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Conditional Inference Trees and Forests for Feature Selection
Milletich, Robert, Downes, Justin, Goley, Steve, Hirst, Newel
Conditional inference trees (CIT) and conditional inference forests (CIF) reduce split-selection bias by testing features before choosing split thresholds, but repeated permutation tests and threshold searches can make these methods computationally expensive. We study CIT and CIF as top-$k$ feature-ranking methods for downstream prediction using real-data benchmarks, runtime ablations, and synthetic feature-recovery experiments. At a fixed node, if the features and permutation budget do not depend on the node responses, Bonferroni-corrected $+1$ Monte Carlo permutation $p$-values control nodewise rejection under the complete permutation null. CIF ranks 4th among 17 classification methods on 22 datasets and 3rd among 18 regression methods on 8 datasets. With Bonferroni correction held fixed, the CIF runtime ablations indicate that adaptive stopping and the number of thresholds searched have the largest measured effect on runtime: turning off adaptive stopping and using exact threshold search increase fitting time by 4.0--8.4$\times$ and 1.9--10.8$\times$, respectively, while downstream score changes are at most 0.011. Sparse high-$p$ simulations indicate that forest feature sampling can leave informative features out of many split decisions. Overall, the results support CIF as a top-$k$ feature-ranking method in the evaluated downstream prediction benchmarks.
Relational and Sequential Conformal Inference for Energy Time Series over Graphs via Foundation Models
Niresi, Keivan Faghih, Cicirello, Alice, Fink, Olga
Accurate energy demand forecasting is essential for the reliable operation and planning of modern sustainable energy systems. Spatial-temporal graph neural networks (STGNNs) have recently achieved strong performance in point forecasting by jointly modeling temporal dynamics and relational dependencies across interconnected energy nodes. However, in real-world energy systems, accurate point forecasts alone are insufficient, as operators also require reliable uncertainty estimates to support risk-aware decision-making, grid stability, and operational planning under uncertainty. Conformal prediction provides a principled and model-agnostic framework for uncertainty quantification with statistical coverage guarantees, making it particularly attractive for safety-critical energy applications. However, existing conformal prediction approaches often fail to fully capture the complex spatial-temporal structure of energy systems. To address these limitations, we propose STOIC (Spatial-Temporal Graph Conformal Prediction with In-Context Learning), a novel framework that integrates graph-based forecasting with the zero-shot calibration capabilities of tabular foundation models. STOIC first generates point forecasts using an STGNN and subsequently reformulates spatial-temporal residuals into a tabular representation suitable for in-context learning. Leveraging a tabular foundation model, STOIC calibrates prediction intervals without task-specific retraining, effectively capturing both sequential and relational dependencies. We evaluate STOIC on five diverse benchmarks, including synthetic simulations as well as real-world electricity and district heating networks. Across all datasets, STOIC consistently outperforms existing conformal prediction baselines, delivering more reliable and robust uncertainty estimates for complex graph-structured energy time series.
Tensor-based second-order causal discovery
Ouyang, Nathan, Wang, Kexin, Seigal, Anna
Causal discovery seeks to uncover the causal dependencies among variables. For this purpose, we propose an algorithm called Tensor-based Second-order Causal Discovery (TSCD). Its input is a tensor obtained from the covariance matrices of observational and interventional data. Assuming the causal dependencies follow a linear structural equation model on a directed acyclic graph (DAG), TSCD outputs the DAG and the functions on its edges, requiring only that the noise variables are uncorrelated. We also implement a version of the approach for nonlinear models. Our focus on second-order statistics (via the covariance matrices) is motivated by their statistical and computational efficiency relative to higher-order moments, their identifiability relative to first-order statistics, and that they work regardless of whether the variables are Gaussian. We show that TSCD has identifiable causal order and parameters from a number of interventions that is logarithmic in the number of variables. Experiments show that TSCD is robust to noise, competitive with existing methods, and scales to hundreds of variables.
Graph Few-Shot Learning via Adaptive Spectrum Experts and Cross-Set Distribution Calibration
Graph few-shot learning has attracted increasing attention due to its ability to rapidly adapt models to new tasks with only limited labeled nodes. Despite the remarkable progress made by existing graph few-shot learning methods, several key limitations remain. First, most current approaches rely on predefined and unified graph filters (e.g., low-pass or high-pass filters) to globally enhance or suppress node frequency signals. Such fixed spectral operations fail to account for the heterogeneity of local topological structures inherent in real-world graphs. Moreover, these methods often assume that the support and query sets are drawn from the same distribution. However, under few-shot conditions, the limited labeled data in the support set may not sufficiently capture the complex distribution of the query set, leading to suboptimal generalization.
Dynamic Bundling with Large Language Models for Zero-Shot Inference on Text-Attributed Graphs
Large language models (LLMs) have been used in many zero-shot learning problems, with their strong generalization ability. Recently, adopting LLMs in textattributed graphs (TAGs) has drawn increasing attention. However, the adoption of LLMs faces two major challenges: limited information on graph structure and unreliable responses. LLMs struggle with text attributes isolated from the graph topology. Worse still, they yield unreliable predictions due to both information insufficiency and the inherent weakness of LLMs (e.g., hallucination). Towards this end, this paper proposes a novel method named Dynamic Text Bundling Supervision (DENSE) that queries LLMs with bundles of texts to obtain bundle-level labels and uses these labels to supervise graph neural networks.
FlowNet Modeling Dynamic Temporal Systems via Flow Propagation
Accurately modeling complex dynamic spatio-temporal systems requires capturing flow-mediated interdependencies and context-sensitive interaction dynamics. Existing methods, predominantly graph-based or attention-driven, rely on similaritydriven connectivity assumptions, neglecting asymmetric flow exchanges that govern system evolution. We propose Spatio-Temporal Flow, a physics-inspired paradigm that explicitly models dynamic node couplings through quantifiable flow transfers governed by conservation principles. Building on this, we design FlowNet, a novel architecture leveraging flow tokens as information carriers to simulate source-todestination transfers via Flow Allocation Modules, ensuring state redistribution aligns with conservation laws. FlowNet dynamically adjusts the interaction radius through an Adaptive Spatial Masking module, suppressing irrelevant noise while enabling context-aware propagation. A cascaded architecture enhances scalability and nonlinear representation capacity. Experiments demonstrate that FlowNet significantly outperforms existing state-of-the-art approaches on seven metrics in the modeling of three real-world systems, validating its efficiency and physical interpretability. We establish a principled methodology for modeling complex systems through spatio-temporal flow interactions.
Return of ChebNet: Understanding and Improving an Overlooked GNN on Long-Range Tasks
ChebNet, one of the earliest spectral GNNs, has largely been overshadowed by Message Passing Neural Networks (MPNNs), which gained popularity for their simplicity and effectiveness in capturing local graph structure. Despite their success, MPNNs are limited in their ability to capture long-range dependencies between nodes. This has led researchers to adapt MPNNs through rewiring or make use of Graph Transformers, which compromises the computational efficiency that characterized early spatial message-passing architectures, and typically disregards the graph structure. Almost a decade after its original introduction, we revisit ChebNet to shed light on its ability to model distant node interactions. We find that out-of-box, ChebNet already shows competitive advantages relative to classical MPNNs and GTs on long-range benchmarks, while maintaining good scalability properties for high-order polynomials. However, we uncover that this polynomial expansion leads ChebNet to an unstable regime during training. To address this limitation, we cast ChebNet as a stable and non-dissipative dynamical system, which we coin Stable-ChebNet. Our Stable-ChebNetmodel allows for stable information propagation, and has controllable dynamics which do not require the use of eigendecompositions, positional encodings, or graph rewiring.
Probing Neural Combinatorial Optimization Models
Neural combinatorial optimization (NCO) has achieved remarkable performance, yet its learned model representations and decision rationale remain a black box. This impedes both academic research and practical deployment, since researchers and stakeholders require deeper insights into NCO models. In this paper, we take the first critical step towards interpreting NCO models by investigating their representations through various probing tasks. Moreover, we introduce a novel probing tool named Coefficient Significance Probing (CS-Probing) to enable deeper analysis of NCO representations by examining the coefficients and statistical significance during probing. Extensive experiments and analysis reveal that NCO models encode low-level information essential for solution construction, while capturing high-level knowledge to facilitate better decisions. Using CS-Probing, we find that prevalent NCO models impose varying inductive biases on their learned representations, uncover direct evidence related to model generalization, and identify key embedding dimensions associated with specific knowledge. These insights can be potentially translated into practice, for example, with minor code modifications, we improve the generalization of the analyzed model. Our work represents a first systematic attempt to interpret black-box NCO models, showcasing probing as a promising tool for analyzing their internal mechanisms and revealing insights for the NCO community. The source code is publicly available 2.
Ultrametric Cluster Hierarchies: IWant'em All!
Hierarchical clustering is a powerful tool for exploratory data analysis, organizing data into a tree of clusterings from which a partition can be chosen. This paper generalizes these ideas by proving that, for any reasonable hierarchy, one can optimally solve any center-based clustering objective over it (such as k-means). Moreover, these solutions can be found exceedingly quickly and are themselves necessarily hierarchical. Thus, given a cluster tree, we show that one can quickly access a plethora of new, equally meaningful hierarchies. Just as in standard hierarchical clustering, one can then choose any desired partition from these new hierarchies. We conclude by verifying the utility of our proposed techniques across datasets, hierarchies, and partitioning schemes.
Rethinking Neural Combinatorial Optimization for Vehicle Routing Problems with Different Constraint Tightness Degrees
Recent neural combinatorial optimization (NCO) methods have shown promising problem-solving ability without requiring domain-specific expertise. Most existing NCO methods use training and testing data with a fixed constraint value and lack research on the effect of constraint tightness on the performance of NCO methods. This paper takes the capacity-constrained vehicle routing problem (CVRP) as an example to empirically analyze the NCO performance under different tightness degrees of the capacity constraint. Our analysis reveals that existing NCO methods overfit the capacity constraint, and they can only perform satisfactorily on a small range of the constraint values but poorly on other values. To tackle this drawback of existing NCO methods, we develop an efficient training scheme that explicitly considers varying degrees of constraint tightness and propose a multiexpert module to learn a generally adaptable solving strategy. Experimental results show that the proposed method can effectively overcome the overfitting issue, demonstrating superior performance on the CVRP and CVRP with time windows (CVRPTW) with various constraint tightness degrees.