Daily Papers

This paper introduces CoMuRoS (Collaborative Multi-Robot System), a generalizable hierarchical architecture for heterogeneous robot teams that unifies centralized deliberation with decentralized execution, and supports event-driven replanning. A Task Manager LLM interprets natural-language goals, classifies tasks, and allocates subtasks using static rules plus dynamic contexts (task, history, robot and task status, and events).Each robot runs a local LLM that composes executable Python code from primitive skills (ROS2 nodes, policies), while onboard perception (VLMs/image processing) continuously monitors events and classifies them into relevant or irrelevant to the task. Task failures or user intent changes trigger replanning, allowing robots to assist teammates, resume tasks, or request human help. Hardware studies demonstrate autonomous recovery from disruptive events, filtering of irrelevant distractions, and tightly coordinated transport with emergent human-robot cooperation (e.g., multirobot collaborative object recovery success rate: 9/10, coordinated transport: 8/8, human-assisted recovery: 5/5).Simulation studies show intention-aware replanning. A curated textual benchmark spanning 22 scenarios (3 tasks each, around 20 robots) evaluates task allocation, classification, IoU, executability, and correctness, with high average scores (e.g., correctness up to 0.91) across multiple LLMs, a separate replanning set (5 scenarios) achieves 1.0 correctness. Compared with prior LLM-based systems, CoMuRoS uniquely demonstrates runtime, event-driven replanning on physical robots, delivering robust, flexible multi-robot and human-robot collaboration.

The increasing complexity and interconnectivity of digital infrastructures make scalable and reliable security assessment methods essential. Robotic systems represent a particularly important class of operational technology, as modern robots are highly networked cyber-physical systems deployed in domains such as industrial automation, logistics, and autonomous services. This paper explores the use of large language models for automated penetration testing in robotic environments. We propose an environment-grounded multi-agent architecture tailored to Robotics-based systems. The approach dynamically constructs a shared graph-based memory during execution that captures the observable system state, including network topology, communication channels, vulnerabilities, and attempted exploits. This enables structured automation while maintaining traceability and effective context management throughout the testing process. Evaluated across multiple iterations within a specialized robotics Capture-the-Flag scenario (ROS/ROS2), the system demonstrated high reliability, successfully completing the challenge in 100\% of test runs (n=5). This performance significantly exceeds literature benchmarks while maintaining the traceability and human oversight required by frameworks like the EU AI Act.

A spanning tree T of graph G is a rho-approximate universal Steiner tree (UST) for root vertex r if, for any subset of vertices S containing r, the cost of the minimal subgraph of T connecting S is within a rho factor of the minimum cost tree connecting S in G. Busch et al. (FOCS 2012) showed that every graph admits 2^{O(log n)}-approximate USTs by showing that USTs are equivalent to strong sparse partition hierarchies (up to poly-logs). Further, they posed poly-logarithmic USTs and strong sparse partition hierarchies as open questions. We settle these open questions by giving polynomial-time algorithms for computing both O(log ^ 7 n)-approximate USTs and poly-logarithmic strong sparse partition hierarchies. For graphs with constant doubling dimension or constant pathwidth we improve this to O(log n)-approximate USTs and O(1) strong sparse partition hierarchies. Our doubling dimension result is tight up to second order terms. We reduce the existence of these objects to the previously studied cluster aggregation problem and what we call dangling nets.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

We study the problem of constructing Steiner Minimal Trees (SMTs) in hyperbolic space. Exact SMT computation is NP-hard, and existing hyperbolic heuristics such as HyperSteiner are deterministic and often get trapped in locally suboptimal configurations. We introduce Randomized HyperSteiner (RHS), a stochastic Delaunay triangulation heuristic that incorporates randomness into the expansion process and refines candidate trees via Riemannian gradient descent optimization. Experiments on synthetic data sets and a real-world single-cell transcriptomic data show that RHS outperforms Minimum Spanning Tree (MST), Neighbour Joining, and vanilla HyperSteiner (HS). In near-boundary configurations, RHS can achieve a 32% reduction in total length over HS, demonstrating its effectiveness and robustness in diverse data regimes.

Collaborative Simultaneous Localization And Mapping (C-SLAM) is a vital component for successful multi-robot operations in environments without an external positioning system, such as indoors, underground or underwater. In this paper, we introduce Swarm-SLAM, an open-source C-SLAM system that is designed to be scalable, flexible, decentralized, and sparse, which are all key properties in swarm robotics. Our system supports inertial, lidar, stereo, and RGB-D sensing, and it includes a novel inter-robot loop closure prioritization technique that reduces communication and accelerates convergence. We evaluated our ROS-2 implementation on five different datasets, and in a real-world experiment with three robots communicating through an ad-hoc network. Our code is publicly available: https://github.com/MISTLab/Swarm-SLAM

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

Deploying robots in human-shared environments requires a deep understanding of how nearby agents and objects interact. Employing causal inference to model cause-and-effect relationships facilitates the prediction of human behaviours and enables the anticipation of robot interventions. However, a significant challenge arises due to the absence of implementation of existing causal discovery methods within the ROS ecosystem, the standard de-facto framework in robotics, hindering effective utilisation on real robots. To bridge this gap, in our previous work we proposed ROS-Causal, a ROS-based framework designed for onboard data collection and causal discovery in human-robot spatial interactions. In this work, we present an experimental evaluation of ROS-Causal both in simulation and on a new dataset of human-robot spatial interactions in a lab scenario, to assess its performance and effectiveness. Our analysis demonstrates the efficacy of this approach, showcasing how causal models can be extracted directly onboard by robots during data collection. The online causal models generated from the simulation are consistent with those from lab experiments. These findings can help researchers to enhance the performance of robotic systems in shared environments, firstly by studying the causal relations between variables in simulation without real people, and then facilitating the actual robot deployment in real human environments. ROS-Causal: https://lcastri.github.io/roscausal

In this paper, we design a simple yet powerful deep network architecture, U^2-Net, for salient object detection (SOD). The architecture of our U^2-Net is a two-level nested U-structure. The design has the following advantages: (1) it is able to capture more contextual information from different scales thanks to the mixture of receptive fields of different sizes in our proposed ReSidual U-blocks (RSU), (2) it increases the depth of the whole architecture without significantly increasing the computational cost because of the pooling operations used in these RSU blocks. This architecture enables us to train a deep network from scratch without using backbones from image classification tasks. We instantiate two models of the proposed architecture, U^2-Net (176.3 MB, 30 FPS on GTX 1080Ti GPU) and U^2-Net^{dagger} (4.7 MB, 40 FPS), to facilitate the usage in different environments. Both models achieve competitive performance on six SOD datasets. The code is available: https://github.com/NathanUA/U-2-Net.

Understanding a plant's root system architecture (RSA) is crucial for a variety of plant science problem domains including sustainability and climate adaptation. Minirhizotron (MR) technology is a widely-used approach for phenotyping RSA non-destructively by capturing root imagery over time. Precisely segmenting roots from the soil in MR imagery is a critical step in studying RSA features. In this paper, we introduce a large-scale dataset of plant root images captured by MR technology. In total, there are over 72K RGB root images across six different species including cotton, papaya, peanut, sesame, sunflower, and switchgrass in the dataset. The images span a variety of conditions including varied root age, root structures, soil types, and depths under the soil surface. All of the images have been annotated with weak image-level labels indicating whether each image contains roots or not. The image-level labels can be used to support weakly supervised learning in plant root segmentation tasks. In addition, 63K images have been manually annotated to generate pixel-level binary masks indicating whether each pixel corresponds to root or not. These pixel-level binary masks can be used as ground truth for supervised learning in semantic segmentation tasks. By introducing this dataset, we aim to facilitate the automatic segmentation of roots and the research of RSA with deep learning and other image analysis algorithms.

Visual programming languages (VPLs) provide coding without typing texts. VPL makes coding easy to programmers with automatically adding usually used some code structure. Beginners in coding have generally two main challenges; transforming ideas into logical expressions and syntax errors. Syntax errors are impossible with VPLs because of there is no forgotten parentheses and semicolons. VPLs provide to focus on algorithm for programmers. VPL is a new trend for educational robotic environments. In this study, Robot Operating System (ROS) compatible web based visual programming system has been developed for evarobot. ROS provides libraries and tools to help software developers create robot applications. It provides hardware abstraction, device drivers, libraries, visualizers, message-passing, package management, and more. Blockly has been used as VPL for the study and to generate / use blocks (commucation, sensing etc.). Some applications were generated like teleoperation, SLAM and wander etc. In this system, communication between server and client is supported by rosbridge package. Web page connected to ROS which runs on server using roslibjs library. Rosbridge provides a JSON API to ROS functionality for non-ROS programs.

We algorithmically determine the regions and facets of all dimensions of the canonical polyhedral complex, the universal object into which a ReLU network decomposes its input space. We show that the locations of the vertices of the canonical polyhedral complex along with their signs with respect to layer maps determine the full facet structure across all dimensions. We present an algorithm which calculates this full combinatorial structure, making use of our theorems that the dual complex to the canonical polyhedral complex is cubical and it possesses a multiplication compatible with its facet structure. The resulting algorithm is numerically stable, polynomial time in the number of intermediate neurons, and obtains accurate information across all dimensions. This permits us to obtain, for example, the true topology of the decision boundaries of networks with low-dimensional inputs. We run empirics on such networks at initialization, finding that width alone does not increase observed topology, but width in the presence of depth does. Source code for our algorithms is accessible online at https://github.com/mmasden/canonicalpoly.

Rotary Position Embedding (RoPE) performs remarkably on language models, especially for length extrapolation of Transformers. However, the impacts of RoPE on computer vision domains have been underexplored, even though RoPE appears capable of enhancing Vision Transformer (ViT) performance in a way similar to the language domain. This study provides a comprehensive analysis of RoPE when applied to ViTs, utilizing practical implementations of RoPE for 2D vision data. The analysis reveals that RoPE demonstrates impressive extrapolation performance, i.e., maintaining precision while increasing image resolution at inference. It eventually leads to performance improvement for ImageNet-1k, COCO detection, and ADE-20k segmentation. We believe this study provides thorough guidelines to apply RoPE into ViT, promising improved backbone performance with minimal extra computational overhead. Our code and pre-trained models are available at https://github.com/naver-ai/rope-vit

We show that in a drive-response coupling framework extreme events are suppressed in the response system by the dominance of a single driving signal. We validate this approach across three distinct response network topologies, namely (i) a pair of coupled neurons, (ii) a monolayer network of N coupled neurons and (iii) a two-layer multiplex network each composed of FitzHugh-Nagumo neuronal units. The response networks inherently exhibit extreme events. Our results demonstrate that influencing just one neuron in the response network with an appropriately tuned driving signal is sufficient to control extreme events across all three configurations. In the two-neuron case, suppression of extreme events occurs due to the breaking of phase-locking between the driving neuron and the targeted response neuron. In the case of monolayer and multiplex networks, suppression of extreme events results from the disruption of protoevent frequency dynamics and a subsequent frequency decoupling of the driven neuron from the rest of the network. We also observe that when the size of the neurons in response network connected to the drive increases, the onset of control occurs earlier indicating a scaling advantage of the method.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

This paper discusses the experiences gained from designing, deploying, and maintaining low-power Wireless Sensor Networks (WSN) in three geothermally active remote locations in Iceland. The network was deployed for environmental monitoring and real-time data collection to assist in investigating the impact of global warming on the (sub)Arctic climate and the resulting carbon release from the region. Functional networks with more than 50 sensor nodes from three sites with extreme weather conditions and hard-to-access terrain have been collecting data since 2021. The networks employ primary cell-powered wireless sensor nodes equipped with DASH7 Alliance Protocol (D7A) for low-power data transmission and solar-powered D7A-cellular gateways for the backend connection. The WSNs have so far achieved over three years of uptime with minimal maintenance required throughout this period. We present a detailed discussion of different network components, their architecture, and the networks' overall performance and reliability.

We present a framework for intuitive robot programming by non-experts, leveraging natural language prompts and contextual information from the Robot Operating System (ROS). Our system integrates large language models (LLMs), enabling non-experts to articulate task requirements to the system through a chat interface. Key features of the framework include: integration of ROS with an AI agent connected to a plethora of open-source and commercial LLMs, automatic extraction of a behavior from the LLM output and execution of ROS actions/services, support for three behavior modes (sequence, behavior tree, state machine), imitation learning for adding new robot actions to the library of possible actions, and LLM reflection via human and environment feedback. Extensive experiments validate the framework, showcasing robustness, scalability, and versatility in diverse scenarios, including long-horizon tasks, tabletop rearrangements, and remote supervisory control. To facilitate the adoption of our framework and support the reproduction of our results, we have made our code open-source. You can access it at: https://github.com/huawei-noah/HEBO/tree/master/ROSLLM.

Recent works in self-supervised learning have demonstrated strong performance on scene-level dense prediction tasks by pretraining with object-centric or region-based correspondence objectives. In this paper, we present Region-to-Object Representation Learning (R2O) which unifies region-based and object-centric pretraining. R2O operates by training an encoder to dynamically refine region-based segments into object-centric masks and then jointly learns representations of the contents within the mask. R2O uses a "region refinement module" to group small image regions, generated using a region-level prior, into larger regions which tend to correspond to objects by clustering region-level features. As pretraining progresses, R2O follows a region-to-object curriculum which encourages learning region-level features early on and gradually progresses to train object-centric representations. Representations learned using R2O lead to state-of-the art performance in semantic segmentation for PASCAL VOC (+0.7 mIOU) and Cityscapes (+0.4 mIOU) and instance segmentation on MS COCO (+0.3 mask AP). Further, after pretraining on ImageNet, R2O pretrained models are able to surpass existing state-of-the-art in unsupervised object segmentation on the Caltech-UCSD Birds 200-2011 dataset (+2.9 mIoU) without any further training. We provide the code/models from this work at https://github.com/KKallidromitis/r2o.

Neurological diseases are the leading global cause of disability, yet most lack disease-modifying treatments. We present PROTON, a heterogeneous graph transformer that generates testable hypotheses across molecular, organoid, and clinical systems. To evaluate PROTON, we apply it to Parkinson's disease (PD), bipolar disorder (BD), and Alzheimer's disease (AD). In PD, PROTON linked genetic risk loci to genes essential for dopaminergic neuron survival and predicted pesticides toxic to patient-derived neurons, including the insecticide endosulfan, which ranked within the top 1.29% of predictions. In silico screens performed by PROTON reproduced six genome-wide α-synuclein experiments, including a split-ubiquitin yeast two-hybrid system (normalized enrichment score [NES] = 2.30, FDR-adjusted p < 1 times 10^{-4}), an ascorbate peroxidase proximity labeling assay (NES = 2.16, FDR < 1 times 10^{-4}), and a high-depth targeted exome sequencing study in 496 synucleinopathy patients (NES = 2.13, FDR < 1 times 10^{-4}). In BD, PROTON predicted calcitriol as a candidate drug that reversed proteomic alterations observed in cortical organoids derived from BD patients. In AD, we evaluated PROTON predictions in health records from n = 610,524 patients at Mass General Brigham, confirming that five PROTON-predicted drugs were associated with reduced seven-year dementia risk (minimum hazard ratio = 0.63, 95% CI: 0.53-0.75, p < 1 times 10^{-7}). PROTON generated neurological hypotheses that were evaluated across molecular, organoid, and clinical systems, defining a path for AI-driven discovery in neurological disease.

Graph neural networks (GNNs) are increasingly applied to physical design tasks such as congestion prediction and wirelength estimation, yet progress is hindered by inconsistent circuit representations and the absence of controlled evaluation protocols. We present R2G (RTL-to-GDSII), a multi-view circuit-graph benchmark suite that standardizes five stage-aware views with information parity (every view encodes the same attribute set, differing only in where features attach) over 30 open-source IP cores (up to 10^6 nodes/edges). R2G provides an end-to-end DEF-to-graph pipeline spanning synthesis, placement, and routing stages, together with loaders, unified splits, domain metrics, and reproducible baselines. By decoupling representation choice from model choice, R2G isolates a confound that prior EDA and graph-ML benchmarks leave uncontrolled. In systematic studies with GINE, GAT, and ResGatedGCN, we find: (i) view choice dominates model choice, with Test R^2 varying by more than 0.3 across representations for a fixed GNN; (ii) node-centric views generalize best across both placement and routing; and (iii) decoder-head depth (3--4 layers) is the primary accuracy driver, turning divergent training into near-perfect predictions (R^2>0.99). Code and datasets are available at https://github.com/ShenShan123/R2G.

Large Language Models (LLMs) are increasingly deployed as computer-use agents, autonomously performing tasks within real desktop or web environments. While this evolution greatly expands practical use cases for humans, it also creates serious security exposures. We present SUDO (Screen-based Universal Detox2Tox Offense), a novel attack framework that systematically bypasses refusal-trained safeguards in commercial computer-use agents, such as Claude for Computer Use. The core mechanism, Detox2Tox, transforms harmful requests (that agents initially reject) into seemingly benign requests via detoxification, secures detailed instructions from advanced vision language models (VLMs), and then reintroduces malicious content via toxification just before execution. Unlike conventional jailbreaks, SUDO iteratively refines its attacks based on a built-in refusal feedback, making it increasingly effective against robust policy filters. In extensive tests spanning 50 real-world tasks and multiple state-of-the-art VLMs, SUDO achieves a stark attack success rate of 24.41% (with no refinement), and up to 41.33% (by its iterative refinement) in Claude for Computer Use. By revealing these vulnerabilities and demonstrating the ease with which they can be exploited in real-world computing environments, this paper highlights an immediate need for robust, context-aware safeguards. WARNING: This paper includes harmful or offensive model outputs

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

We introduce Topological Neural Operators (TNOs), a principled framework for operator learning on cell complexes that lifts neural operators (NOs) from functions on points and/or edges to topological domains. TNOs represent data as features defined on cells of varying dimension and model their interactions through Discrete Exterior Calculus, enabling explicit cross-dimensional coupling via gradient-, curl-, and divergence-type operators. The key design principle is to decouple where information flows, as governed by fixed topological operators, from how it is transformed (which is learned), yielding models that respect the geometric support of physical quantities and expose conservation and compatibility structure. We further propose Hierarchical TNOs (HTNOs), which incorporate learned coarse complexes to propagate long-range and topology-dependent information. Our framework subsumes existing NOs as a special case, providing a unified perspective on operator learning across discretizations. Across a range of PDE benchmarks, including irregular-geometry flow problems, TNOs and HTNOs improve accuracy; controlled studies further isolate the benefits of native higher-rank and topological structure. Project page: https://circle-group.github.io/research/TNO

We prepared Na_xTO_2 (T = Mn, Co) nanostructures to use as cathode material in Na-ion batteries. The Rietveld refinement of x-ray diffraction data confirms the hexagonal symmetry. Scanning and transmission electron microscopy measurements show hexagonal and rod-shape morphology for T = Co and Mn, respectively. The magnetic measurements indicate the presence of variable oxidation states of Mn/Co ions, but no long range ordering till 5~K. We find that the Na_{0.6}MnO_2 is highly insulating whereas Na_{0.7}CoO_2 is semiconducting in nature. The conduction in Na_{0.7}CoO_2 takes place through both variable range hopping (VRH) as well as activation mechanisms in different temperature ranges. However, for Na_{0.6}MnO_2 the VRH prevails at elevated temperatures. Furthermore, the coin cells have been fabricated and tested the electrochemical behavior using cyclic voltammetry, which confirms the reversibility of Na--ions during intercalation/de-intercalation.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

Sparse Mixture-of-Experts (MoE) architectures employ increasingly sophisticated routing mechanisms -- learned routers, multi-hop trajectories, token-dependent gating. We ask: does routing topology actually determine language modeling quality? We build a geometric MoE (ST-MoE) using cosine-similarity routing against learned centroids in a low-dimensional space (d_{space} = 64), requiring 80% fewer routing parameters than standard linear routers. Through 62 controlled experiments on WikiText-103 at 76--84M parameters trained to convergence (50K steps, 1.64B tokens), we find that routing topology does not determine asymptotic perplexity (PPL): five cosine-routing variants are statistically equivalent within a 1-PPL margin (Two One-Sided Tests [TOST], p < 0.05 for all 10 pairwise comparisons; 15 runs across 3 seeds, observed range 33.93--34.72). The finding extends to hash, random-fixed, and top-1 routing (single-seed; graceful 1.1--2.2 PPL degradation) and replicates on OpenWebText (0.03 PPL gap, 6 runs, 3 seeds each). A standard linear router with 5.3times more routing parameters reaches PPL 32.76, but iso-parameter cosine routing closes 67% of this gap -- the true mechanism advantage is sim1.2%. The mechanistic explanation is convergent redundancy: multi-hop updates are collinear (cos(Δh_0, Δh_1) = 0.805), implementing magnitude amplification rather than compositional reasoning; a single learnable scalar replicates multi-hop performance. As a practical payoff, zero-shot relative-norm halting saves 25% of MoE FLOPs at +0.12% PPL. Expert-level specialization and causal controllability -- which coexist with topology-level equifinality -- are explored in a companion paper.

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.

Complex tables with multi-level headers, merged cells and heterogeneous layouts pose persistent challenges for LLMs in both understanding and reasoning. Existing approaches typically rely on table linearization or normalized grid modeling. However, these representations struggle to explicitly capture hierarchical structures and cross-dimensional dependencies, which can lead to misalignment between structural semantics and textual representations for non-standard tables. To address this issue, we propose an Orthogonal Hierarchical Decomposition (OHD) framework that constructs structure-preserving input representations of complex tables for LLMs. OHD introduces an Orthogonal Tree Induction (OTI) method based on spatial--semantic co-constraints, which decomposes irregular tables into a column tree and a row tree to capture vertical and horizontal hierarchical dependencies, respectively. Building on this representation, we design a dual-pathway association protocol to symmetrically reconstruct semantic lineage of each cell, and incorporate an LLM as a semantic arbitrator to align multi-level semantic information. We evaluate OHD framework on two complex table question answering benchmarks, AITQA and HiTab. Experimental results show that OHD consistently outperforms existing representation paradigms across multiple evaluation metrics.

Single-atom catalysts (SACs) have emerged as frontiers for catalyzing chemical reactions, yet the diverse combinations of active elements and support materials, the nature of coordination environments, elude traditional methodologies in searching optimal SAC systems with superior catalytic performance. Herein, by integrating multi-branch Convolutional Neural Network (CNN) analysis models to hybrid descriptor based activity volcano plot, 2D SAC system composed of diverse metallic single atoms anchored on six type of 2D supports, including graphitic carbon nitride, nitrogen-doped graphene, graphene with dual-vacancy, black phosphorous, boron nitride, and C2N, are screened for efficient CO2RR. Starting from establishing a correlation map between the adsorption energies of intermediates and diverse electronic and elementary descriptors, sole singular descriptor lost magic to predict catalytic activity. Deep learning method utilizing multi-branch CNN model therefore was employed, using 2D electronic density of states as input to predict adsorption energies. Hybrid-descriptor enveloping both C- and O-types of CO2RR intermediates was introduced to construct volcano plots and limiting potential periodic table, aiming for intuitive screening of catalyst candidates for efficient CO2 reduction to CH4. The eDOS occlusion experiments were performed to unravel individual orbital contribution to adsorption energy. To explore the electronic scale principle governing practical engineering catalytic CO2RR activity, orbitalwise eDOS shifting experiments based on CNN model were employed. The study involves examining the adsorption energy and, consequently, catalytic activities while varying supported single atoms. This work offers a tangible framework to inform both theoretical screening and experimental synthesis, thereby paving the way for systematically designing efficient SACs.

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA

Virtual cell modeling predicts molecular state changes under genetic perturbations in silico, which is essential for biological mechanism studies. However, existing approaches suffer from unconstrained reasoning, uninterpretable predictions, and retrieval signals that are weakly aligned with regulatory topology. To address these limitations, we propose AROMA, an Augmented Reasoning Over a Multimodal Architecture for virtual cell genetic perturbation modeling. AROMA integrates textual evidence, graph-topology information, and protein sequence features to model perturbation-target dependencies, and is trained with a two-stage optimization strategy to yield predictions that are both accurate and interpretable. We also construct two knowledge graphs and a perturbation reasoning dataset, PerturbReason, containing more than 498k samples, as reusable resources for the virtual cell domain. Experiments show that AROMA outperforms existing methods across multiple cell lines, and remains robust under zero-shot evaluation on an unseen cell line, as well as in knowledge-sparse, long-tail scenarios. Overall, AROMA demonstrates that combining knowledge-driven multimodal modeling with evidence retrieval provides a promising pathway toward more reliable and interpretable virtual cell perturbation prediction. Model weights are available at https://huggingface.co/blazerye/AROMA. Code is available at https://github.com/blazerye/AROMA.

In the era of large foundation models, the quality of embeddings has become a central determinant of downstream task performance and overall system capability. Yet widely used dense embeddings are often extremely high-dimensional, incurring substantial costs in storage, memory, and inference latency. To address these, Contrastive Sparse Representation (CSR) is recently proposed as a promising direction, mapping dense embeddings into high-dimensional but k-sparse vectors, in contrast to compact dense embeddings such as Matryoshka Representation Learning (MRL). Despite its promise, CSR suffers severe degradation in the ultra-sparse regime, where over 80% of neurons remain inactive, leaving much of its efficiency potential unrealized. In this paper, we introduce CSRv2, a principled training approach designed to make ultra-sparse embeddings viable. CSRv2 stabilizes sparsity learning through progressive k-annealing, enhances representational quality via supervised contrastive objectives, and ensures end-to-end adaptability with full backbone finetuning. CSRv2 reduces dead neurons from 80% to 20% and delivers a 14% accuracy gain at k=2, bringing ultra-sparse embeddings on par with CSR at k=8 and MRL at 32 dimensions, all with only two active features. While maintaining comparable performance, CSRv2 delivers a 7x speedup over MRL, and yields up to 300x improvements in compute and memory efficiency relative to dense embeddings in text representation. Extensive experiments across text and vision demonstrate that CSRv2 makes ultra-sparse embeddings practical without compromising performance, where CSRv2 achieves 7%/4% improvement over CSR when k=4 and further increases this gap to 14%/6% when k=2 in text/vision representation. By making extreme sparsity viable, CSRv2 broadens the design space for real-time and edge-deployable AI systems where both embedding quality and efficiency are critical.

We present a distributed data structure, which we call the rainbow skip graph. To our knowledge, this is the first peer-to-peer data structure that simultaneously achieves high fault tolerance, constant-sized nodes, and fast update and query times for ordered data. It is a non-trivial adaptation of the SkipNet/skip-graph structures of Harvey et al. and Aspnes and Shah, so as to provide fault-tolerance as these structures do, but to do so using constant-sized nodes, as in the family tree structure of Zatloukal and Harvey. It supports successor queries on a set of n items using O(log n) messages with high probability, an improvement over the expected O(log n) messages of the family tree.

Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical organization inherent in protein structures. We introduce Topotein, a comprehensive framework that applies topological deep learning to PRL through the novel Protein Combinatorial Complex (PCC) and Topology-Complete Perceptron Network (TCPNet). Our PCC represents proteins at multiple hierarchical levels -- from residues to secondary structures to complete proteins -- while preserving geometric information at each level. TCPNet employs SE(3)-equivariant message passing across these hierarchical structures, enabling more effective capture of multi-scale structural patterns. Through extensive experiments on four PRL tasks, TCPNet consistently outperforms state-of-the-art geometric graph neural networks. Our approach demonstrates particular strength in tasks such as fold classification which require understanding of secondary structure arrangements, validating the importance of hierarchical topological features for protein analysis.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

In theoretical neuroscience, recent work leverages deep learning tools to explore how some network attributes critically influence its learning dynamics. Notably, initial weight distributions with small (resp. large) variance may yield a rich (resp. lazy) regime, where significant (resp. minor) changes to network states and representation are observed over the course of learning. However, in biology, neural circuit connectivity could exhibit a low-rank structure and therefore differs markedly from the random initializations generally used for these studies. As such, here we investigate how the structure of the initial weights -- in particular their effective rank -- influences the network learning regime. Through both empirical and theoretical analyses, we discover that high-rank initializations typically yield smaller network changes indicative of lazier learning, a finding we also confirm with experimentally-driven initial connectivity in recurrent neural networks. Conversely, low-rank initialization biases learning towards richer learning. Importantly, however, as an exception to this rule, we find lazier learning can still occur with a low-rank initialization that aligns with task and data statistics. Our research highlights the pivotal role of initial weight structures in shaping learning regimes, with implications for metabolic costs of plasticity and risks of catastrophic forgetting.

Interdisciplinary scientific breakthroughs mostly emerge unexpectedly, and forecasting the formation of novel research fields remains a major challenge. We introduce FOS (Future Of Science), a comprehensive time-aware graph-based benchmark that reconstructs annual co-occurrence graphs of 65,027 research sub-fields (spanning 19 general domains) over the period 1827-2024. In these graphs, edges denote the co-occurrence of two fields in a single publication and are timestamped with the corresponding publication year. Nodes are enriched with semantic embeddings, and edges are characterized by temporal and topological descriptors. We formulate the prediction of new field-pair linkages as a temporal link-prediction task, emphasizing the "first-time" connections that signify pioneering interdisciplinary directions. Through extensive experiments, we evaluate a suite of state-of-the-art temporal graph architectures under multiple negative-sampling regimes and show that (i) embedding long-form textual descriptions of fields significantly boosts prediction accuracy, and (ii) distinct model classes excel under different evaluation settings. Case analyses show that top-ranked link predictions on FOS align with field pairings that emerge in subsequent years of academic publications. We publicly release FOS, along with its temporal data splits and evaluation code, to establish a reproducible benchmark for advancing research in predicting scientific frontiers.

Vision-language models (VLMs) achieve strong multimodal performance, yet how computation is organized across populations of neurons remains poorly understood. In this work, we study VLMs through the lens of neural topology, representing each layer as a within-layer correlation graph derived from neuron-neuron co-activations. This view allows us to ask whether population-level structure is behaviorally meaningful, how it changes across modalities and depth, and whether it identifies causally influential internal components under intervention. We show that correlation topology carries recoverable behavioral signal; moreover, cross-modal structure progressively consolidates with depth around a compact set of recurrent hub neurons, whose targeted perturbation substantially alters model output. Neural topology thus emerges as a meaningful intermediate scale for VLM interpretability: richer than local attribution, more tractable than full circuit recovery, and empirically tied to multimodal behavior. Code is publicly available at https://github.com/he-h/vlm-graph-probing.

Modern machine learning is still largely organized around a single recipe: choose a parameterized model family and optimize its weights. Although highly successful, this paradigm is too narrow for many structured prediction problems, where the main bottleneck is not parameter fitting but discovering what should be computed from the data. Success often depends on identifying the right transformations, statistics, invariances, interaction structures, temporal summaries, gates, or nonlinear compositions, especially when objectives are non-differentiable, evaluation is cross-validation-based, interpretability matters, or continual adaptation is required. We present EvoForest, a hybrid neuro-symbolic system for end-to-end open-ended evolution of computation. Rather than merely generating features, EvoForest jointly evolves reusable computational structure, callable function families, and trainable low-dimensional continuous components inside a shared directed acyclic graph. Intermediate nodes store alternative implementations, callable nodes encode reusable transformation families such as projections, gates, and activations, output nodes define candidate predictive computations, and persistent global parameters can be refined by gradient descent. For each graph configuration, EvoForest evaluates the discovered computation and uses a lightweight Ridge-based readout to score the resulting representation against a non-differentiable cross-validation target. The evaluator also produces structured feedback that guides future LLM-driven mutations. In the 2025 ADIA Lab Structural Break Challenge, EvoForest reached 94.13% ROC-AUC after 600 evolution steps, exceeding the publicly reported winning score of 90.14% under the same evaluation protocol.

We present HERCULES, an open-source simulator and data-collection pipeline for heterogeneous multi-robot autonomy. Built upon the Unreal Engine 5 (UE5)-based simulators AirSim and Cosys-AirSim, HERCULES resolves key architectural limitations of prior frameworks to enable concurrent unmanned aerial and ground vehicle (UAV-UGV) operation in large-scale, photorealistic, dynamic environments. It introduces a new waypoint-tracking UGV controller that mirrors existing UAV control interfaces, and provides a shared navigation stack for mapping, traversability analysis, planning, and control across heterogeneous platforms. Expanding inherited sensor suites, it adds physics-based long-wave infrared (LWIR) cameras and configurable night-vision modes for degraded visual environments. HERCULES provides lightweight APIs, ROS 2 wrappers, and rigorous time synchronization across sensors and platforms, and brings state-of-the-art game-engine capabilities into robotics simulation, integrating intelligent agents such as pedestrians, traffic, and wildlife with high-fidelity dynamic phenomena, including fire, flooding, and crop disease spread. HERCULES runs in two modes: passively, replaying offline-designed trajectories to generate reproducible multi-modal datasets, and actively, running an online planner in closed loop from live observations. Our experiments in heterogeneous multi-robot SLAM, collaborative perception, and exploration, using both HERCULES-generated data and active closed-loop execution, demonstrate its utility for advancing heterogeneous multi-robot autonomy. We publicly release our source code, experiment code, documentation, and datasets, including a heterogeneous multi-robot SLAM benchmark collected with two UAVs and two UGVs across kilometer-scale desert, forest, and city environments, at https://lunarlab-gatech.github.io/HERCULES-website.

Autonomous embedded nodes deployed in connectivity-denied environments - remote forest perimeters, farm boundaries, and cargo in transit across highways or open ocean - share a common set of engineering requirements that are usually addressed by separate, purpose-built systems: passive-infrared (PIR) triggered wake-up, inertial-measurement-unit (IMU) driven active stabilization, and long-range communication under strict power budgets. This paper argues that a perimeter/wildlife security turret and a high-value cargo protection crate are, from a systems perspective, two parametrizations of the same generalized node architecture rather than two unrelated designs. We formalize this generalized architecture, extend it with three sensing/communication modalities not present in either original design - single-point LiDAR ranging, a LoRa/LoRaWAN regional mesh tier, and a satellite short-burst-data (SBD) global tier - and couple the resulting telemetry to a Geographic Information System (GIS) layer via a proposed Composite Risk Index (CRI) that fuses breach events, impact severity, and connectivity state into a single spatially-referenced score. We present the sensor-fusion, proportional-integral-derivative (PID) stabilization, link-budget, received-signal-strength-indicator (RSSI) localization, and CRI formulations that unify the two deployment modes, provide a simulated closed-loop stabilization response and a tiered-communication trade-off analysis, and instantiate the two original projects as case studies of the generalized architecture. The framework is intended as an engineering blueprint and a starting point for field validation rather than as a report of field-tested results.

Stomata play a crucial role in regulating plant physiological processes and reflecting environmental responses. However, accurate and high-throughput stomatal phenotyping remains challenging, as conventional approaches rely on destructive sampling and manual annotation, restricting large-scale and field deployment. To overcome these limitations, a noninvasive restoration-detection integrated framework, termed StomaD2, is developed to achieve accurate and fast stomatal phenotyping under complex imaging conditions. The framework incorporates a diffusion-based restoration module to recover degraded images and a specialized rotated object detection network tailored to the small, dense, and cluttered characteristics of stomata. The proposed network enhances feature representation through three key innovations: a column-wise structure for global feature interaction, context-aware resampling and reweighting mechanism to improve multi-scale consistency, and a feature reassembly module to boost discrimination against complex backgrounds. In extensive comparisons, StomaD2 demonstrated state-of-the-art performance. On public Maize and Wheat datasets, it achieved accuracies of 0.994 and 0.992, respectively, significantly outperforming existing benchmarks. When benchmarked against ten other advanced models, including Oriented Former and YOLOv12, StomaD2 achieved a top-tier F1-score/mAP of 0.989. The framework is integrated into a user-friendly, field-operable system that supports the fast extraction of eight stomatal phenotypes, such as density and conductance. Validated on more than 130 plant species, StomaD2's results highlight its strong generalizability and potential for large-scale phenotyping, plant physiology analysis, and precision agriculture applications.

Cypher, the query language for Neo4j graph databases, plays a critical role in enabling graph-based analytics and data exploration. While substantial research has been dedicated to natural language to SQL query generation (Text2SQL), the analogous problem for graph databases referred to as Text2Cypher remains underexplored. In this work, we introduce SynthCypher, a fully synthetic and automated data generation pipeline designed to address this gap. SynthCypher employs a novel LLMSupervised Generation-Verification framework, ensuring syntactically and semantically correct Cypher queries across diverse domains and query complexities. Using this pipeline, we create SynthCypher Dataset, a large-scale benchmark containing 29.8k Text2Cypher instances. Fine-tuning open-source large language models (LLMs), including LLaMa-3.1- 8B, Mistral-7B, and QWEN-7B, on SynthCypher yields significant performance improvements of up to 40% on the Text2Cypher test set and 30% on the SPIDER benchmark adapted for graph databases. This work demonstrates that high-quality synthetic data can effectively advance the state-of-the-art in Text2Cypher tasks.

Methods for carefully selecting or generating a small set of training data to learn from, i.e., data pruning, coreset selection, and data distillation, have been shown to be effective in reducing the ever-increasing cost of training neural networks. Behind this success are rigorously designed strategies for identifying informative training examples out of large datasets. However, these strategies come with additional computational costs associated with subset selection or data distillation before training begins, and furthermore, many are shown to even under-perform random sampling in high data compression regimes. As such, many data pruning, coreset selection, or distillation methods may not reduce 'time-to-accuracy', which has become a critical efficiency measure of training deep neural networks over large datasets. In this work, we revisit a powerful yet overlooked random sampling strategy to address these challenges and introduce an approach called Repeated Sampling of Random Subsets (RSRS or RS2), where we randomly sample the subset of training data for each epoch of model training. We test RS2 against thirty state-of-the-art data pruning and data distillation methods across four datasets including ImageNet. Our results demonstrate that RS2 significantly reduces time-to-accuracy compared to existing techniques. For example, when training on ImageNet in the high-compression regime (using less than 10% of the dataset each epoch), RS2 yields accuracy improvements up to 29% compared to competing pruning methods while offering a runtime reduction of 7x. Beyond the above meta-study, we provide a convergence analysis for RS2 and discuss its generalization capability. The primary goal of our work is to establish RS2 as a competitive baseline for future data selection or distillation techniques aimed at efficient training.

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.