Daily Papers

The rapid expansion of long-context Large Language Models (LLMs) has reignited debate on whether Retrieval-Augmented Generation (RAG) remains necessary. However, empirical evidence reveals persistent limitations of long-context inference, including the lost-in-the-middle phenomenon, high computational cost, and poor scalability for multi-document reasoning. Conversely, traditional RAG systems, while efficient, are constrained by flat chunk-level retrieval that introduces semantic noise and fails to support structured cross-document synthesis. We present FABLE, a Forest-based Adaptive Bi-path LLM-Enhanced retrieval framework that integrates LLMs into both knowledge organization and retrieval. FABLE constructs LLM-enhanced hierarchical forest indexes with multi-granularity semantic structures, then employs a bi-path strategy combining LLM-guided hierarchical traversal with structure-aware propagation for fine-grained evidence acquisition, with explicit budget control for adaptive efficiency trade-offs. Extensive experiments demonstrate that FABLE consistently outperforms SOTA RAG methods and achieves comparable accuracy to full-context LLM inference with up to 94\% token reduction, showing that long-context LLMs amplify rather than fully replace the need for structured retrieval.

A heuristic extending the Squarified Treemap technique for the representation of hierarchical information as treemaps is presented. The original technique gives high quality treemap views, since items are laid out with rectangles that approximate squares, allowing easy comparison and selection operations. New key steps, with a low computational impact, have been introduced to yield treemaps with even better aspect ratios and higher homogeneity among items.

We present a novel method for hierarchical topic detection where topics are obtained by clustering documents in multiple ways. Specifically, we model document collections using a class of graphical models called hierarchical latent tree models (HLTMs). The variables at the bottom level of an HLTM are observed binary variables that represent the presence/absence of words in a document. The variables at other levels are binary latent variables, with those at the lowest latent level representing word co-occurrence patterns and those at higher levels representing co-occurrence of patterns at the level below. Each latent variable gives a soft partition of the documents, and document clusters in the partitions are interpreted as topics. Latent variables at high levels of the hierarchy capture long-range word co-occurrence patterns and hence give thematically more general topics, while those at low levels of the hierarchy capture short-range word co-occurrence patterns and give thematically more specific topics. Unlike LDA-based topic models, HLTMs do not refer to a document generation process and use word variables instead of token variables. They use a tree structure to model the relationships between topics and words, which is conducive to the discovery of meaningful topics and topic hierarchies.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

Treemaps are a popular technique to visualize hierarchical data. The input is a weighted tree tree where the weight of each node is the sum of the weights of its children. A treemap for tree is a hierarchical partition of a rectangle into simply connected regions, usually rectangles. Each region represents a node of tree and its area is proportional to the weight of the corresponding node. An important quality criterion for treemaps is the aspect ratio of its regions. One cannot bound the aspect ratio if the regions are restricted to be rectangles. In contrast, polygonal partitions, that use convex polygons, have bounded aspect ratio. We are the first to obtain convex partitions with optimal aspect ratio O(depth(tree)). However, depth(tree) still depends on the input tree. Hence we introduce a new type of treemaps, namely orthoconvex treemaps, where regions representing leaves are rectangles, L-, and S-shapes, and regions representing internal nodes are orthoconvex polygons. We prove that any input tree, irrespective of the weights of the nodes and the depth of the tree, admits an orthoconvex treemap of constant aspect ratio. We also obtain several specialized results for single-level treemaps, that is, treemaps where the input tree has depth~1.

The increasing demand for commodities is leading to changes in land use worldwide. In the tropics, deforestation, which causes high carbon emissions and threatens biodiversity, is often linked to agricultural expansion. While the need for deforestation-free global supply chains is widely recognized, making progress in practice remains a challenge. Here, we propose an automated approach that aims to support conservation and sustainable land use planning decisions by mapping tropical landscapes at large scale and high spatial resolution following the High Carbon Stock (HCS) approach. A deep learning approach is developed that estimates canopy height for each 10 m Sentinel-2 pixel by learning from sparse GEDI LIDAR reference data, achieving an overall RMSE of 6.3 m. We show that these wall-to-wall maps of canopy top height are predictive for classifying HCS forests and degraded areas with an overall accuracy of 86 % and produce a first high carbon stock map for Indonesia, Malaysia, and the Philippines.

Document retrieval is a core component of question-answering systems, as it enables conditioning answer generation on new and large-scale corpora. While effective, the standard practice of encoding documents into high-dimensional embeddings for similarity search entails large memory and compute footprints, and also makes it hard to inspect the inner workings of the system. In this paper, we propose a tree-based method for organizing and representing reference documents at various granular levels, which offers the flexibility to balance cost and utility, and eases the inspection of the corpus content and retrieval operations. Our method, called ReTreever, jointly learns a routing function per internal node of a binary tree such that query and reference documents are assigned to similar tree branches, hence directly optimizing for retrieval performance. Our evaluations show that ReTreever generally preserves full representation accuracy. Its hierarchical structure further provides strong coarse representations and enhances transparency by indirectly learning meaningful semantic groupings. Among hierarchical retrieval methods, ReTreever achieves the best retrieval accuracy at the lowest latency, proving that this family of techniques can be viable in practical applications.

As an effective method to boost the performance of Large Language Models (LLMs) on the question answering (QA) task, Retrieval-Augmented Generation (RAG), which queries highly relevant information from external complex documents, has attracted tremendous attention from both industry and academia. Existing RAG approaches often focus on general documents, and they overlook the fact that many real-world documents (such as books, booklets, handbooks, etc.) have a hierarchical structure, which organizes their content from different granularity levels, leading to poor performance for the QA task. To address these limitations, we introduce BookRAG, a novel RAG approach targeted for documents with a hierarchical structure, which exploits logical hierarchies and traces entity relations to query the highly relevant information. Specifically, we build a novel index structure, called BookIndex, by extracting a hierarchical tree from the document, which serves as the role of its table of contents, using a graph to capture the intricate relationships between entities, and mapping entities to tree nodes. Leveraging the BookIndex, we then propose an agent-based query method inspired by the Information Foraging Theory, which dynamically classifies queries and employs a tailored retrieval workflow. Extensive experiments on three widely adopted benchmarks demonstrate that BookRAG achieves state-of-the-art performance, significantly outperforming baselines in both retrieval recall and QA accuracy while maintaining competitive efficiency.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

We present a new approach for the approximate K-nearest neighbor search based on navigable small world graphs with controllable hierarchy (Hierarchical NSW, HNSW). The proposed solution is fully graph-based, without any need for additional search structures, which are typically used at the coarse search stage of the most proximity graph techniques. Hierarchical NSW incrementally builds a multi-layer structure consisting from hierarchical set of proximity graphs (layers) for nested subsets of the stored elements. The maximum layer in which an element is present is selected randomly with an exponentially decaying probability distribution. This allows producing graphs similar to the previously studied Navigable Small World (NSW) structures while additionally having the links separated by their characteristic distance scales. Starting search from the upper layer together with utilizing the scale separation boosts the performance compared to NSW and allows a logarithmic complexity scaling. Additional employment of a heuristic for selecting proximity graph neighbors significantly increases performance at high recall and in case of highly clustered data. Performance evaluation has demonstrated that the proposed general metric space search index is able to strongly outperform previous opensource state-of-the-art vector-only approaches. Similarity of the algorithm to the skip list structure allows straightforward balanced distributed implementation.

Taxonomy is a hierarchically structured knowledge graph that plays a crucial role in machine intelligence. The taxonomy expansion task aims to find a position for a new term in an existing taxonomy to capture the emerging knowledge in the world and keep the taxonomy dynamically updated. Previous taxonomy expansion solutions neglect valuable information brought by the hierarchical structure and evaluate the correctness of merely an added edge, which downgrade the problem to node-pair scoring or mini-path classification. In this paper, we propose the Hierarchy Expansion Framework (HEF), which fully exploits the hierarchical structure's properties to maximize the coherence of expanded taxonomy. HEF makes use of taxonomy's hierarchical structure in multiple aspects: i) HEF utilizes subtrees containing most relevant nodes as self-supervision data for a complete comparison of parental and sibling relations; ii) HEF adopts a coherence modeling module to evaluate the coherence of a taxonomy's subtree by integrating hypernymy relation detection and several tree-exclusive features; iii) HEF introduces the Fitting Score for position selection, which explicitly evaluates both path and level selections and takes full advantage of parental relations to interchange information for disambiguation and self-correction. Extensive experiments show that by better exploiting the hierarchical structure and optimizing taxonomy's coherence, HEF vastly surpasses the prior state-of-the-art on three benchmark datasets by an average improvement of 46.7% in accuracy and 32.3% in mean reciprocal rank.

Let T be a rooted and weighted tree, where the weight of any node is equal to the sum of the weights of its children. The popular Treemap algorithm visualizes such a tree as a hierarchical partition of a square into rectangles, where the area of the rectangle corresponding to any node in T is equal to the weight of that node. The aspect ratio of the rectangles in such a rectangular partition necessarily depends on the weights and can become arbitrarily high. We introduce a new hierarchical partition scheme, called a polygonal partition, which uses convex polygons rather than just rectangles. We present two methods for constructing polygonal partitions, both having guarantees on the worst-case aspect ratio of the constructed polygons; in particular, both methods guarantee a bound on the aspect ratio that is independent of the weights of the nodes. We also consider rectangular partitions with slack, where the areas of the rectangles may differ slightly from the weights of the corresponding nodes. We show that this makes it possible to obtain partitions with constant aspect ratio. This result generalizes to hyper-rectangular partitions in R^d. We use these partitions with slack for embedding ultrametrics into d-dimensional Euclidean space: we give a rm polylog(Delta)-approximation algorithm for embedding n-point ultrametrics into R^d with minimum distortion, where Delta denotes the spread of the metric, i.e., the ratio between the largest and the smallest distance between two points. The previously best-known approximation ratio for this problem was polynomial in n. This is the first algorithm for embedding a non-trivial family of weighted-graph metrics into a space of constant dimension that achieves polylogarithmic approximation ratio.

Paper search is an important activity for researchers, typically involving using a query with description of a topic to find relevant papers. As research deepens, paper search requirements may become more flexible, sometimes involving specific details such as module configuration rather than being limited to coarse-grained topics. However, previous paper search systems are unable to meet these flexible-grained requirements, as these systems mainly collect paper abstracts to construct index of corpus, which lack detailed information to support retrieval by finer-grained queries. In this work, we propose PaperRegister, consisted of offline hierarchical indexing and online adaptive retrieval, transforming traditional abstract-based index into hierarchical index tree for paper search, thereby supporting queries at flexible granularity. Experiments on paper search tasks across a range of granularity demonstrate that PaperRegister achieves the state-of-the-art performance, and particularly excels in fine-grained scenarios, highlighting the good potential as an effective solution for flexible-grained paper search in real-world applications. Code for this work is in https://github.com/Li-Z-Q/PaperRegister.

This paper presents algorithms for hierarchical, agglomerative clustering which perform most efficiently in the general-purpose setup that is given in modern standard software. Requirements are: (1) the input data is given by pairwise dissimilarities between data points, but extensions to vector data are also discussed (2) the output is a "stepwise dendrogram", a data structure which is shared by all implementations in current standard software. We present algorithms (old and new) which perform clustering in this setting efficiently, both in an asymptotic worst-case analysis and from a practical point of view. The main contributions of this paper are: (1) We present a new algorithm which is suitable for any distance update scheme and performs significantly better than the existing algorithms. (2) We prove the correctness of two algorithms by Rohlf and Murtagh, which is necessary in each case for different reasons. (3) We give well-founded recommendations for the best current algorithms for the various agglomerative clustering schemes.

Knowledge of tree species distribution is fundamental to managing forests. New deep learning approaches promise significant accuracy gains for forest mapping, and are becoming a critical tool for mapping multiple tree species at scale. To advance the field, deep learning researchers need large benchmark datasets with high-quality annotations. To this end, we present the PureForest dataset: a large-scale, open, multimodal dataset designed for tree species classification from both Aerial Lidar Scanning (ALS) point clouds and Very High Resolution (VHR) aerial images. Most current public Lidar datasets for tree species classification have low diversity as they only span a small area of a few dozen annotated hectares at most. In contrast, PureForest has 18 tree species grouped into 13 semantic classes, and spans 339 km^2 across 449 distinct monospecific forests, and is to date the largest and most comprehensive Lidar dataset for the identification of tree species. By making PureForest publicly available, we hope to provide a challenging benchmark dataset to support the development of deep learning approaches for tree species identification from Lidar and/or aerial imagery. In this data paper, we describe the annotation workflow, the dataset, the recommended evaluation methodology, and establish a baseline performance from both 3D and 2D modalities.

Hierarchical clustering of networks consists in finding a tree of communities, such that lower levels of the hierarchy reveal finer-grained community structures. There are two main classes of algorithms tackling this problem. Divisive (top-down) algorithms recursively partition the nodes into two communities, until a stopping rule indicates that no further split is needed. In contrast, agglomerative (bottom-up) algorithms first identify the smallest community structure and then repeatedly merge the communities using a linkage method. In this article, we establish theoretical guarantees for the recovery of the hierarchical tree and community structure of a Hierarchical Stochastic Block Model by a bottom-up algorithm. We also establish that this bottom-up algorithm attains the information-theoretic threshold for exact recovery at intermediate levels of the hierarchy. Notably, these recovery conditions are less restrictive compared to those existing for top-down algorithms. This shows that bottom-up algorithms extend the feasible region for achieving exact recovery at intermediate levels. Numerical experiments on both synthetic and real data sets confirm the superiority of bottom-up algorithms over top-down algorithms. We also observe that top-down algorithms can produce dendrograms with inversions. These findings contribute to a better understanding of hierarchical clustering techniques and their applications in network analysis.

Detailed forest inventories are critical for sustainable and flexible management of forest resources, to conserve various ecosystem services. Modern airborne laser scanners deliver high-density point clouds with great potential for fine-scale forest inventory and analysis, but automatically partitioning those point clouds into meaningful entities like individual trees or tree components remains a challenge. The present study aims to fill this gap and introduces a deep learning framework, termed ForAINet, that is able to perform such a segmentation across diverse forest types and geographic regions. From the segmented data, we then derive relevant biophysical parameters of individual trees as well as stands. The system has been tested on FOR-Instance, a dataset of point clouds that have been acquired in five different countries using surveying drones. The segmentation back-end achieves over 85% F-score for individual trees, respectively over 73% mean IoU across five semantic categories: ground, low vegetation, stems, live branches and dead branches. Building on the segmentation results our pipeline then densely calculates biophysical features of each individual tree (height, crown diameter, crown volume, DBH, and location) and properties per stand (digital terrain model and stand density). Especially crown-related features are in most cases retrieved with high accuracy, whereas the estimates for DBH and location are less reliable, due to the airborne scanning setup.

We provide a reproducible, end-to-end demonstration of vector search with OpenAI embeddings using Lucene on the popular MS MARCO passage ranking test collection. The main goal of our work is to challenge the prevailing narrative that a dedicated vector store is necessary to take advantage of recent advances in deep neural networks as applied to search. Quite the contrary, we show that hierarchical navigable small-world network (HNSW) indexes in Lucene are adequate to provide vector search capabilities in a standard bi-encoder architecture. This suggests that, from a simple cost-benefit analysis, there does not appear to be a compelling reason to introduce a dedicated vector store into a modern "AI stack" for search, since such applications have already received substantial investments in existing, widely deployed infrastructure.

We present PrediTree, the first comprehensive open-source dataset designed for training and evaluating tree height prediction models at sub-meter resolution. This dataset combines very high-resolution (0.5m) LiDAR-derived canopy height maps, spatially aligned with multi-temporal and multi-spectral imagery, across diverse forest ecosystems in France, totaling 3,141,568 images. PrediTree addresses a critical gap in forest monitoring capabilities by enabling the training of deep learning methods that can predict tree growth based on multiple past observations. %Initially focused on French forests, PrediTree is designed as an expanding resource with ongoing efforts to incorporate data from other countries. To make use of this PrediTree dataset, we propose an encoder-decoder framework that requires the multi-temporal multi-spectral imagery and the relative time differences in years between the canopy height map timestamp (target) and each image acquisition date for which this framework predicts the canopy height. The conducted experiments demonstrate that a U-Net architecture trained on the PrediTree dataset provides the highest masked mean squared error of 11.78%, outperforming the next-best architecture, ResNet-50, by around 12%, and cutting the error of the same experiments but on fewer bands (red, green, blue only), by around 30%. This dataset is publicly available on URL{HuggingFace}, and both processing and training codebases are available on URL{GitHub}.

Hierarchical classification offers an approach to incorporate the concept of mistake severity by leveraging a structured, labeled hierarchy. However, decoding in such settings frequently relies on heuristic decision rules, which may not align with task-specific evaluation metrics. In this work, we propose a framework for the optimal decoding of an output probability distribution with respect to a target metric. We derive optimal decision rules for increasingly complex prediction settings, providing universal algorithms when candidates are limited to the set of nodes. In the most general case of predicting a subset of nodes, we focus on rules dedicated to the hierarchical hF_{beta} scores, tailored to hierarchical settings. To demonstrate the practical utility of our approach, we conduct extensive empirical evaluations, showcasing the superiority of our proposed optimal strategies, particularly in underdetermined scenarios. These results highlight the potential of our methods to enhance the performance and reliability of hierarchical classifiers in real-world applications. The code is available at https://github.com/RomanPlaud/hierarchical_decision_rules

This research advances individual tree crown (ITC) segmentation in lidar data, using a deep learning model applicable to various laser scanning types: airborne (ULS), terrestrial (TLS), and mobile (MLS). It addresses the challenge of transferability across different data characteristics in 3D forest scene analysis. The study evaluates the model's performance based on platform (ULS, MLS) and data density, testing five scenarios with varying input data, including sparse versions, to gauge adaptability and canopy layer efficacy. The model, based on PointGroup architecture, is a 3D CNN with separate heads for semantic and instance segmentation, validated on diverse point cloud datasets. Results show point cloud sparsification enhances performance, aiding sparse data handling and improving detection in dense forests. The model performs well with >50 points per sq. m densities but less so at 10 points per sq. m due to higher omission rates. It outperforms existing methods (e.g., Point2Tree, TLS2trees) in detection, omission, commission rates, and F1 score, setting new benchmarks on LAUTx, Wytham Woods, and TreeLearn datasets. In conclusion, this study shows the feasibility of a sensor-agnostic model for diverse lidar data, surpassing sensor-specific approaches and setting new standards in tree segmentation, particularly in complex forests. This contributes to future ecological modeling and forest management advancements.

Accurately quantifying tree cover is an important metric for ecosystem monitoring and for assessing progress in restored sites. Recent works have shown that deep learning-based segmentation algorithms are capable of accurately mapping trees at country and continental scales using high-resolution aerial and satellite imagery. Mapping at high (ideally sub-meter) resolution is necessary to identify individual trees, however there are few open-access datasets containing instance level annotations and those that exist are small or not geographically diverse. We present a novel open-access dataset for individual tree crown delineation (TCD) in high-resolution aerial imagery sourced from OpenAerialMap (OAM). Our dataset, OAM-TCD, comprises 5072 2048x2048 px images at 10 cm/px resolution with associated human-labeled instance masks for over 280k individual and 56k groups of trees. By sampling imagery from around the world, we are able to better capture the diversity and morphology of trees in different terrestrial biomes and in both urban and natural environments. Using our dataset, we train reference instance and semantic segmentation models that compare favorably to existing state-of-the-art models. We assess performance through k-fold cross-validation and comparison with existing datasets; additionally we demonstrate compelling results on independent aerial imagery captured over Switzerland and compare to municipal tree inventories and LIDAR-derived canopy maps in the city of Zurich. Our dataset, models and training/benchmark code are publicly released under permissive open-source licenses: Creative Commons (majority CC BY 4.0), and Apache 2.0 respectively.

Accurate estimation of forest biomass, a major carbon sink, relies heavily on tree-level traits such as height and species. Unoccupied Aerial Vehicles (UAVs) capturing high-resolution imagery from a single RGB camera offer a cost-effective and scalable approach for mapping and measuring individual trees. We introduce BIRCH-Trees, the first benchmark for individual tree height and species estimation from tree-centered UAV images, spanning three datasets: temperate forests, tropical forests, and boreal plantations. We also present DINOvTree, a unified approach using a Vision Foundation Model (VFM) backbone with task-specific heads for simultaneous height and species prediction. Through extensive evaluations on BIRCH-Trees, we compare DINOvTree against commonly used vision methods, including VFMs, as well as biological allometric equations. We find that DINOvTree achieves top overall results with accurate height predictions and competitive classification accuracy while using only 54% to 58% of the parameters of the second-best approach.

Hierarchical Text Classification (HTC) is a natural language processing task with the objective to classify text documents into a set of classes from a structured class hierarchy. Many HTC approaches have been proposed which attempt to leverage the class hierarchy information in various ways to improve classification performance. Machine learning-based classification approaches require large amounts of training data and are most-commonly compared through three established benchmark datasets, which include the Web Of Science (WOS), Reuters Corpus Volume 1 Version 2 (RCV1-V2) and New York Times (NYT) datasets. However, apart from the RCV1-V2 dataset which is well-documented, these datasets are not accompanied with detailed description methodologies. In this paper, we introduce three new HTC benchmark datasets in the domain of research publications which comprise the titles and abstracts of papers from the Web of Science publication database. We first create two baseline datasets which use existing journal-and citation-based classification schemas. Due to the respective shortcomings of these two existing schemas, we propose an approach which combines their classifications to improve the reliability and robustness of the dataset. We evaluate the three created datasets with a clustering-based analysis and show that our proposed approach results in a higher quality dataset where documents that belong to the same class are semantically more similar compared to the other datasets. Finally, we provide the classification performance of four state-of-the-art HTC approaches on these three new datasets to provide baselines for future studies on machine learning-based techniques for scientific publication classification.

Very High Resolution (VHR) forest structure data at individual-tree scale is essential for carbon, biodiversity, and ecosystem monitoring. Still, airborne LiDAR remains costly and infrequent despite being the reference for forest structure metrics like Canopy Height Model (CHM), Plant Area Index (PAI), and Foliage Height Diversity (FHD). We propose FSKD: a LiDAR-to-RGB-Infrared (RGBI) knowledge distillation (KD) framework in which a multi-modal teacher fuses RGBI imagery with LiDAR-derived planar metrics and vertical profiles via cross-attention, and an RGBI-only SegFormer student learns to reproduce these outputs. Trained on 384 km^2 of forests in Saxony, Germany (20 cm ground sampling distance (GSD)) and evaluated on eight geographically distinct test tiles, the student achieves state-of-the-art (SOTA) zero-shot CHM performance (MedAE 4.17 m, R^2=0.51, IoU 0.87), outperforming HRCHM/DAC baselines by 29--46% in MAE (5.81 m vs. 8.14--10.84 m) with stronger correlation coefficients (0.713 vs. 0.166--0.652). Ablations show that multi-modal fusion improves performance by 10--26% over RGBI-only training, and that asymmetric distillation with appropriate model capacity is critical. The method jointly predicts CHM, PAI, and FHD, a multi-metric capability not provided by current monocular CHM estimators, although PAI/FHD transfer remains region-dependent and benefits from local calibration. The framework also remains effective under temporal mismatch (winter LiDAR, summer RGBI), removing strict co-acquisition constraints and enabling scalable 20 cm operational monitoring for workflows such as Digital Twin Germany and national Digital Orthophoto programs.

Hyperbolic embeddings offer excellent quality with few dimensions when embedding hierarchical data structures like synonym or type hierarchies. Given a tree, we give a combinatorial construction that embeds the tree in hyperbolic space with arbitrarily low distortion without using optimization. On WordNet, our combinatorial embedding obtains a mean-average-precision of 0.989 with only two dimensions, while Nickel et al.'s recent construction obtains 0.87 using 200 dimensions. We provide upper and lower bounds that allow us to characterize the precision-dimensionality tradeoff inherent in any hyperbolic embedding. To embed general metric spaces, we propose a hyperbolic generalization of multidimensional scaling (h-MDS). We show how to perform exact recovery of hyperbolic points from distances, provide a perturbation analysis, and give a recovery result that allows us to reduce dimensionality. The h-MDS approach offers consistently low distortion even with few dimensions across several datasets. Finally, we extract lessons from the algorithms and theory above to design a PyTorch-based implementation that can handle incomplete information and is scalable.

Modern forest monitoring workflows increasingly benefit from the growing availability of high-resolution satellite imagery and advances in deep learning. Two persistent challenges in this context are accurate pixel-level change detection and meaningful semantic change captioning for complex forest dynamics. While large language models (LLMs) are being adapted for interactive data exploration, their integration with vision-language models (VLMs) for remote sensing image change interpretation (RSICI) remains underexplored. To address this gap, we introduce an LLM-driven agent for integrated forest change analysis that supports natural language querying across multiple RSICI tasks. The proposed system builds upon a multi-level change interpretation (MCI) vision-language backbone with LLM-based orchestration. To facilitate adaptation and evaluation in forest environments, we further introduce the Forest-Change dataset, which comprises bi-temporal satellite imagery, pixel-level change masks, and multi-granularity semantic change captions generated using a combination of human annotation and rule-based methods. Experimental results show that the proposed system achieves mIoU and BLEU-4 scores of 67.10% and 40.17% on the Forest-Change dataset, and 88.13% and 34.41% on LEVIR-MCI-Trees, a tree-focused subset of LEVIR-MCI benchmark for joint change detection and captioning. These results highlight the potential of interactive, LLM-driven RSICI systems to improve accessibility, interpretability, and efficiency of forest change analysis. All data and code are publicly available at https://github.com/JamesBrockUoB/ForestChat.

In this paper, we present DendroMap, a novel approach to interactively exploring large-scale image datasets for machine learning (ML). ML practitioners often explore image datasets by generating a grid of images or projecting high-dimensional representations of images into 2-D using dimensionality reduction techniques (e.g., t-SNE). However, neither approach effectively scales to large datasets because images are ineffectively organized and interactions are insufficiently supported. To address these challenges, we develop DendroMap by adapting Treemaps, a well-known visualization technique. DendroMap effectively organizes images by extracting hierarchical cluster structures from high-dimensional representations of images. It enables users to make sense of the overall distributions of datasets and interactively zoom into specific areas of interests at multiple levels of abstraction. Our case studies with widely-used image datasets for deep learning demonstrate that users can discover insights about datasets and trained models by examining the diversity of images, identifying underperforming subgroups, and analyzing classification errors. We conducted a user study that evaluates the effectiveness of DendroMap in grouping and searching tasks by comparing it with a gridified version of t-SNE and found that participants preferred DendroMap. DendroMap is available at https://div-lab.github.io/dendromap/.

Hierarchical text classification (HTC) is the task of assigning labels to a text within a structured space organized as a hierarchy. Recent works treat HTC as a conventional multilabel classification problem, therefore evaluating it as such. We instead propose to evaluate models based on specifically designed hierarchical metrics and we demonstrate the intricacy of metric choice and prediction inference method. We introduce a new challenging dataset and we evaluate fairly, recent sophisticated models, comparing them with a range of simple but strong baselines, including a new theoretically motivated loss. Finally, we show that those baselines are very often competitive with the latest models. This highlights the importance of carefully considering the evaluation methodology when proposing new methods for HTC. Code implementation and dataset are available at https://github.com/RomanPlaud/revisitingHTC.

Hierarchical text classification aims to categorize each document into a set of classes in a label taxonomy, which is a fundamental web text mining task with broad applications such as web content analysis and semantic indexing. Most earlier works focus on fully or semi-supervised methods that require a large amount of human annotated data which is costly and time-consuming to acquire. To alleviate human efforts, in this paper, we work on hierarchical text classification with a minimal amount of supervision: using the sole class name of each node as the only supervision. Recently, large language models (LLM) have shown competitive performance on various tasks through zero-shot prompting, but this method performs poorly in the hierarchical setting because it is ineffective to include the large and structured label space in a prompt. On the other hand, previous weakly-supervised hierarchical text classification methods only utilize the raw taxonomy skeleton and ignore the rich information hidden in the text corpus that can serve as additional class-indicative features. To tackle the above challenges, we propose TELEClass, Taxonomy Enrichment and LLM-Enhanced weakly-supervised hierarchical text Classification, which combines the general knowledge of LLMs and task-specific features mined from an unlabeled corpus. TELEClass automatically enriches the raw taxonomy with class-indicative features for better label space understanding and utilizes novel LLM-based data annotation and generation methods specifically tailored for the hierarchical setting. Experiments show that TELEClass can significantly outperform previous baselines while achieving comparable performance to zero-shot prompting of LLMs with drastically less inference cost.

Accurate canopy height information is essential for quantifying forest carbon, monitoring restoration and degradation, and assessing habitat structure, yet high-fidelity measurements from airborne laser scanning (ALS) remain unevenly available globally. Here we present CHMv2, a global, meter-resolution canopy height map derived from high-resolution optical satellite imagery using a depth-estimation model built on DINOv3 and trained against ALS canopy height models. Compared to existing products, CHMv2 substantially improves accuracy, reduces bias in tall forests, and better preserves fine-scale structure such as canopy edges and gaps. These gains are enabled by a large expansion of geographically diverse training data, automated data curation and registration, and a loss formulation and data sampling strategy tailored to canopy height distributions. We validate CHMv2 against independent ALS test sets and against tens of millions of GEDI and ICESat-2 observations, demonstrating consistent performance across major forest biomes.

Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring methods involve ground measurements, requiring extensive cost, time and labor. Advances in drone remote sensing and computer vision offer great potential for mapping individual trees from aerial imagery at broad-scale. Large pre-trained vision models, such as the Segment Anything Model (SAM), represent a particularly compelling choice given limited labeled data. In this work, we compare methods leveraging SAM for the task of automatic tree crown instance segmentation in high resolution drone imagery in three use cases: 1) boreal plantations, 2) temperate forests and 3) tropical forests. We also study the integration of elevation data into models, in the form of Digital Surface Model (DSM) information, which can readily be obtained at no additional cost from RGB drone imagery. We present BalSAM, a model leveraging SAM and DSM information, which shows potential over other methods, particularly in the context of plantations. We find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts. However, efficiently tuning SAM end-to-end and integrating DSM information are both promising avenues for tree crown instance segmentation models.

Given a massive graph, how can we exploit its hierarchical structure for concisely but exactly summarizing the graph? By exploiting the structure, can we achieve better compression rates than state-of-the-art graph summarization methods? The explosive proliferation of the Web has accelerated the emergence of large graphs, such as online social networks and hyperlink networks. Consequently, graph compression has become increasingly important to process such large graphs without expensive I/O over the network or to disk. Among a number of approaches, graph summarization, which in essence combines similar nodes into a supernode and describe their connectivity concisely, protrudes with several advantages. However, we note that it fails to exploit pervasive hierarchical structures of real-world graphs as its underlying representation model enforces supernodes to be disjoint. In this work, we propose the hierarchical graph summarization model, which is an expressive graph representation model that includes the previous one proposed by Navlakha et al. as a special case. The new model represents an unweighted graph using positive and negative edges between hierarchical supernodes, each of which can contain others. Then, we propose Slugger, a scalable heuristic for concisely and exactly representing a given graph under our new model. Slugger greedily merges nodes into supernodes while maintaining and exploiting their hierarchy, which is later pruned. Slugger significantly accelerates this process by sampling, approximation, and memoization. Our experiments on 16 real-world graphs show that Slugger is (a) Effective: yielding up to 29.6% more concise summary than state-of-the-art lossless summarization methods, (b) Fast: summarizing a graph with 0.8 billion edges in a few hours, and (c) Scalable: scaling linearly with the number of edges in the input graph.

While the availability of large and diverse datasets has contributed to significant breakthroughs in autonomous driving and indoor applications, forestry applications are still lagging behind and new forest datasets would most certainly contribute to achieving significant progress in the development of data-driven methods for forest-like scenarios. This paper introduces a forest dataset called FinnWoodlands, which consists of RGB stereo images, point clouds, and sparse depth maps, as well as ground truth manual annotations for semantic, instance, and panoptic segmentation. FinnWoodlands comprises a total of 4226 objects manually annotated, out of which 2562 objects (60.6\%) correspond to tree trunks classified into three different instance categories, namely "Spruce Tree", "Birch Tree", and "Pine Tree". Besides tree trunks, we also annotated "Obstacles" objects as instances as well as the semantic stuff classes "Lake", "Ground", and "Track". Our dataset can be used in forestry applications where a holistic representation of the environment is relevant. We provide an initial benchmark using three models for instance segmentation, panoptic segmentation, and depth completion, and illustrate the challenges that such unstructured scenarios introduce.

We define and investigate the problem of c-approximate window search: approximate nearest neighbor search where each point in the dataset has a numeric label, and the goal is to find nearest neighbors to queries within arbitrary label ranges. Many semantic search problems, such as image and document search with timestamp filters, or product search with cost filters, are natural examples of this problem. We propose and theoretically analyze a modular tree-based framework for transforming an index that solves the traditional c-approximate nearest neighbor problem into a data structure that solves window search. On standard nearest neighbor benchmark datasets equipped with random label values, adversarially constructed embeddings, and image search embeddings with real timestamps, we obtain up to a 75times speedup over existing solutions at the same level of recall.

Hyperbolic geometry is gaining traction in machine learning for its effectiveness at capturing hierarchical structures in real-world data. Hyperbolic spaces, where neighborhoods grow exponentially, offer substantial advantages and consistently deliver state-of-the-art results across diverse applications. However, hyperbolic classifiers often grapple with computational challenges. Methods reliant on Riemannian optimization frequently exhibit sluggishness, stemming from the increased computational demands of operations on Riemannian manifolds. In response to these challenges, we present hyperDT, a novel extension of decision tree algorithms into hyperbolic space. Crucially, hyperDT eliminates the need for computationally intensive Riemannian optimization, numerically unstable exponential and logarithmic maps, or pairwise comparisons between points by leveraging inner products to adapt Euclidean decision tree algorithms to hyperbolic space. Our approach is conceptually straightforward and maintains constant-time decision complexity while mitigating the scalability issues inherent in high-dimensional Euclidean spaces. Building upon hyperDT we introduce hyperRF, a hyperbolic random forest model. Extensive benchmarking across diverse datasets underscores the superior performance of these models, providing a swift, precise, accurate, and user-friendly toolkit for hyperbolic data analysis.

Object categories are typically organized into a multi-granularity taxonomic hierarchy. When classifying categories at different hierarchy levels, traditional uni-modal approaches focus primarily on image features, revealing limitations in complex scenarios. Recent studies integrating Vision-Language Models (VLMs) with class hierarchies have shown promise, yet they fall short of fully exploiting the hierarchical relationships. These efforts are constrained by their inability to perform effectively across varied granularity of categories. To tackle this issue, we propose a novel framework (HGCLIP) that effectively combines CLIP with a deeper exploitation of the Hierarchical class structure via Graph representation learning. We explore constructing the class hierarchy into a graph, with its nodes representing the textual or image features of each category. After passing through a graph encoder, the textual features incorporate hierarchical structure information, while the image features emphasize class-aware features derived from prototypes through the attention mechanism. Our approach demonstrates significant improvements on 11 diverse visual recognition benchmarks. Our codes are fully available at https://github.com/richard-peng-xia/HGCLIP.

Accurate estimates of Above Ground Biomass (AGB) are essential in addressing two of humanity's biggest challenges, climate change and biodiversity loss. Existing datasets for AGB estimation from satellite imagery are limited. Either they focus on specific, local regions at high resolution, or they offer global coverage at low resolution. There is a need for a machine learning-ready, globally representative, high-resolution benchmark. Our findings indicate significant variability in biomass estimates across different vegetation types, emphasizing the necessity for a dataset that accurately captures global diversity. To address these gaps, we introduce a comprehensive new dataset that is globally distributed, covers a range of vegetation types, and spans several years. This dataset combines AGB reference data from the GEDI mission with data from Sentinel-2 and PALSAR-2 imagery. Additionally, it includes pre-processed high-level features such as a dense canopy height map, an elevation map, and a land-cover classification map. We also produce a dense, high-resolution (10m) map of AGB predictions for the entire area covered by the dataset. Rigorously tested, our dataset is accompanied by several benchmark models and is publicly available. It can be easily accessed using a single line of code, offering a solid basis for efforts towards global AGB estimation. The GitHub repository github.com/ghjuliasialelli/AGBD serves as a one-stop shop for all code and data.

Document structure analysis (aka document layout analysis) is crucial for understanding the physical layout and logical structure of documents, with applications in information retrieval, document summarization, knowledge extraction, etc. In this paper, we concentrate on Hierarchical Document Structure Analysis (HDSA) to explore hierarchical relationships within structured documents created using authoring software employing hierarchical schemas, such as LaTeX, Microsoft Word, and HTML. To comprehensively analyze hierarchical document structures, we propose a tree construction based approach that addresses multiple subtasks concurrently, including page object detection (Detect), reading order prediction of identified objects (Order), and the construction of intended hierarchical structure (Construct). We present an effective end-to-end solution based on this framework to demonstrate its performance. To assess our approach, we develop a comprehensive benchmark called Comp-HRDoc, which evaluates the above subtasks simultaneously. Our end-to-end system achieves state-of-the-art performance on two large-scale document layout analysis datasets (PubLayNet and DocLayNet), a high-quality hierarchical document structure reconstruction dataset (HRDoc), and our Comp-HRDoc benchmark. The Comp-HRDoc benchmark will be released to facilitate further research in this field.

Hierarchical Text Classification (HTC) aims to assign texts to structured label hierarchies; however, it faces challenges due to data scarcity and model complexity. This study explores the feasibility of using black box Large Language Models (LLMs) accessed via APIs for HTC, as an alternative to traditional machine learning methods that require extensive labeled data and computational resources. We evaluate three prompting strategies -- Direct Leaf Label Prediction (DL), Direct Hierarchical Label Prediction (DH), and Top-down Multi-step Hierarchical Label Prediction (TMH) -- in both zero-shot and few-shot settings, comparing the accuracy and cost-effectiveness of these strategies. Experiments on two datasets show that a few-shot setting consistently improves classification accuracy compared to a zero-shot setting. While a traditional machine learning model achieves high accuracy on a dataset with a shallow hierarchy, LLMs, especially DH strategy, tend to outperform the machine learning model on a dataset with a deeper hierarchy. API costs increase significantly due to the higher input tokens required for deeper label hierarchies on DH strategy. These results emphasize the trade-off between accuracy improvement and the computational cost of prompt strategy. These findings highlight the potential of black box LLMs for HTC while underscoring the need to carefully select a prompt strategy to balance performance and cost.

Estimating canopy height and canopy height change at meter resolution from satellite imagery has numerous applications, such as monitoring forest health, logging activities, wood resources, and carbon stocks. However, many existing forest datasets are based on commercial or closed data sources, restricting the reproducibility and evaluation of new approaches. To address this gap, we introduce Open-Canopy, the first open-access and country-scale benchmark for very high resolution (1.5 m) canopy height estimation. Covering more than 87,000 km^2 across France, Open-Canopy combines SPOT satellite imagery with high resolution aerial LiDAR data. We also propose Open-Canopy-Delta, the first benchmark for canopy height change detection between two images taken at different years, a particularly challenging task even for recent models. To establish a robust foundation for these benchmarks, we evaluate a comprehensive list of state-of-the-art computer vision models for canopy height estimation. The dataset and associated codes can be accessed at https://github.com/fajwel/Open-Canopy.

Forest monitoring and education are key to forest protection, education and management, which is an effective way to measure the progress of a country's forest and climate commitments. Due to the lack of a large-scale wild forest monitoring benchmark, the common practice is to train the model on a common outdoor benchmark (e.g., KITTI) and evaluate it on real forest datasets (e.g., CanaTree100). However, there is a large domain gap in this setting, which makes the evaluation and deployment difficult. In this paper, we propose a new photorealistic virtual forest dataset and a multimodal transformer-based algorithm for tree detection and instance segmentation. To the best of our knowledge, it is the first time that a multimodal detection and segmentation algorithm is applied to large-scale forest scenes. We believe that the proposed dataset and method will inspire the simulation, computer vision, education, and forestry communities towards a more comprehensive multi-modal understanding.

The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that models evolution and the hierarchical relationship that characterises real-world datasets. We present Neural Distance Embeddings (NeuroSEED), a general framework to embed sequences in geometric vector spaces, and illustrate the effectiveness of the hyperbolic space that captures the hierarchical structure and provides an average 22% reduction in embedding RMSE against the best competing geometry. The capacity of the framework and the significance of these improvements are then demonstrated devising supervised and unsupervised NeuroSEED approaches to multiple core tasks in bioinformatics. Benchmarked with common baselines, the proposed approaches display significant accuracy and/or runtime improvements on real-world datasets. As an example for hierarchical clustering, the proposed pretrained and from-scratch methods match the quality of competing baselines with 30x and 15x runtime reduction, respectively.

The segmentation of forest LiDAR 3D point clouds, including both individual tree and semantic segmentation, is fundamental for advancing forest management and ecological research. However, current approaches often struggle with the complexity and variability of natural forest environments. We present ForestFormer3D, a new unified and end-to-end framework designed for precise individual tree and semantic segmentation. ForestFormer3D incorporates ISA-guided query point selection, a score-based block merging strategy during inference, and a one-to-many association mechanism for effective training. By combining these new components, our model achieves state-of-the-art performance for individual tree segmentation on the newly introduced FOR-instanceV2 dataset, which spans diverse forest types and regions. Additionally, ForestFormer3D generalizes well to unseen test sets (Wytham woods and LAUTx), showcasing its robustness across different forest conditions and sensor modalities. The FOR-instanceV2 dataset and the ForestFormer3D code are publicly available at https://bxiang233.github.io/FF3D/.

Forest wildfires represent one of the catastrophic events that, over the last decades, caused huge environmental and humanitarian damages. In addition to a significant amount of carbon dioxide emission, they are a source of risk to society in both short-term (e.g., temporary city evacuation due to fire) and long-term (e.g., higher risks of landslides) cases. Consequently, the availability of tools to support local authorities in automatically identifying burned areas plays an important role in the continuous monitoring requirement to alleviate the aftereffects of such catastrophic events. The great availability of satellite acquisitions coupled with computer vision techniques represents an important step in developing such tools. This paper introduces a novel open dataset that tackles the burned area delineation problem, a binary segmentation problem applied to satellite imagery. The presented resource consists of pre- and post-fire Sentinel-2 L2A acquisitions of California forest fires that took place starting in 2015. Raster annotations were generated from the data released by California's Department of Forestry and Fire Protection. Moreover, in conjunction with the dataset, we release three different baselines based on spectral indexes analyses, SegFormer, and U-Net models.

Estimating global tree canopy height is crucial for forest conservation and climate change applications. However, capturing high-resolution ground truth canopy height using LiDAR is expensive and not available globally. An efficient alternative is to train a canopy height estimator to operate on single-view remotely sensed imagery. The primary obstacle to this approach is that these methods require significant training data to generalize well globally and across uncommon edge cases. Recent monocular depth estimation foundation models have show strong zero-shot performance even for complex scenes. In this paper we leverage the representations learned by these models to transfer to the remote sensing domain for measuring canopy height. Our findings suggest that our proposed Depth Any Canopy, the result of fine-tuning the Depth Anything v2 model for canopy height estimation, provides a performant and efficient solution, surpassing the current state-of-the-art with superior or comparable performance using only a fraction of the computational resources and parameters. Furthermore, our approach requires less than \$1.30 in compute and results in an estimated carbon footprint of 0.14 kgCO2. Code, experimental results, and model checkpoints are openly available at https://github.com/DarthReca/depth-any-canopy.

Approximate nearest neighbor search (ANNS) is a fundamental building block in information retrieval with graph-based indices being the current state-of-the-art and widely used in the industry. Recent advances in graph-based indices have made it possible to index and search billion-point datasets with high recall and millisecond-level latency on a single commodity machine with an SSD. However, existing graph algorithms for ANNS support only static indices that cannot reflect real-time changes to the corpus required by many key real-world scenarios (e.g. index of sentences in documents, email, or a news index). To overcome this drawback, the current industry practice for manifesting updates into such indices is to periodically re-build these indices, which can be prohibitively expensive. In this paper, we present the first graph-based ANNS index that reflects corpus updates into the index in real-time without compromising on search performance. Using update rules for this index, we design FreshDiskANN, a system that can index over a billion points on a workstation with an SSD and limited memory, and support thousands of concurrent real-time inserts, deletes and searches per second each, while retaining >95% 5-recall@5. This represents a 5-10x reduction in the cost of maintaining freshness in indices when compared to existing methods.

With the rapid advancement of Large Language Models (LLMs), there is an increasing need for challenging benchmarks to evaluate their capabilities in handling complex tabular data. However, existing benchmarks are either based on outdated data setups or focus solely on simple, flat table structures. In this paper, we introduce RealHiTBench, a comprehensive benchmark designed to evaluate the performance of both LLMs and Multimodal LLMs (MLLMs) across a variety of input formats for complex tabular data, including LaTeX, HTML, and PNG. RealHiTBench also includes a diverse collection of tables with intricate structures, spanning a wide range of task types. Our experimental results, using 25 state-of-the-art LLMs, demonstrate that RealHiTBench is indeed a challenging benchmark. Moreover, we also develop TreeThinker, a tree-based pipeline that organizes hierarchical headers into a tree structure for enhanced tabular reasoning, validating the importance of improving LLMs' perception of table hierarchies. We hope that our work will inspire further research on tabular data reasoning and the development of more robust models. The code and data are available at https://github.com/cspzyy/RealHiTBench.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as their size or depth. We are not aware of such research for tree ensembles and aim to contribute to this area. Mainly, we provide two novel algorithms and corresponding lower bounds. First, we are able to carry over and substantially improve on tractability results for decision trees, obtaining a (6delta D S)^S cdot poly-time algorithm, where S is the number of cuts in the tree ensemble, D the largest domain size, and delta is the largest number of features in which two examples differ. To achieve this, we introduce the witness-tree technique which also seems promising for practice. Second, we show that dynamic programming, which has been successful for decision trees, may also be viable for tree ensembles, providing an ell^n cdot poly-time algorithm, where ell is the number of trees and n the number of examples. Finally, we compare the number of cuts necessary to classify training data sets for decision trees and tree ensembles, showing that ensembles may need exponentially fewer cuts for increasing number of trees.

Semi-structured documents integrate diverse interleaved data elements (e.g., tables, charts, hierarchical paragraphs) arranged in various and often irregular layouts. These documents are widely observed across domains and account for a large portion of real-world data. However, existing methods struggle to support natural language question answering over these documents due to three main technical challenges: (1) The elements extracted by techniques like OCR are often fragmented and stripped of their original semantic context, making them inadequate for analysis. (2) Existing approaches lack effective representations to capture hierarchical structures within documents (e.g., associating tables with nested chapter titles) and to preserve layout-specific distinctions (e.g., differentiating sidebars from main content). (3) Answering questions often requires retrieving and aligning relevant information scattered across multiple regions or pages, such as linking a descriptive paragraph to table cells located elsewhere in the document. To address these issues, we propose MoDora, an LLM-powered system for semi-structured document analysis. First, we adopt a local-alignment aggregation strategy to convert OCR-parsed elements into layout-aware components, and conduct type-specific information extraction for components with hierarchical titles or non-text elements. Second, we design the Component-Correlation Tree (CCTree) to hierarchically organize components, explicitly modeling inter-component relations and layout distinctions through a bottom-up cascade summarization process. Finally, we propose a question-type-aware retrieval strategy that supports (1) layout-based grid partitioning for location-based retrieval and (2) LLM-guided pruning for semantic-based retrieval. Experiments show MoDora outperforms baselines by 5.97%-61.07% in accuracy. The code is at https://github.com/weAIDB/MoDora.

The increasing availability of high-resolution satellite imagery, together with advances in deep learning, creates new opportunities for enhancing forest monitoring workflows. Two central challenges in this domain are pixel-level change detection and semantic change interpretation, particularly for complex forest dynamics. While large language models (LLMs) are increasingly adopted for data exploration, their integration with vision-language models (VLMs) for remote sensing image change interpretation (RSICI) remains underexplored, especially beyond urban environments. We introduce Forest-Chat, an LLM-driven agent designed for integrated forest change analysis. The proposed framework enables natural language querying and supports multiple RSICI tasks, including change detection, change captioning, object counting, deforestation percentage estimation, and change reasoning. Forest-Chat builds upon a multi-level change interpretation (MCI) vision-language backbone with LLM-based orchestration, and incorporates zero-shot change detection via a foundation change detection model together with an interactive point-prompt interface to support fine-grained user guidance. To facilitate adaptation and evaluation in forest environments, we introduce the Forest-Change dataset, comprising bi-temporal satellite imagery, pixel-level change masks, and multi-granularity semantic change captions generated through a combination of human annotation and rule-based methods. Experimental results demonstrate that Forest-Chat achieves strong performance on Forest-Change and on LEVIR-MCI-Trees, a tree-focused subset of LEVIR-MCI, for joint change detection and captioning, highlighting the potential of interactive, LLM-driven RSICI systems to improve accessibility, interpretability, and analytical efficiency in forest change analysis.

Finding meaningful representations and distances of hierarchical data is important in many fields. This paper presents a new method for hierarchical data embedding and distance. Our method relies on combining diffusion geometry, a central approach to manifold learning, and hyperbolic geometry. Specifically, using diffusion geometry, we build multi-scale densities on the data, aimed to reveal their hierarchical structure, and then embed them into a product of hyperbolic spaces. We show theoretically that our embedding and distance recover the underlying hierarchical structure. In addition, we demonstrate the efficacy of the proposed method and its advantages compared to existing methods on graph embedding benchmarks and hierarchical datasets.

Semantic text classification has undergone significant advances in recent years due to the rise of large language models (LLMs) and their high dimensional embeddings. While LLM-embeddings are frequently used to store and retrieve text by semantic similarity in vector databases, the global structure semantic relationships in text corpora often remains opaque. Herein we propose a nested density clustering approach, to infer hierarchical trees of semantically related texts. The method starts by identifying texts of strong semantic similarity as it searches for dense clusters in LLM embedding space. As the density criterion is gradually relaxed, these dense clusters merge into more diffuse clusters, until the whole dataset is represented by a single cluster -- the root of the tree. By embedding dense clusters into increasingly diffuse ones, we construct a tree structure that captures hierarchical semantic relationships among texts. We outline how this approach can be used to classify textual data for abstracts of scientific abstracts as a case study. This enables the data-driven discovery research areas and their subfields without predefined categories. To evaluate the general applicability of the method, we further apply it to established benchmark datasets such as the 20 Newsgroups and IMDB 50k Movie Reviews, demonstrating its robustness across domains. Finally we discuss possible applications on scientometrics, topic evolution, highlighting how nested density trees can reveal semantic structure and evolution in textual datasets.

Scientific literature review generation aims to extract and organize important information from an abundant collection of reference papers and produces corresponding reviews while lacking a clear and logical hierarchy. We observe that a high-quality catalogue-guided generation process can effectively alleviate this problem. Therefore, we present an atomic and challenging task named Hierarchical Catalogue Generation for Literature Review as the first step for review generation, which aims to produce a hierarchical catalogue of a review paper given various references. We construct a novel English Hierarchical Catalogues of Literature Reviews Dataset with 7.6k literature review catalogues and 389k reference papers. To accurately assess the model performance, we design two evaluation metrics for informativeness and similarity to ground truth from semantics and structure.Our extensive analyses verify the high quality of our dataset and the effectiveness of our evaluation metrics. We further benchmark diverse experiments on state-of-the-art summarization models like BART and large language models like ChatGPT to evaluate their capabilities. We further discuss potential directions for this task to motivate future research.

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.

Characterizing the processes leading to deforestation is critical to the development and implementation of targeted forest conservation and management policies. In this work, we develop a deep learning model called ForestNet to classify the drivers of primary forest loss in Indonesia, a country with one of the highest deforestation rates in the world. Using satellite imagery, ForestNet identifies the direct drivers of deforestation in forest loss patches of any size. We curate a dataset of Landsat 8 satellite images of known forest loss events paired with driver annotations from expert interpreters. We use the dataset to train and validate the models and demonstrate that ForestNet substantially outperforms other standard driver classification approaches. In order to support future research on automated approaches to deforestation driver classification, the dataset curated in this study is publicly available at https://stanfordmlgroup.github.io/projects/forestnet .

Global vegetation structure mapping is critical for understanding the global carbon cycle and maximizing the efficacy of nature-based carbon sequestration initiatives. Moreover, vegetation structure mapping can help reduce the impacts of climate change by, for example, guiding actions to improve water security, increase biodiversity and reduce flood risk. Global satellite measurements provide an important set of observations for monitoring and managing deforestation and degradation of existing forests, natural forest regeneration, reforestation, biodiversity restoration, and the implementation of sustainable agricultural practices. In this paper, we explore the effectiveness of fine-tuning of a geospatial foundation model to estimate above-ground biomass (AGB) using space-borne data collected across different eco-regions in Brazil. The fine-tuned model architecture consisted of a Swin-B transformer as the encoder (i.e., backbone) and a single convolutional layer for the decoder head. All results were compared to a U-Net which was trained as the baseline model Experimental results of this sparse-label prediction task demonstrate that the fine-tuned geospatial foundation model with a frozen encoder has comparable performance to a U-Net trained from scratch. This is despite the fine-tuned model having 13 times less parameters requiring optimization, which saves both time and compute resources. Further, we explore the transfer-learning capabilities of the geospatial foundation models by fine-tuning on satellite imagery with sparse labels from different eco-regions in Brazil.

The in-memory algorithms for approximate nearest neighbor search (ANNS) have achieved great success for fast high-recall search, but are extremely expensive when handling very large scale database. Thus, there is an increasing request for the hybrid ANNS solutions with small memory and inexpensive solid-state drive (SSD). In this paper, we present a simple but efficient memory-disk hybrid indexing and search system, named SPANN, that follows the inverted index methodology. It stores the centroid points of the posting lists in the memory and the large posting lists in the disk. We guarantee both disk-access efficiency (low latency) and high recall by effectively reducing the disk-access number and retrieving high-quality posting lists. In the index-building stage, we adopt a hierarchical balanced clustering algorithm to balance the length of posting lists and augment the posting list by adding the points in the closure of the corresponding clusters. In the search stage, we use a query-aware scheme to dynamically prune the access of unnecessary posting lists. Experiment results demonstrate that SPANN is 2times faster than the state-of-the-art ANNS solution DiskANN to reach the same recall quality 90% with same memory cost in three billion-scale datasets. It can reach 90% recall@1 and recall@10 in just around one millisecond with only 32GB memory cost. Code is available at: {\footnotesizeblue{https://github.com/microsoft/SPTAG}}.

Nowadays, data is represented by vectors. Retrieving those vectors, among millions and billions, that are similar to a given query is a ubiquitous problem, known as similarity search, of relevance for a wide range of applications. Graph-based indices are currently the best performing techniques for billion-scale similarity search. However, their random-access memory pattern presents challenges to realize their full potential. In this work, we present new techniques and systems for creating faster and smaller graph-based indices. To this end, we introduce a novel vector compression method, Locally-adaptive Vector Quantization (LVQ), that uses per-vector scaling and scalar quantization to improve search performance with fast similarity computations and a reduced effective bandwidth, while decreasing memory footprint and barely impacting accuracy. LVQ, when combined with a new high-performance computing system for graph-based similarity search, establishes the new state of the art in terms of performance and memory footprint. For billions of vectors, LVQ outcompetes the second-best alternatives: (1) in the low-memory regime, by up to 20.7x in throughput with up to a 3x memory footprint reduction, and (2) in the high-throughput regime by 5.8x with 1.4x less memory.

Automatic tree density estimation and counting using single aerial and satellite images is a challenging task in photogrammetry and remote sensing, yet has an important role in forest management. In this paper, we propose the first semisupervised transformer-based framework for tree counting which reduces the expensive tree annotations for remote sensing images. Our method, termed as TreeFormer, first develops a pyramid tree representation module based on transformer blocks to extract multi-scale features during the encoding stage. Contextual attention-based feature fusion and tree density regressor modules are further designed to utilize the robust features from the encoder to estimate tree density maps in the decoder. Moreover, we propose a pyramid learning strategy that includes local tree density consistency and local tree count ranking losses to utilize unlabeled images into the training process. Finally, the tree counter token is introduced to regulate the network by computing the global tree counts for both labeled and unlabeled images. Our model was evaluated on two benchmark tree counting datasets, Jiangsu, and Yosemite, as well as a new dataset, KCL-London, created by ourselves. Our TreeFormer outperforms the state of the art semi-supervised methods under the same setting and exceeds the fully-supervised methods using the same number of labeled images. The codes and datasets are available at https://github.com/HAAClassic/TreeFormer.

Accurately predicting stock market movements remains a formidable challenge due to the inherent volatility and complex interdependencies among stocks. Although multi-scale Graph Neural Networks (GNNs) hold potential for modeling these relationships, they frequently neglect two key points: the subtle intra-attribute patterns within each stock affecting inter-stock correlation, and the biased attention to coarse- and fine-grained features during multi-scale sampling. To overcome these challenges, we introduce MS-HGFN (Multi-Scale Hierarchical Graph Fusion Network). The model features a hierarchical GNN module that forms dynamic graphs by learning patterns from intra-attributes and features from inter-attributes over different time scales, thus comprehensively capturing spatio-temporal dependencies. Additionally, a top-down gating approach facilitates the integration of multi-scale spatio-temporal features, preserving critical coarse- and fine-grained features without too much interference. Experiments utilizing real-world datasets from U.S. and Chinese stock markets demonstrate that MS-HGFN outperforms both traditional and advanced models, yielding up to a 1.4% improvement in prediction accuracy and enhanced stability in return simulations. The code is available at https://anonymous.4open.science/r/MS-HGFN.

Scientific surveys require not only summarizing large bodies of literature, but also organizing them into clear and coherent conceptual structures. Existing automatic survey generation methods typically focus on linear text generation and struggle to explicitly model hierarchical relations among research topics and structured methodological comparisons, resulting in gaps in structural organization compared to expert-written surveys. We propose MVSS, a multi-view structured survey generation framework that jointly generates and aligns citation-grounded hierarchical trees, structured comparison tables, and survey text. MVSS follows a structure-first paradigm: it first constructs a conceptual tree of the research domain, then generates comparison tables constrained by the tree, and finally uses both as structural constraints for text generation. This enables complementary multi-view representations across structure, comparison, and narrative. We introduce an evaluation framework assessing structural quality, comparative completeness, and citation fidelity. Experiments on 76 computer science topics show MVSS outperforms existing methods in organization and evidence grounding, achieving performance comparable to expert surveys.

Modern NLP tasks increasingly rely on dense retrieval methods to access up-to-date and relevant contextual information. We are motivated by the premise that retrieval benefits from segments that can vary in size such that a content's semantic independence is better captured. We propose LumberChunker, a method leveraging an LLM to dynamically segment documents, which iteratively prompts the LLM to identify the point within a group of sequential passages where the content begins to shift. To evaluate our method, we introduce GutenQA, a benchmark with 3000 "needle in a haystack" type of question-answer pairs derived from 100 public domain narrative books available on Project Gutenberg. Our experiments show that LumberChunker not only outperforms the most competitive baseline by 7.37% in retrieval performance (DCG@20) but also that, when integrated into a RAG pipeline, LumberChunker proves to be more effective than other chunking methods and competitive baselines, such as the Gemini 1.5M Pro. Our Code and Data are available at https://github.com/joaodsmarques/LumberChunker

Large language models (LLMs) have achieved remarkable success and demonstrated superior performance across various tasks, including natural language processing (NLP), weather forecasting, biological protein folding, text generation, and solving mathematical problems. However, many real-world data exhibit highly non-Euclidean latent hierarchical anatomy, such as protein networks, transportation networks, financial networks, brain networks, and linguistic structures or syntactic trees in natural languages. Effectively learning intrinsic semantic entailment and hierarchical relationships from these raw, unstructured input data using LLMs remains an underexplored area. Due to its effectiveness in modeling tree-like hierarchical structures, hyperbolic geometry -- a non-Euclidean space -- has rapidly gained popularity as an expressive latent representation space for complex data modeling across domains such as graphs, images, languages, and multi-modal data. Here, we provide a comprehensive and contextual exposition of recent advancements in LLMs that leverage hyperbolic geometry as a representation space to enhance semantic representation learning and multi-scale reasoning. Specifically, the paper presents a taxonomy of the principal techniques of Hyperbolic LLMs (HypLLMs) in terms of four main categories: (1) hyperbolic LLMs through exp/log maps; (2) hyperbolic fine-tuned models; (3) fully hyperbolic LLMs, and (4) hyperbolic state-space models. We also explore crucial potential applications and outline future research directions. A repository of key papers, models, datasets, and code implementations is available at https://github.com/sarangp2402/Hyperbolic-LLM-Models/tree/main.

Assessing the effectiveness of large language models (LLMs) in addressing diverse tasks is essential for comprehending their strengths and weaknesses. Conventional evaluation techniques typically apply a single prompting strategy uniformly across datasets, not considering the varying degrees of task complexity. We introduce the Hierarchical Prompting Taxonomy (HPT), a taxonomy that employs a Hierarchical Prompt Framework (HPF) composed of five unique prompting strategies, arranged from the simplest to the most complex, to assess LLMs more precisely and to offer a clearer perspective. This taxonomy assigns a score, called the Hierarchical Prompting Score (HP-Score), to datasets as well as LLMs based on the rules of the taxonomy, providing a nuanced understanding of their ability to solve diverse tasks and offering a universal measure of task complexity. Additionally, we introduce the Adaptive Hierarchical Prompt framework, which automates the selection of appropriate prompting strategies for each task. This study compares manual and adaptive hierarchical prompt frameworks using four instruction-tuned LLMs, namely Llama 3 8B, Phi 3 3.8B, Mistral 7B, and Gemma 7B, across four datasets: BoolQ, CommonSenseQA (CSQA), IWSLT-2017 en-fr (IWSLT), and SamSum. Experiments demonstrate the effectiveness of HPT, providing a reliable way to compare different tasks and LLM capabilities. This paper leads to the development of a universal evaluation metric that can be used to evaluate both the complexity of the datasets and the capabilities of LLMs. The implementation of both manual HPF and adaptive HPF is publicly available.

Although retrieval-augmented generation(RAG) significantly improves generation quality by retrieving external knowledge bases and integrating generated content, it faces computational efficiency bottlenecks, particularly in knowledge retrieval tasks involving hierarchical structures for Tree-RAG. This paper proposes a Tree-RAG acceleration method based on the improved Cuckoo Filter, which optimizes entity localization during the retrieval process to achieve significant performance improvements. Tree-RAG effectively organizes entities through the introduction of a hierarchical tree structure, while the Cuckoo Filter serves as an efficient data structure that supports rapid membership queries and dynamic updates. The experiment results demonstrate that our method is much faster than naive Tree-RAG while maintaining high levels of generative quality. When the number of trees is large, our method is hundreds of times faster than naive Tree-RAG. Our work is available at https://github.com/TUPYP7180/CFT-RAG-2025.

Language models are trained mainly on massive text data from the Internet, and it becomes increasingly important to understand this data source. Exact-match search engines enable searching in large text corpora -- counting string appearances and retrieving the enclosing documents -- yet the high storage overhead hinders their application on Internet-scale data. We present Infini-gram mini, an efficient and scalable system that can make petabyte-level text corpora searchable. Based on the FM-index data structure (Ferragina and Manzini, 2000), which simultaneously indexes and compresses text, our system creates indexes with size only 44% of the corpus. Infini-gram mini greatly improves upon the best existing implementation of FM-index in terms of indexing speed (18times) and memory use during both indexing (3.2times reduction) and querying (down to a negligible amount). We index 46TB of Internet text in 50 days with a single 128-core CPU node (or 19 hours if using 75 such nodes). We show one important use case of Infini-gram mini in a large-scale analysis of benchmark contamination. We find several core LM evaluation benchmarks to be heavily contaminated in Internet crawls (up to 40% in SQuAD), which could lead to overestimating the capabilities of language models if trained on such data. We host a benchmark contamination bulletin to share the contamination rate of many core and community-contributed benchmarks. We also release a web interface and an API endpoint to serve general search queries on Infini-gram mini indexes.

In this paper, we propose the Hierarchical Document Transformer (HDT), a novel sparse Transformer architecture tailored for structured hierarchical documents. Such documents are extremely important in numerous domains, including science, law or medicine. However, most existing solutions are inefficient and fail to make use of the structure inherent to documents. HDT exploits document structure by introducing auxiliary anchor tokens and redesigning the attention mechanism into a sparse multi-level hierarchy. This approach facilitates information exchange between tokens at different levels while maintaining sparsity, thereby enhancing computational and memory efficiency while exploiting the document structure as an inductive bias. We address the technical challenge of implementing HDT's sample-dependent hierarchical attention pattern by developing a novel sparse attention kernel that considers the hierarchical structure of documents. As demonstrated by our experiments, utilizing structural information present in documents leads to faster convergence, higher sample efficiency and better performance on downstream tasks.

The continually increasing number of documents produced each year necessitates ever improving information processing methods for searching, retrieving, and organizing text. Central to these information processing methods is document classification, which has become an important application for supervised learning. Recently the performance of these traditional classifiers has degraded as the number of documents has increased. This is because along with this growth in the number of documents has come an increase in the number of categories. This paper approaches this problem differently from current document classification methods that view the problem as multi-class classification. Instead we perform hierarchical classification using an approach we call Hierarchical Deep Learning for Text classification (HDLTex). HDLTex employs stacks of deep learning architectures to provide specialized understanding at each level of the document hierarchy.

Given thousands of equally accurate machine learning (ML) models, how can users choose among them? A recent ML technique enables domain experts and data scientists to generate a complete Rashomon set for sparse decision trees--a huge set of almost-optimal interpretable ML models. To help ML practitioners identify models with desirable properties from this Rashomon set, we develop TimberTrek, the first interactive visualization system that summarizes thousands of sparse decision trees at scale. Two usage scenarios highlight how TimberTrek can empower users to easily explore, compare, and curate models that align with their domain knowledge and values. Our open-source tool runs directly in users' computational notebooks and web browsers, lowering the barrier to creating more responsible ML models. TimberTrek is available at the following public demo link: https://poloclub.github.io/timbertrek.

Hierarchical text classification (HTC) depends on taxonomies that organize labels into structured hierarchies. However, many real-world taxonomies introduce ambiguities, such as identical leaf names under similar parent nodes, which prevent language models (LMs) from learning clear decision boundaries. In this paper, we present TaxMorph, a framework that uses large language models (LLMs) to transform entire taxonomies through operations such as renaming, merging, splitting, and reordering. Unlike prior work, our method revises the full hierarchy to better match the semantics encoded by LMs. Experiments across three HTC benchmarks show that LLM-refined taxonomies consistently outperform human-curated ones in various settings up to +2.9pp. in F1. To better understand these improvements, we compare how well LMs can assign leaf nodes to parent nodes and vice versa across human-curated and LLM-refined taxonomies. We find that human-curated taxonomies lead to more easily separable clusters in embedding space. However, the LLM-refined taxonomies align more closely with the model's actual confusion patterns during classification. In other words, even though they are harder to separate, they better reflect the model's inductive biases. These findings suggest that LLM-guided refinement creates taxonomies that are more compatible with how models learn, improving HTC performance.

Many real-world machine learning problems involve inherently hierarchical data, yet traditional approaches rely on Euclidean metrics that fail to capture the discrete, branching nature of hierarchical relationships. We present a theoretical foundation for machine learning in p-adic metric spaces, which naturally respect hierarchical structure. Our main result proves that an n-dimensional plane minimizing the p-adic sum of distances to points in a dataset must pass through at least n + 1 of those points -- a striking contrast to Euclidean regression that highlights how p-adic metrics better align with the discrete nature of hierarchical data. As a corollary, a polynomial of degree n constructed to minimise the p-adic sum of residuals will pass through at least n + 1 points. As a further corollary, a polynomial of degree n approximating a higher degree polynomial at a finite number of points will yield a difference polynomial that has distinct rational roots. We demonstrate the practical significance of this result through two applications in natural language processing: analyzing hierarchical taxonomies and modeling grammatical morphology. These results suggest that p-adic metrics may be fundamental to properly handling hierarchical data structures in machine learning. In hierarchical data, interpolation between points often makes less sense than selecting actual observed points as representatives.

Robust scene understanding is essential for intelligent vehicles operating in natural, unstructured environments. While semantic segmentation datasets for structured urban driving are abundant, the datasets for extremely unstructured wild environments remain scarce due to the difficulty and cost of generating pixel-accurate annotations. These limitations hinder the development of perception systems needed for intelligent ground vehicles tasked with forestry automation, agricultural robotics, disaster response, and all-terrain mobility. To address this gap, we present ForestSim, a high-fidelity synthetic dataset designed for training and evaluating semantic segmentation models for intelligent vehicles in forested off-road and no-road environments. ForestSim contains 2094 photorealistic images across 25 diverse environments, covering multiple seasons, terrain types, and foliage densities. Using Unreal Engine environments integrated with Microsoft AirSim, we generate consistent, pixel-accurate labels across 20 classes relevant to autonomous navigation. We benchmark ForestSim using state-of-the-art architectures and report strong performance despite the inherent challenges of unstructured scenes. ForestSim provides a scalable and accessible foundation for perception research supporting the next generation of intelligent off-road vehicles. The dataset and code are publicly available: Dataset: https://vailforestsim.github.io Code: https://github.com/pragatwagle/ForestSim

Foundation segmentation models achieve reasonable leaf instance extraction from top-view crop images without training (i.e., zero-shot). However, segmenting entire plant individuals with each consisting of multiple overlapping leaves remains challenging. This problem is referred to as a hierarchical segmentation task, typically requiring annotated training datasets, which are often species-specific and require notable human labor. To address this, we introduce ZeroPlantSeg, a zero-shot segmentation for rosette-shaped plant individuals from top-view images. We integrate a foundation segmentation model, extracting leaf instances, and a vision-language model, reasoning about plants' structures to extract plant individuals without additional training. Evaluations on datasets with multiple plant species, growth stages, and shooting environments demonstrate that our method surpasses existing zero-shot methods and achieves better cross-domain performance than supervised methods. Implementations are available at https://github.com/JunhaoXing/ZeroPlantSeg.

Timber represents an increasingly valuable and versatile resource. However, forestry operations such as harvesting, handling and measuring logs still require substantial human labor in remote environments posing significant safety risks. Progressively automating these tasks has the potential of increasing their efficiency as well as safety, but requires an accurate detection of individual logs as well as live trees and their context. Although initial approaches have been proposed for this challenging application domain, specialized data and algorithms are still too scarce to develop robust solutions. To mitigate this gap, we introduce the TimberVision dataset, consisting of more than 2k annotated RGB images containing a total of 51k trunk components including cut and lateral surfaces, thereby surpassing any existing dataset in this domain in terms of both quantity and detail by a large margin. Based on this data, we conduct a series of ablation experiments for oriented object detection and instance segmentation and evaluate the influence of multiple scene parameters on model performance. We introduce a generic framework to fuse the components detected by our models for both tasks into unified trunk representations. Furthermore, we automatically derive geometric properties and apply multi-object tracking to further enhance robustness. Our detection and tracking approach provides highly descriptive and accurate trunk representations solely from RGB image data, even under challenging environmental conditions. Our solution is suitable for a wide range of application scenarios and can be readily combined with other sensor modalities.

In natural language processing (NLP), lexical function is a concept to unambiguously represent semantic and syntactic features of words and phrases in text first crafted in the Meaning-Text Theory. Hierarchical classification of lexical functions involves organizing these features into a tree-like hierarchy of categories or labels. This is a challenging task as it requires a good understanding of the context and the relationships among words and phrases in text. It also needs large amounts of labeled data to train language models effectively. In this paper, we present a dataset of most frequent Spanish verb-noun collocations and sentences where they occur, each collocation is assigned to one of 37 lexical functions defined as classes for a hierarchical classification task. Each class represents a relation between the noun and the verb in a collocation involving their semantic and syntactic features. We combine the classes in a tree-based structure, and introduce classification objectives for each level of the structure. The dataset was created by dependency tree parsing and matching of the phrases in Spanish news. We provide baselines and data splits for each objective.

The K-core of a graph is the unique maximum subgraph within which each vertex connects to K or more other vertices. The optimal K-core attack problem asks to delete the minimum number of vertices from the K-core to induce its complete collapse. A hierarchical cycle-tree packing model is introduced here for this challenging combinatorial optimization problem. We convert the temporally long-range correlated K-core pruning dynamics into locally tree-like static patterns and analyze this model through the replica-symmetric cavity method of statistical physics. A set of coarse-grained belief propagation equations are derived to predict single vertex marginal probabilities efficiently. The associated hierarchical cycle-tree guided attack ({\tt hCTGA}) algorithm is able to construct nearly optimal attack solutions for regular random graphs and Erd\"os-R\'enyi random graphs. Our cycle-tree packing model may also be helpful for constructing optimal initial conditions for other irreversible dynamical processes on sparse random graphs.

Despite their remarkable effectiveness and broad application, the drivers of success underlying ensembles of trees are still not fully understood. In this paper, we highlight how interpreting tree ensembles as adaptive and self-regularizing smoothers can provide new intuition and deeper insight to this topic. We use this perspective to show that, when studied as smoothers, randomized tree ensembles not only make predictions that are quantifiably more smooth than the predictions of the individual trees they consist of, but also further regulate their smoothness at test-time based on the dissimilarity between testing and training inputs. First, we use this insight to revisit, refine and reconcile two recent explanations of forest success by providing a new way of quantifying the conjectured behaviors of tree ensembles objectively by measuring the effective degree of smoothing they imply. Then, we move beyond existing explanations for the mechanisms by which tree ensembles improve upon individual trees and challenge the popular wisdom that the superior performance of forests should be understood as a consequence of variance reduction alone. We argue that the current high-level dichotomy into bias- and variance-reduction prevalent in statistics is insufficient to understand tree ensembles -- because the prevailing definition of bias does not capture differences in the expressivity of the hypothesis classes formed by trees and forests. Instead, we show that forests can improve upon trees by three distinct mechanisms that are usually implicitly entangled. In particular, we demonstrate that the smoothing effect of ensembling can reduce variance in predictions due to noise in outcome generation, reduce variability in the quality of the learned function given fixed input data and reduce potential bias in learnable functions by enriching the available hypothesis space.

Large language models (LLMs) are increasingly adopted for automating survey paper generation wang2406autosurvey, liang2025surveyx, yan2025surveyforge,su2025benchmarking,wen2025interactivesurvey. Existing approaches typically extract content from a large collection of related papers and prompt LLMs to summarize them directly. However, such methods often overlook the structural relationships among papers, resulting in generated surveys that lack a coherent taxonomy and a deeper contextual understanding of research progress. To address these shortcomings, we propose SurveyG, an LLM-based agent framework that integrates hierarchical citation graph, where nodes denote research papers and edges capture both citation dependencies and semantic relatedness between their contents, thereby embedding structural and contextual knowledge into the survey generation process. The graph is organized into three layers: Foundation, Development, and Frontier, to capture the evolution of research from seminal works to incremental advances and emerging directions. By combining horizontal search within layers and vertical depth traversal across layers, the agent produces multi-level summaries, which are consolidated into a structured survey outline. A multi-agent validation stage then ensures consistency, coverage, and factual accuracy in generating the final survey. Experiments, including evaluations by human experts and LLM-as-a-judge, demonstrate that SurveyG outperforms state-of-the-art frameworks, producing surveys that are more comprehensive and better structured to the underlying knowledge taxonomy of a field.

Multi-hop Question Answering (QA) necessitates complex reasoning by integrating multiple pieces of information to resolve intricate questions. However, existing QA systems encounter challenges such as outdated information, context window length limitations, and an accuracy-quantity trade-off. To address these issues, we propose a novel framework, the Hierarchical Retrieval-Augmented Generation Model with Rethink (HiRAG), comprising Decomposer, Definer, Retriever, Filter, and Summarizer five key modules. We introduce a new hierarchical retrieval strategy that incorporates both sparse retrieval at the document level and dense retrieval at the chunk level, effectively integrating their strengths. Additionally, we propose a single-candidate retrieval method to mitigate the limitations of multi-candidate retrieval. We also construct two new corpora, Indexed Wikicorpus and Profile Wikicorpus, to address the issues of outdated and insufficient knowledge. Our experimental results on four datasets demonstrate that HiRAG outperforms state-of-the-art models across most metrics, and our Indexed Wikicorpus is effective. The code for HiRAG is available at https://github.com/2282588541a/HiRAG

Hierarchical graph pooling(HGP) are designed to consider the fact that conventional graph neural networks(GNN) are inherently flat and are also not multiscale. However, most HGP methods suffer not only from lack of considering global topology of the graph and focusing on the feature learning aspect, but also they do not align local and global features since graphs should inherently be analyzed in a multiscale way. LGRPool is proposed in the present paper as a HGP in the framework of expectation maximization in machine learning that aligns local and global aspects of message passing with each other using a regularizer to force the global topological information to be inline with the local message passing at different scales through the representations at different layers of HGP. Experimental results on some graph classification benchmarks show that it slightly outperforms some baselines.

Neural document ranking approaches, specifically transformer models, have achieved impressive gains in ranking performance. However, query processing using such over-parameterized models is both resource and time intensive. In this paper, we propose the Fast-Forward index -- a simple vector forward index that facilitates ranking documents using interpolation of lexical and semantic scores -- as a replacement for contextual re-rankers and dense indexes based on nearest neighbor search. Fast-Forward indexes rely on efficient sparse models for retrieval and merely look up pre-computed dense transformer-based vector representations of documents and passages in constant time for fast CPU-based semantic similarity computation during query processing. We propose index pruning and theoretically grounded early stopping techniques to improve the query processing throughput. We conduct extensive large-scale experiments on TREC-DL datasets and show improvements over hybrid indexes in performance and query processing efficiency using only CPUs. Fast-Forward indexes can provide superior ranking performance using interpolation due to the complementary benefits of lexical and semantic similarities.

Information on standing dead trees is important for understanding forest ecosystem functioning and resilience but has been lacking over large geographic regions. Climate change has caused large-scale tree mortality events that can remain undetected due to limited data. In this study, we propose a novel method for segmenting standing dead trees using aerial multispectral orthoimages. Because access to annotated datasets has been a significant problem in forest remote sensing due to the need for forest expertise, we introduce a method for domain transfer by leveraging domain adaptation to learn a transformation from a source domain X to target domain Y. In this Image-to-Image translation task, we aim to utilize available annotations in the target domain by pre-training a segmentation network. When images from a new study site without annotations are introduced (source domain X), these images are transformed into the target domain. Then, transfer learning is applied by inferring the pre-trained network on domain-adapted images. In addition to investigating the feasibility of current domain adaptation approaches for this objective, we propose a novel approach called the Attention-guided Domain Adaptation Network (ADA-Net) with enhanced contrastive learning. Accordingly, the ADA-Net approach provides new state-of-the-art domain adaptation performance levels outperforming existing approaches. We have evaluated the proposed approach using two datasets from Finland and the US. The USA images are converted to the Finland domain, and we show that the synthetic USA2Finland dataset exhibits similar characteristics to the Finland domain images. The software implementation is shared at https://github.com/meteahishali/ADA-Net. The data is publicly available at https://www.kaggle.com/datasets/meteahishali/aerial-imagery-for-standing-dead-tree-segmentation.

Computing distances and finding shortest paths in massive real-world networks is a fundamental algorithmic task in network analysis. There are two main approaches to solving this task. On one hand are traversal-based algorithms like bidirectional breadth-first search (BiBFS) with no preprocessing step and slow individual distance inquiries. On the other hand are indexing-based approaches, which maintain a large index. This allows for answering individual inquiries very fast; however, index creation is prohibitively expensive. We seek to bridge these two extremes: quickly answer distance inquiries without the need for costly preprocessing. In this work, we propose a new algorithm and data structure, WormHole, for approximate shortest path computations. WormHole leverages structural properties of social networks to build a sublinearly sized index, drawing upon the explicit core-periphery decomposition of Ben-Eliezer et al. Empirically, the preprocessing time of WormHole improves upon index-based solutions by orders of magnitude, and individual inquiries are consistently much faster than in BiBFS. The acceleration comes at the cost of a minor accuracy trade-off. Nonetheless, our empirical evidence demonstrates that WormHole accurately answers essentially all inquiries within a maximum additive error of 2. We complement these empirical results with provable theoretical guarantees, showing that WormHole requires n^{o(1)} node queries per distance inquiry in random power-law networks. In contrast, any approach without a preprocessing step requires n^{Ω(1)} queries for the same task. WormHole does not require reading the whole graph. Unlike the vast majority of index-based algorithms, it returns paths, not just distances. For faster inquiry times, it can be combined effectively with other index-based solutions, by running them only on the sublinear core.

Non-hierarchical sparse attention Transformer-based models, such as Longformer and Big Bird, are popular approaches to working with long documents. There are clear benefits to these approaches compared to the original Transformer in terms of efficiency, but Hierarchical Attention Transformer (HAT) models are a vastly understudied alternative. We develop and release fully pre-trained HAT models that use segment-wise followed by cross-segment encoders and compare them with Longformer models and partially pre-trained HATs. In several long document downstream classification tasks, our best HAT model outperforms equally-sized Longformer models while using 10-20% less GPU memory and processing documents 40-45% faster. In a series of ablation studies, we find that HATs perform best with cross-segment contextualization throughout the model than alternative configurations that implement either early or late cross-segment contextualization. Our code is on GitHub: https://github.com/coastalcph/hierarchical-transformers.

This paper develops a hierarchical clustering algorithm for weighted projective spaces P_{q}, utilizing a Finsler metric d_F([z], [w]) and its rational analogue d_{F,Q}([z], [w]) to define distances that preserve the non-Euclidean geometry of these quotient manifolds. Defined via geodesic integrals of a scaling invariant Finsler norm weighted by the grades q = (q_0, q_1, dots, q_n), these metrics satisfy true metric properties including the triangle inequality, overcoming the limitations of the non-metric dissimilarity measure from prior work.

Clustering is a fundamental building block of modern statistical analysis pipelines. Fair clustering has seen much attention from the machine learning community in recent years. We are some of the first to study fairness in the context of hierarchical clustering, after the results of Ahmadian et al. from NeurIPS in 2020. We evaluate our results using Dasgupta's cost function, perhaps one of the most prevalent theoretical metrics for hierarchical clustering evaluation. Our work vastly improves the previous O(n^{5/6}polylog(n)) fair approximation for cost to a near polylogarithmic O(n^delta polylog(n)) fair approximation for any constant deltain(0,1). This result establishes a cost-fairness tradeoff and extends to broader fairness constraints than the previous work. We also show how to alter existing hierarchical clusterings to guarantee fairness and cluster balance across any level in the hierarchy.

We have compared three common visualisations for hierarchical quantitative data, treemaps, icicle plots and sunburst charts as well as a semicircular variant of sunburst charts we call the sundown chart. In a pilot study, we found that the sunburst chart was least preferred. In a controlled study with 12 participants, we compared treemaps, icicle plots and sundown charts. Treemap was the least preferred and had a slower performance on a basic navigation task and slower performance and accuracy in hierarchy understanding tasks. The icicle plot and sundown chart had similar performance with slight user preference for the icicle plot.

Vector search systems, pivotal in AI applications, often rely on the Hierarchical Navigable Small Worlds (HNSW) algorithm. However, the behaviour of HNSW under real-world scenarios using vectors generated with deep learning models remains under-explored. Existing Approximate Nearest Neighbours (ANN) benchmarks and research typically has an over-reliance on simplistic datasets like MNIST or SIFT1M and fail to reflect the complexity of current use-cases. Our investigation focuses on HNSW's efficacy across a spectrum of datasets, including synthetic vectors tailored to mimic specific intrinsic dimensionalities, widely-used retrieval benchmarks with popular embedding models, and proprietary e-commerce image data with CLIP models. We survey the most popular HNSW vector databases and collate their default parameters to provide a realistic fixed parameterisation for the duration of the paper. We discover that the recall of approximate HNSW search, in comparison to exact K Nearest Neighbours (KNN) search, is linked to the vector space's intrinsic dimensionality and significantly influenced by the data insertion sequence. Our methodology highlights how insertion order, informed by measurable properties such as the pointwise Local Intrinsic Dimensionality (LID) or known categories, can shift recall by up to 12 percentage points. We also observe that running popular benchmark datasets with HNSW instead of KNN can shift rankings by up to three positions for some models. This work underscores the need for more nuanced benchmarks and design considerations in developing robust vector search systems using approximate vector search algorithms. This study presents a number of scenarios with varying real world applicability which aim to better increase understanding and future development of ANN algorithms and embedding

Skiplists are widely used for in-memory indexing in many key-value stores, such as RocksDB and LevelDB, due to their ease of implementation and simple concurrency control mechanisms. However, traditional skiplists suffer from poor cache locality, as they store only a single element per node, leaving performance on the table. Minimizing last-level cache misses is key to maximizing in-memory index performance, making high cache locality essential. In this paper, we present a practical concurrent B-skiplist that enhances cache locality and performance while preserving the simplicity of traditional skiplist structures and concurrency control schemes. Our key contributions include a top-down, single-pass insertion algorithm for B-skiplists and a corresponding simple and efficient top-down concurrency control scheme. On 128 threads, the proposed concurrent B-skiplist achieves between 2x-9x higher throughput compared to state-of-the-art concurrent skiplist implementations, including Facebook's concurrent skiplist from Folly and the Java ConcurrentSkipListMap. Furthermore, we find that the B-skiplist achieves competitive (0.9x-1.7x) throughput on point workloads compared to state-of-the-art cache-optimized tree-based indices (e.g., Masstree). For a more complete picture of the performance, we also measure the latency of skiplist and tree-based indices and find that the B-skiplist achieves between 3.5x-103x lower 99% latency compared to other concurrent skiplists and between 0.85x-64x lower 99% latency compared to tree-based indices on point workloads with inserts.

Vector databases have emerged as key enablers for bridging intelligent applications with unstructured data, providing generic search and management support for embedding vectors extracted from the raw unstructured data. As multiple data users can share the same database infrastructure, multi-tenancy support for vector databases is increasingly desirable. This hinges on an efficient filtered search operation, i.e., only querying the vectors accessible to a particular tenant. Multi-tenancy in vector databases is currently achieved by building either a single, shared index among all tenants, or a per-tenant index. The former optimizes for memory efficiency at the expense of search performance, while the latter does the opposite. Instead, this paper presents Curator, an in-memory vector index design tailored for multi-tenant queries that simultaneously achieves the two conflicting goals, low memory overhead and high performance for queries, vector insertion, and deletion. Curator indexes each tenant's vectors with a tenant-specific clustering tree and encodes these trees compactly as sub-trees of a shared clustering tree. Each tenant's clustering tree adapts dynamically to its unique vector distribution, while maintaining a low per-tenant memory footprint. Our evaluation, based on two widely used data sets, confirms that Curator delivers search performance on par with per-tenant indexing, while maintaining memory consumption at the same level as metadata filtering on a single, shared index.

Local graph clustering methods aim to detect small clusters in very large graphs without the need to process the whole graph. They are fundamental and scalable tools for a wide range of tasks such as local community detection, node ranking and node embedding. While prior work on local graph clustering mainly focuses on graphs without node attributes, modern real-world graph datasets typically come with node attributes that provide valuable additional information. We present a simple local graph clustering algorithm for graphs with node attributes, based on the idea of diffusing mass locally in the graph while accounting for both structural and attribute proximities. Using high-dimensional concentration results, we provide statistical guarantees on the performance of the algorithm for the recovery of a target cluster with a single seed node. We give conditions under which a target cluster generated from a fairly general contextual random graph model, which includes both the stochastic block model and the planted cluster model as special cases, can be fully recovered with bounded false positives. Empirically, we validate all theoretical claims using synthetic data, and we show that incorporating node attributes leads to superior local clustering performances using real-world graph datasets.

Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.

In orchard automation, dense foliage during the canopy season severely occludes tree structures, minimizing visibility to various canopy parts such as trunks and branches, which limits the ability of a machine vision system. However, canopy structure is more open and visible during the dormant season when trees are defoliated. In this work, we present an information fusion framework that integrates multi-seasonal structural data to support robotic and automated crop load management during the entire growing season. The framework combines high-resolution RGB-D imagery from both dormant and canopy periods using YOLOv9-Seg for instance segmentation, Kinect Fusion for 3D reconstruction, and Fast Generalized Iterative Closest Point (Fast GICP) for model alignment. Segmentation outputs from YOLOv9-Seg were used to extract depth-informed masks, which enabled accurate 3D point cloud reconstruction via Kinect Fusion; these reconstructed models from each season were subsequently aligned using Fast GICP to achieve spatially coherent multi-season fusion. The YOLOv9-Seg model, trained on manually annotated images, achieved a mean squared error (MSE) of 0.0047 and segmentation mAP@50 scores up to 0.78 for trunks in dormant season dataset. Kinect Fusion enabled accurate reconstruction of tree geometry, validated with field measurements resulting in root mean square errors (RMSE) of 5.23 mm for trunk diameter, 4.50 mm for branch diameter, and 13.72 mm for branch spacing. Fast GICP achieved precise cross-seasonal registration with a minimum fitness score of 0.00197, allowing integrated, comprehensive tree structure modeling despite heavy occlusions during the growing season. This fused structural representation enables robotic systems to access otherwise obscured architectural information, improving the precision of pruning, thinning, and other automated orchard operations.

Generative retrieval has recently emerged as a new alternative of traditional information retrieval approaches. However, existing generative retrieval methods directly decode docid when a query is given, making it impossible to provide users with explanations as an answer for "Why this document is retrieved?". To address this limitation, we propose Hierarchical Category Path-Enhanced Generative Retrieval(HyPE), which enhances explainability by generating hierarchical category paths step-by-step before decoding docid. HyPE leverages hierarchical category paths as explanation, progressing from broad to specific semantic categories. This approach enables diverse explanations for the same document depending on the query by using shared category paths between the query and the document, and provides reasonable explanation by reflecting the document's semantic structure through a coarse-to-fine manner. HyPE constructs category paths with external high-quality semantic hierarchy, leverages LLM to select appropriate candidate paths for each document, and optimizes the generative retrieval model with path-augmented dataset. During inference, HyPE utilizes path-aware reranking strategy to aggregate diverse topic information, allowing the most relevant documents to be prioritized in the final ranked list of docids. Our extensive experiments demonstrate that HyPE not only offers a high level of explainability but also improves the retrieval performance in the document retrieval task.

Few-shot Hierarchical Text Classification (few-shot HTC) is a challenging task that involves mapping texts to a predefined tree-structured label hierarchy under data-scarce conditions. While current approaches utilize structural constraints from the label hierarchy to maintain parent-child prediction consistency, they face a critical bottleneck, the difficulty in distinguishing semantically similar sibling classes due to insufficient domain knowledge. We introduce an innovative method named Sibling Contrastive Learning with Hierarchical Knowledge-aware Prompt Tuning for few-shot HTC tasks (SCHK-HTC). Our work enhances the model's perception of subtle differences between sibling classes at deeper levels, rather than just enforcing hierarchical rules. Specifically, we propose a novel framework featuring two core components: a hierarchical knowledge extraction module and a sibling contrastive learning mechanism. This design guides model to encode discriminative features at each hierarchy level, thus improving the separability of confusable classes. Our approach achieves superior performance across three benchmark datasets, surpassing existing state-of-the-art methods in most cases. Our code is available at https://github.com/happywinder/SCHK-HTC.

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) that are traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time-series of climatic variables, and satellite time-series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

While learning models are typically studied for inputs in the form of a fixed dimensional feature vector, real world data is rarely found in this form. In order to meet the basic requirement of traditional learning models, structural data generally have to be converted into fix-length vectors in a handcrafted manner, which is tedious and may even incur information loss. A common form of structured data is what we term "semantic tree-structures", corresponding to data where rich semantic information is encoded in a compositional manner, such as those expressed in JavaScript Object Notation (JSON) and eXtensible Markup Language (XML). For tree-structured data, several learning models have been studied to allow for working directly on raw tree-structure data, However such learning models are limited to either a specific tree-topology or a specific tree-structured data format, e.g., synthetic parse trees. In this paper, we propose a novel framework for end-to-end learning on generic semantic tree-structured data of arbitrary topology and heterogeneous data types, such as data expressed in JSON, XML and so on. Motivated by the works in recursive and recurrent neural networks, we develop exemplar neural implementations of our framework for the JSON format. We evaluate our approach on several UCI benchmark datasets, including ablation and data-efficiency studies, and on a toy reinforcement learning task. Experimental results suggest that our framework yields comparable performance to use of standard models with dedicated feature-vectors in general, and even exceeds baseline performance in cases where compositional nature of the data is particularly important. The source code for a JSON-based implementation of our framework along with experiments can be downloaded at https://github.com/EndingCredits/json2vec.

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks. The Comp-HRDoc benchmark and UniHDSA's configurations are publicly available at https://github.com/microsoft/CompHRDoc.

Model customization necessitates high-quality and diverse datasets, but acquiring such data remains time-consuming and labor-intensive. Despite the great potential of large language models (LLMs) for data synthesis, current approaches are constrained by limited seed data, model biases, and low-variation prompts, resulting in limited diversity and biased distributions with the increase of data scales. To tackle this challenge, we introduce TREESYNTH, a tree-guided subspace-based data synthesis approach inspired by decision trees. It constructs a spatial partitioning tree to recursively divide a task-specific full data space (i.e., root node) into numerous atomic subspaces (i.e., leaf nodes) with mutually exclusive and exhaustive attributes to ensure both distinctiveness and comprehensiveness before synthesizing samples within each atomic subspace. This globally dividing-and-synthesizing method finally collects subspace samples into a comprehensive dataset, effectively circumventing repetition and space collapse to ensure the diversity of large-scale data synthesis. Furthermore, the spatial partitioning tree enables sample allocation into atomic subspaces, allowing the rebalancing of existing datasets for more balanced and comprehensive distributions. Empirically, extensive experiments across diverse benchmarks consistently demonstrate the superior data diversity, model performance, and robust scalability of TREESYNTH compared to both human-crafted datasets and peer data synthesis methods, with an average performance gain reaching 10%. Besides, the consistent improvements of TREESYNTH-balanced datasets highlight its efficacious application to redistribute existing datasets for more comprehensive coverage and the induced performance enhancement. The code is available at https://github.com/cpa2001/TreeSynth.

Many practical applications, such as recommender systems and learning to rank, involve solving multiple similar tasks. One example is learning of recommendation policies for users with similar movie preferences, where the users may still rank the individual movies slightly differently. Such tasks can be organized in a hierarchy, where similar tasks are related through a shared structure. In this work, we formulate this problem as a contextual off-policy optimization in a hierarchical graphical model from logged bandit feedback. To solve the problem, we propose a hierarchical off-policy optimization algorithm (HierOPO), which estimates the parameters of the hierarchical model and then acts pessimistically with respect to them. We instantiate HierOPO in linear Gaussian models, for which we also provide an efficient implementation and analysis. We prove per-task bounds on the suboptimality of the learned policies, which show a clear improvement over not using the hierarchical model. We also evaluate the policies empirically. Our theoretical and empirical results show a clear advantage of using the hierarchy over solving each task independently.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

We consider the hierarchical representation of documents as graphs and use geometric deep learning to classify them into different categories. While graph neural networks can efficiently handle the variable structure of hierarchical documents using the permutation invariant message passing operations, we show that we can gain extra performance improvements using our proposed selective graph pooling operation that arises from the fact that some parts of the hierarchy are invariable across different documents. We applied our model to classify clinical trial (CT) protocols into completed and terminated categories. We use bag-of-words based, as well as pre-trained transformer-based embeddings to featurize the graph nodes, achieving f1-scores around 0.85 on a publicly available large scale CT registry of around 360K protocols. We further demonstrate how the selective pooling can add insights into the CT termination status prediction. We make the source code and dataset splits accessible.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

In this era of information explosion, a personalized recommendation system is convenient for users to get information they are interested in. To deal with billions of users and items, large-scale online recommendation services usually consist of three stages: candidate generation, coarse-grained ranking, and fine-grained ranking. The success of each stage depends on whether the model accurately captures the interests of users, which are usually hidden in users' behavior data. Previous research shows that users' interests are diverse, and one vector is not sufficient to capture users' different preferences. Therefore, many methods use multiple vectors to encode users' interests. However, there are two unsolved problems: (1) The similarity of different vectors in existing methods is too high, with too much redundant information. Consequently, the interests of users are not fully represented. (2) Existing methods model the long-term and short-term behaviors together, ignoring the differences between them. This paper proposes a Hierarchical Multi-Interest Co-Network (HCN) to capture users' diverse interests in the coarse-grained ranking stage. Specifically, we design a hierarchical multi-interest extraction layer to update users' diverse interest centers iteratively. The multiple embedded vectors obtained in this way contain more information and represent the interests of users better in various aspects. Furthermore, we develop a Co-Interest Network to integrate users' long-term and short-term interests. Experiments on several real-world datasets and one large-scale industrial dataset show that HCN effectively outperforms the state-of-the-art methods. We deploy HCN into a large-scale real world E-commerce system and achieve extra 2.5\% improvements on GMV (Gross Merchandise Value).

Recommending novel content, which expands user horizons by introducing them to new interests, has been shown to improve users' long-term experience on recommendation platforms chen2021values. Users however are not constantly looking to explore novel content. It is therefore crucial to understand their novelty-seeking intent and adjust the recommendation policy accordingly. Most existing literature models a user's propensity to choose novel content or to prefer a more diverse set of recommendations at individual interactions. Hierarchical structure, on the other hand, exists in a user's novelty-seeking intent, which is manifested as a static and intrinsic user preference for seeking novelty along with a dynamic session-based propensity. To this end, we propose a novel hierarchical reinforcement learning-based method to model the hierarchical user novelty-seeking intent, and to adapt the recommendation policy accordingly based on the extracted user novelty-seeking propensity. We further incorporate diversity and novelty-related measurement in the reward function of the hierarchical RL (HRL) agent to encourage user exploration chen2021values. We demonstrate the benefits of explicitly modeling hierarchical user novelty-seeking intent in recommendations through extensive experiments on simulated and real-world datasets. In particular, we demonstrate that the effectiveness of our proposed hierarchical RL-based method lies in its ability to capture such hierarchically-structured intent. As a result, the proposed HRL model achieves superior performance on several public datasets, compared with state-of-art baselines.

Recent advances in representation learning on graphs, mainly leveraging graph convolutional networks, have brought a substantial improvement on many graph-based benchmark tasks. While novel approaches to learning node embeddings are highly suitable for node classification and link prediction, their application to graph classification (predicting a single label for the entire graph) remains mostly rudimentary, typically using a single global pooling step to aggregate node features or a hand-designed, fixed heuristic for hierarchical coarsening of the graph structure. An important step towards ameliorating this is differentiable graph coarsening---the ability to reduce the size of the graph in an adaptive, data-dependent manner within a graph neural network pipeline, analogous to image downsampling within CNNs. However, the previous prominent approach to pooling has quadratic memory requirements during training and is therefore not scalable to large graphs. Here we combine several recent advances in graph neural network design to demonstrate that competitive hierarchical graph classification results are possible without sacrificing sparsity. Our results are verified on several established graph classification benchmarks, and highlight an important direction for future research in graph-based neural networks.

We present TreeON, a novel neural-based framework for reconstructing detailed 3D tree point clouds from sparse top-down geodata, using only a single orthophoto and its corresponding Digital Surface Model (DSM). Our method introduces a new training supervision strategy that combines both geometric supervision and differentiable shadow and silhouette losses to learn point cloud representations of trees without requiring species labels, procedural rules, terrestrial reconstruction data, or ground laser scans. To address the lack of ground truth data, we generate a synthetic dataset of point clouds from procedurally modeled trees and train our network on it. Quantitative and qualitative experiments demonstrate better reconstruction quality and coverage compared to existing methods, as well as strong generalization to real-world data, producing visually appealing and structurally plausible tree point cloud representations suitable for integration into interactive digital 3D maps. The codebase, synthetic dataset, and pretrained model are publicly available at https://angelikigram.github.io/treeON/.

Canada experienced in 2023 one of the most severe wildfire seasons in recent history, causing damage across ecosystems, destroying communities, and emitting large quantities of CO2. This extreme wildfire season is symptomatic of a climate-change-induced increase in the length and severity of the fire season that affects the boreal ecosystem. Therefore, it is critical to empower wildfire management in boreal communities with better mitigation solutions. Wildfire probability maps represent an important tool for understanding the likelihood of wildfire occurrence and the potential severity of future wildfires. The massive increase in the availability of Earth observation data has enabled the development of deep learning-based wildfire forecasting models, aiming at providing precise wildfire probability maps at different spatial and temporal scales. A main limitation of such methods is their reliance on coarse-resolution environmental drivers and satellite products, leading to wildfire occurrence prediction of reduced resolution, typically around sim 0.1{\deg}. This paper presents a benchmark dataset: CanadaFireSat, and baseline methods for high-resolution: 100 m wildfire forecasting across Canada, leveraging multi-modal data from high-resolution multi-spectral satellite images (Sentinel-2 L1C), mid-resolution satellite products (MODIS), and environmental factors (ERA5 reanalysis data). Our experiments consider two major deep learning architectures. We observe that using multi-modal temporal inputs outperforms single-modal temporal inputs across all metrics, achieving a peak performance of 60.3% in F1 score for the 2023 wildfire season, a season never seen during model training. This demonstrates the potential of multi-modal deep learning models for wildfire forecasting at high-resolution and continental scale.

Vision foundation models (FMs) are accelerating the development of digital pathology algorithms and transforming biomedical research. These models learn, in a self-supervised manner, to represent histological features in highly heterogeneous tiles extracted from whole-slide images (WSIs) of real-world patient samples. The performance of these FMs is significantly influenced by the size, diversity, and balance of the pre-training data. However, data selection has been primarily guided by expert knowledge at the WSI level, focusing on factors such as disease classification and tissue types, while largely overlooking the granular details available at the tile level. In this paper, we investigate the potential of unsupervised automatic data curation at the tile-level, taking into account 350 million tiles. Specifically, we apply hierarchical clustering trees to pre-extracted tile embeddings, allowing us to sample balanced datasets uniformly across the embedding space of the pretrained FM. We further identify these datasets are subject to a trade-off between size and balance, potentially compromising the quality of representations learned by FMs, and propose tailored batch sampling strategies to mitigate this effect. We demonstrate the effectiveness of our method through improved performance on a diverse range of clinically relevant downstream tasks.

Open vocabulary models (e.g. CLIP) have shown strong performance on zero-shot classification through their ability generate embeddings for each class based on their (natural language) names. Prior work has focused on improving the accuracy of these models through prompt engineering or by incorporating a small amount of labeled downstream data (via finetuning). However, there has been little focus on improving the richness of the class names themselves, which can pose issues when class labels are coarsely-defined and are uninformative. We propose Classification with Hierarchical Label Sets (or CHiLS), an alternative strategy for zero-shot classification specifically designed for datasets with implicit semantic hierarchies. CHiLS proceeds in three steps: (i) for each class, produce a set of subclasses, using either existing label hierarchies or by querying GPT-3; (ii) perform the standard zero-shot CLIP procedure as though these subclasses were the labels of interest; (iii) map the predicted subclass back to its parent to produce the final prediction. Across numerous datasets with underlying hierarchical structure, CHiLS leads to improved accuracy in situations both with and without ground-truth hierarchical information. CHiLS is simple to implement within existing zero-shot pipelines and requires no additional training cost. Code is available at: https://github.com/acmi-lab/CHILS.

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.