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01.
arXiv (CS.CL) 2026-06-16

Agentic Retrieval and Reinforcement Learned Equation Chains: A Controlled Generation Framework for Complex and Novel Physics Word Problems

Generating high-quality Physics Word Problems (PWPs) that are novel, complex, and solvable remains a challenging and underexplored problem in educational content generation. Existing approaches, many adapted from Math Word Problem (MWP) generation, often produce ambiguous, unsolvable, or structurally simple questions with limited linguistic diversity. We introduce ARVRE (Agentic Retrieval Value Reinforced Equation-chain), a two-stage framework for generating diverse and mathematically valid PWPs. In the first stage, a form of offline temporal-difference learning is used to construct valid chains of physics equations, while an agentic retrieval-augmented generation (RAG) framework dynamically selects topic-specific concepts and vocabulary. This design enables explicit control over problem structure and difficulty. In the second stage, a Large Language Model (LLM) converts the equation chain and retrieved concepts into a natural-language physics question. By grounding generation in valid equation chains, our method preserves mathematical correctness while promoting linguistic diversity and contextual richness. Human and automated evaluations demonstrate that ARVRE generates PWPs that are more complex, novel, and solvable than those produced by existing approaches. These results highlight the potential of combining reinforcement learning, retrieval, and LLMs for reliable generation of educational physics content.

02.
arXiv (CS.LG) 2026-06-11

Tree-Structured Orthonormal Decomposition of the Aitchison Simplex

arXiv:2606.11646v1 Announce Type: new Abstract: Compositional data – vectors encoding relative proportions – arise across scientific domains, including ecology, geochemistry, and genomics. The features in these data often come with known hierarchical structure (e.g., taxonomies, phylogenies, ontologies), yet existing methods either ignore this structure, discard the intrinsic Aitchison geometry, are designed for binary trees, or yield incomplete coordinate systems. We describe PolyILR, a canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology. Our construction defines a weighted local geometry at each internal node capturing full branching structure, then lifts these to a global orthonormal basis where every coordinate corresponds to a specific tree location. On microbiome and single-cell benchmarks, PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution. We also establish a novel theoretical connection to softmax classifiers, suggesting possible applications to probabilistic modeling.

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

Deep Temporal Modeling and Ensemble Fusion for Multimodal Emotion Recognition from Physiological Signals

Physiological stress and emotion recognition are important for health monitoring and affective computing. In this work, we present a comprehensive evaluation of deep learning models such as Long Short-Term Memory (LSTM), Temporal Convolutional Networks (TCN), and Transformer on the WESAD dataset for multimodal affect recognition using wrist and chest sensor signals. We perform ablation studies to assess the individual contributions of each modality by training models on wrist-only and chest-only inputs. In addition, we implement a late-fusion ensemble strategy that combines predictions from all three architectures trained on multimodal input. We also employ early fusion at the sensor level by concatenating wrist and chest signals before feeding them into each model. Our results show that Transformer models consistently achieve the highest accuracy in multimodal settings, while TCN models perform best in the wrist-only configuration. The ensemble method yields the highest overall accuracy (98.91 +/- 0.13%) and macro-F1 score (98.56 +/- 0.17%). These findings demonstrate the effectiveness of sensor fusion and ensemble-based fusion in developing robust systems for physiological emotion recognition.

04.
PLOS Computational Biology 2026-06-09

Multi-stable oscillations in cortical networks with two classes of inhibition

by Arnab Dey Sarkar, Bard Ermentrout In the classical view of cortical rhythms, interactions between excitatory pyramidal neurons (E) and inhibitory parvalbumin-expressing interneurons (I) are sufficient to generate gamma- and beta-band oscillations. However, it is now well established that multiple inhibitory interneuron subtypes exist and that they play important roles in the generation and modulation of these rhythms. In this paper, we develop a spiking network model consisting of populations of E, I, and an additional interneuron type, somatostatin-expressing neurons (S), which receive excitation from the E cells and inhibit both the E and I populations. The S cells are further modulated by a third inhibitory subtype, vasoactive intestinal peptide (VIP) neurons, which receive inputs from other cortical areas. We reduce the spiking network to a system of nine differential equations that describe the mean membrane potential, firing rate, and synaptic conductance for each population. Using this reduced model, we identify a wide range of parameters that exhibit multiple coexisting rhythms. Employing tools from nonlinear dynamics, we then explore the roles of the two classes of inhibition, as well as VIP modulation, in shaping the properties of these rhythms.

05.
arXiv (quant-ph) 2026-06-16

Experimental realization of the complete seven-phase Anderson-localization landscape

arXiv:2606.14825v1 Announce Type: cross Abstract: Anderson localization has evolved far beyond the conventional dichotomy between extended and localized states. Modern localization theory predicts a complete transport hierarchy comprising extended, critical, and localized phases together with all coexistence phases among them, forming a seven-phase Anderson-localization landscape. Despite its fundamental importance, this hierarchy has never been experimentally realized within a single system. Here we realize the complete seven-phase Anderson-localization landscape in a one-dimensional Floquet photonic lattice. By engineering quasiperiodic hopping profiles containing inhomogeneously distributed hopping zeros, we generate critical states and enable their coexistence with extended and localized sectors. The resulting transport regimes are directly resolved through their distinct spatiotemporal dynamics, including ballistic expansion, confined critical oscillations, and persistent localization. We observe all seven phases, including the elusive triply coexisting extended-critical-localized phase, and experimentally track the phase transitions connecting them. Our results establish the first complete experimental map of the Anderson-localization landscape and provide a unified platform for investigating mobility edges, multifractality, and programmable coherent transport.

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

Task-guided cross-subject latent alignment: a multi-encoder-decoder VAE

arXiv:2606.15989v1 Announce Type: cross Abstract: Aligning neural activity across subjects offers the promise of discovering shared computational principles and generalizable decoders. However, traditional alignment methods require shared stimuli across subjects, a constraint that limits applicability to naturalistic paradigms with limited or non-overlapping data. We introduce a Multi-Encoder-Decoder Variational Autoencoder (MED-VAE) that achieves cross-subject alignment without shared stimuli by anchoring representations to a common scaffold provided by a pretrained ANN. Using the Natural Scenes Dataset, we show that MED-VAE creates common latent spaces with superior semantic organisation, achieving higher cross-subject alignment than common methods while maintaining robust generalisation to held-out stimuli where traditional methods degrade. Reconstructing from these common spaces back to each subject's original neural space, MED-VAE preserves equal stimulus-driven signal in its cross-subject latent space. Finally, we show that this superior alignment directly enables cross-subject neural prediction, as demonstrated via cross-subject image decoding. In summary, we introduce a framework to identify generalisable common subspaces for cross-subject predictions and downstream tasks, demonstrated here for visual cortex responses to static images.

07.
arXiv (CS.LG) 2026-06-12

Multi-Token Residual Prediction

arXiv:2605.18817v2 Announce Type: replace Abstract: Diffusion Language Models (DLMs) generate text by iteratively denoising masked token sequences, offering a tradeoff between parallelism and quality compared to autoregressive models. In current practice, the number of tokens decoded per step is controlled by a confidence threshold, and quality degrades monotonically as more tokens are denoised per step. We introduce Multi-token Residual Prediction (MRP), a lightweight module that enables dependency-aware multi-token denoising within a single backbone forward pass. MRP exploits a key property of the denoising process: the logit distributions at adjacent denoising steps are remarkably similar. Rather than running the backbone a second time to obtain the next-step logits, MRP predicts the residual between steps from the backbone's hidden states, effectively denoising more tokens per backbone forward at a fraction of the cost. We apply MRP across the two operating regimes of DLM decoding. In the high-quality-low-throughput static denoising regime, MRP serves as a drafter for speculative decoding: its proposals are verified against the backbone, yielding lossless acceleration of up to 1.4x in SGLang. In the low-quality-high-throughput dynamic denoising regime, MRP instead drives a remasking scheme that revokes over-eager reveals, recovering most of the accuracy lost to aggressive low-threshold decoding and improving accuracy by up to 22.6 points on code generation task HumanEval and 17.7 points on reasoning task GSM8K.

08.
arXiv (CS.CL) 2026-06-11

Schützen: Evaluating LLM Safety in Bulgarian and German Contexts

Large language models are increasingly deployed across professional domains, bringing hard-to-predict risks, including the generation of harmful or disrespectful content. Although substantial progress has been made in developing safety evaluation datasets, existing resources remain overwhelmingly English- and Chinese-centric. This limitation is particularly pronounced when evaluating languages that operate within shared sociocultural, legal, and ethical contexts. To address this gap, we introduce Sch\"{u}tzen: a German–Bulgarian safety dataset designed to assess model answerability under risk, covering both a low-resource language (Bulgarian) and a high-resource language (German). Experiments with multilingual and language-specific LLMs reveal pronounced cross-language differences in safety behavior, highlighting the necessity of tailored, region-specific evaluation resources to support the responsible deployment of LLMs in Germany and Bulgaria. Datasets and code are available at https://github.com/xnlp-lab/Schutzen. Warning: this paper contains examples that may be offensive, harmful, or biased.

09.
arXiv (CS.AI) 2026-06-16

DualGauge: Automated Joint Security-Functionality Benchmarking of Specification-Only Code Generation by LLMs and Coding Agents

arXiv:2511.20709v2 Announce Type: replace-cross Abstract: Large language models (LLMs) and LLM-based coding agents are now used to generate code from natural-language specifications, yet ensuring such code is both functionally correct and secure remains a challenge. We present DualGauge, the first fully automated framework for jointly evaluating correctness and security of specification-only code generation, supported by DualGauge-Bench, a language-agnostic benchmark of 307 coding tasks each paired with functional and security tests derived from the same specification. Evaluating 10 representative LLMs across Python, C++, and JavaScript, we find that functional correctness substantially overestimates reliable code generation: even the strongest model remains below 15% joint security-functionality success in every language. Common model-side factors–scale, extended thinking, quantization, instruction tuning, and code specialization–do not reliably improve joint performance, suggesting secure-and-correct code generation does not simply emerge from stronger coding capability. Evaluation of 3 leading agentic coding systems (Codex, OpenHands, and Claude Code) shows that iterative scaffolding provides no advantage over direct (LLM-based) generation on specification-only tasks. A qualitative audit reveals failures concentrate at the output contract boundary and in guards that exist but are insufficient–patterns that only joint benchmarking reliably exposes.

10.
arXiv (CS.LG) 2026-06-19

BLISS: A Lightweight Bilevel Influence Scoring Method for Data Selection in Language Model Pretraining

arXiv:2510.06048v5 Announce Type: replace Abstract: Effective data selection is essential for pretraining large language models (LLMs), enhancing efficiency and improving generalization to downstream tasks. However, existing approaches often require leveraging external pretrained models, making it difficult to disentangle the effects of data selection from those of the external pretrained models. In addition, they often overlook the long-term impact of selected data if the model is trained to convergence, primarily due to the prohibitive cost of full-scale LLM pretraining. In this paper, we introduce BLISS (BileveL Influence Scoring method for data Selection): a lightweight data selection method that operates entirely from scratch, without relying on any external pretrained oracle models, while explicitly accounting for the long-term impact of selected data. BLISS leverages a small proxy model as a surrogate for the LLM and employs a score model to estimate the long-term influence of training samples if the proxy model is trained to convergence. We formulate data selection as a bilevel optimization problem, where the upper-level objective optimizes the score model to assign importance weights to training samples, ensuring that minimizing the lower-level objective (i.e., training the proxy model over the weighted training loss until convergence) leads to best validation performance. Once optimized, the trained score model predicts influence scores for the dataset, enabling efficient selection of high-quality samples for LLM pretraining. We validate BLISS by pretraining 410M/1B/2.8B Pythia and LLaMA-0.5B models on selected subsets of the C4 dataset. Notably, under the 1B model setting, BLISS achieves $1.7\times$ speedup in reaching the same performance as the state-of-the-art method, demonstrating superior performance across multiple downstream tasks.

11.
arXiv (CS.CL) 2026-06-17

Evaluating Second-Order Bias of LLMs Through Epistemic Entitlement

Evaluations of social bias in LLMs largely focus on whether models generate or imply biased content. However, as LLMs are increasingly used as judges of bias, they may exhibit social biases in subtler ways in how they evaluate biased content, which current methods do not systematically capture. We call this second-order bias: social bias in an LLM's judgment about social bias, which we evaluate through a novel, philosophically grounded reasoning task. Drawing on entitlement epistemology, we conceptualize bias as misplaced foundational knowledge that shapes an agent's rational inquiry, and derive a logical reasoning task for LLMs to judge to whom a biased text is acceptable or non-acceptable. We develop two simple metrics to measure how biased LLM judges are in inferring demographics for acceptability without sufficient support, and how these inferences vary across groups targeted by biased texts. Evaluating open and closed models, we find that our task evades safety guardrails by surfacing bias in model judgment. It varies systematically across target groups, reflects implicit social maps, and shows how models are still triggered by demographic labels. Our work points to the need for LLM bias evaluation in judgment tasks and broadly, for more theoretically grounded approaches to bias evaluation in NLP. We release our code and model responses at https://github.com/uofthcdslab/second-order-bias.

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

Dynamic Rollout Editing for Reducing Overthinking in RL-Trained Reasoning Models

Long-form chain-of-thought reasoning can improve LLM performance on complex tasks, but models often continue generating unnecessary reasoning after a correct answer has emerged. We refer to this behavior as overthinking. We study this phenomenon from the perspective of GRPO-style reinforcement learning (RL) post-training, framing it as a training-time credit-assignment problem rather than merely a decoding-time stopping problem. In rollouts sampled at the onset of GRPO training, we observe that successful trajectories can exhibit a slightly higher degree of overthinking than unsuccessful trajectories for the same prompts. This early imbalance provides a starting point for an undesirable feedback loop: because GRPO assigns sequence-level credit, it cannot distinguish the solution-reaching prefix from the unnecessary continuation that lengthens a successful trajectory. Both receive positive update signal, allowing the initial imbalance to grow into more severe overthinking during training. To address this issue, we introduce Dynamic Rollout Editing (DRE), a training-time intervention for successful trajectories that continue thinking after answer emergence. DRE preserves the accepted verified prefix, edits the remaining thinking, and prefers the edited trajectory within the same RL group, weakening the preference signal for unnecessary thinking without penalizing the reasoning needed to reach the answer. Experiments across diverse tasks show the effectiveness of DRE.

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

Patients With Personality: Realistic Patient Simulation through Controlled Diversity and Selective Disclosure

arXiv:2606.17441v1 Announce Type: cross Abstract: Simulating realistic patient interactions is a key requirement to testing clinical applications of LLMs at scale without time-consuming and expensive user studies. However, existing approaches often lack realism and controllability, often oversharing information unprompted, and failing to capture the wide variability of patient behavior. Here, we introduce PatientsWithPersonality (PWP), a patient simulation framework that generates realistic yet diverse virtual patient responses through explicit personality parametrization over a latent patient state. Grounded in HEXACO, a six-dimensional personality space used to quantify and parameterize human behavioral traits, our approach enables fine-grained control over conversational style, cooperativeness, and information disclosure within a unified framework. In a clinician evaluation, PWP is judged nearly as realistic as recorded human actors and clearly ahead of prior simulators, while being flagged as "too informative" far less often. Conditioning on HEXACO axes yields personas whose configured traits are recoverable by both clinicians and an autorater, span a substantially wider behavioral footprint than the closest baseline, and prevent oversharing. Altogether, our framework paves the way for more accurate and informative LLM benchmarking through our realistic and steerable patient simulator.

14.
PLOS Computational Biology 2026-06-10

Interpreting higher-order dependence in multimorbidity using cohort data: A partial information decomposition approach

by Cillian Hourican, Geeske Peeters, René J. F. Melis, Almar Kok, Natasja M. van Schoor, Sandra Wezeman, Mike Lees, Marcel G. M. Olde Rikkert, Rick Quax In the context of multimorbidity, clinical features seldom act in isolation: symptoms, signs and behaviours form interdependent systems in which joint effects on function can be demonstrated only when features are considered together. We introduce an open, reusable workflow that detects and interprets these “together-only” interactions using bivariate Partial Information Decomposition (PID; two sources to one target), linking synergy-based dependence to the broader network of clinical variables rather than to a single target. The workflow estimates synergy with small-sample bias correction and summarises each pair in a Breadth–Uniformity–Synergy–Total (BUST) map: breadth of synergy across target variables (broad “generalist” vs narrow “specialist” patterns), cross-stratum uniformity across age, sex and multimorbidity (uniform vs subgroup-specific), synergy strength, and total shared information. Simple diagnostics contrast observed targets with additive expectations, revealing the specific joint configurations through which non-additive effects arise. Applied to data from the Longitudinal Ageing Study Amsterdam, we treated all health-related variables—covering symptoms, clinical signs, behaviours, lifestyle factors, and self-rated health indicators—as both sources and targets in the PID framework. This symmetric design permits synergy to be quantified for every pair of variables with respect to every other variable. The workflow identifies synergistic constellations that additive models miss. Multidomain cliques involving subjective health, pain, cognition and grip strength showed multiple non-additive configurations, whereas pairs such as alcohol use with grip strength exhibited focused, narrow but uniform synergy. Notably, the pairs with the strongest synergistic contributions were largely distinct from those with the highest total mutual information, indicating that synergy captures dependency structure overlooked by conventional association measures. Rather than a new measure, this work provides a bias-aware workflow that makes higher-order dependence visible and transferable. Our results support synergy-aware mapping as a practical complement to conventional multimorbidity analyses: it highlights specific combinations of routinely assessed features whose joint states may be especially informative across multiple health targets and therefore candidates for prioritised joint assessment and future multi-domain intervention studies.

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

Q-Learning with Fine-Grained Gap-Dependent Regret

arXiv:2510.06647v2 Announce Type: replace-cross Abstract: We study fine-grained gap-dependent regret bounds for model-free reinforcement learning in episodic tabular Markov Decision Processes. Existing model-free algorithms achieve minimax worst-case regret, but their gap-dependent bounds remain coarse and fail to fully capture the structure of suboptimality gaps. We address this limitation by establishing fine-grained gap-dependent regret bounds for both UCB-based and non-UCB-based algorithms. In the UCB-based setting, we develop a novel analytical framework that explicitly separates the analysis of optimal and suboptimal state-action pairs, yielding the first fine-grained regret upper bound for UCB-Hoeffding (Jin et al., 2018). To highlight the generality of this framework, we introduce ULCB-Hoeffding, a new UCB-based algorithm inspired by AMB (Xu et al.,2021) but with a simplified structure, which enjoys fine-grained regret guarantees and empirically outperforms AMB. In the non-UCB-based setting, we revisit the only known algorithm AMB, and identify two key issues in its algorithm design and analysis: improper truncation in the $Q$-updates and violation of the martingale difference condition in its concentration argument. We propose a refined version of AMB that addresses these issues, establishing the first rigorous fine-grained gap-dependent regret for a non-UCB-based method, with experiments demonstrating improved performance over AMB.

16.
arXiv (CS.LG) 2026-06-18

AGDN: Learning to Solve Traveling Salesman Problem with Anisotropic Graph Diffusion Network

arXiv:2606.19185v1 Announce Type: new Abstract: The Traveling Salesman Problem (TSP) is a cornerstone of combinatorial optimization and arises in many practical scenarios. Although graph-based learning approaches have been explored for TSP, the question of how to exploit graph structure more effectively remains open. We present the Anisotropic Graph Diffusion Network (AGDN), a new Graph Neural Network framework designed to solve TSP. Our method tackles two central difficulties: (1) the lack of informative topological prior in fully connected TSP graphs, and (2) losing connected nodes in the optimal solution after the commonly used graph sparsification techniques. To overcome these issues, we construct a MixScore transition matrix that merges node similarity with pairwise distance, and we develop an anisotropic graph diffusion strategy that supports efficient information exchange across multiple hops. Comprehensive experiments spanning diverse instance sizes and node distributions show that AGDN consistently outperforms existing methods while keeping computation time competitive. Furthermore, AGDN generalizes well to problem sizes and distributions beyond those seen during training. The implementation is publicly available at: https://github.com/LabRAI/AGDN.

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

AnonShield: Scalable On-Premise Pseudonymization for CSIRT Vulnerability Data

arXiv:2606.15650v1 Announce Type: cross Abstract: We present AnonShield, a high-throughput, on-premise pseudonymization system that combines GPU-accelerated NER, streaming processing, caching, and schema-aware configuration. Evaluated on datasets up to 550 MB (70,951 records), AnonShield reduces processing time from over 92 hours to under 10 minutes (up to 738x speedup) while achieving up to 94.2% F1-score and 96.7% recall. Our results show that scalable pseudonymization of vulnerability data is feasible without sacrificing analytical utility, enabling compliant data sharing in operational CSIRT environments.

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

HierSVA: A Data Synthesis Pipeline, Dataset, and Benchmark for LLM-Driven Hierarchical Hardware Formal Verification

arXiv:2606.13706v1 Announce Type: cross Abstract: We present HierSVA, an integrated suite that combines a pipeline, dataset, and benchmark for LLM-driven hierarchical hardware formal verification. HierSVA-SP pairs an RTL preprocessing toolchain with an LLM-in-the-loop formal verification flow to produce reference SystemVerilog Assertions (SVA) on hierarchical RTL. Applying it to BaseJump STL yields HierSVA-DS, a dataset of 342 modules, with hierarchy metadata and depths 0–9, accompanied by a deep subset of 28 module-bug pairs with natural-language specifications and bug variants. HierSVA-B decomposes assertion quality into six metric axes: syntax correctness, assertion proof success rate, vacuity, specification faithfulness, mutation coverage, and formal core coverage. Applying HierSVA-B to twelve recent LLMs reveals three findings. First, the module-level compile rate is 67.1\%; among generated assertions in evaluable runs, 82.1\% prove non-vacuously, but the corresponding assertion sets detect only 70.2\% of eligible injected faults and cover 36.2\% of the formal core. Second, on 211 evaluable model–module entries in the deep subset, assertion sets flag buggy RTL with 0.87 recall, but 40\% of predicted-buggy outcomes are false positives on correct RTL, limiting precision to 0.60. Third, agentic mode improves S1-style provability and strength metrics, but gains plateau and oscillate. Codes and artifacts are available at \href{https://github.com/HierSVAAnon/HierSVACodeAndArtifacts}{https://github.com/HierSVAAnon/HierSVACodeAndArtifacts}. Dataset is available at \href{https://huggingface.co/datasets/AnonymousHierSVA/HierSVA}{https://huggingface.co/datasets/AnonymousHierSVA/HierSVA}.

20.
arXiv (CS.CV) 2026-06-12

Bridging Modal Isolation in Interleaved Thinking: Supervising Modality Transitions via Stepwise Reinforcement

Interleaved thinking, where a unified multimodal model alternates between textual reasoning and visual generation, has shown promise on spatial and physical tasks. However, in complex long-chain scenarios, we identify a fundamental failure mode: generated images diverge from the textual context while subsequent text ignores the visual evidence, causing the two modalities to alternate without genuinely informing each other. We term this Modal Isolation and attribute it to compounding information loss at modality boundaries. We decompose each reasoning cycle into atomic operations and define modality transition loss, quantifying cross-modal hallucination (text-to-image) and visual utilization deficit (image-to-text) at each boundary. We propose MoTiF (Modality Tiransition Fidelity), a two-stage training framework that directly optimizes these transitions: Reflective SFT trains the model to detect and recover from erroneous visual outputs; Flow-GRPO improves image generation fidelity via reinforcement learning. All training signals in MoTiF derive from transition-level fidelity rather than end-task accuracy. Across four visual puzzle benchmarks, this transition-level supervision substantially improves both cross-modal coherence and final task accuracy. The results demonstrate that effective interleaved reasoning requires explicit structural supervision at modality boundaries, not merely scaling or end-task optimization.

21.
PLOS Computational Biology 2026-06-22

CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data

by Irene Creus-Martí, Andrés Moya, Francisco J. Santonja In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.

22.
arXiv (CS.AI) 2026-06-15

Universal Manipulation Exoskeleton: Learning Compliant Whole-body Policies with Real-time Torque Feedback

arXiv:2606.14218v1 Announce Type: cross Abstract: For robots to work safely in household environments, they need to be compliant and react to torque and force feedback during contact. However, the majority of existing data collection pipelines still lack the ability to capture force and torque data for learning active compliant policies. In this paper, we present Universal Manipulation Exoskeleton (UME), an upper-limb exoskeleton that provides real-time haptic torque feedback while recording whole-arm configurations and joint torque signals for teleoperation. With transparent torque feedback, human operators can even unsheathe kinematically constrained objects while blindfolded. UME is low-cost, lightweight, and portable. Equipped with an embedded IMU, it enables teleoperation for mobile manipulation. With our proposed universal retargeting algorithm, UME can teleoperate a range of robots, including the 7DoF OpenArm, 7DoF Franka, and 6DoF X-ARM. We demonstrate that this combination of capabilities enables learning bimanual, whole-body, and active compliant policies that operate effectively in highly constrained spaces. The learned robust autonomous policies achieve high success rates across a variety of tasks, including long-horizon mobile manipulation, force-mediated box flipping, visually occluded box pushing, and space-constrained tabletop manipulation. Videos, code, and additional information can be found at https://ume-exo.github.io.

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

GraspLLM: Towards Zero-Shot Generalization on Text-Attributed Graphs with LLMs

Research on Text-Attributed Graphs (TAGs) has gained significant attention recently due to its broad applications across various real-world data scenarios, such as citation networks, e-commerce platforms, social media, and web pages. Inspired by the remarkable semantic understanding ability of Large Language Models (LLMs), there have been numerous attempts to integrate LLMs into TAGs. However, existing methods still struggle to generalize across diverse graphs and tasks, and their ability to capture transferable graph structural patterns remains limited. To address this, we introduce the GraspLLM, a framework that combines Graph structural comprehension with semantic understanding prowess of LLMs to enhance the cross-dataset and cross-task generalizability. Specifically, we represent node texts from different graphs in a unified semantic space with a frozen general embedding model, on top of which we perform motif-aware contrastive learning across multiple motif-induced adjacency matrices to extract dataset-agnostic structural information. Then, with our proposed optimal contextual subgraph, we extract the most contextually relevant subgraph for each target node and align these subgraphs to the token space of LLM via an alignment projector. Extensive experiments on TAG benchmark datasets spanning diverse domains reveal that GraspLLM consistently outperforms previous LLM-based methods for TAGs, especially in zero-shot scenarios, highlighting its strong generalizability across different datasets and tasks. Our code is available at https://github.com/Heinz217/GraspLLM.

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

HyPE: Category-Aware Hypergraph Encoding with Persistent Edge Embeddings for Persona-Grounded Dialogue

Persona-grounded dialogue systems aim to produce responses consistent with a speaker's persona, yet existing methods treat personas as a flat set of sentences and fail to model the high-order relations among persona attributes-e.g., that several persona sentences share a topical category. We propose HyPE (Hypergraph Persona Encoder), a framework that (i) analyzes each persona-bearing text as a (Core, Expression, Sentiment, Category) quadruple, and (ii) organizes persona elements into a hypergraph whose hyperedges are induced by shared category labels. An HyperGCN hypergraph neural network propagates this structure into a persona summary vector and a soft-memory bank that condition the response generator. We further propose Persistent Edge Embeddings (PEE), lightweight per-category learnable priors fused into the HyperGCN message-passing step. On PersonaChat under greedy decoding, HyPE consistently outperforms sentence-level pooling baselines across GPT-2, LLaMA-3.2-3B, and Qwen2.5-3B backbones by demonstrating that structured hyperedge-level persona encoding provides a transferable advantage across model scales.

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

Skill-Constrained Model Predictive Control for Resilient Manufacturing Supply Chains

arXiv:2606.17269v1 Announce Type: new Abstract: In skill-constrained production-inventory systems, the qualified human capacity available tomorrow depends on training decisions made today: production requires certified workers, certifications decay unless maintained, and training consumes the same scarce worker hours that production needs now. We study a closed-loop skill-constrained model predictive controller that, at every shift, solves a finite-horizon mixed-integer program over production, inventory, backlog, and training, with binary predicted certification, hard production eligibility, and an interpretable terminal value that prices certified-capacity gaps at the horizon boundary; only the first-period action is applied before replanning. On synthetic, seed-controlled SkillChain-Gym scenarios - announced and surprise new-skill shocks, demand shocks, absenteeism, forecast- and availability-quality modes, capacity-boundary and training-rate sweeps, and negative controls - we evaluate the controller against production-only and maintenance-only ablations, static cross-training insurance plans, and a strong reactive heuristic, under an ex-ante locked configuration and paired statistics. The result is regime dependence, not superiority: no policy class dominates. Predictive control helps when skill or labor bottlenecks are forecastable early enough for training to complete; lean static insurance remains hard to beat under surprise shocks, near the demand-capacity boundary, and wherever pre-shock slack makes insurance cheap. Attribution ablations separate certification maintenance, re-acquisition of lapsed certifications, and greenfield skill acquisition. Forecastability, not adaptivity per se, decides when predictive control pays.