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STARK denoises spatial transcriptomics images via adaptive regularization

Kubal, Sharvaj, Graham, Naomi, Heitz, Matthieu, Warren, Andrew, Friedlander, Michael P., Plan, Yaniv, Schiebinger, Geoffrey

arXiv.org Machine Learning

We present an approach to denoising spatial transcriptomics images that is particularly effective for uncovering cell identities in the regime of ultra-low sequencing depths, and also allows for interpolation of gene expression. The method -- Spatial Transcriptomics via Adaptive Regularization and Kernels (STARK) -- augments kernel ridge regression with an incrementally adaptive graph Laplacian regularizer. In each iteration, we (1) perform kernel ridge regression with a fixed graph to update the image, and (2) update the graph based on the new image. The kernel ridge regression step involves reducing the infinite dimensional problem on a space of images to finite dimensions via a modified representer theorem. Starting with a purely spatial graph, and updating it as we improve our image makes the graph more robust to noise in low sequencing depth regimes. We show that the aforementioned approach optimizes a block-convex objective through an alternating minimization scheme wherein the sub-problems have closed form expressions that are easily computed. This perspective allows us to prove convergence of the iterates to a stationary point of this non-convex objective. Statistically, such stationary points converge to the ground truth with rate $\mathcal{O}(R^{-1/2})$ where $R$ is the number of reads. In numerical experiments on real spatial transcriptomics data, the denoising performance of STARK, evaluated in terms of label transfer accuracy, shows consistent improvement over the competing methods tested.


How Should the Law Treat Future AI Systems? Fictional Legal Personhood versus Legal Identity

Alexander, Heather J., Simon, Jonathan A., Pinard, Frédéric

arXiv.org Artificial Intelligence

The law draws a sharp distinction between objects and persons, and between two kinds of persons, the ''fictional'' kind (i.e. corporations), and the ''non-fictional'' kind (individual or ''natural'' persons). This paper will assess whether we maximize overall long-term legal coherence by (A) maintaining an object classification for all future AI systems, (B) creating fictional legal persons associated with suitably advanced, individuated AI systems (giving these fictional legal persons derogable rights and duties associated with certified groups of existing persons, potentially including free speech, contract rights, and standing to sue ''on behalf of'' the AI system), or (C) recognizing non-fictional legal personhood through legal identity for suitably advanced, individuated AI systems (recognizing them as entities meriting legal standing with non-derogable rights which for the human case include life, due process, habeas corpus, freedom from slavery, and freedom of conscience). We will clarify the meaning and implications of each option along the way, considering liability, copyright, family law, fundamental rights, civil rights, citizenship, and AI safety regulation. We will tentatively find that the non-fictional personhood approach may be best from a coherence perspective, for at least some advanced AI systems. An object approach may prove untenable for sufficiently humanoid advanced systems, though we suggest that it is adequate for currently existing systems as of 2025. While fictional personhood would resolve some coherence issues for future systems, it would create others and provide solutions that are neither durable nor fit for purpose. Finally, our review will suggest that ''hybrid'' approaches are likely to fail and lead to further incoherence: the choice between object, fictional person and non-fictional person is unavoidable.



Open-Set Fault Diagnosis in Multimode Processes via Fine-Grained Deep Feature Representation

Li, Guangqiang, Atoui, M. Amine, Li, Xiangshun

arXiv.org Artificial Intelligence

A reliable fault diagnosis system should not only accurately classify known health states but also effectively identify unknown faults. In multimode processes, samples belonging to the same health state often show multiple cluster distributions, making it difficult to construct compact and accurate decision boundaries for that state. To address this challenge, a novel open-set fault diagnosis model named fine-grained clustering and rejection network (FGCRN) is proposed. It combines multiscale depthwise convolution, bidirectional gated recurrent unit and temporal attention mechanism to capture discriminative features. A distance-based loss function is designed to enhance the intra-class compactness. Fine-grained feature representations are constructed through unsupervised learning to uncover the intrinsic structures of each health state. Extreme value theory is employed to model the distance between sample features and their corresponding fine-grained representations, enabling effective identification of unknown faults. Extensive experiments demonstrate the superior performance of the proposed method.


OR-R1: Automating Modeling and Solving of Operations Research Optimization Problem via Test-Time Reinforcement Learning

Ding, Zezhen, Tan, Zhen, Zhang, Jiheng, Chen, Tianlong

arXiv.org Artificial Intelligence

Optimization modeling and solving are fundamental to the application of Operations Research (OR) in real-world decision making, yet the process of translating natural language problem descriptions into formal models and solver code remains highly expertise intensive. While recent advances in large language models (LLMs) have opened new opportunities for automation, the generalization ability and data efficiency of existing LLM-based methods are still limited, asmost require vast amounts of annotated or synthetic data, resulting in high costs and scalability barriers. In this work, we present OR-R1, a data-efficient training framework for automated optimization modeling and solving. OR-R1 first employs supervised fine-tuning (SFT) to help the model acquire the essential reasoning patterns for problem formulation and code generation from limited labeled data. In addition, it improves the capability and consistency through Test-Time Group Relative Policy Optimization (TGRPO). This two-stage design enables OR-R1 to leverage both scarce labeled and abundant unlabeled data for effective learning. Experiments show that OR-R1 achieves state-of-the-art performance with an average solving accuracy of $67.7\%$, using only $1/10$ the synthetic data required by prior methods such as ORLM, exceeding ORLM's solving accuracy by up to $4.2\%$. Remarkably, OR-R1 outperforms ORLM by over $2.4\%$ with just $100$ synthetic samples. Furthermore, TGRPO contributes an additional $3.1\%-6.4\%$ improvement in accuracy, significantly narrowing the gap between single-attempt (Pass@1) and multi-attempt (Pass@8) performance from $13\%$ to $7\%$. Extensive evaluations across diverse real-world benchmarks demonstrate that OR-R1 provides a robust, scalable, and cost-effective solution for automated OR optimization problem modeling and solving, lowering the expertise and data barriers for industrial OR applications.


Explaining Decisions in ML Models: a Parameterized Complexity Analysis (Part I)

Ordyniak, Sebastian, Paesani, Giacomo, Rychlicki, Mateusz, Szeider, Stefan

arXiv.org Artificial Intelligence

This paper presents a comprehensive theoretical investigation into the parameterized complexity of explanation problems in various machine learning (ML) models. Contrary to the prevalent black-box perception, our study focuses on models with transparent internal mechanisms. We address two principal types of explanation problems: abductive and contrastive, both in their local and global variants. Our analysis encompasses diverse ML models, including Decision Trees, Decision Sets, Decision Lists, Boolean Circuits, and ensembles thereof, each offering unique explanatory challenges. This research fills a significant gap in explainable AI (XAI) by providing a foundational understanding of the complexities of generating explanations for these models. This work provides insights vital for further research in the domain of XAI, contributing to the broader discourse on the necessity of transparency and accountability in AI systems.


An Adaptive Inspection Planning Approach Towards Routine Monitoring in Uncertain Environments

Viswanathan, Vignesh Kottayam, Bai, Yifan, Fredriksson, Scott, Satpute, Sumeet, Kanellakis, Christoforos, Nikolakopoulos, George

arXiv.org Artificial Intelligence

In this work, we present a hierarchical framework designed to support robotic inspection under environment uncertainty. By leveraging a known environment model, existing methods plan and safely track inspection routes to visit points of interest. However, discrepancies between the model and actual site conditions, caused by either natural or human activities, can alter the surface morphology or introduce path obstructions. To address this challenge, the proposed framework divides the inspection task into: (a) generating the initial global view-plan for region of interests based on a historical map and (b) local view replanning to adapt to the current morphology of the inspection scene. The proposed hierarchy preserves global coverage objectives while enabling reactive adaptation to the local surface morphology. This enables the local autonomy to remain robust against environment uncertainty and complete the inspection tasks. We validate the approach through deployments in real-world subterranean mines using quadrupedal robot.


Assessing the robustness of heterogeneous treatment effects in survival analysis under informative censoring

Wang, Yuxin, Frauen, Dennis, Schweisthal, Jonas, Schröder, Maresa, Feuerriegel, Stefan

arXiv.org Machine Learning

Dropout is common in clinical studies, with up to half of patients leaving early due to side effects or other reasons. When dropout is informative (i.e., dependent on survival time), it introduces censoring bias, because of which treatment effect estimates are also biased. In this paper, we propose an assumption-lean framework to assess the robustness of conditional average treatment effect (CATE) estimates in survival analysis when facing censoring bias. Unlike existing works that rely on strong assumptions, such as non-informative censoring, to obtain point estimation, we use partial identification to derive informative bounds on the CATE. Thereby, our framework helps to identify patient subgroups where treatment is effective despite informative censoring. We further develop a novel meta-learner that estimates the bounds using arbitrary machine learning models and with favorable theoretical properties, including double robustness and quasi-oracle efficiency. We demonstrate the practical value of our meta-learner through numerical experiments and in an application to a cancer drug trial. Together, our framework offers a practical tool for assessing the robustness of estimated treatment effects in the presence of censoring and thus promotes the reliable use of survival data for evidence generation in medicine and epidemiology.


Beyond Static Responses: Multi-Agent LLM Systems as a New Paradigm for Social Science Research

Haase, Jennifer, Pokutta, Sebastian

arXiv.org Artificial Intelligence

As large language models (LLMs) transition from static tools to fully agentic systems, their potential for transforming social science research has become increasingly evident. This paper introduces a structured framework for understanding the diverse applications of LLM-based agents, ranging from simple data processors to complex, multi-agent systems capable of simulating emergent social dynamics. By mapping this developmental continuum across six levels, the paper clarifies the technical and methodological boundaries between different agentic architectures, providing a comprehensive overview of current capabilities and future potential. It highlights how lower-tier systems streamline conventional tasks like text classification and data annotation, while higher-tier systems enable novel forms of inquiry, including the study of group dynamics, norm formation, and large-scale social processes. However, these advancements also introduce significant challenges, including issues of reproducibility, ethical oversight, and the risk of emergent biases. The paper critically examines these concerns, emphasizing the need for robust validation protocols, interdisciplinary collaboration, and standardized evaluation metrics. It argues that while LLM-based agents hold transformative potential for the social sciences, realizing this promise will require careful, context-sensitive deployment and ongoing methodological refinement. The paper concludes with a call for future research that balances technical innovation with ethical responsibility, encouraging the development of agentic systems that not only replicate but also extend the frontiers of social science, offering new insights into the complexities of human behavior.


Predicting butterfly species presence from satellite imagery using soft contrastive regularisation

van der Plas, Thijs L, Law, Stephen, Pocock, Michael JO

arXiv.org Artificial Intelligence

The growing demand for scalable biodiversity monitoring methods has fuelled interest in remote sensing data, due to its widespread availability and extensive coverage. Traditionally, the application of remote sensing to biodiversity research has focused on mapping and monitoring habitats, but with increasing availability of large-scale citizen-science wildlife observation data, recent methods have started to explore predicting multi-species presence directly from satellite images. This paper presents a new data set for predicting butterfly species presence from satellite data in the United Kingdom. W e experimentally optimise a Resnet-based model to predict multi-species presence from 4-band satellite images, and find that this model especially outperforms the mean rate baseline for locations with high species biodiversity. T o improve performance, we develop a soft, supervised contrastive regularisation loss that is tailored to probabilistic labels (such as species-presence data), and demonstrate that this improves prediction accuracy. In summary, our new data set and contrastive regularisation method contribute to the open challenge of accurately predicting species biodiversity from remote sensing data, which is key for efficient biodiversity monitoring.