unintended mixing matrix in the labels. Splitting the training objective into the ReLU term and the mixing term, we find that performance gains scale with the magnitude of the mixing matrix and vanish when the matrix is removed. The learned neuron directions concentrate in the subspace associated with the top 50 eigenvalues of the mixing matrix, suggesting that the mixing term governs the solution. Finally, a semi-non-negative matrix factorization (SNMF) baseline derived solely from the mixing matrix reproduces the qualitative loss profile and improves on prior baselines, though it does not match the trained model. These results suggest CC is not a suitable toy model of computation in superposition.

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

Estimating Tail Risks in Language Model Output Distributions

arXiv:2604.22167v2 Announce Type: replace-cross Abstract: Language models are increasingly capable and are being rapidly deployed on a population-level scale. As a result, the safety of these models is increasingly high-stakes. Fortunately, advances in alignment have significantly reduced the likelihood of harmful model outputs. However, when models are queried billions of times in a day, even rare worst-case behaviors will occur. Current safety evaluations focus on capturing the distribution of inputs that yield harmful outputs. These evaluations disregard the probabilistic nature of models and their tail output behavior. To measure this tail risk, we propose a method to efficiently estimate the probability of harmful outputs for any input query. Instead of naive brute-force sampling from the target model, where harmful outputs could be rare, we operationalize importance sampling by creating unsafe versions of the target model. These unsafe versions enable sample-efficient estimation by making harmful outputs more probable. On benchmarks measuring misuse and misalignment, these estimates match brute-force Monte Carlo estimates using 10-20x fewer samples. For example, we can estimate probability of harmful outputs on the order of 10^-4 with just 500 samples. Additionally, we find that these harmfulness estimates can reveal the sensitivity of models to perturbations in model input and predict deployment risks. Our work demonstrates that accurate rare-event estimation is both critical and feasible for safety evaluations. Code is available at https://github.com/rangell/LMTailRisk

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

PCFootprint: A Large-Scale Dataset and Benchmark for Vectorized Building Footprint Extraction from Aerial LiDAR Point Clouds

Building footprint extraction is a fundamental task in photogrammetry, remote sensing, and computer vision. Recent image-based methods have achieved remarkable progress in extracting vectorized footprints from high-resolution optical imagery. However, optical imagery inherently susceptible to occlusions, perspective distortions, and residual relief displacement, yielding incomplete or misaligned footprint extraction. Furthermore, the lack of explicit elevation information limits its direct applicability to Level of Detail building modeling. In this paper, we present PCFootprint, the first large-scale public dataset for footprint extraction from airborne laser scanning point clouds. PCFootprint comprises \num{33000} tiles derived from the Estonian Land and Spatial Development Board, covering diverse urban and rural landscapes. Each tile spans \qtyproduct{128 x 128}{\m} with systematically aligned vectorized footprints aligned to point clouds. The dataset includes a \num{3000} tiles cross-domain test set for evaluating generalization across geographic regions. We establish comprehensive benchmarks by evaluating mainstream methods. Experimental results reveal significant challenges including high intra-class variance, data imbalance, and noise across complex geospatial environments. We believe PCFootprint will advance future research in building modeling, urban scene understanding, and geospatial analysis. The PCFootprint dataset is publicly available at \url{https://huggingface.co/datasets/Haoyuan-Shen/PCFootprint}.

20.
medRxiv (Medicine) 2026-06-12

Cancer care disruption during the COVID-19 pandemic in Ontario, Canada: A sequential mixed-methods study

Introduction The COVID-19 pandemic profoundly disrupted healthcare delivery worldwide, with cancer care among the most affected services. Prior studies documented delays in referrals, reduced specialist access, and increased provider burden. However, the extent to which these experiences were reflected at the system level remains unclear. Objective To document cancer care experiences and examine whether these experiences were reflected in population-level health system indicators across Ontario, Canada. Methods We used an exploratory sequential mixed-methods design. Qualitative data were collected through focus groups and semi-structured interviews with 32 participants, including patients with cancer (n=8), caregivers (n=5), healthcare providers (n=14), and decision-makers (n=5) across two hospital settings in Ontario, Canada. Emergent themes informed the development of quantitative indicators. We then conducted a retrospective population-based analysis of linked administrative health databases for cancer patients in Ontario (n=87,786) to assess the prevalence of identified themes. Results Four themes emerged: (I) delays in diagnosis and screening; (II) disrupted access to primary care; (III) barriers to specialist and mental health services; and (IV) fragmented care for patients with multimorbidity. Quantitative findings corroborated major themes. Screening rates declined for cervical (64.8% to 57.5%) and breast cancer (64.5% to 57.2%). While in-person primary care shifted almost entirely to virtual modalities (8.5% to 95.4%), overall visit volumes remained stable. Specialist care showed uneven patterns, with increased oncology visits but declines in cardiology and mental health services. Patients with multiple comorbidities experienced the largest reductions in non-oncology specialist care. Conclusion The pandemic disrupted key components of cancer care, particularly screening, access to certain specialist services, and care for patients with complex needs. Integrating qualitative and quantitative evidence highlights areas of system vulnerability and underscores the need for coordinated, resilient cancer care capable of maintaining essential services during future crises.

21.
arXiv (CS.AI) 2026-06-17

Evaluating Interactive 2D Visualization as a Sample Selection Strategy for Biomedical Time-Series Data Annotation

arXiv:2603.26592v2 Announce Type: replace-cross Abstract: Reliable machine-learning models in biomedical settings depend on accurate labels, yet annotating biomedical time-series data remains challenging. Algorithmic sample selection may support annotation, but evidence from studies involving real human annotators is scarce. Consequently, we compare three sample selection methods for annotation: random sampling (RND), farthest-first traversal (FAFT), and a graphical user interface-based method enabling exploration of complementary 2D visualizations (2DVs) of high-dimensional data. We evaluated the methods across four classification tasks in infant motility assessment (IMA) and speech emotion recognition (SER). Twelve annotators, categorized as experts or non-experts, performed data annotation under a limited annotation budget, and post-annotation experiments were conducted to evaluate the sampling methods. Across all classification tasks, 2DV performed best when aggregating labels across annotators. In IMA, 2DV most effectively captured rare classes, but also exhibited greater annotator-to-annotator label distribution variability resulting from the limited annotation budget, decreasing classification performance when models were trained on individual annotators' labels; in these cases, FAFT excelled. For SER, 2DV outperformed the other methods among expert annotators and matched their performance for non-experts in the individual-annotator setting. A failure risk analysis revealed that RND was the safest choice when annotator count or annotator expertise was uncertain, whereas 2DV had the highest risk due to its greater label distribution variability. Furthermore, post-experiment interviews indicated that 2DV made the annotation task more interesting and enjoyable. Overall, 2DV-based sampling appears promising for biomedical time-series data annotation, particularly when the annotation budget is not highly constrained.

23.
bioRxiv (Bioinfo) 2026-06-22

PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search

Antimicrobial resistance databases are central to genomic surveillance, but resistance determinants remain distributed across resources with different scopes, structures, and annotations. We developed PanRes, a curated resistance database of 11,717 genes integrating acquired and latent determinants of antibiotic, biocide, and metal resistance within a unified ontology. We predicted representative protein structures and clustered them by structural similarity, grouping proteins into 598 structurally conserved clusters coherent despite sequence divergence. Their structure-guided alignments were used to build Hidden Markov Models (HMMs) for remote homology search. In wastewater metagenomes from seven European cities, PanRes 3D-based HMMs expanded detection beyond high-confidence BLAST, with 35.2% of retained hits identified only by the HMMs and generally showing greater divergence from known proteins. For beta-lactamases, several proteins retained beta-lactamase-like folds and catalytic geometry despite weak sequence similarity. PanRes is available through an interactive web platform (https://panres.rambio.dk/), a structure-informed resource for exploring the whole resistome.

24.
bioRxiv (Bioinfo) 2026-06-16

THEOBROMA: an aggregated open database of 1.13 million natural products with per-compound license auditing, three-tier classification, and stereochemistry-aware deduplication

Natural products remain one of the most productive sources of pharmacologically active compounds for drug discovery, yet the current open aggregator landscape attributes licenses at database rather than compound granularity, with consequences that have become tangible as the field grows. A recent relicensing event in one constituent source (the September 2024 transition of the Natural Products Atlas to CC BY-NC 4.0) demonstrates how database-level licensing propagates across an aggregate and motivates the per-compound audit framework presented here. The same peer cohort separately leaves classification provenance and stereoisomer-family relations coarser than either layer warrants. THEOBROMA, accessible at url{https://theobroma.l3s.uni-hannover.de}, integrates 1{,}133{,}004 natural products from 29 open sources under a per-compound license audit that resolves each compound's license tier across all attesting sources under a most-restrictive-wins rule, identifying 900{,}170 compounds (79.4%) under open-use licenses and exposing the per-source attestation chain and resolved tier through a dedicated audit endpoint and a query-time license filter. A three-tier classification stratifies 89.3% coverage into 35.1% curated, 43.9% high-confidence inferred, and 10.3% exploratory tiers, with 486{,}215 stereoisomer families preserved by full 27-character InChIKey deduplication and exposed via a dedicated texttt{/api/stereoisomers/} endpoint and a radial-family display. Per-compound license provenance is the primary differentiator. Classification stratification and stereoisomer-family exposure add finer-grained access to two related axes, supporting license-compatible virtual screening and isomer-specific bioactivity analysis at corpus scale. As an evolving open resource, THEOBROMA pairs continuous pipeline maintenance with interactive geographic, taxonomic, and chemical-space exploration.

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

The Morse Transform for Discrete Shape Analysis

arXiv:2503.04507v2 Announce Type: replace-cross Abstract: The geometry of an object plays a vital role in modulating its interactions with the physical world. It nevertheless remains difficult to describe geometric information numerically for the purposes of statistical inference or classification tasks. Here, we introduce a new topological transform which leverages directional piecewise-linear Morse theory to quantify the geometry of an embedded object by cataloguing critical points across multiple height-functions. The output of this Morse transform records both the heights and the local topological type (peak, trough or saddle) of the critical points that characterise the underlying shape, retaining finer information than the Euler characteristic transform whilst naturally prioritising a shape's outermost regions. Crucially, this output can be further compressed into a rich but compact feature vector. We benchmark the Morse feature vector as a descriptor for ligand-based virtual screening (LBVS), which intrinsically depends on the shape of molecules. Under a common gradient-boosted tree classification pipeline, Morse descriptors achieve the highest mean AUROC when compared to other topological transform descriptors and to standard shape-based LBVS descriptors.