Daily Papers

In this paper, we present gfnx, a fast and scalable package for training and evaluating Generative Flow Networks (GFlowNets) written in JAX. gfnx provides an extensive set of environments and metrics for benchmarking, accompanied with single-file implementations of core objectives for training GFlowNets. We include synthetic hypergrids, multiple sequence generation environments with various editing regimes and particular reward designs for molecular generation, phylogenetic tree construction, Bayesian structure learning, and sampling from the Ising model energy. Across different tasks, gfnx achieves significant wall-clock speedups compared to Pytorch-based benchmarks (such as torchgfn library) and author implementations. For example, gfnx achieves up to 55 times speedup on CPU-based sequence generation environments, and up to 80 times speedup with the GPU-based Bayesian network structure learning setup. Our package provides a diverse set of benchmarks and aims to standardize empirical evaluation and accelerate research and applications of GFlowNets. The library is available on GitHub (https://github.com/d-tiapkin/gfnx) and on pypi (https://pypi.org/project/gfnx/). Documentation is available on https://gfnx.readthedocs.io.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a phylogenetic distance metrics based on the similarity of LLMs' output. The resulting metric is then used to construct dendrograms, which satisfactorily capture known relationships across a set of 111 open-source and 45 closed models. Furthermore, our phylogenetic distance predicts performance in standard benchmarks, thus demonstrating its functional validity and paving the way for a time and cost-effective estimation of LLM capabilities. To sum up, by translating population genetic concepts to machine learning, we propose and validate a tool to evaluate LLM development, relationships and capabilities, even in the absence of transparent training information.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce THE-Tree (Technology History Evolution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

We introduce Tree D-fusion, featuring the first collection of 600,000 environmentally aware, 3D simulation-ready tree models generated through Diffusion priors. Each reconstructed 3D tree model corresponds to an image from Google's Auto Arborist Dataset, comprising street view images and associated genus labels of trees across North America. Our method distills the scores of two tree-adapted diffusion models by utilizing text prompts to specify a tree genus, thus facilitating shape reconstruction. This process involves reconstructing a 3D tree envelope filled with point markers, which are subsequently utilized to estimate the tree's branching structure using the space colonization algorithm conditioned on a specified genus.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell) which is inherently non-treelike. Currently available tools for reconstructing the evolutionary past of a polyploid dataset generally start with a multi-labelled tree obtained for a dataset of interest and then derive a (phylogenetic) network from that tree in some way that reflects that past by interpreting the networks's vertices of indegree at least two as polyploidization events. Since obtaining such a tree can be computationally expensive it is paramount to have alternative approaches available that allow one to shed light into the reticulate evolutionary past of a polyploid dataset. SPRINT aims to reconstruct the evolutionary past of a polyploid dataset in terms of a binary network which realises the dataset's ploidy profile (vector of ploidy levels of the dataset's taxa) and requires the fewest number of polyploidization events. It does this by representing the ploidy level of a species x in terms of the number of directed paths from the root of the network to the leaf of the network labelled by x. SPRINT is distributed on GitHub: https://github.com/lmaher1/SPRINT.

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

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.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face limitations such as suboptimal solutions from greedy methods or prohibitive computational costs and limited applicability of exact optimization approaches. To address these challenges, we propose an evolutionary optimization method for decision tree induction based on genetic programming (GP). Our key innovation is the integration of semantic priors and domain-specific knowledge about the search space into the optimization algorithm. To this end, we introduce LLEGO, a framework that incorporates semantic priors into genetic search operators through the use of Large Language Models (LLMs), thereby enhancing search efficiency and targeting regions of the search space that yield decision trees with superior generalization performance. This is operationalized through novel genetic operators that work with structured natural language prompts, effectively utilizing LLMs as conditional generative models and sources of semantic knowledge. Specifically, we introduce fitness-guided crossover to exploit high-performing regions, and diversity-guided mutation for efficient global exploration of the search space. These operators are controlled by corresponding hyperparameters that enable a more nuanced balance between exploration and exploitation across the search space. Empirically, we demonstrate across various benchmarks that LLEGO evolves superior-performing trees compared to existing tree induction methods, and exhibits significantly more efficient search performance compared to conventional GP approaches.

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.

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

Large Reasoning Models (LRMs) achieve remarkable inference-time improvements through parallel thinking. However, existing methods rely on redundant sampling of reasoning trajectories, failing to effectively explore the reasoning space to uncover high-quality solutions. To address these limitations, we propose Decoding Tree Sketching (DTS), a plug-and-play decoding framework for structural multi-trajectory exploration and reasoning selection. For reasoning exploration, DTS sketches a backbone tree of the reasoning space by selectively branching at decision tokens. For reasoning selection, guided by length-accuracy anti-correlation, DTS designs an early termination to prioritize short and reliable trajectories during decoding. Experimental results across four LRMs and datasets demonstrate that DTS significantly enhances accuracy by 14% and reduces repetitive generation by 8% on average. Notably, DTS enables smaller models to outperform larger models with 10times the size, highlighting its potential to strengthen reasoning capabilities.

Competition-level code generation tasks pose significant challenges for current state-of-the-art large language models (LLMs). For example, on the LiveCodeBench-Hard dataset, models such as O1-Mini and O1-Preview achieve pass@1 rates of only 0.366 and 0.143, respectively. While tree search techniques have proven effective in domains like mathematics and general coding, their potential in competition-level code generation remains under-explored. In this work, we propose a novel token-level tree search method specifically designed for code generation. Leveraging Qwen2.5-Coder-32B-Instruct, our approach achieves a pass rate of 0.305 on LiveCodeBench-Hard, surpassing the pass@100 performance of GPT4o-0513 (0.245). Furthermore, by integrating Chain-of-Thought (CoT) prompting, we improve our method's performance to 0.351, approaching O1-Mini's pass@1 rate. To ensure reproducibility, we report the average number of generations required per problem by our tree search method on the test set. Our findings underscore the potential of tree search to significantly enhance performance on competition-level code generation tasks. This opens up new possibilities for large-scale synthesis of challenging code problems supervised fine-tuning (SFT) data, advancing competition-level code generation tasks.

Training multiple tasks jointly in one deep network yields reduced latency during inference and better performance over the single-task counterpart by sharing certain layers of a network. However, over-sharing a network could erroneously enforce over-generalization, causing negative knowledge transfer across tasks. Prior works rely on human intuition or pre-computed task relatedness scores for ad hoc branching structures. They provide sub-optimal end results and often require huge efforts for the trial-and-error process. In this work, we present an automated multi-task learning algorithm that learns where to share or branch within a network, designing an effective network topology that is directly optimized for multiple objectives across tasks. Specifically, we propose a novel tree-structured design space that casts a tree branching operation as a gumbel-softmax sampling procedure. This enables differentiable network splitting that is end-to-end trainable. We validate the proposed method on controlled synthetic data, CelebA, and Taskonomy.

We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving code repository. This graph-based structure supports fine-grained branching, implicit concurrency, and scalable agent interaction while preserving a consistent historical record. Human involvement is minimal but strategic: users define high-level goals, periodically review the graph, and provide lightweight feedback to promote promising directions or prune unproductive ones. Experiments demonstrate EvoGit's ability to autonomously produce functional and modular software artifacts across two real-world tasks: (1) building a web application from scratch using modern frameworks, and (2) constructing a meta-level system that evolves its own language-model-guided solver for the bin-packing optimization problem. Our results underscore EvoGit's potential to establish a new paradigm for decentralized, automated, and continual software development. EvoGit is open-sourced at https://github.com/BillHuang2001/evogit.

Large language models (LLMs) have shown remarkable ability to generate code, yet their outputs often violate syntactic or semantic constraints when guided only through natural language prompts. We introduce TreeCoder, the most general and flexible framework to date for exploring decoding strategies, constraints, and hyperparameters in LLMs, and use it in code generation to enforce correctness and structure during decoding rather than relying on prompt engineering. TreeCoder represents decoding as a tree search over candidate programs, where both decoding strategies and constraint functions - such as style, syntax, execution - are treated as first-class, optimisable components. This design enables systematic exploration and automatic tuning of decoding configurations using standard optimisation techniques. Experiments on the MBPP (Python) and SQL-Spider benchmarks show that TreeCoder consistently improves accuracy across open-source models such as CodeLlama, Mistral and DeepSeek, often outperforming their unconstrained baselines by considerable margins.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Since its emergence, SARS-CoV-2 has demonstrated a rapid and unpredictable evolutionary trajectory, characterized by the continual emergence of immune-evasive variants. This poses persistent challenges to public health and vaccine development. While large-scale generative pre-trained transformers (GPTs) have revolutionized the modeling of sequential data, their direct applications to noisy viral genomic sequences are limited. In this paper, we introduce PETRA(Pretrained Evolutionary TRAnsformer), a novel transformer approach based on evolutionary trajectories derived from phylogenetic trees rather than raw RNA sequences. This method effectively mitigates sequencing noise and captures the hierarchical structure of viral evolution. With a weighted training framework to address substantial geographical and temporal imbalances in global sequence data, PETRA excels in predicting future SARS-CoV-2 mutations, achieving a weighted recall@1 of 9.45% for nucleotide mutations and 17.10\% for spike amino-acid mutations, compared to 0.49% and 6.64% respectively for the best baseline. PETRA also demonstrates its ability to aid in the real-time mutation prediction of major clades like 24F(XEC) and 25A(LP.8.1). The code is open sourced on https://github.com/xz-keg/PETra

Speculative decoding is an inference-acceleration method for large language models (LLMs) where a small language model generates a draft-token sequence which is further verified by the target LLM in parallel. Recent works have advanced this method by establishing a draft-token tree, achieving superior performance over a single-sequence speculative decoding. However, those works independently generate tokens at each level of the tree, not leveraging the tree's entire diversifiability. Besides, their empirical superiority has been shown for fixed length of sequences, implicitly granting more computational resource to LLM for the tree-based methods. None of the existing works has conducted empirical studies with fixed target computational budgets despite its importance to resource-bounded devices. We present Recursive Speculative Decoding (RSD), a novel tree-based method that samples draft tokens without replacement and maximizes the diversity of the tree. During RSD's drafting, the tree is built by either Gumbel-Top-k trick that draws tokens without replacement in parallel or Stochastic Beam Search that samples sequences without replacement while early-truncating unlikely draft sequences and reducing the computational cost of LLM. We empirically evaluate RSD with Llama 2 and OPT models, showing that RSD outperforms the baseline methods, consistently for fixed draft sequence length and in most cases for fixed computational budgets at LLM.

Scientific posters play a vital role in academic communication by presenting ideas through visual summaries. Analyzing reading order and parent-child relations of posters is essential for building structure-aware interfaces that facilitate clear and accurate understanding of research content. Despite their prevalence in academic communication, posters remain underexplored in structural analysis research, which has primarily focused on papers. To address this gap, we constructed SciPostLayoutTree, a dataset of approximately 8,000 posters annotated with reading order and parent-child relations. Compared to an existing structural analysis dataset, SciPostLayoutTree contains more instances of spatially challenging relations, including upward, horizontal, and long-distance relations. As a solution to these challenges, we develop Layout Tree Decoder, which incorporates visual features as well as bounding box features including position and category information. The model also uses beam search to predict relations while capturing sequence-level plausibility. Experimental results demonstrate that our model improves the prediction accuracy for spatially challenging relations and establishes a solid baseline for poster structure analysis. The dataset is publicly available at https://huggingface.co/datasets/omron-sinicx/scipostlayouttree. The code is also publicly available at https://github.com/omron-sinicx/scipostlayouttree.

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.

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.

Recent research suggests that tree search algorithms (e.g. Monte Carlo Tree Search) can dramatically boost LLM performance on complex mathematical reasoning tasks. However, they often require more than 10 times the computational resources of greedy decoding due to wasteful search strategies, making them difficult to be deployed in practical applications. This study introduces a novel guided tree search algorithm with dynamic node selection and node-level exploration budget (maximum number of children) calculation to tackle this issue. By considering the search progress towards the final answer (history) and the guidance from a value network (future) trained without any step-wise annotations, our algorithm iteratively selects the most promising tree node before expanding it within the boundaries of the allocated computational budget. Experiments conducted on the GSM8K and TabMWP datasets demonstrate that our approach not only offers competitive performance but also enjoys significantly lower computational costs compared to baseline methods.

Agentic retrieval-augmented generation (RAG) formulates question answering as a multi-step interaction between reasoning and information retrieval, and has recently been advanced by reinforcement learning (RL) with outcome-based supervision. While effective, relying solely on sparse final rewards limits step-wise credit assignment and provides weak guidance for intermediate reasoning and actions. Recent efforts explore process-level supervision, but typically depend on offline constructed training data, which risks distribution shift, or require costly intermediate annotations. We present TreePS-RAG, an online, tree-based RL framework for agentic RAG that enables step-wise credit assignment while retaining standard outcome-only rewards. Our key insight is to model agentic RAG reasoning as a rollout tree, where each reasoning step naturally maps to a node. This tree structure allows step utility to be estimated via Monte Carlo estimation over its descendant outcomes, yielding fine-grained process advantages without requiring intermediate labels. To make this paradigm practical, we introduce an efficient online tree construction strategy that preserves exploration diversity under a constrained computational budget. With a rollout cost comparable to strong baselines like Search-R1, experiments on seven multi-hop and general QA benchmarks across multiple model scales show that TreePS-RAG consistently and significantly outperforms both outcome-supervised and leading process-supervised RL methods.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

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.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Autoregressive language models demonstrate excellent performance in various scenarios. However, the inference efficiency is limited by its one-step-one-word generation mode, which has become a pressing problem recently as the models become increasingly larger. Speculative decoding employs a "draft and then verify" mechanism to allow multiple tokens to be generated in one step, realizing lossless acceleration. Existing methods mainly adopt fixed heuristic draft structures, which fail to adapt to different situations to maximize the acceptance length during verification. To alleviate this dilemma, we proposed OPT-Tree, an algorithm to construct adaptive and scalable draft trees. It searches the optimal tree structure that maximizes the mathematical expectation of the acceptance length in each decoding step. Experimental results reveal that OPT-Tree outperforms the existing draft structures and achieves a speed-up ratio of up to 3.2 compared with autoregressive decoding. If the draft model is powerful enough and the node budget is sufficient, it can generate more than ten tokens in a single step. Our code is available at https://github.com/Jikai0Wang/OPT-Tree.

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.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

Prototype-based methods use interpretable representations to address the black-box nature of deep learning models, in contrast to post-hoc explanation methods that only approximate such models. We propose the Neural Prototype Tree (ProtoTree), an intrinsically interpretable deep learning method for fine-grained image recognition. ProtoTree combines prototype learning with decision trees, and thus results in a globally interpretable model by design. Additionally, ProtoTree can locally explain a single prediction by outlining a decision path through the tree. Each node in our binary tree contains a trainable prototypical part. The presence or absence of this learned prototype in an image determines the routing through a node. Decision making is therefore similar to human reasoning: Does the bird have a red throat? And an elongated beak? Then it's a hummingbird! We tune the accuracy-interpretability trade-off using ensemble methods, pruning and binarizing. We apply pruning without sacrificing accuracy, resulting in a small tree with only 8 learned prototypes along a path to classify a bird from 200 species. An ensemble of 5 ProtoTrees achieves competitive accuracy on the CUB-200- 2011 and Stanford Cars data sets. Code is available at https://github.com/M-Nauta/ProtoTree

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the R programming language with easy-to-use tools for reading and writing NeXML documents, including rich metadata, in a way that interfaces seamlessly with the extensive library of phylogenetic tools already available in the R ecosystem.

Speculative decoding has been widely used to accelerate autoregressive (AR) text generation. However, its effectiveness in visual AR models remains limited due to token selection ambiguity, where multiple tokens receive similarly low probabilities, reducing acceptance rates. While dynamic tree drafting has been proposed to improve speculative decoding, we show that it fails to mitigate token selection ambiguity, resulting in shallow draft trees and suboptimal acceleration. To address this, we introduce LANTERN++, a novel framework that integrates static tree drafting with a relaxed acceptance condition, allowing drafts to be selected independently of low-confidence predictions. This enables deeper accepted sequences, improving decoding efficiency while preserving image quality. Extensive experiments on state-of-the-art visual AR models demonstrate that LANTERN++ significantly accelerates inference, achieving up to times 2.56 speedup over standard AR decoding while maintaining high image quality.

Decision trees are renowned for their interpretability capability to achieve high predictive performance, especially on tabular data. Traditionally, they are constructed through recursive algorithms, where they partition the data at every node in a tree. However, identifying the best partition is challenging, as decision trees optimized for local segments may not bring global generalization. To address this, we introduce MetaTree, which trains a transformer-based model on filtered outputs from classical algorithms to produce strong decision trees for classification. Specifically, we fit both greedy decision trees and optimized decision trees on a large number of datasets. We then train MetaTree to produce the trees that achieve strong generalization performance. This training enables MetaTree to not only emulate these algorithms, but also to intelligently adapt its strategy according to the context, thereby achieving superior generalization performance.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

We introduce HunyuanProver, an language model finetuned from the Hunyuan 7B for interactive automatic theorem proving with LEAN4. To alleviate the data sparsity issue, we design a scalable framework to iterative synthesize data with low cost. Besides, guided tree search algorithms are designed to enable effective ``system 2 thinking`` of the prover. HunyuanProver achieves state-of-the-art (SOTA) performances on major benchmarks. Specifically, it achieves a pass of 68.4% on the miniF2F-test compared to 65.9%, the current SOTA results. It proves 4 IMO statements (imo_1960_p2, imo_1962_p2}, imo_1964_p2 and imo_1983_p6) in miniF2F-test. To benefit the community, we will open-source a dataset of 30k synthesized instances, where each instance contains the original question in natural language, the converted statement by autoformalization, and the proof by HunyuanProver.

This paper presents UD-NewsCrawl, the largest Tagalog treebank to date, containing 15.6k trees manually annotated according to the Universal Dependencies framework. We detail our treebank development process, including data collection, pre-processing, manual annotation, and quality assurance procedures. We provide baseline evaluations using multiple transformer-based models to assess the performance of state-of-the-art dependency parsers on Tagalog. We also highlight challenges in the syntactic analysis of Tagalog given its distinctive grammatical properties, and discuss its implications for the annotation of this treebank. We anticipate that UD-NewsCrawl and our baseline model implementations will serve as valuable resources for advancing computational linguistics research in underrepresented languages like Tagalog.

Pre-trained on massive amounts of code and text data, large language models (LLMs) have demonstrated remarkable achievements in performing code generation tasks. With additional execution-based feedback, these models can act as agents with capabilities to self-refine and improve generated code autonomously. However, on challenging coding tasks with extremely large search space, current agentic approaches still struggle with multi-stage planning, generating, and debugging. To address this problem, we propose CodeTree, a framework for LLM agents to efficiently explore the search space in different stages of the code generation process. Specifically, we adopted a unified tree structure to explicitly explore different coding strategies, generate corresponding coding solutions, and subsequently refine the solutions. In each stage, critical decision-making (ranking, termination, expanding) of the exploration process is guided by both the environmental execution-based feedback and LLM-agent-generated feedback. We comprehensively evaluated CodeTree on 7 code generation benchmarks and demonstrated the significant performance gains of CodeTree against strong baselines. Using GPT-4o as the base model, we consistently achieved top results of 95.1 on HumanEval, 98.7 on MBPP, and 43.0 on CodeContests. On the challenging SWEBench benchmark, our approach led to significant performance gains.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

Multilingual language models have pushed state-of-the-art in cross-lingual NLP transfer. The majority of zero-shot cross-lingual transfer, however, use one and the same massively multilingual transformer (e.g., mBERT or XLM-R) to transfer to all target languages, irrespective of their typological, etymological, and phylogenetic relations to other languages. In particular, readily available data and models of resource-rich sibling languages are often ignored. In this work, we empirically show, in a case study for Faroese -- a low-resource language from a high-resource language family -- that by leveraging the phylogenetic information and departing from the 'one-size-fits-all' paradigm, one can improve cross-lingual transfer to low-resource languages. In particular, we leverage abundant resources of other Scandinavian languages (i.e., Danish, Norwegian, Swedish, and Icelandic) for the benefit of Faroese. Our evaluation results show that we can substantially improve the transfer performance to Faroese by exploiting data and models of closely-related high-resource languages. Further, we release a new web corpus of Faroese and Faroese datasets for named entity recognition (NER), semantic text similarity (STS), and new language models trained on all Scandinavian languages.

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}

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Generative Knowledge Graph Construction (KGC) refers to those methods that leverage the sequence-to-sequence framework for building knowledge graphs, which is flexible and can be adapted to widespread tasks. In this study, we summarize the recent compelling progress in generative knowledge graph construction. We present the advantages and weaknesses of each paradigm in terms of different generation targets and provide theoretical insight and empirical analysis. Based on the review, we suggest promising research directions for the future. Our contributions are threefold: (1) We present a detailed, complete taxonomy for the generative KGC methods; (2) We provide a theoretical and empirical analysis of the generative KGC methods; (3) We propose several research directions that can be developed in the future.

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.

Large Reasoning Models(LRMs) such as OpenAI o1 and DeepSeek-R1 have shown remarkable reasoning capabilities by scaling test-time compute and generating long Chain-of-Thought(CoT). Distillation--post-training on LRMs-generated data--is a straightforward yet effective method to enhance the reasoning abilities of smaller models, but faces a critical bottleneck: we found that distilled long CoT data poses learning difficulty for small models and leads to the inheritance of biases (i.e. over-thinking) when using Supervised Fine-tuning(SFT) and Reinforcement Learning(RL) methods. To alleviate this bottleneck, we propose constructing tree-based CoT data from scratch via Monte Carlo Tree Search(MCTS). We then exploit a set of CoT-aware approaches, including Thoughts Length Balance, Fine-grained DPO, and Joint Post-training Objective, to enhance SFT and RL on the construted data.

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats

In the field of decision trees, most previous studies have difficulty ensuring the statistical optimality of a prediction of new data and suffer from overfitting because trees are usually used only to represent prediction functions to be constructed from given data. In contrast, some studies, including this paper, used the trees to represent stochastic data observation processes behind given data. Moreover, they derived the statistically optimal prediction, which is robust against overfitting, based on the Bayesian decision theory by assuming a prior distribution for the trees. However, these studies still have a problem in computing this Bayes optimal prediction because it involves an infeasible summation for all division patterns of a feature space, which is represented by the trees and some parameters. In particular, an open problem is a summation with respect to combinations of division axes, i.e., the assignment of features to inner nodes of the tree. We solve this by a Markov chain Monte Carlo method, whose step size is adaptively tuned according to a posterior distribution for the trees.

We investigate the utility of Large Language Models for automated taxonomy generation and completion specifically applied to taxonomies from the food technology industry. We explore the extent to which taxonomies can be completed from a seed taxonomy or generated without a seed from a set of known concepts, in an iterative fashion using recent prompting techniques. Experiments on five taxonomies using an open-source LLM (Llama-3), while promising, point to the difficulty of correctly placing inner nodes.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

We present Muses, the first training-free method for fantastic 3D creature generation in a feed-forward paradigm. Previous methods, which rely on part-aware optimization, manual assembly, or 2D image generation, often produce unrealistic or incoherent 3D assets due to the challenges of intricate part-level manipulation and limited out-of-domain generation. In contrast, Muses leverages the 3D skeleton, a fundamental representation of biological forms, to explicitly and rationally compose diverse elements. This skeletal foundation formalizes 3D content creation as a structure-aware pipeline of design, composition, and generation. Muses begins by constructing a creatively composed 3D skeleton with coherent layout and scale through graph-constrained reasoning. This skeleton then guides a voxel-based assembly process within a structured latent space, integrating regions from different objects. Finally, image-guided appearance modeling under skeletal conditions is applied to generate a style-consistent and harmonious texture for the assembled shape. Extensive experiments establish Muses' state-of-the-art performance in terms of visual fidelity and alignment with textual descriptions, and potential on flexible 3D object editing. Project page: https://luhexiao.github.io/Muses.github.io/.

Understanding the underlying linguistic rules of plant genomes remains a fundamental challenge in computational biology. Recent advances including AgroNT and PDLLMs have made notable progress although, they suffer from excessive parameter size and limited ability to model the bidirectional nature of DNA strands respectively. To address these limitations, we propose PlantBiMoE, a lightweight and expressive plant genome language model that integrates bidirectional Mamba and a Sparse Mixture-of-Experts (SparseMoE) framework. The bidirectional Mamba enables the model to effectively capture structural dependencies across both the forward and reverse DNA strands, while SparseMoE significantly reduces the number of active parameters, improving computational efficiency without sacrificing modeling capacity. We evaluated and tested our model on the Modified Plants Genome Benchmark (MPGB), an enhanced genomic benchmark, which consolidates 31 datasets across 11 representative tasks, with input sequence lengths ranging from 50 to 6,000 bp. Experimental results demonstrate that PlantBiMoE achieves the best performance on 20 out of 31 datasets and the average best when comparing with existing models. In summary, all above results demonstrate that our model can effectively represent plant genomic sequences, serving as a robust computational tool for diverse genomic tasks, while making substantive contributions to plant genomics, gene editing, and synthetic biology. The code is available at: https://github.com/HUST-Keep-Lin/PlantBiMoE

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.

Reinforcement learning (RL) post-training is crucial for aligning generative models with human preferences, but its prohibitive computational cost remains a major barrier to widespread adoption. We introduce TreeGRPO, a novel RL framework that dramatically improves training efficiency by recasting the denoising process as a search tree. From shared initial noise samples, TreeGRPO strategically branches to generate multiple candidate trajectories while efficiently reusing their common prefixes. This tree-structured approach delivers three key advantages: (1) High sample efficiency, achieving better performance under same training samples (2) Fine-grained credit assignment via reward backpropagation that computes step-specific advantages, overcoming the uniform credit assignment limitation of trajectory-based methods, and (3) Amortized computation where multi-child branching enables multiple policy updates per forward pass. Extensive experiments on both diffusion and flow-based models demonstrate that TreeGRPO achieves 2.4times faster training while establishing a superior Pareto frontier in the efficiency-reward trade-off space. Our method consistently outperforms GRPO baselines across multiple benchmarks and reward models, providing a scalable and effective pathway for RL-based visual generative model alignment. The project website is available at treegrpo.github.io.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

The rapid growth in the parameters of large language models (LLMs) has made inference latency a fundamental bottleneck, limiting broader application of LLMs. Speculative decoding represents a lossless approach to accelerate inference through a guess-and-verify paradigm, leveraging the parallel capabilities of modern hardware. Some speculative decoding methods rely on additional structures to guess draft tokens, such as small models or parameter-efficient architectures, which need extra training before use. Alternatively, retrieval-based train-free techniques build libraries from pre-existing corpora or by n-gram generation. However, they face challenges like large storage requirements, time-consuming retrieval, and limited adaptability. Observing that candidate tokens generated during the decoding process are likely to reoccur in future sequences, we propose Token Recycling. This approach stores candidate tokens in an adjacency matrix and employs a breadth-first search (BFS)-like algorithm on the matrix to construct a draft tree. The tree is then validated through tree attention. New candidate tokens from the decoding process are then used to update the matrix. Token Recycling requires \textless2MB of additional storage and achieves approximately 2x speedup across all sizes of LLMs. It significantly outperforms existing train-free methods by 30\% and even a training method by 25\%. It can be directly applied to any existing LLMs and tasks without the need for adaptation.

Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method Wei2022ChainOT can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at https://tianchi.aliyun.com/dataset/95414, and the source codes are open-sourced at https://github.com/michael-wzhu/text2dt.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

We propose a transformer architecture and training strategy for tree generation. The architecture processes data at multiple resolutions and has an hourglass shape, with middle layers processing fewer tokens than outer layers. Similar to convolutional networks, we introduce longer range skip connections to completent this multi-resolution approach. The key advantage of this architecture is the faster processing speed and lower memory consumption. We are therefore able to process more complex trees than would be possible with a vanilla transformer architecture. Furthermore, we extend this approach to perform image-to-tree and point-cloud-to-tree conditional generation and to simulate the tree growth processes, generating 4D trees. Empirical results validate our approach in terms of speed, memory consumption, and generation quality.

Reasoning is a distinctive human capacity, enabling us to address complex problems by breaking them down into a series of manageable cognitive steps. Yet, complex logical reasoning is still cumbersome for language models. Based on the dual process theory in cognitive science, we are the first to unravel the cognitive reasoning abilities of language models. Our framework employs an iterative methodology to construct a Cognitive Tree (CogTree). The root node of this tree represents the initial query, while the leaf nodes consist of straightforward questions that can be answered directly. This construction involves two main components: the implicit extraction module (referred to as the intuitive system) and the explicit reasoning module (referred to as the reflective system). The intuitive system rapidly generates multiple responses by utilizing in-context examples, while the reflective system scores these responses using comparative learning. The scores guide the intuitive system in its subsequent generation step. Our experimental results on two popular and challenging reasoning tasks indicate that it is possible to achieve a performance level comparable to that of GPT-3.5 (with 175B parameters), using a significantly smaller language model that contains fewer parameters (<=7B) than 5% of GPT-3.5.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

We study the problem of optimizing biological sequences, e.g., proteins, DNA, and RNA, to maximize a black-box score function that is only evaluated in an offline dataset. We propose a novel solution, bootstrapped training of score-conditioned generator (BootGen) algorithm. Our algorithm repeats a two-stage process. In the first stage, our algorithm trains the biological sequence generator with rank-based weights to enhance the accuracy of sequence generation based on high scores. The subsequent stage involves bootstrapping, which augments the training dataset with self-generated data labeled by a proxy score function. Our key idea is to align the score-based generation with a proxy score function, which distills the knowledge of the proxy score function to the generator. After training, we aggregate samples from multiple bootstrapped generators and proxies to produce a diverse design. Extensive experiments show that our method outperforms competitive baselines on biological sequential design tasks. We provide reproducible source code: https://github.com/kaist-silab/bootgen{https://github.com/kaist-silab/bootgen}.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

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}.

Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches rely on various local heuristics for enforcing the acyclicity constraint. In this paper, we introduce a fundamentally different strategy: We formulate the structure learning problem as a purely continuous optimization problem over real matrices that avoids this combinatorial constraint entirely. This is achieved by a novel characterization of acyclicity that is not only smooth but also exact. The resulting problem can be efficiently solved by standard numerical algorithms, which also makes implementation effortless. The proposed method outperforms existing ones, without imposing any structural assumptions on the graph such as bounded treewidth or in-degree. Code implementing the proposed algorithm is open-source and publicly available at https://github.com/xunzheng/notears.

The notion of shortcut partition, introduced recently by Chang, Conroy, Le, Milenkovi\'c, Solomon, and Than [CCLMST23], is a new type of graph partition into low-diameter clusters. Roughly speaking, the shortcut partition guarantees that for every two vertices u and v in the graph, there exists a path between u and v that intersects only a few clusters. They proved that any planar graph admits a shortcut partition and gave several applications, including a construction of tree cover for arbitrary planar graphs with stretch 1+varepsilon and O(1) many trees for any fixed varepsilon in (0,1). However, the construction heavily exploits planarity in multiple steps, and is thus inherently limited to planar graphs. In this work, we breach the "planarity barrier" to construct a shortcut partition for K_r-minor-free graphs for any r. To this end, we take a completely different approach -- our key contribution is a novel deterministic variant of the cop decomposition in minor-free graphs [And86, AGG14]. Our shortcut partition for K_r-minor-free graphs yields several direct applications. Most notably, we construct the first optimal distance oracle for K_r-minor-free graphs, with 1+varepsilon stretch, linear space, and constant query time for any fixed varepsilon in (0,1). The previous best distance oracle [AG06] uses O(nlog n) space and O(log n) query time, and its construction relies on Robertson-Seymour structural theorem and other sophisticated tools. We also obtain the first tree cover of O(1) size for minor-free graphs with stretch 1+varepsilon, while the previous best (1+varepsilon)-tree cover has size O(log^2 n) [BFN19].

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Large Language Models (LLMs) have achieved significant success across various NLP tasks. However, their massive computational costs limit their widespread use, particularly in real-time applications. Structured pruning offers an effective solution by compressing models and directly providing end-to-end speed improvements, regardless of the hardware environment. Meanwhile, different components of the model exhibit varying sensitivities towards pruning, calling for non-uniform model compression. However, a pruning method should not only identify a capable substructure, but also account for post-compression training. To this end, we propose \sysname, a method for training-aware structured pruning. \sysname builds upon an evolutionary search process, generating multiple offspring models in each generation through mutation, and selecting the fittest for survival. To assess the effect of post-training, we incorporate a lightweight, multistep training process within the offspring population, progressively increasing the number of tokens and eliminating poorly performing models in each selection stage. We validate our method through extensive experiments on Llama-2-7B, Llama-3.1-8B and Qwen-2.5-14B-Instruct, achieving state-of-the-art performance for structured pruning. For instance, \sysname surpasses ShearedLlama while requiring 5times less training data during post-compression training.

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.

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.

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.

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.

Adapting a pretrained diffusion model to new objectives at inference time remains an open problem in generative modeling. Existing steering methods suffer from inaccurate value estimation, especially at high noise levels, which biases guidance. Moreover, information from past runs is not reused to improve sample quality, resulting in inefficient use of compute. Inspired by the success of Monte Carlo Tree Search, we address these limitations by casting inference-time alignment as a search problem that reuses past computations. We introduce a tree-based approach that samples from the reward-aligned target density by propagating terminal rewards back through the diffusion chain and iteratively refining value estimates with each additional generation. Our proposed method, Diffusion Tree Sampling (DTS), produces asymptotically exact samples from the target distribution in the limit of infinite rollouts, and its greedy variant, Diffusion Tree Search (DTS^star), performs a global search for high reward samples. On MNIST and CIFAR-10 class-conditional generation, DTS matches the FID of the best-performing baseline with up to 10times less compute. In text-to-image generation and language completion tasks, DTS^star effectively searches for high reward samples that match best-of-N with up to 5times less compute. By reusing information from previous generations, we get an anytime algorithm that turns additional compute into steadily better samples, providing a scalable approach for inference-time alignment of diffusion models.

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.

Federated learning has emerged as a promising distributed learning paradigm that facilitates collaborative learning among multiple parties without transferring raw data. However, most existing federated learning studies focus on either horizontal or vertical data settings, where the data of different parties are assumed to be from the same feature or sample space. In practice, a common scenario is the hybrid data setting, where data from different parties may differ both in the features and samples. To address this, we propose HybridTree, a novel federated learning approach that enables federated tree learning on hybrid data. We observe the existence of consistent split rules in trees. With the help of these split rules, we theoretically show that the knowledge of parties can be incorporated into the lower layers of a tree. Based on our theoretical analysis, we propose a layer-level solution that does not need frequent communication traffic to train a tree. Our experiments demonstrate that HybridTree can achieve comparable accuracy to the centralized setting with low computational and communication overhead. HybridTree can achieve up to 8 times speedup compared with the other baselines.

Tree search has become as a representative framework for test-time reasoning with large language models (LLMs), exemplified by methods such as Tree-of-Thought and Monte Carlo Tree Search that explore multiple reasoning paths. However, it remains difficult to provide instant and reliable quantitative assessments of intermediate reasoning step quality, and extensive path exploration is computationally costly. To address this, we propose Mutual Information Tree Search (MITS), a novel framework that guides reasoning with information-theoretic principles. MITS introduces an effective scoring function based on pointwise mutual information (PMI), which enables step-wise evaluation of reasoning paths and search tree expansion via beam search without expensive look-ahead simulations, achieving superior reasoning performances while maintaining computational efficiency. The framework is complemented by an entropy-based dynamic sampling strategy that adaptively allocates computational resources to uncertain reasoning steps where exploration is most beneficial. For final prediction, MITS employs a weighted voting scheme that combines PMI scores with prediction consensus. Through comprehensive experiments on diverse reasoning benchmarks, MITS consistently surpasses baseline methods, establishing a principled and efficient framework for LLM reasoning.

Natural language understanding (NLU) is an essential branch of natural language processing, which relies on representations generated by pre-trained language models (PLMs). However, PLMs primarily focus on acquiring lexico-semantic information, while they may be unable to adequately handle the meaning of constructions. To address this issue, we introduce construction grammar (CxG), which highlights the pairings of form and meaning, to enrich language representation. We adopt usage-based construction grammar as the basis of our work, which is highly compatible with statistical models such as PLMs. Then a HyCxG framework is proposed to enhance language representation through a three-stage solution. First, all constructions are extracted from sentences via a slot-constraints approach. As constructions can overlap with each other, bringing redundancy and imbalance, we formulate the conditional max coverage problem for selecting the discriminative constructions. Finally, we propose a relational hypergraph attention network to acquire representation from constructional information by capturing high-order word interactions among constructions. Extensive experiments demonstrate the superiority of the proposed model on a variety of NLU tasks.

Data quality determines foundation model performance, yet systematic processing frameworks are lacking. We introduce Data Darwinism, a ten-level taxonomy (L0-L9) that conceptualizes data-model co-evolution: advanced models produce superior data for next-generation systems. We validate this on scientific literature by constructing Darwin-Science, a 900B-token corpus (L0-L5). We identify a learnability gap in raw scientific text, which we bridge via L4 (Generative Refinement) and L5 (Cognitive Completion) using frontier LLMs to explicate reasoning and terminology. To ensure rigorous attribution, we pre-trained daVinci-origin-3B/7B models from scratch, excluding scientific content to create contamination-free baselines. After 600B tokens of continued pre-training, Darwin-Science outperforms baselines by +2.12 (3B) and +2.95 (7B) points across 20+ benchmarks, rising to +5.60 and +8.40 points on domain-aligned tasks. Systematic progression to L5 yields a +1.36 total gain, confirming that higher-level processing unlocks latent data value. We release the Darwin-Science corpus and daVinci-origin models to enable principled, co-evolutionary development.

Recent advancements in aligning large language models via reinforcement learning have achieved remarkable gains in solving complex reasoning problems, but at the cost of expensive on-policy rollouts and limited exploration of diverse reasoning paths. In this work, we introduce TreePO, involving a self-guided rollout algorithm that views sequence generation as a tree-structured searching process. Composed of dynamic tree sampling policy and fixed-length segment decoding, TreePO leverages local uncertainty to warrant additional branches. By amortizing computation across common prefixes and pruning low-value paths early, TreePO essentially reduces the per-update compute burden while preserving or enhancing exploration diversity. Key contributions include: (1) a segment-wise sampling algorithm that alleviates the KV cache burden through contiguous segments and spawns new branches along with an early-stop mechanism; (2) a tree-based segment-level advantage estimation that considers both global and local proximal policy optimization. and (3) analysis on the effectiveness of probability and quality-driven dynamic divergence and fallback strategy. We empirically validate the performance gain of TreePO on a set reasoning benchmarks and the efficiency saving of GPU hours from 22\% up to 43\% of the sampling design for the trained models, meanwhile showing up to 40\% reduction at trajectory-level and 35\% at token-level sampling compute for the existing models. While offering a free lunch of inference efficiency, TreePO reveals a practical path toward scaling RL-based post-training with fewer samples and less compute. Home page locates at https://m-a-p.ai/TreePO.

Speculative decoding accelerates inference in large language models (LLMs) by generating draft tokens for target model verification. Current approaches for obtaining draft tokens rely on lightweight draft models or additional model structures to generate draft tokens and retrieve context from databases. Due to the draft model's small size and limited training data, model-based speculative decoding frequently becomes less effective in out-of-domain scenarios. Additionally, the time cost of the drafting phase results in a low upper limit on acceptance length during the verification step, limiting overall efficiency. This paper proposes RASD (Retrieval-Augmented Speculative Decoding), which adopts retrieval methods to enhance model-based speculative decoding. We introduce tree pruning and tree fusion to achieve this. Specifically, we develop a pruning method based on the draft model's probability distribution to construct the optimal retrieval tree. Second, we employ the longest prefix matching algorithm to merge the tree generated by the draft model with the retrieval tree, resulting in a unified tree for verification. Experimental results demonstrate that RASD achieves state-of-the-art inference acceleration across tasks such as DocQA, Summary, Code, and In-Domain QA. Moreover, RASD exhibits strong scalability, seamlessly integrating with various speculative decoding approaches, including both generation-based and retrieval-based methods.

The rapid evolution of scientific fields introduces challenges in organizing and retrieving scientific literature. While expert-curated taxonomies have traditionally addressed this need, the process is time-consuming and expensive. Furthermore, recent automatic taxonomy construction methods either (1) over-rely on a specific corpus, sacrificing generalizability, or (2) depend heavily on the general knowledge of large language models (LLMs) contained within their pre-training datasets, often overlooking the dynamic nature of evolving scientific domains. Additionally, these approaches fail to account for the multi-faceted nature of scientific literature, where a single research paper may contribute to multiple dimensions (e.g., methodology, new tasks, evaluation metrics, benchmarks). To address these gaps, we propose TaxoAdapt, a framework that dynamically adapts an LLM-generated taxonomy to a given corpus across multiple dimensions. TaxoAdapt performs iterative hierarchical classification, expanding both the taxonomy width and depth based on corpus' topical distribution. We demonstrate its state-of-the-art performance across a diverse set of computer science conferences over the years to showcase its ability to structure and capture the evolution of scientific fields. As a multidimensional method, TaxoAdapt generates taxonomies that are 26.51% more granularity-preserving and 50.41% more coherent than the most competitive baselines judged by LLMs.

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.

We study inferring a tree-structured representation from a single image for object shading. Prior work typically uses the parametric or measured representation to model shading, which is neither interpretable nor easily editable. We propose using the shade tree representation, which combines basic shading nodes and compositing methods to factorize object surface shading. The shade tree representation enables novice users who are unfamiliar with the physical shading process to edit object shading in an efficient and intuitive manner. A main challenge in inferring the shade tree is that the inference problem involves both the discrete tree structure and the continuous parameters of the tree nodes. We propose a hybrid approach to address this issue. We introduce an auto-regressive inference model to generate a rough estimation of the tree structure and node parameters, and then we fine-tune the inferred shade tree through an optimization algorithm. We show experiments on synthetic images, captured reflectance, real images, and non-realistic vector drawings, allowing downstream applications such as material editing, vectorized shading, and relighting. Project website: https://chen-geng.com/inv-shade-trees

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.

Given the generational gap in available hardware between lay practitioners and the most endowed institutions, LLMs are becoming increasingly inaccessible as they grow in size. Whilst many approaches have been proposed to compress LLMs to make their resource consumption manageable, these methods themselves tend to be resource intensive, putting them out of the reach of the very user groups they target. In this work, we explore the problem of structured pruning of LLMs using only forward passes. We seek to empower practitioners to prune models so large that their available hardware has just enough memory to run inference. We develop Bonsai, a gradient-free, perturbative pruning method capable of delivering small, fast, and accurate pruned models. We observe that Bonsai outputs pruned models that (i) outperform those generated by more expensive gradient-based structured pruning methods, and (ii) are twice as fast (with comparable accuracy) as those generated by semi-structured pruning methods requiring comparable resources as Bonsai. We also leverage Bonsai to produce a new sub-2B model using a single A6000 that yields state-of-the-art performance on 4/6 tasks on the Huggingface Open LLM leaderboard.

This paper presents a reinforced genetic approach to a defined d-resource system optimization problem. The classical evolution schema was ineffective due to a very strict feasibility function in the studied problem. Hence, the presented strategy has introduced several modifications and adaptations to standard genetic routines, e.g.: a migration operator which is an analogy to the biological random genetic drift.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

Socratic questioning is an effective teaching strategy, encouraging critical thinking and problem-solving. The conversational capabilities of large language models (LLMs) show great potential for providing scalable, real-time student guidance. However, current LLMs often give away solutions directly, making them ineffective instructors. We tackle this issue in the code debugging domain with TreeInstruct, an Instructor agent guided by a novel state space-based planning algorithm. TreeInstruct asks probing questions to help students independently identify and resolve errors. It estimates a student's conceptual and syntactical knowledge to dynamically construct a question tree based on their responses and current knowledge state, effectively addressing both independent and dependent mistakes concurrently in a multi-turn interaction setting. In addition to using an existing single-bug debugging benchmark, we construct a more challenging multi-bug dataset of 150 coding problems, incorrect solutions, and bug fixes -- all carefully constructed and annotated by experts. Extensive evaluation shows TreeInstruct's state-of-the-art performance on both datasets, proving it to be a more effective instructor than baselines. Furthermore, a real-world case study with five students of varying skill levels further demonstrates TreeInstruct's ability to guide students to debug their code efficiently with minimal turns and highly Socratic questioning.

Semi-structured tables, widely used in real-world applications (e.g., financial reports, medical records, transactional orders), often involve flexible and complex layouts (e.g., hierarchical headers and merged cells). These tables generally rely on human analysts to interpret table layouts and answer relevant natural language questions, which is costly and inefficient. To automate the procedure, existing methods face significant challenges. First, methods like NL2SQL require converting semi-structured tables into structured ones, which often causes substantial information loss. Second, methods like NL2Code and multi-modal LLM QA struggle to understand the complex layouts of semi-structured tables and cannot accurately answer corresponding questions. To this end, we propose ST-Raptor, a tree-based framework for semi-structured table question answering using large language models. First, we introduce the Hierarchical Orthogonal Tree (HO-Tree), a structural model that captures complex semi-structured table layouts, along with an effective algorithm for constructing the tree. Second, we define a set of basic tree operations to guide LLMs in executing common QA tasks. Given a user question, ST-Raptor decomposes it into simpler sub-questions, generates corresponding tree operation pipelines, and conducts operation-table alignment for accurate pipeline execution. Third, we incorporate a two-stage verification mechanism: forward validation checks the correctness of execution steps, while backward validation evaluates answer reliability by reconstructing queries from predicted answers. To benchmark the performance, we present SSTQA, a dataset of 764 questions over 102 real-world semi-structured tables. Experiments show that ST-Raptor outperforms nine baselines by up to 20% in answer accuracy. The code is available at https://github.com/weAIDB/ST-Raptor.

Training effective Text-to-SQL models remains challenging due to the scarcity of high-quality, diverse, and structurally complex datasets. Existing methods either rely on limited human-annotated corpora, or synthesize datasets directly by simply prompting LLMs without explicit control over SQL structures, often resulting in limited structural diversity and complexity. To address this, we introduce EvolSQL, a structure-aware data synthesis framework that evolves SQL queries from seed data into richer and more semantically diverse forms. EvolSQL starts with an exploratory Query-SQL expansion to broaden question diversity and improve schema coverage, and then applies an adaptive directional evolution strategy using six atomic transformation operators derived from the SQL Abstract Syntax Tree to progressively increase query complexity across relational, predicate, aggregation, and nesting dimensions. An execution-grounded SQL refinement module and schema-aware deduplication further ensure the creation of high-quality, structurally diverse mapping pairs. Experimental results show that a 7B model fine-tuned on our data outperforms one trained on the much larger SynSQL dataset using only 1/18 of the data.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Autonomous scientific discovery with large language model (LLM)-based agents has recently made substantial progress, demonstrating the ability to automate end-to-end research workflows. However, existing systems largely rely on runtime-centric execution paradigms, repeatedly reading, summarizing, and reasoning over large volumes of scientific literature online. This on-the-spot computation strategy incurs high computational cost, suffers from context window limitations, and often leads to brittle reasoning and hallucination. We propose Idea2Story, a pre-computation-driven framework for autonomous scientific discovery that shifts literature understanding from online reasoning to offline knowledge construction. Idea2Story continuously collects peer-reviewed papers together with their review feedback, extracts core methodological units, composes reusable research patterns, and organizes them into a structured methodological knowledge graph. At runtime, underspecified user research intents are aligned to established research paradigms, enabling efficient retrieval and reuse of high-quality research patterns instead of open-ended generation and trial-and-error. By grounding research planning and execution in a pre-built knowledge graph, Idea2Story alleviates the context window bottleneck of LLMs and substantially reduces repeated runtime reasoning over literature. We conduct qualitative analyses and preliminary empirical studies demonstrating that Idea2Story can generate coherent, methodologically grounded, and novel research patterns, and can produce several high-quality research demonstrations in an end-to-end setting. These results suggest that offline knowledge construction provides a practical and scalable foundation for reliable autonomous scientific discovery.

We propose an online training procedure for a transformer-based automated theorem prover. Our approach leverages a new search algorithm, HyperTree Proof Search (HTPS), inspired by the recent success of AlphaZero. Our model learns from previous proof searches through online training, allowing it to generalize to domains far from the training distribution. We report detailed ablations of our pipeline's main components by studying performance on three environments of increasing complexity. In particular, we show that with HTPS alone, a model trained on annotated proofs manages to prove 65.4% of a held-out set of Metamath theorems, significantly outperforming the previous state of the art of 56.5% by GPT-f. Online training on these unproved theorems increases accuracy to 82.6%. With a similar computational budget, we improve the state of the art on the Lean-based miniF2F-curriculum dataset from 31% to 42% proving accuracy.

A creative idea is often born from transforming, combining, and modifying ideas from existing visual examples capturing various concepts. However, one cannot simply copy the concept as a whole, and inspiration is achieved by examining certain aspects of the concept. Hence, it is often necessary to separate a concept into different aspects to provide new perspectives. In this paper, we propose a method to decompose a visual concept, represented as a set of images, into different visual aspects encoded in a hierarchical tree structure. We utilize large vision-language models and their rich latent space for concept decomposition and generation. Each node in the tree represents a sub-concept using a learned vector embedding injected into the latent space of a pretrained text-to-image model. We use a set of regularizations to guide the optimization of the embedding vectors encoded in the nodes to follow the hierarchical structure of the tree. Our method allows to explore and discover new concepts derived from the original one. The tree provides the possibility of endless visual sampling at each node, allowing the user to explore the hidden sub-concepts of the object of interest. The learned aspects in each node can be combined within and across trees to create new visual ideas, and can be used in natural language sentences to apply such aspects to new designs.

Retrosynthesis planning is a fundamental challenge in chemistry which aims at designing reaction pathways from commercially available starting materials to a target molecule. Each step in multi-step retrosynthesis planning requires accurate prediction of possible precursor molecules given the target molecule and confidence estimates to guide heuristic search algorithms. We model single-step retrosynthesis planning as a distribution learning problem in a discrete state space. First, we introduce the Markov Bridge Model, a generative framework aimed to approximate the dependency between two intractable discrete distributions accessible via a finite sample of coupled data points. Our framework is based on the concept of a Markov bridge, a Markov process pinned at its endpoints. Unlike diffusion-based methods, our Markov Bridge Model does not need a tractable noise distribution as a sampling proxy and directly operates on the input product molecules as samples from the intractable prior distribution. We then address the retrosynthesis planning problem with our novel framework and introduce RetroBridge, a template-free retrosynthesis modeling approach that achieves state-of-the-art results on standard evaluation benchmarks.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Test-time compute scaling has emerged as a new axis along which to improve model accuracy, where additional computation is used at inference time to allow the model to think longer for more challenging problems. One promising approach for test-time compute scaling is search against a process reward model, where a model generates multiple potential candidates at each step of the search, and these partial trajectories are then scored by a separate reward model in order to guide the search process. The diversity of trajectories in the tree search process affects the accuracy of the search, since increasing diversity promotes more exploration. However, this diversity comes at a cost, as divergent trajectories have less KV sharing, which means they consume more memory and slow down the search process. Previous search methods either do not perform sufficient exploration, or else explore diverse trajectories but have high latency. We address this challenge by proposing Efficient Tree Search (ETS), which promotes KV sharing by pruning redundant trajectories while maintaining necessary diverse trajectories. ETS incorporates a linear programming cost model to promote KV cache sharing by penalizing the number of nodes retained, while incorporating a semantic coverage term into the cost model to ensure that we retain trajectories which are semantically different. We demonstrate how ETS can achieve 1.8times reduction in average KV cache size during the search process, leading to 1.4times increased throughput relative to prior state-of-the-art methods, with minimal accuracy degradation and without requiring any custom kernel implementation. Code is available at: https://github.com/SqueezeAILab/ETS.

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

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.

Robotic assembly tasks are open challenges due to the long task horizon and complex part relations. Behavior trees (BTs) are increasingly used in robot task planning for their modularity and flexibility, but manually designing them can be effort-intensive. Large language models (LLMs) have recently been applied in robotic task planning for generating action sequences, but their ability to generate BTs has not been fully investigated. To this end, We propose LLM as BT-planner, a novel framework to leverage LLMs for BT generation in robotic assembly task planning and execution. Four in-context learning methods are introduced to utilize the natural language processing and inference capabilities of LLMs to produce task plans in BT format, reducing manual effort and ensuring robustness and comprehensibility. We also evaluate the performance of fine-tuned, fewer-parameter LLMs on the same tasks. Experiments in simulated and real-world settings show that our framework enhances LLMs' performance in BT generation, improving success rates in BT generation through in-context learning and supervised fine-tuning.

Despite their outstanding capabilities, large language models (LLMs) are prone to hallucination and producing factually incorrect information. This challenge has spurred efforts in attributed text generation, which prompts LLMs to generate content with supporting evidence. In this paper, we propose a novel framework, called Think&Cite, and formulate attributed text generation as a multi-step reasoning problem integrated with search. Specifically, we propose Self-Guided Monte Carlo Tree Search (SG-MCTS), which capitalizes on the self-reflection capability of LLMs to reflect on the intermediate states of MCTS for guiding the tree expansion process. To provide reliable and comprehensive feedback, we introduce Progress Reward Models to measure the progress of tree search from the root to the current state from two aspects, i.e., generation and attribution progress. We conduct extensive experiments on three datasets and the results show that our approach significantly outperforms baseline approaches.

Code completion is a prominent application of Large Language Models (LLMs) in software engineering. Due to the near real-time response requirements of this task, base models with small to medium-sized parameters are typically employed, supplemented by various optimization and post-training techniques. However, these optimization methods often have trade-offs, leading to a seesaw effect where performance improvements on certain datasets or metrics are accompanied by degradations on others -- sometimes even falling below the baseline model's performance. This paper proposes SynthCoder, a model that integrates leading industry practices to achieve state-of-the-art performance on the Fill-in-the-Middle (FIM) code completion task. In specific, we first construct a diverse dataset by combining Abstract Syntax Tree (AST) node extraction with heuristics that simulate developer behavior. Then we enrich our training corpus with cross-file contextual information using the BM25 algorithm and call graphs, enhancing the model's ability to perform code completion in both file-level and repository-level scenarios. As the last step, we employ a two-stage training process using the Seed-Coder-8B-Base as the base model. First, we fine-tune the model using Curriculum Learning technology. Following this, we perform alignment using Direct Preference Optimization (DPO) with preference pairs generated through Rejection Sampling. Experimental results demonstrate that our final model excels on mainstream repository-level code completion benchmarks, including aiXcoder, ExecRepoBench, CrossCodeEval, and CoLT. Furthermore, our carefully curated training set effectively mitigates the model's tendency to just repeat existing code, a common issue existing in various code completion models.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Effectively scaling GUI automation is essential for computer-use agents (CUAs); however, existing work primarily focuses on scaling GUI grounding rather than the more crucial GUI planning, which requires more sophisticated data collection. In reality, the exploration process of a CUA across apps/desktops/web pages typically follows a tree structure, with earlier functional entry points often being explored more frequently. Thus, organizing large-scale trajectories into tree structures can reduce data cost and streamline the data scaling of GUI planning. In this work, we propose TreeCUA to efficiently scale GUI automation with tree-structured verifiable evolution. We propose a multi-agent collaborative framework to explore the environment, verify actions, summarize trajectories, and evaluate quality to generate high-quality and scalable GUI trajectories. To improve efficiency, we devise a novel tree-based topology to store and replay duplicate exploration nodes, and design an adaptive exploration algorithm to balance the depth (i.e., trajectory difficulty) and breadth (i.e., trajectory diversity). Moreover, we develop world knowledge guidance and global memory backtracking to avoid low-quality generation. Finally, we naturally extend and propose the TreeCUA-DPO method from abundant tree node information, improving GUI planning capability by referring to the branch information of adjacent trajectories. Experimental results show that TreeCUA and TreeCUA-DPO offer significant improvements, and out-of-domain (OOD) studies further demonstrate strong generalization. All trajectory node information and code will be available at https://github.com/UITron-hub/TreeCUA.

Handcrafting heuristics for solving complex planning tasks (e.g., NP-hard combinatorial optimization (CO) problems) is a common practice but requires extensive domain knowledge. Recently, Large Language Model (LLM)-based automatic heuristics design (AHD) methods have shown promise in generating high-quality heuristics without manual intervention. Existing LLM-based AHD methods employ a population to maintain a fixed number of top-performing LLM-generated heuristics and introduce evolutionary computation (EC) to enhance the population iteratively. However, the population-based procedure brings greedy properties, often resulting in convergence to local optima. Instead, to more comprehensively explore the space of heuristics, we propose using Monte Carlo Tree Search (MCTS) for LLM-based heuristic evolution while preserving all LLM-generated heuristics in a tree structure. With a novel thought-alignment process and an exploration-decay technique, the proposed MCTS-AHD method delivers significantly higher-quality heuristics on various complex tasks. Our code is available at https://github.com/zz1358m/MCTS-AHD-master.

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.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM

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.

Kinodynamic motion planning is concerned with computing collision-free trajectories while abiding by the robot's dynamic constraints. This critical problem is often tackled using sampling-based planners (SBPs) that explore the robot's high-dimensional state space by constructing a search tree via action propagations. Although SBPs can offer global guarantees on completeness and solution quality, their performance is often hindered by slow exploration due to uninformed action sampling. Learning-based approaches can yield significantly faster runtimes, yet they fail to generalize to out-of-distribution (OOD) scenarios and lack critical guarantees, e.g., safety, thus limiting their deployment on physical robots. We present Diffusion Tree (DiTree): a provably-generalizable framework leveraging diffusion policies (DPs) as informed samplers to efficiently guide state-space search within SBPs. DiTree combines DP's ability to model complex distributions of expert trajectories, conditioned on local observations, with the completeness of SBPs to yield provably-safe solutions within a few action propagation iterations for complex dynamical systems. We demonstrate DiTree's power with an implementation combining the popular RRT planner with a DP action sampler trained on a single environment. In comprehensive evaluations on OOD scenarios, % DiTree has comparable runtimes to a standalone DP (3x faster than classical SBPs), while improving the average success rate over DP and SBPs. DiTree is on average 3x faster than classical SBPs, and outperforms all other approaches by achieving roughly 30\% higher success rate. Project webpage: https://sites.google.com/view/ditree.

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.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

We present Connection-Aware Motif Sequencing (CamS), a graph-to-sequence representation that enables decoder-only Transformers to learn molecular graphs via standard next-token prediction (NTP). For molecular property prediction, SMILES-based NTP scales well but lacks explicit topology, whereas graph-native masked modeling captures connectivity but risks disrupting the pivotal chemical details (e.g., activity cliffs). CamS bridges this gap by serializing molecular graphs into structure-rich causal sequences. CamS first mines data-driven connection-aware motifs. It then serializes motifs via scaffold-rooted breadth-first search (BFS) to establish a stable core-to-periphery order. Crucially, CamS enables hierarchical modeling by concatenating sequences from fine to coarse motif scales, allowing the model to condition global scaffolds on dense, uncorrupted local structural evidence. We instantiate CamS-LLaMA by pre-training a vanilla LLaMA backbone on CamS sequences. It achieves state-of-the-art performance on MoleculeNet and the activity-cliff benchmark MoleculeACE, outperforming both SMILES-based language models and strong graph baselines. Interpretability analysis confirms that our multi-scale causal serialization effectively drives attention toward cliff-determining differences.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.