OpenRaiser/Intern-Atlas huggingface dataset:
SPHENIC: Topology-Aware Multi-View Clustering for Spatial Transcriptomics
Venue: arXiv cs.LG 2026
Year: 2026

Spatial transcriptomics clustering is pivotal for identifying cell subpopulations by leveraging spatial location information. While recent graph-based methods modeling cell-cell interactions have improved clustering accuracy, they remain limited in two key aspects: (i) reliance on local aggregation in static graphs often fails to capture robust global topological structures (e.g., loops and voids) and is vulnerable to noisy edges; and (ii) dimensionality reduction techniques frequently neglect spatial coherence, causing physically adjacent spots to be erroneously separated in the latent space. To overcome these challenges, we propose SPHENIC, a Spatial Persistent Homology-Enhanced Neighborhood Integrative Clustering method. Specifically, it explicitly incorporates topology-invariant features into the clustering network to ensure robust representation learning against noise. Furthermore, we design a dual-regularized optimization module that imposes spatial constraints alongside distributional optimization, ensuring that the embedding space preserves the physical proximity of cells. Extensive experiments on 11 benchmark datasets demonstrate that SPHENIC outperforms state-of-the-art methods by 4.19%-9.14%, validating its superiority in characterizing complex tissue architectures.
Generating Compilers for Qubit Mapping and Routing
Venue: arXiv cs.PL 2026
Year: 2026

To evaluate a quantum circuit on a quantum processor, one must find a mapping from circuit qubits to processor qubits and plan the instruction execution while satisfying the processor's constraints. This is known as the qubit mapping and routing (QMR) problem. High-quality QMR solutions are key to maximizing the utility of scarce quantum resources and minimizing the probability of logical errors affecting computation. The challenge is that the landscape of quantum processors is incredibly diverse and fast-evolving. Given this diversity, dozens of papers have addressed the QMR problem for different qubit hardware, connectivity constraints, and quantum error correction schemes by a developing a new algorithm for a particular context. We present an alternative approach: automatically generating qubit mapping and routing compilers for arbitrary quantum processors. Though each QMR problem is different, we identify a common core structure-device state machine-that we use to formulate an abstract QMR problem. Our formulation naturally leads to a compact domain-specific language for specifying QMR problems and a powerful parametric algorithm that can be instantiated for any QMR specification. Our thorough evaluation on case studies of important QMR problems shows that generated compilers are competitive with handwritten, specialized compilers in terms of runtime and solution quality.
Zono-Conformal Prediction: Zonotope-Based Uncertainty Quantification for Regression and Classification Tasks
Venue: arXiv cs.LG 2026
Year: 2026

Conformal prediction is a popular uncertainty quantification method that augments a base predictor to return sets of predictions with statistically valid coverage guarantees. However, current methods are often computationally expensive and data-intensive, as they require constructing an uncertainty model before calibration. Moreover, existing approaches typically represent the prediction sets with intervals, which limits their ability to capture dependencies in multi-dimensional outputs. We address these limitations by introducing zono-conformal prediction, a novel approach inspired by interval predictor models and reachset-conformant identification that constructs prediction zonotopes with assured coverage. By placing zonotopic uncertainty sets directly into the model of the base predictor, zono-conformal predictors can be identified via a single, data-efficient linear program. While we can apply zono-conformal prediction to arbitrary nonlinear base predictors, we focus on feed-forward neural networks in this work. Aside from regression tasks, we also construct optimal zono-conformal predictors in classification settings where the output of an uncertain predictor is a set of possible classes. We provide probabilistic coverage guarantees and present methods for detecting outliers in the identification data. In extensive numerical experiments, we show that zono-conformal predictors are less conservative than interval predictor models and standard conformal prediction methods, while achieving a similar coverage over the test data.
Aligning the Spectrum: Hybrid Graph Pre-training and Prompt Tuning across Homophily and Heterophily
Venue: arXiv cs.LG 2026
Year: 2026

Graph ``pre-training and prompt-tuning'' aligns downstream tasks with pre-trained objectives to enable efficient knowledge transfer under limited supervision. However, current methods typically rely on single-filter backbones (e.g., low-pass), whereas real-world graphs exhibit inherent spectral diversity. Our theoretical \textit{Spectral Specificity} principle reveals that effective knowledge transfer requires alignment between pre-trained spectral filters and the intrinsic spectrum of downstream graphs. This identifies two fundamental limitations: (1) Knowledge Bottleneck: single-filter models suffer from irreversible information loss by suppressing signals from other frequency bands (e.g., high-frequency); (2) Utilization Bottleneck: spectral mismatches between pre-trained filters and downstream spectra lead to significant underutilization of pre-trained knowledge. To bridge this gap, we propose HS-GPPT. We utilize a hybrid spectral backbone to construct an abundant knowledge basis. Crucially, we introduce Spectral-Aligned Prompt Tuning to actively align the downstream graph's spectrum with diverse pre-trained filters, facilitating comprehensive knowledge utilization across both homophily and heterophily. Extensive experiments validate the effectiveness under both transductive and inductive learning settings.
Calibrated and uncertain? Evaluating uncertainty estimates in binary classification models
Venue: arXiv cs.LG 2026
Year: 2026

Rigorous statistical methods, including parameter estimation with accompanying uncertainties, underpin the validity of scientific discovery, especially in the natural sciences. With increasingly complex data models such as deep learning techniques, uncertainty quantification has become exceedingly difficult and a plethora of techniques have been proposed. In this case study, we use the unifying framework of approximate Bayesian inference combined with empirical tests on carefully created synthetic classification datasets to investigate qualitative properties of six different probabilistic machine learning algorithms for class probability and uncertainty estimation: (i) a neural network ensemble, (ii) neural network ensemble with conflictual loss, (iii) evidential deep learning, (iv) a single neural network with Monte Carlo Dropout, (v) Gaussian process classification and (vi) a Dirichlet process mixture model. We check if the algorithms produce uncertainty estimates which reflect commonly desired properties, such as being well calibrated and exhibiting an increase in uncertainty for out-of-distribution data points. Our results indicate that all algorithms show reasonably good calibration performance on our synthetic test sets, but none of the deep learning based algorithms provide uncertainties that consistently reflect lack of experimental evidence for out-of-distribution data points. We hope our study may serve as a clarifying example for researchers that are using or developing methods of uncertainty estimation for scientific data-driven modeling and analysis.
Guided Perturbation Sensitivity (GPS): Detecting Adversarial Text via Embedding Stability and Word Importance
Venue: arXiv cs.LG 2026
Year: 2026

Adversarial text attacks remain a persistent threat to transformer models, yet existing defenses are typically attack-specific or require costly model retraining, leaving a gap for attack-agnostic detection. We introduce Guided Perturbation Sensitivity (GPS), a detection framework that identifies adversarial examples by measuring how embedding representations change when important words are masked. GPS first ranks words using importance heuristics, then measures embedding sensitivity to masking top-k critical words, and processes the resulting patterns with a BiLSTM detector. Experiments show that adversarially perturbed words exhibit disproportionately high masking sensitivity compared to naturally important words. Across three datasets, three attack types, and two victim models, GPS achieves over 85% detection accuracy and demonstrates competitive performance compared to existing state-of-the-art methods, often at lower computational cost. Using Normalized Discounted Cumulative Gain (NDCG) to measure perturbation identification quality, we demonstrate that gradient-based ranking significantly outperforms attention, hybrid, and random selection approaches, with identification quality strongly correlating with detection performance for word-level attacks ($ρ= 0.65$). GPS generalizes to unseen datasets, attacks, and models without retraining, providing a practical solution for adversarial text detection.
Collaborative Learning-Enhanced Lightweight Models for Predicting Arterial Blood Pressure Waveform in a Large-scale Perioperative Dataset
Venue: arXiv cs.LG 2026
Year: 2026

Noninvasive arterial blood pressure (ABP) monitoring is essential for patient management in critical care and perioperative settings, providing continuous assessment of cardiovascular hemodynamics with minimal risks. Numerous deep learning models have developed to reconstruct ABP waveform from noninvasively acquired physiological signals such as electrocardiogram and photoplethysmogram. However, limited research has addressed the issue of model performance and computational load for deployment on embedded systems. The study introduces a lightweight sInvResUNet, along with a collaborative learning scheme named KDCL_sInvResUNet. With only 0.89 million parameters and a computational load of 0.02 GFLOPS, real-time ABP estimation was successfully achieved on embedded devices with an inference time of just 8.49 milliseconds for a 10-second output. We performed subject-independent validation in a large-scale and heterogeneous perioperative dataset containing 1,257,141 data segments from 2,154 patients, with a wide BP range (41-257 mmHg for SBP, and 31-234 mmHg for DBP). The proposed KDCL_sInvResUNet achieved lightly better performance compared to large models, with a mean absolute error of 10.06 mmHg and mean Pearson correlation of 0.88 in tracking ABP changes. Despite these promising results, all deep learning models showed significant performance variations across different demographic and cardiovascular conditions, highlighting their limited ability to generalize across such a broad and diverse population. This study lays a foundation work for real-time, unobtrusive ABP monitoring in real-world perioperative settings, providing baseline for future advancements in this area.
Mutually Assured Deregulation
Venue: arXiv cs.CY 2026
Year: 2026

We have convinced ourselves that the way to make AI safe is to make it unsafe. Since 2022, policymakers worldwide have embraced the Regulation Sacrifice - the belief that dismantling safety oversight will deliver security through AI dominance. Fearing China or USA will gain advantage, nations rush to eliminate safeguards that might slow progress. This Essay reveals the fatal flaw: though AI poses national security challenges, the solution demands stronger regulatory frameworks, not weaker ones. A race without guardrails breeds shared danger, not competitive strength. The Regulation Sacrifice makes three false promises. First, it promises durable technological leads. But AI capabilities spread rapidly - performance gaps between U.S. and Chinese systems collapsed from 9 percent to 2 percent in thirteen months. When advantages evaporate in months, sacrificing permanent safety for temporary speed makes no sense. Second, it promises deregulation accelerates innovation. The opposite often proves true. Companies report well-designed governance streamlines development. Investment flows toward regulated markets. Clear rules reduce uncertainty; uncertain liability creates paralysis. Environmental standards did not kill the auto industry; they created Tesla and BYD. Third, enhanced national security through deregulation actually undermines security across all timeframes. Near term: it hands adversaries information warfare tools. Medium term: it democratizes bioweapon capabilities. Long term: it guarantees deployment of uncontrollable AGI systems. The Regulation Sacrifice persists because it serves powerful interests, not security. Tech companies prefer freedom to accountability. Politicians prefer simple stories to complex truths. This creates mutually assured deregulation, where each nation's sprint for advantage guarantees collective vulnerability. The only way to win is not to play.
Constructing 3D Rotational Invariance and Equivariance with Symmetric Tensor Networks
Venue: arXiv cs.LG 2026
Year: 2026

Symmetry-aware architectures are central to geometric deep learning. We present a systematic approach for constructing continuous rotationally invariant and equivariant functions using symmetric tensor networks. The proposed framework supports inputs and outputs given as a tuple of Cartesian tensors of different rank as well as spherical tensors of different type. We introduce tensor network generators for invariant maps and obtain equivariant maps via differentiation. Specifically, we derive general continuous equivariant maps from vector inputs to Cartesian or spherical tensor output. Finally, we clarify how common equivariant primitives in geometric graph neural networks arise within our construction.
Ensured Energy: How a Serious Game can Reach and Engage Diverse Societal Groups in Swiss Energy Transition
Venue: arXiv cs.CE 2026
Year: 2026

In support of Switzerland's energy and climate strategy for 2050, researchers investigate scenarios for the transition of energy systems towards a higher share of renewables, assessing their social, environmental and economic impact. Their results guide stakeholders and policy makers in designing resilient and sustainable systems. A crucial condition to successfully implement these solution in the real-world is that the population supports these transitions. Social scientists have identified the high complexity of energy systems and energy policy as one reason why popular support for the implementation of the energy transition is often limited. This paper proposes serious gaming as a novel approach to inform and sensitize a broader public for the transition of the energy system in Switzerland. We motivate and describe the design of an online game in which players experience an accurate simulation of current and future energy provision and manage transition towards a sustainable future. We present the embedding of this serious game into a large-scale population survey and report findings on player characteristics and engagement. We show that a serious game can successfully attract participants from diverse societal groups and highlight the challenge of balancing complexity and entertainment.
Empirical Analysis of Decoding Biases in Masked Diffusion Models
Venue: arXiv cs.AI 2026
Year: 2026

Masked diffusion models (MDMs), which leverage bidirectional attention and a denoising process, are narrowing the performance gap with autoregressive models (ARMs). However, their internal attention mechanisms remain under-explored. This paper investigates the attention behaviors in MDMs, revealing the phenomenon of Attention Floating. Unlike ARMs, where attention converges to a fixed sink, MDMs exhibit dynamic, dispersed attention anchors that shift across denoising steps and layers. Further analysis reveals its Shallow Structure-Aware, Deep Content-Focused attention mechanism: shallow layers utilize floating tokens to build a global structural framework, while deeper layers allocate more capability toward capturing semantic content. Empirically, this distinctive attention pattern provides a mechanistic explanation for the strong in-context learning capabilities of MDMs, allowing them to double the performance compared to ARMs in knowledge-intensive tasks. All codes are available at https://github.com/NEUIR/Uncode.
Improving Detection of Watermarked Language Models
Venue: arXiv cs.CL 2026
Year: 2026

Watermarking has recently emerged as an effective strategy for detecting the generations of large language models (LLMs). The strength of a watermark typically depends strongly on the entropy afforded by the language model and the set of input prompts. However, entropy can be quite limited in practice, especially for models that are post-trained, for example via instruction tuning or reinforcement learning from human feedback (RLHF), which makes detection based on watermarking alone challenging. In this work, we investigate whether detection can be improved by combining watermark detectors with non-watermark ones. We explore a number of hybrid schemes that combine the two, observing performance gains over either class of detector under a wide range of experimental conditions.
OrbitChain: Orchestrating In-orbit Real-time Analytics of Earth Observation Data
Venue: arXiv cs.DC 2026
Year: 2026

Earth observation analytics have the potential to transform many sectors. However, due to limited ground connections, it currently takes hours to days to download and analyze Earth observation data, diminishing the value of data for time-sensitive applications like disaster monitoring or search-and-rescue. To enable real-time analytics, we propose OrbitChain, an in-orbit multi-satellite Earth analytics framework. OrbitChain uses a pipelined design to decompose workflows into analytics functions, and orchestrates constellation-wide resources to finish real-time analytics tasks. It provides timely insights to Earth sensing applications and enables advanced workflows like in-orbit tip-and-cue. Hardware-in-the-loop experiments show that OrbitChain can deliver analytics results in minutes, supports up to 60% more analytics workload than existing frameworks, and reduces inter-satellite communication overhead by up to 45%.
CASPER: Concept-integrated Sparse Representation for Scientific Retrieval
Venue: arXiv cs.IR 2026
Year: 2026

Identifying relevant research concepts is crucial for effective scientific search. However, primary sparse retrieval methods often lack concept-aware representations. To address this, we propose CASPER, a sparse retrieval model for scientific search that utilizes both tokens and keyphrases as representation units (i.e., dimensions in the sparse embedding space). This enables CASPER to represent queries and documents via research concepts and match them at both granular and conceptual levels. Furthermore, we construct training data by leveraging abundant scholarly references (including titles, citation contexts, author-assigned keyphrases, and co-citations), which capture how research concepts are expressed in diverse settings. Empirically, CASPER outperforms strong dense and sparse retrieval baselines across eight scientific retrieval benchmarks. We also explore the effectiveness-efficiency trade-off via representation pruning and demonstrate CASPER's interpretability by showing that it can serve as an effective and efficient keyphrase generation model.
MAVIS: Multi-Objective Alignment via Inference-Time Value-Guided Selection
Venue: arXiv cs.LG 2026
Year: 2026

Large Language Models (LLMs) are increasingly deployed across diverse applications that demand balancing multiple, often conflicting, objectives -- such as helpfulness, harmlessness, or humor. Many traditional methods for aligning outputs to user-specific preferences require fine-tuning models for each objective or for specific preference configurations, which is computationally expensive and inflexible. We introduce \textbf{MAVIS} -- \textit{Multi-Objective Alignment via Inference-Time Value-Guided Selection} -- a lightweight inference-time alignment framework that enables dynamic control over LLM behavior without modifying the base model's weights. MAVIS trains a set of small value models, each corresponding to a distinct objective. At inference time, these value models are combined using user-specified weights to produce a tilting function that adjusts the base model's output distribution toward desired trade-offs. The value models are trained using a simple iterative algorithm that enables monotonic improvement of the KL-regularized policy. We show empirically that MAVIS achieves a superior pareto front compared to baselines which fine-tune per-objective models and combine them post hoc or train a single preference-conditioned value model for guidance. Our code is available at https://github.com/5-Jeremy/MAVIS/tree/main.
Virtuous Machines: Towards Artificial General Science
Venue: arXiv cs.AI 2026
Year: 2026

Artificial intelligence systems are transforming scientific discovery by accelerating specific research tasks, from protein structure prediction to materials design, yet remain confined to narrow domains requiring substantial human oversight. The exponential growth of scientific literature and increasing domain specialisation constrain researchers' capacity to synthesise knowledge across disciplines and develop unifying theories, motivating exploration of more general-purpose AI systems for science. Here we show that a domain-agnostic, agentic AI Scientist system can independently navigate the scientific workflow - from hypothesis generation through data collection to manuscript preparation. The system autonomously designed and executed three psychological studies on visual working memory, mental rotation, and imagery vividness, executed one new online data collection with 288 participants, developed analysis pipelines through 8-hour+ continuous coding sessions, and produced completed manuscripts. The results demonstrate the capability of AI scientific discovery pipelines to conduct non-trivial research with theoretical reasoning and methodological rigour comparable to experienced researchers, though with limitations in conceptual nuance and theoretical interpretation. This is a step toward embodied AI that can test hypotheses through real-world experiments, accelerating discovery by autonomously exploring regions of scientific space that human cognitive and resource constraints might otherwise leave unexplored. It raises important questions about the nature of scientific understanding and the attribution of scientific credit.
A Three-Level Whole-Body Disturbance Rejection Control Framework for Dynamic Motions in Legged Robots
Venue: arXiv cs.RO 2026
Year: 2026

This paper presents a control framework designed to enhance the stability and robustness of legged robots in the presence of uncertainties, including model uncertainties, external disturbances, and faults. The framework enables the full-state feedback estimator to estimate and compensate for uncertainties in the whole-body dynamics of the legged robots. First, we propose a novel moving horizon extended state observer (MH-ESO) to estimate uncertainties and mitigate noise in legged systems, which can be integrated into the framework for disturbance compensation. Second, we introduce a three-level whole-body disturbance rejection control framework (T-WB-DRC). Unlike the previous two-level approach, this three-level framework considers both the plan based on whole-body dynamics without uncertainties and the plan based on dynamics with uncertainties, significantly improving payload transportation, external disturbance rejection, and fault tolerance. Third, simulations of both humanoid and quadruped robots in the Gazebo simulator demonstrate the effectiveness and versatility of T-WB-DRC. Finally, extensive experimental trials on a quadruped robot validate the robustness and stability of the system when using T-WB-DRC under various disturbance conditions.