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

Quantifying Consistency in LLM Logical Reasoning via Structural Uncertainty

arXiv:2606.17312v1 Announce Type: new Abstract: Large language models can arrive at the same answer through reasoning paths that are unstable, contradictory, or difficult to rank consistently – a failure mode especially prevalent in multi-step deductive reasoning. Existing methods assess reliability primarily through output dispersion – measuring how much sampled answers differ – but this discards a complementary signal: whether the model can consistently rank competing reasoning candidates. We propose structural uncertainty, a consistency-aware framework derived from the stability of self-preference-induced rankings over sampled reasoning solutions. Given a query, we generate multiple candidate solutions and ask the model to judge pairwise preferences among its own outputs. We aggregate self-preferences into ranking distributions via Bradley-Terry modeling with PageRank, and decompose the signal into two entropy-based components: across-trial ranking instability and within-trial candidate ambiguity. Across five LLMs and eight benchmarks, structural signals provide information complementary to answer dispersion: on logical and mathematical reasoning tasks, the combination improves identification of unreliable instances, while on factual retrieval the structural signal collapses toward uniformity, diagnosing a regime boundary where reasoning-level consistency evaluation is uninformative. The two components relate differently to accuracy: within-trial ambiguity correlates positively with correctness – consistent with settings where multiple plausible solution paths remain competitive – while across-trial instability correlates negatively, signaling unreliable reasoning. Structural uncertainty is best understood not as a universal confidence estimator, but as a regime-sensitive evaluator of logical reasoning consistency.

02.
arXiv (CS.CV) 2026-06-15

A Unified Theory of Sinusoidal Activation Families for Implicit Neural Representations

Implicit Neural Representations (INRs) model continuous signals with compact neural networks and have become a standard tool in vision, graphics, and signal processing. A central challenge is accurately capturing fine detail without heavy hand-crafted encodings or brittle training heuristics. Across the literature, periodic activations have emerged as a compelling remedy: from SIREN, which uses a single sinusoid with a fixed global frequency, to more recent architectures employing multiple sinusoids and, in some cases, trainable frequencies and phases. We study this family of sinusoidal activations and develop a principled theoretical and practical framework for trainable sinusoidal activations in INRs. Concretely, we instantiate this framework with Sinusoidal Trainable Activation Functions (STAF), a Fourier-like activation whose amplitudes, frequencies, and phases are learned. Our analysis (i) establishes a Kronecker-equivalence construction that expresses trainable sinusoidal activations with standard sine networks and quantifies expressive growth, (ii) characterizes how the Neural Tangent Kernel (NTK) spectrum changes under trainable sinusoidal parameterization, and (iii) provides an initialization that yields standard normal post-activations without asymptotic central limit theorem (CLT) arguments. Empirically, on images, audio, shapes, inverse problems (super-resolution, denoising) and NeRF, STAF is competitive and often stronger on distortion-oriented reconstruction metrics such as PSNR/SSIM across the evaluated INR tasks, with favorable parameter efficiency under layer-wise sharing. While periodic activations can alleviate practical manifestations of spectral bias, our results indicate they do not eliminate it; instead, trainable sinusoids can improve the observed capacity-optimization trade-off in the evaluated settings.

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

Small Initialization Matters for Large Language Models

arXiv:2606.17945v1 Announce Type: new Abstract: Large language models provide a tractable system for asking how intelligence itself emerges, rather than only how LLMs can be engineered. Although progress is usually attributed to scale, data and architecture, we show that parameter initialization is a gene-like determinant of training and, in particular, of model capacity. Reducing the initialization scale consistently improves pretraining, with the largest gains on reasoning-demanding tasks. We identify two widely used empirical settings that restrain the advantage of small initialization, and show how relaxing them restores favorable scaling. We further uncover a critical initialization that balances the reasoning and training. Mechanistically, small initialization drives a distinct developmental trajectory: parameters first condense into low-complexity structures and later expand into richer representations, giving concrete form to the idea that compression is intelligence. Token-level analyses show that the gains concentrate on non-trivial, context-constrained predictions rather than all tokens uniformly. These results motivate a simple $\gamma$-initialization rule: expose initialization rage as an explicit knob and use small initialization by default, an almost cost-free intervention that improves pretraining and strengthens reasoning across model scales.

04.
arXiv (CS.AI) 2026-06-16

IoT-Zoo: A Container-Based Framework for Heterogeneous IoT Device Profiles and Reproducible Traffic Capture

arXiv:2606.15653v1 Announce Type: cross Abstract: The validation of networking and security solutions for the Internet of Things (IoT) requires realistic and reproducible experimental data. However, existing platforms often achieve scalability by replicating a limited set of device types, which restricts profile diversity and fails to capture the heterogeneity of real-world IoT environments. In this paper, we present IoT-Zoo, a container-based testbed designed to support reproducible experimentation through heterogeneous, dataset-driven IoT device profiles. Built upon Containernet, IoT-Zoo automates the deployment of multi-domain scenarios and supports real application protocols such as MQTT and RTSP. The platform provides a single-command interface for environment provisioning and automated traffic capture (PCAP), enabling the generation of consistent traffic baselines and reducing the operational effort required to evaluate networking and security solutions.

05.
arXiv (CS.LG) 2026-06-11

JGRA: Jacobian Geometry Robustness Assessment in NISQ Noise-Aware Quantum Neural Networks

arXiv:2606.09964v2 Announce Type: replace-cross Abstract: The NISQ era places stringent constraints on quantum computation, where noise and decoherence fundamentally limit performance. In classical deep learning, model robustness and resilience to perturbations are well studied: deep neural networks (DNNs) maintain high performance despite pruning, noise injection, and structural perturbations due to inherent redundancy in their representations. A central challenge in quantum machine learning is to transfer this notion of robustness to quantum neural networks (QNNs) under realistic NISQ noise. While classical deep learning exhibits robustness through structural redundancy, analogous principles for QNNs remain underdeveloped. We propose JGRA: a framework for assessing robustness in noise-aware QNNs via Jacobian geometry, capturing model sensitivity to parameter perturbations induced by noise. Our method includes entropy-matched noise calibration, noise-aware training, and noise-conditioned Jacobian extraction, yielding geometric descriptors that link clean-regime structure to noisy inference behaviour. We also empirically demonstrate that these descriptors encode predictive information about robustness under unseen noise.

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

Pretraining A Large Language Model using Distributed GPUs: A Memory-Efficient Decentralized Paradigm

Pretraining large language models (LLMs) typically requires centralized clusters with thousands of high-memory GPUs (e.g., H100/A100). Recent decentralized training methods reduce communication overhead by employing federated optimization; however, they still need to train the entire model on each node, remaining constrained by GPU memory limitations. In this work, we propose SParse Expert Synchronization (SPES), a memory-efficient decentralized framework for pretraining mixture-of-experts (MoE) LLMs. SPES trains only a subset of experts per node, substantially lowering the memory footprint. Each node updates its local experts and periodically synchronizes with other nodes, eliminating full-parameter transmission while ensuring efficient knowledge sharing. To mitigate limited per-expert data utilization under sparse expert updates, we introduce an expert-merging warm-up strategy, where experts exchange knowledge early in training, to rapidly establish foundational capabilities. With SPES, we train a 2B-parameter MoE LLM using 16 standalone 48GB GPUs over internet connections, which achieves competitive performance with centrally trained LLMs under similar computational budgets. We further demonstrate scalability by training a 7B model from scratch and a 9B model upcycled from a dense checkpoint, both of which match prior centralized baselines. Our code is available at https://github.com/zjr2000/SPES.

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

Light Forcing: Accelerating Autoregressive Video Diffusion via Sparse Attention

Advanced autoregressive (AR) video generation models have improved visual fidelity and interactivity, but the quadratic complexity of attention remains a primary bottleneck for efficient deployment. While existing sparse attention solutions have shown promise on bidirectional models, we identify that applying these solutions to AR models leads to considerable performance degradation for two reasons: isolated consideration of chunk generation and insufficient utilization of past informative context. Motivated by these observations, we propose \textsc{Light Forcing}, the first sparse attention solution tailored for AR video generation models. It incorporates a Chunk-Aware Growth mechanism to quantitatively estimate the contribution of each chunk, which determines their sparsity allocation. This progressive sparsity increase strategy enables the current chunk to inherit prior knowledge in earlier chunks during generation. Additionally, we introduce a Hierarchical Sparse Attention to capture informative historical and local context in a coarse-to-fine manner. Such two-level mask selection strategy (i.e., frame and block level) can adaptively handle diverse attention patterns. Extensive experiments demonstrate that our method outperforms existing sparse attention in quality (e.g., 84.5 on VBench) and efficiency (e.g., $1.2{\sim}1.3\times$ end-to-end speedup). Combined with other efficient solutions, \textsc{Light Forcing} further achieves a $2.0{\sim}3.0\times$ end-to-end speedup across diverse GPUs (e.g., 27.4\,FPS on RTX 5090 and 33.9\,FPS on H100). Code is released via this \href{https://github.com/chengtao-lv/LightForcing}{link}.

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

Conditional Local Importance by Quantile Expectations

arXiv:2411.08821v4 Announce Type: replace-cross Abstract: Global variable importance measures are commonly used to interpret the results of machine learning models. Local variable importance techniques assess how variables contribute to individual observations. Current, popular methods, including LIME and SHAP, provide useful measures of feature contribution in the prediction space, while leaving opportunities for improved characterization of local structure in the model loss space. Additionally, they are not natively adapted for multi-class classification problems. We propose a new model-agnostic method for calculating local variable importance, CLIQUE, that highlights locally dependent relationships, provides improved stability over permutation-based methods, and can be directly applied to multi-class classification problems. Simulated and real-world examples show that CLIQUE emphasizes locally dependent information, captures interaction behavior beyond what can be evaluated by correlations, and assigns zero importance in regions where the response is invariant to changes in variables.

09.
arXiv (quant-ph) 2026-06-19

Topological Codes Based on Space Groups

arXiv:2606.20548v1 Announce Type: new Abstract: Topological codes form one of the most important classes of stabilizer codes. Most existing algebraic constructions and analyses of topological codes assume translation invariance. Here we show that topological codes can arise in more general settings by incorporating point group operations. The central construction is a class of Calderbank-Shor-Steane (CSS) codes called space-group codes, whose check operators are built from group-algebra templates over space groups that combine translations with point-group operations. We develop methods for analyzing topological properties of space-group codes using ring-modules and their invariant theory. At first glance, space-group codes might appear to complicate practical implementation; however, we find that they can exhibit greater locality than previous codes based purely on translations. Our framework thus extends the landscape of topological codes and opens up a broader design space for the co-design of topological codes with quantum computing platforms.

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

LongSpike: Fractional Order Spiking State Space Models for Efficient Long Sequence Learning

arXiv:2606.12895v1 Announce Type: new Abstract: Spiking Neural Networks (SNNs) are well-regarded for their biological plausibility and energy efficiency in processing sequential data. However, dominant SNN architectures typically rely on first-order Ordinary Differential Equations (ODEs) to govern neuronal state transitions. This first-order assumption imposes a "memoryless" bottleneck, limiting the model's capacity to capture the complex, long-range dependencies inherent in long-sequence tasks. In this work, we propose LongSpike, a novel SNN framework that integrates fractional-order State-Space Modeling, or f-SSM, from control theory into the spiking domain. By extending traditional integer-order SSMs to the fractional-calculus regime, LongSpike enables the hierarchical integration of neuronal dynamics with long-memory kernels. To mitigate the computational overhead and parallelization challenges typically associated with fractional operators, we leverage a state-space formulation that supports efficient, parallel training. Empirical evaluations on challenging benchmarks, including Long Range Arena (LRA), large-scale WikiText-103, and Speech Commands, demonstrate that LongSpike outperforms state-of-the-art SNNs in accuracy while preserving sparse synaptic computation. The code is available at https://github.com/xinruihe389-commits/LongSpike.

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

From Bounding Boxes to Visual Reasoning: An On-Policy Data Annotation Tool for Vision-Language Models

Vision-language models (VLMs) are rapidly advancing toward sophisticated grounded structured visual reasoning. Training models for such advanced capabilities demands a new genre of data that seamlessly unifies spatial coordinates, open-vocabulary descriptions, structured attributes, and topological relationships into a singular representation. However, existing data annotation tools fundamentally fail to meet these intricate demands, suffering from three systematic bottlenecks: limited expressiveness, severe annotation-training decoupling, and poor data reusability. To bridge this infrastructure gap, we introduce an open-source annotation tool, ScreenAnnotator. First, we define a unified annotation atom schema that binds spatial, semantic, and structural primitives into a single unit. Second, we implement an on-policy annotation loop embedded with a Bayesian Annotation Verifier (BAV). Finally, we design a template-driven multi-task data synthesis process dynamically transforms static atoms into diverse multi-dimensional reasoning tasks, eliminating redundant re-annotation. The on-policy loop drives the annotation accept rate to nearly 100% on flowcharts and 77% on GUI screenshots, while steadily reducing per-image annotation time as labeled data accumulate. In the flowchart scenario, fine-tuning a VLM yields 76.1% average accuracy, which is a 35.1% point absolute gain. Our code is available at: https://github.com/WnQinm/Annotator.

12.
arXiv (CS.CV) 2026-06-17

Reinforcing Dual-Path Reasoning in Spatial Vision Language Models

Spatial VLMs have made substantial progress in geometric perception, yet complex spatial reasoning requiring multi-step inference over depth, distance, and scene relations remains challenging. Moreover, different spatial queries call for fundamentally different strategies: some are best addressed through purely linguistic, step-by-step deduction, while others require explicit 3D grounding before quantitative inference. We present Dual-Path Spatial Reasoning via Reinforcement Learning for Spatial VLMs (SR-REAL), a unified framework that equips a spatial VLM with two complementary reasoning paths: Language-Only Reasoning (LOR), which performs step-by-step linguistic deduction, and Detect-Then-Reason (DTR), which detects 3D geometric cues (e.g., centers or bounding boxes) via region tokens before explicit geometric inference. SR-REAL begins with a cold-start supervised fine-tuning stage that constructs LOR and DTR chain-of-thought supervision and exposes a region-to-3D interface, followed by RL that optimizes the policy model with accuracy and format rewards; for DTR, a discrete center-based detection reward further refines geometric alignment. Across diverse spatial benchmarks, SR-REAL significantly outperforms spatial VLM baselines: (i) a single RL-trained model supports both reasoning paths, with DTR excelling in region-aware tasks through precise 3D localization and LOR enhancing general spatial reasoning; (ii) jointly training both paths fosters mutual reinforcement; (iii) high-quality, blended cold-start data is crucial for stable RL optimization; and (iv) the model generalizes across datasets and domains without per-task tuning, demonstrating positive transfer between LOR and DTR.

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

A fully GPU-based workflow for building physics emulators of hypersonic flows

arXiv:2606.13742v1 Announce Type: cross Abstract: The ability to resolve complex physical phenomena with high fidelity and at low computational cost is central to addressing key challenges in modern engineering. A prime example lies in hypersonic flows, where the precise prediction of the full flowfield topology, in particular with respect to shock wave location and intensity, is critical. Yet supersonic and hypersonic flows continue to be a stumbling block for traditional reduced-order models and neural emulators that struggle to capture steep gradients in flow states with physical consistency in applications of industrial relevance. To that end, we introduce a fully GPU based workflow that integrates accelerated data generation with the training of neural emulators augmented by uncertainty quantification and physics-aware refinement. Our workflow is enabled by a differentiable high-fidelity solver (JAX-Fluids) which we employ for rapid dataset creation and residual-based improvement of the neural emulator to enhance physical consistency. Building on this framework, we first present a suite of model architectures and analyze their scaling behavior to expose their strengths and shortcomings. We then show that residual-based refinement enables training on cases where only mesh and input parameters are available, substantially reducing residuals and improving physical consistency. Together, differentiable simulation and residual-based refinement yield physics emulators that remain reliable beyond their training distribution, a key requirement for deploying surrogates in real-world engineering design loops.

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

Generalized two-qubit Hamiltonian for Projective Quantum Feature Maps

arXiv:2606.13641v1 Announce Type: new Abstract: Projected quantum feature maps provide a strategy for using quantum processors as feature generators for classical machine-learning models. Building on counterdiabatic Ising-glass and one-dimensional Heisenberg PQFMs, we introduce a generalized two-qubit Hamiltonian-based PQFM that provides a unified way to encode classical features through local Pauli fields and pairwise two-qubit Pauli interactions. This construction allows distinct classical variables to be embedded along different Pauli axes of the same qubit, increasing the information density of shallow circuits while remaining compatible with hardware constraints. We develop and implement these methods in pqfmlib, a publicly available Python library for constructing, executing, and benchmarking Hamiltonian-based PQFMs.We then benchmark the generalized Hamiltonian PQFMs against reference PQFMs on four biomedical classification datasets under a nested cross-validation protocol with paired statistical tests. Quantum features are generated using both IBM quantum processors with up to 156 qubits and statevector simulations. Our results show that the generalized two-qubit Hamiltonian family provides the most consistent pattern of statistically supported gains over matched classical baselines, although the performance of all methods depends on the dataset, encoding strategy, measured observables, and hardware conditions. These findings support generalized Hamiltonian PQFMs as a promising route toward near-term quantum utility.

16.
medRxiv (Medicine) 2026-06-17

Silent Manipulation of Mental Health Treatment Recommendations from a Large Language Model

Importance. Large language models (LLMs) increasingly inform mental health decisions by patients and clinicians. Inference-time activation steering can shift model behavior on a target dimension without altering weights or prompts and without disclosure to users, allowing treatment recommendations to be silently changed for commercial or ideological reasons. Objective. To determine whether directional activation steering can shift an open-weights LLM's depression treatment recommendations. Design, Setting, and Participants. This non-human subjects study applied directional activation steering to an open-weights LLM (DeepSeek V4 Flash) responding to 12 depression-advice scenarios (4 favoring medication, 4 favoring avoidance, 4 neutral), generated at 30 amplitudes from -1.5 to +1.5 in 0.1 increments plus an unsteered baseline. Exposures. A single steering direction contrasting antidepressant medication with self-directed approaches (diet, exercise, meditation, dietary supplements), constructed from 16 paired training prompts and applied at the attention output of every transformer block; weights and system prompt were held constant. Main Outcomes and Measures. The extent to which medication and four self-care categories were addressed, scored 0 to 3 by a human-validated LLM rater (Claude Opus 4.7), the medication-versus-self-care balance, and clinician referral, estimated per unit of amplitude using mixed-effects models with a scenario random intercept. Results. Across 372 generations, steering produced a graded, dose-dependent shift in the medication-versus-self-care balance, which declined by 0.32 per unit of amplitude (beta=-0.32; 95% CI, -0.39 to -0.25; P < .001); medication extent fell and self-care extent rose. The shift was largest for scenarios with no stated treatment preference (beta = -0.44; 95% CI, -0.54 to -0.34; P < .001). A clinician referral appeared in 322 of 372 responses (87%) and did not vary with steering amplitude (P = .63). Conclusions and Relevance. In this open-weights LLM providing depression treatment information, inference-time activation steering shifted treatment recommendations without altering weights, prompt structure, or safety outputs, with the largest effect among users expressing no treatment preference. These findings suggest a need for LLM disclosure standards and independent auditing as such models inform clinical decisions.

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

CoIRL-AD: Collaborative-Competitive Imitation-Reinforcement Learning in Latent World Models for Autonomous Driving

End-to-end autonomous driving models trained with imitation learning (IL) often generalize poorly, particularly in long-tail scenarios where expert demonstrations are sparse. Reinforcement learning (RL) can provide complementary task-level supervision, but applying RL to real-world autonomous driving is challenging in offline settings without interactive simulators, where datasets are dominated by expert actions and provide limited behavioral diversity. We propose CoIRL-AD, a competitive dual-policy framework that integrates IL and RL under a unified offline training regime. CoIRL-AD decouples imitation and reward optimization into separate actors to alleviate objective conflicts, uses imagined future rollouts for long-horizon reward estimation, and introduces a competition mechanism that selectively transfers beneficial behaviors while keeping RL anchored to expert-like driving. Experiments on the nuScenes benchmark show that CoIRL-AD consistently improves robustness over strong IL-based baselines, with especially large gains in cross-city generalization and long-tail scenarios. Code is available at: https://github.com/SEU-zxj/CoIRL-AD.

18.
arXiv (CS.CL) 2026-06-15

MedLatentDx: Latent Multi-Agent Communication for Cross-Hospital Rare-Disease Diagnosis

Rare diseases affect over $300$ million patients across more than $7{,}000$ conditions, yet no single hospital encounters enough cases of any one condition for reliable diagnosis. Cross-hospital collaboration could help by allowing a diagnosing institution to use distributed, case-specific diagnostic evidence, but privacy regulations restrict the transmission of identifiable clinical text across institutional boundaries. This setting raises two challenges: existing medical agent systems often rely on textual evidence exchange, while raw latent states such as hidden states and KV caches may still reveal prompt-derived clinical content. We introduce MedLatentDx, a latent multi-agent communication framework in which hospital agents keep private clinical records and retrieved cases local, and send compact latent KV blocks to a host agent for rare-disease diagnosis. MedLatentDx supports two deployment settings: same-backbone hospital agents use latent KV distillation, while hospitals with different LLM backbones use cross-family latent alignment. On CrossRare-Bench, a self-built large-scale rare-disease benchmark with hospital-level partitions, MedLatentDx improves cross-hospital diagnostic performance while reducing reconstructable clinical content relative to raw-latent communication baselines.

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

Unifying Acoustic Features and Text with Multimodal LLMs for Neurodegenerative Screening

arXiv:2606.14788v1 Announce Type: cross Abstract: Voice-based screening offers a scalable and non-invasive way to assess neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD), but their staging remains challenging due to the difficulty of integrating heterogeneous data. This paper presents NeurMLLM, an efficient multimodal generative framework for neurodegenerative disease staging. NeurMLLM first encodes the spectrograms and Mel-frequency cepstral coefficients of audio data with vision transformers and projects their representations into the embedding space of a large language model (LLM), where they are concatenated with transcript and demographic instruction tokens as a single unified sequence. The LLM is then instruction-tuned via Low-Rank Adaptation using task prompts to autoregressively predict a constrained label token, enabling a generative classification. By evaluating on the Bridge2AI-Voice dataset for fine-grained staging of AD and PD, we observe that NeurMLLM achieves strong performance, consistently outperforming classical machine learning methods and existing LLM-based approaches. The results show the high potential of multimodal LLMs in neurodegenerative disease staging, improving staging accuracy and supporting accessible deployment.

20.
arXiv (quant-ph) 2026-06-12

Positive Conserved Quantities in the Klein-Gordon Equation

作者:

arXiv:2410.04666v3 Announce Type: replace Abstract: We introduce an embedding of the Klein-Gordon equation into a pair of coupled equations that are first-order in time. The existence of such an embedding is based on a positivity property exhibited by the Klein-Gordon equation. These coupled equations provide a more satisfactory reduction of the Klein-Gordon equation to first-order differential equations in time than the Schrodinger equation. Using this embedding, we show that the ``negative probabilities" associated with the Klein-Gordon equation do not need to be resolved by introducing matrices as Dirac did with his eponymous equation. For the case of the massive Klein-Gordon equation, the coupled equations are equivalent to a forward Schrodinger equation in time and a backward Schrodinger equation in time, respectively, corresponding to a particle and its antiparticle. We show that there are two positive integrals that are conserved (constant in time) in the Klein-Gordon equation and thus provide a concrete resolution of the historical puzzle regarding the previously supposed lack of a probabilistic interpretation for the field governed by the Klein-Gordon equation. A significant consequence is that the Schrodinger equation is given a relativistic formulation, which does not require creation and annihilation operators, i.e. quantum fields. Physically, this corresponds to a theory in which the positive and negative energy parts do not directly interact, hence there will be no annihilation events–for example, particle-antiparticle collisions which do not result in photon emission. Thus, one practical consequence of this relativistically consistent theory is a simple explanation for dark matter.

21.
bioRxiv (Bioinfo) 2026-06-14

Prediction of parsimonious and temporally sensitive sets of cell fate engineering transcription factors with IMCell

Transcription factor (TF) cocktails used in cell identity reprogramming protocols have largely been developed from experimental approaches. A handful of computational approaches have been reported, though have not been widely adopted by the scientific community. To standardize their use and assess their performance, we built CompForce, a platform that integrates these tools. Using CompForce, we found that existing computational methods offer modest improvements over differential expression on both synthetic and literature-curated data, and that their lackluster and inconsistent performance could be attributed to a reliance on local centrality metrics. To improve upon these methods, we developed IMCell, a prediction method that is inspired by the influence maximization problem. Unlike existing tools, IMCell returns optimized TF sets rather than ranked TF lists. We demonstrate that IMCell vastly out-performs existing tools, and further extend it to dynamic, stepwise contexts. The tools presented here are available in the R packages CompForce and IMCell.

22.
medRxiv (Medicine) 2026-06-15

HPV Self-Sampling in Cervical Screening: A Rapid Review

Introduction Cervical cancer is the fourth largest cause of cancer deaths in women. HPV self-sampling could increase uptake of cervical screening. This rapid review aimed to determine the accuracy, concordance, uptake and acceptability of self-sampling over clinician-collected samples in high income countries. Method We followed Cochrane Rapid Reviews Methods. Top-up of 4 systematic reviews and meta-analyses was performed. Narrative data synthesis was conducted and meta-analysis where applicable. Databases searched were MEDLINE, EMBASE, CENTRAL and clinical trial registries. Risk of bias was assessed using AMSTAR 2, QUADAS, the Cochrane Risk of Bias (RoB), or the Nudelman and Otto, 2020 tool, depending on the study type. Findings The review included 39 studies for accuracy, 38 studies for concordance, 37 uptake and 48 studies for acceptability. Self-sampling has similar accuracy as clinician-collected samples when PCR-based assays are used. The overall agreement of self-sampling and clinician-collected samples was 87.1%(95%CI;85.6-88.6) with a kappa value of 0.70(95%CI;0.67-0.73). Mail-to-all strategies had higher uptake with participation differences of 11.3%(95%CI:8.4-14.2) in the intention-to-treat analysis and 7.7%(95%CI:4.7-10.8) in the per protocol analysis. Self-sampling is acceptable to non-attendees (91%(95%CI;85.3-94.6). Conclusion and Recommendation Self-sampling shows good performance on the four clinical effectiveness indicators of accuracy, concordance, uptake and acceptability.

23.
arXiv (CS.CV) 2026-06-11

Weakly Supervised Segmentation as Semantic-Based Regularization

Weakly supervised semantic segmentation (WSSS) trains dense pixel-level segmentation models from partial or coarse annotations such as bounding boxes, scribbles, or image-level tags. While recent work leverages foundation models such as the Segment Anything Model (SAM) to generate pseudo-labels, these approaches typically depend on heuristic prompt choices and offer limited ways to incorporate prior knowledge or heterogeneous labels. We address this gap by taking a neurosymbolic perspective: integrating differentiable fuzzy logic with deep segmentation models. Weak annotations and domain-specific priors are unified as continuous logical constraints that fine-tune SAM under weak supervision. The refined foundation model then produces improved pseudo-labels, from which we train a second-stage prompt-free segmentation model. Experiments on Pascal VOC 2012 and the REFUGE2 optic disc/cup segmentation dataset show that our logic-guided fine-tuning yields higher-quality pseudo-labels, leading to state-of-the-art segmentation accuracy that often exceeds densely supervised baselines.

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

Enhancing Graph Neural Networks Using Proximity Graphs for Dust Source Emission Forecasting

arXiv:2606.19825v1 Announce Type: new Abstract: Accurate prediction of dust source emissions is critical for mitigating the significant environmental and health hazards posed by dust storms. Traditional forecasting methods often struggle to capture the complex spatiotemporal dynamics of these phenomena. In this paper, we demonstrate that proximity graphs enable Graph Neural Networks (GNNs) to effectively model the intricate spatial and temporal relationships between data points. Specifically, we use proximity graphs–such as Delaunay triangulation, Gabriel graph, k-Nearest Neighbor graph, and Yao graph–as the input for GNNs (including GraphSAGE, Graph Convolutional Networks, and Graph Attention Networks) to perform message passing. Our approach highlights the effectiveness of integrating proximity graphs with GNNs for robust and accurate dust source forecasting. To emphasize the importance of proximity graph representations, we compare our method against GNNs using random graphs for message passing. The results show that GNNs with proximity graphs significantly outperform those with random graphs and are also far superior to Long Short-Term Memory (LSTM) model in dust source emission forecasting.

25.
PLOS Computational Biology 2026-06-05

A multiscale, Bayesian inference approach to augment mechanistic models of cell signaling with machine-learning predictions of binding affinity

by Holly A. Huber, Stacey D. Finley Computational models in systems biology are often underdetermined—that is, there is little data relative to the complexity and size of the model. This lack of data is primarily due to limits in our ability to observe specific biological systems and restricts the utility of computational models. To reduce this uncertainty, recent methods have explored augmenting parameter inference of systems biology models with predictions from machine learning models. Such approaches expand the pool of data that is applicable for the inference problem. Here, we explore augmenting the parameter inference of intracellular signaling models. We choose to investigate signaling because experimental measurements of the variables of interest, protein dynamics, are still quite limited. To investigate, we propose a novel, multiscale, Bayesian inference approach that augments traditional signaling data with predictions of binding affinity. These predictions are generated using a machine learning pipeline with measurements of amino acid sequence, from the Universal Protein Resource, or protein structure, from the Protein Data Bank, as inputs. We find that we can successfully integrate these measurements into the inference problem using our novel framework. Excitingly, this integration significantly improves the parameter estimates of signaling models. We demonstrate that how much this improvement impacts predictions of signaling depends on the sensitivity of the prediction to perturbations in the parameter values. Overall, the framework we establish here improves the parameter inference of intracellular signaling models by successfully bridging data on protein sequence and structure with systems-level signaling.