Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with noisy data, limited scalability, and inadequate modelling of complex cellular relationships. We present SemanticST, a biologically informed, graph-based deep learning framework that models diverse cellular contexts through multi-semantic graph construction. SemanticST builds multiple context-specific graphs capturing spatial proximity, gene expression similarity, and tissue domain structure, and learns disentangled embeddings for each. These are fused using an attention-inspired strategy to yield a unified, biologically meaningful representation. A community-aware min-cut loss improves robustness over contrastive learning, particularly in sparse ST data. SemanticST supports mini-batch training, making it the first graph neural network scalable to large-scale datasets such as Xenium (500,000 cells). Benchmarking across four platforms (Visium, Slide-seq, Stereo-seq, Xenium) and multiple human and mouse tissues shows consistent 20 percentage gains in ARI, NMI, and trajectory fidelity over DeepST, GraphST, and IRIS. In re-analysis of breast cancer Xenium data, SemanticST revealed rare and clinically significant niches, including triple receptor-positive clusters, spatially distinct DCIS-to-IDC transition zones, and FOXC2 tumour-associated myoepithelial cells, suggesting non-canonical EMT programs with stem-like features. SemanticST thus provides a scalable, interpretable, and biologically grounded framework for spatial transcriptomics analysis, enabling robust discovery across tissue types and diseases, and paving the way for spatially resolved tissue atlases and next-generation precision medicine.
We propose a novel nonparametric regression method that models complex input-output relationships as the sum of convex and concave components. The method-Identifiable Convex-Concave Nonparametric Least Squares (ICCNLS)-decomposes the target function into additive shape-constrained components, each represented via sub-gradient-constrained affine functions. To address the affine ambiguity inherent in convex-concave decompositions, we introduce global statistical orthogonality constraints, ensuring that residuals are uncorrelated with both intercept and input variables. This enforces decomposition identifiability and improves interpretability. We further incorporate L1, L2 and elastic net regularisation on sub-gradients to enhance generalisation and promote structural sparsity. The proposed method is evaluated on synthetic and real-world datasets, including healthcare pricing data, and demonstrates improved predictive accuracy and model simplicity compared to conventional CNLS and difference-of-convex (DC) regression approaches. Our results show that statistical identifiability, when paired with convex-concave structure and sub-gradient regularisation, yields interpretable models suited for forecasting, benchmarking, and policy evaluation.
Hematoxylin and Eosin (H&E) has been the gold standard in tissue analysis for decades, however, tissue specimens stained in different laboratories vary, often significantly, in appearance. This variation poses a challenge for both pathologists' and AI-based downstream analysis. Minimizing stain variation computationally is an active area of research. To further investigate this problem, we collected a unique multi-center tissue image dataset, wherein tissue samples from colon, kidney, and skin tissue blocks were distributed to 66 different labs for routine H&E staining. To isolate staining variation, other factors affecting the tissue appearance were kept constant. Further, we used this tissue image dataset to compare the performance of eight different stain normalization methods, including four traditional methods, namely, histogram matching, Macenko, Vahadane, and Reinhard normalization, and two deep learning-based methods namely CycleGAN and Pixp2pix, both with two variants each. We used both quantitative and qualitative evaluation to assess the performance of these methods. The dataset's inter-laboratory staining variation could also guide strategies to improve model generalizability through varied training data
Comprehensive evaluation of geospatial foundation models (Geo-FMs) requires benchmarking across diverse tasks, sensors, and geographic regions. However, most existing benchmark datasets are limited to segmentation or classification tasks, and focus on specific geographic areas. To address this gap, we introduce a globally distributed dataset for forest aboveground biomass (AGB) estimation, a pixel-wise regression task. This benchmark dataset combines co-located hyperspectral imagery (HSI) from the Environmental Mapping and Analysis Program (EnMAP) satellite and predictions of AGB density estimates derived from the Global Ecosystem Dynamics Investigation lidars, covering seven continental regions. Our experimental results on this dataset demonstrate that the evaluated Geo-FMs can match or, in some cases, surpass the performance of a baseline U-Net, especially when fine-tuning the encoder. We also find that the performance difference between the U-Net and Geo-FMs depends on the dataset size for each region and highlight the importance of the token patch size in the Vision Transformer backbone for accurate predictions in pixel-wise regression tasks. By releasing this globally distributed hyperspectral benchmark dataset, we aim to facilitate the development and evaluation of Geo-FMs for HSI applications. Leveraging this dataset additionally enables research into geographic bias and generalization capacity of Geo-FMs. The dataset and source code will be made publicly available.
Anomaly detection has been widely studied in the context of industrial defect inspection, with numerous methods developed to tackle a range of challenges. In digital pathology, anomaly detection holds significant potential for applications such as rare disease identification, artifact detection, and biomarker discovery. However, the unique characteristics of pathology images, such as their large size, multi-scale structures, stain variability, and repetitive patterns, introduce new challenges that current anomaly detection algorithms struggle to address. In this quantitative study, we benchmark over 20 classical and prevalent anomaly detection methods through extensive experiments. We curated five digital pathology datasets, both real and synthetic, to systematically evaluate these approaches. Our experiments investigate the influence of image scale, anomaly pattern types, and training epoch selection strategies on detection performance. The results provide a detailed comparison of each method's strengths and limitations, establishing a comprehensive benchmark to guide future research in anomaly detection for digital pathology images.
Artificial intelligence (AI) has become a powerful tool for economic research, enabling large-scale simulation and policy optimization. However, applying AI effectively requires simulation platforms for scalable training and evaluation-yet existing environments remain limited to simplified, narrowly scoped tasks, falling short of capturing complex economic challenges such as demographic shifts, multi-government coordination, and large-scale agent interactions. To address this gap, we introduce EconGym, a scalable and modular testbed that connects diverse economic tasks with AI algorithms. Grounded in rigorous economic modeling, EconGym implements 11 heterogeneous role types (e.g., households, firms, banks, governments), their interaction mechanisms, and agent models with well-defined observations, actions, and rewards. Users can flexibly compose economic roles with diverse agent algorithms to simulate rich multi-agent trajectories across 25+ economic tasks for AI-driven policy learning and analysis. Experiments show that EconGym supports diverse and cross-domain tasks-such as coordinating fiscal, pension, and monetary policies-and enables benchmarking across AI, economic methods, and hybrids. Results indicate that richer task composition and algorithm diversity expand the policy space, while AI agents guided by classical economic methods perform best in complex settings. EconGym also scales to 10k agents with high realism and efficiency.
The cross-Modality Domain Adaptation (crossMoDA) challenge series, initiated in 2021 in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), focuses on unsupervised cross-modality segmentation, learning from contrast-enhanced T1 (ceT1) and transferring to T2 MRI. The task is an extreme example of domain shift chosen to serve as a meaningful and illustrative benchmark. From a clinical application perspective, it aims to automate Vestibular Schwannoma (VS) and cochlea segmentation on T2 scans for more cost-effective VS management. Over time, the challenge objectives have evolved to enhance its clinical relevance. The challenge evolved from using single-institutional data and basic segmentation in 2021 to incorporating multi-institutional data and Koos grading in 2022, and by 2023, it included heterogeneous routine data and sub-segmentation of intra- and extra-meatal tumour components. In this work, we report the findings of the 2022 and 2023 editions and perform a retrospective analysis of the challenge progression over the years. The observations from the successive challenge contributions indicate that the number of outliers decreases with an expanding dataset. This is notable since the diversity of scanning protocols of the datasets concurrently increased. The winning approach of the 2023 edition reduced the number of outliers on the 2021 and 2022 testing data, demonstrating how increased data heterogeneity can enhance segmentation performance even on homogeneous data. However, the cochlea Dice score declined in 2023, likely due to the added complexity from tumour sub-annotations affecting overall segmentation performance. While progress is still needed for clinically acceptable VS segmentation, the plateauing performance suggests that a more challenging cross-modal task may better serve future benchmarking.
Quantitative Structure-Activity Relationship (QSAR) modeling is a cornerstone of computational drug discovery. This research demonstrates the successful application of a Quantum Multiple Kernel Learning (QMKL) framework to enhance QSAR classification, showing a notable performance improvement over classical methods. We apply this methodology to a dataset for identifying DYRK1A kinase inhibitors. The workflow involves converting SMILES representations into numerical molecular descriptors, reducing dimensionality via Principal Component Analysis (PCA), and employing a Support Vector Machine (SVM) trained on an optimized combination of multiple quantum and classical kernels. By benchmarking the QMKL-SVM against a classical Gradient Boosting model, we show that the quantum-enhanced approach achieves a superior AUC score, highlighting its potential to provide a quantum advantage in challenging cheminformatics classification tasks.
This paper presents a Model-Inspired Distributionally Robust Data-enabled Predictive Control (MDR-DeePC) framework for systems with partially known and uncertain dynamics. The proposed method integrates model-based equality constraints for known dynamics with a Hankel matrix-based representation of unknown dynamics. A distributionally robust optimization problem is formulated to account for parametric uncertainty and stochastic disturbances. Simulation results on a triple-mass-spring-damper system demonstrate improved disturbance rejection, reduced output oscillations, and lower control cost compared to standard DeePC. The results validate the robustness and effectiveness of MDR-DeePC, with potential for real-time implementation pending further benchmarking.
A sustainable electricity infrastructure requires the explicit integration of carbon emissions into power system modeling and optimization paradigms. However, existing open-source datasets for power system R&D lack generator-level carbon emission profiling, limiting the ability to benchmark and compare various carbon-aware grid operational strategies. To address this gap, this work introduces PGLib-CO2, an open-source extension to the widely adopted PGLib-OPF test case library. PGLib-CO2 enriches standard network cases with CO2 and CO2-equivalent emission intensity factors by expanding the fuel-type categorization used by PGLib-OPF, attaining a realistic generator-level carbon profiling. It is also packaged for both Python's pandapower and Julia's PowerModels.jl, for a seamless, user-friendly integration of emission modeling into grid computation and optimization tasks. The dataset produced by PGLib-CO2 can support grid-based carbon accounting, emission metric evaluation, and integration into AC optimal power flow (OPF) and optimal load shifting (OLS) formulations. We demonstrate PGLib-CO2's utility through case studies that quantify cost-emission trade-offs and optimize a carbon-aware objective function. By standardizing carbon-enhanced test cases, PGLib-CO2 provides an open-source, reproducible foundation for benchmarking carbon-aware computation, facilitating future research in sustainable power system operation.
Recent advancements have brought generated music closer to human-created compositions, yet evaluating these models remains challenging. While human preference is the gold standard for assessing quality, translating these subjective judgments into objective metrics, particularly for text-audio alignment and music quality, has proven difficult. In this work, we generate 6k songs using 12 state-of-the-art models and conduct a survey of 15k pairwise audio comparisons with 2.5k human participants to evaluate the correlation between human preferences and widely used metrics. To the best of our knowledge, this work is the first to rank current state-of-the-art music generation models and metrics based on human preference. To further the field of subjective metric evaluation, we provide open access to our dataset of generated music and human evaluations.
In modern speech synthesis, paralinguistic information--such as a speaker's vocal timbre, emotional state, and dynamic prosody--plays a critical role in conveying nuance beyond mere semantics. Traditional Text-to-Speech (TTS) systems rely on fixed style labels or inserting a speech prompt to control these cues, which severely limits flexibility. Recent attempts seek to employ natural-language instructions to modulate paralinguistic features, substantially improving the generalization of instruction-driven TTS models. Although many TTS systems now support customized synthesis via textual description, their actual ability to interpret and execute complex instructions remains largely unexplored. In addition, there is still a shortage of high-quality benchmarks and automated evaluation metrics specifically designed for instruction-based TTS, which hinders accurate assessment and iterative optimization of these models. To address these limitations, we introduce InstructTTSEval, a benchmark for measuring the capability of complex natural-language style control. We introduce three tasks, namely Acoustic-Parameter Specification, Descriptive-Style Directive, and Role-Play, including English and Chinese subsets, each with 1k test cases (6k in total) paired with reference audio. We leverage Gemini as an automatic judge to assess their instruction-following abilities. Our evaluation of accessible instruction-following TTS systems highlights substantial room for further improvement. We anticipate that InstructTTSEval will drive progress toward more powerful, flexible, and accurate instruction-following TTS.
Learning-based control approaches like reinforcement learning (RL) have recently produced a slew of impressive results for tasks like quadrotor trajectory tracking and drone racing. Naturally, it is common to demonstrate the advantages of these new controllers against established methods like analytical controllers. We observe, however, that reliably comparing the performance of such very different classes of controllers is more complicated than might appear at first sight. As a case study, we take up the problem of agile tracking of an end-effector for a quadrotor with a fixed arm. We develop a set of best practices for synthesizing the best-in-class RL and geometric controllers (GC) for benchmarking. In the process, we resolve widespread RL-favoring biases in prior studies that provide asymmetric access to: (1) the task definition, in the form of an objective function, (2) representative datasets, for parameter optimization, and (3) feedforward information, describing the desired future trajectory. The resulting findings are the following: our improvements to the experimental protocol for comparing learned and classical controllers are critical, and each of the above asymmetries can yield misleading conclusions. Prior works have claimed that RL outperforms GC, but we find the gaps between the two controller classes are much smaller than previously published when accounting for symmetric comparisons. Geometric control achieves lower steady-state error than RL, while RL has better transient performance, resulting in GC performing better in relatively slow or less agile tasks, but RL performing better when greater agility is required. Finally, we open-source implementations of geometric and RL controllers for these aerial vehicles, implementing best practices for future development. Website and code is available at https://pratikkunapuli.github.io/rl-vs-gc/
High-dimensional image data often require dimensionality reduction before further analysis. This paper provides a purely analytical comparison of two linear techniques-Principal Component Analysis (PCA) and Singular Value Decomposition (SVD). After the derivation of each algorithm from first principles, we assess their interpretability, numerical stability, and suitability for differing matrix shapes. We synthesize rule-of-thumb guidelines for choosing one out of the two algorithms without empirical benchmarking, building on classical and recent numerical literature. Limitations and directions for future experimental work are outlined at the end.
Generative AI is being leveraged to solve a variety of computer-use tasks involving desktop applications. State-of-the-art systems have focused solely on improving accuracy on leading benchmarks. However, these systems are practically unusable due to extremely high end-to-end latency (e.g., tens of minutes) for tasks that typically take humans just a few minutes to complete. To understand the cause behind this and to guide future developments of computer agents, we conduct the first study on the temporal performance of computer-use agents on OSWorld, the flagship benchmark in computer-use AI. We find that large model calls for planning and reflection account for the majority of the overall latency, and as an agent uses more steps to complete a task, each successive step can take 3x longer than steps at the beginning of a task. We then construct OSWorld-Human, a manually annotated version of the original OSWorld dataset that contains a human-determined trajectory for each task. We evaluate 16 agents on their efficiency using OSWorld-Human and found that even the highest-scoring agents on OSWorld take 1.4-2.7x more steps than necessary.
Human-Object Interaction (HOI) detection has seen substantial advances in recent years. However, existing works focus on the standard setting with ideal images and natural distribution, far from practical scenarios with inevitable distribution shifts. This hampers the practical applicability of HOI detection. In this work, we investigate this issue by benchmarking, analyzing, and enhancing the robustness of HOI detection models under various distribution shifts. We start by proposing a novel automated approach to create the first robustness evaluation benchmark for HOI detection. Subsequently, we evaluate more than 40 existing HOI detection models on this benchmark, showing their insufficiency, analyzing the features of different frameworks, and discussing how the robustness in HOI is different from other tasks. With the insights from such analyses, we propose to improve the robustness of HOI detection methods through: (1) a cross-domain data augmentation integrated with mixup, and (2) a feature fusion strategy with frozen vision foundation models. Both are simple, plug-and-play, and applicable to various methods. Our experimental results demonstrate that the proposed approach significantly increases the robustness of various methods, with benefits on standard benchmarks, too. The dataset and code will be released.
The rapid growth of AI, data-intensive science, and digital twin technologies has driven an unprecedented demand for high-performance computing (HPC) across the research ecosystem. While national laboratories and industrial hyperscalers have invested heavily in exascale and GPU-centric architectures, university-operated HPC systems remain comparatively under-resourced. This survey presents a comprehensive assessment of the HPC landscape across U.S. universities, benchmarking their capabilities against Department of Energy (DOE) leadership-class systems and industrial AI infrastructures. We examine over 50 premier research institutions, analyzing compute capacity, architectural design, governance models, and energy efficiency. Our findings reveal that university clusters, though vital for academic research, exhibit significantly lower growth trajectories (CAGR $\approx$ 18%) than their national ($\approx$ 43%) and industrial ($\approx$ 78%) counterparts. The increasing skew toward GPU-dense AI workloads has widened the capability gap, highlighting the need for federated computing, idle-GPU harvesting, and cost-sharing models. We also identify emerging paradigms, such as decentralized reinforcement learning, as promising opportunities for democratizing AI training within campus environments. Ultimately, this work provides actionable insights for academic leaders, funding agencies, and technology partners to ensure more equitable and sustainable HPC access in support of national research priorities.
The recent shift in Generative AI (GenAI) applications from cloud-only environments to end-user devices introduces new challenges in resource management, system efficiency, and user experience. This paper presents ConsumerBench, a comprehensive benchmarking framework designed to evaluate the system efficiency and response time of GenAI models running on end-user devices. Unlike existing benchmarks that assume exclusive model access on dedicated GPUs, ConsumerBench simulates realistic multi-application scenarios executing concurrently on constrained hardware. Furthermore, ConsumerBench supports customizable workflows that simulate complex tasks requiring coordination among multiple applications. ConsumerBench captures both application-level metrics, including latency and Service Level Objective (SLO) attainment, and system-level metrics like CPU/GPU utilization and memory bandwidth. Through extensive experiments, ConsumerBench reveals inefficiencies in resource sharing, unfair scheduling under greedy allocation, and performance pitfalls of static model server configurations. The paper also provides practical insights for model developers and system designers, highlighting the benefits of custom kernels tailored to consumer-grade GPU architectures and the value of implementing SLO-aware scheduling strategies.
Face swapping manipulations in video streams represents an increasing threat in remote video communications, due to advances in automated and real-time tools. Recent literature proposes to characterize and exploit visual artifacts introduced in video frames by swapping algorithms when dealing with challenging physical scenes, such as face occlusions. This paper investigates the effectiveness of this approach by benchmarking CNN-based data-driven models on two data corpora (including a newly collected one) and analyzing generalization capabilities with respect to different acquisition sources and swapping algorithms. The results confirm excellent performance of general-purpose CNN architectures when operating within the same data source, but a significant difficulty in robustly characterizing occlusion-based visual cues across datasets. This highlights the need for specialized detection strategies to deal with such artifacts.
Prescriptive Process Monitoring (PresPM) is an emerging area within Process Mining, focused on optimizing processes through real-time interventions for effective decision-making. PresPM holds significant promise for organizations seeking enhanced operational performance. However, the current literature faces two key limitations: a lack of extensive comparisons between techniques and insufficient evaluation approaches. To address these gaps, we introduce SimBank: a simulator designed for accurate benchmarking of PresPM methods. Modeled after a bank's loan application process, SimBank enables extensive comparisons of both online and offline PresPM methods. It incorporates a variety of intervention optimization problems with differing levels of complexity and supports experiments on key causal machine learning challenges, such as assessing a method's robustness to confounding in data. SimBank additionally offers a comprehensive evaluation capability: for each test case, it can generate the true outcome under each intervention action, which is not possible using recorded datasets. The simulator incorporates parallel activities and loops, drawing from common logs to generate cases that closely resemble real-life process instances. Our proof of concept demonstrates SimBank's benchmarking capabilities through experiments with various PresPM methods across different interventions, highlighting its value as a publicly available simulator for advancing research and practice in PresPM.