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Jun 23

SproutRAG: Attention-Guided Tree Search with Progressive Embeddings for Long-Document RAG

Retrieval-augmented generation (RAG) systems must balance retrieval granularity with contextual coherence, a challenge that existing methods address through LLM-guided chunking, single-level context expansion, or hierarchical summarization. These approaches variously depend on costly LLM calls during indexing or retrieval, limit context aggregation to a single granularity level, or introduce information loss through summarization. We present SproutRAG, an attention-guided hierarchical RAG framework that addresses this trade-off by organizing sentence-level chunks into progressively larger but semantically coherent units, using learned inter-sentence attention to construct a binary chunking tree. Unlike prior approaches that rely on external LLMs, fixed context expansion, or lossy summarization, SproutRAG learns which attention heads and layers best capture semantic document structure, enabling multi-granularity retrieval without additional LLM calls or compressed summaries. At retrieval time, SproutRAG uses hierarchical beam search to retrieve candidates at multiple granularities, capturing multi-sentence relevance beyond flat retrieval. The framework is trained end-to-end with a joint objective that improves both embeddings and tree structure. Experiments across four benchmarks spanning scientific, legal, and open-domain settings demonstrate that SproutRAG improves information efficiency (IE) by 6.1% on average over the strongest baseline. Code is available on https://github.com/AmirAbaskohi/SproutRAG.

Adaptive Chunking: Optimizing Chunking-Method Selection for RAG

The effectiveness of Retrieval-Augmented Generation (RAG) is highly dependent on how documents are chunked, that is, segmented into smaller units for indexing and retrieval. Yet, commonly used "one-size-fits-all" approaches often fail to capture the nuanced structure and semantics of diverse texts. Despite its central role, chunking lacks a dedicated evaluation framework, making it difficult to assess and compare strategies independently of downstream performance. We challenge this paradigm by introducing Adaptive Chunking, a framework that selects the most suitable chunking strategy for each document based on a set of five novel intrinsic, document-based metrics: References Completeness (RC), Intrachunk Cohesion (ICC), Document Contextual Coherence (DCC), Block Integrity (BI), and Size Compliance (SC), which directly assess chunking quality across key dimensions. To support this framework, we also introduce two new chunkers, an LLM-regex splitter and a split-then-merge recursive splitter, alongside targeted post-processing techniques. On a diverse corpus spanning legal, technical, and social science domains, our metric-guided adaptive method significantly improves downstream RAG performance. Without changing models or prompts, our framework increases RAG outcomes, raising answers correctness to 72% (from 62-64%) and increasing the number of successfully answered questions by over 30% (65 vs. 49). These results demonstrate that adaptive, document-aware chunking, guided by a complementary suite of intrinsic metrics, offers a practical and effective path to more robust RAG systems. Code available at https://github.com/ekimetrics/adaptive-chunking.

Ekimetrics Ekimetrics
·
Mar 25

Fat Polygonal Partitions with Applications to Visualization and Embeddings

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.

  • 3 authors
·
Sep 9, 2010

Meta-Chunking: Learning Efficient Text Segmentation via Logical Perception

Retrieval-Augmented Generation (RAG), while serving as a viable complement to large language models (LLMs), often overlooks the crucial aspect of text chunking within its pipeline, which impacts the quality of knowledge-intensive tasks. This paper introduces the concept of Meta-Chunking, which refers to a granularity between sentences and paragraphs, consisting of a collection of sentences within a paragraph that have deep linguistic logical connections. To implement Meta-Chunking, we designed two strategies based on LLMs: Margin Sampling Chunking and Perplexity Chunking. The former employs LLMs to perform binary classification on whether consecutive sentences need to be segmented, making decisions based on the probability difference obtained from margin sampling. The latter precisely identifies text chunk boundaries by analyzing the characteristics of perplexity distribution. Additionally, considering the inherent complexity of different texts, we propose a strategy that combines Meta-Chunking with dynamic merging to achieve a balance between fine-grained and coarse-grained text chunking. Experiments conducted on eleven datasets demonstrate that Meta-Chunking can more efficiently improve the performance of single-hop and multi-hop question answering based on RAG. For instance, on the 2WikiMultihopQA dataset, it outperforms similarity chunking by 1.32 while only consuming 45.8% of the time. Our code is available at https://github.com/IAAR-Shanghai/Meta-Chunking.

  • 7 authors
·
Oct 16, 2024 4

CORAG: A Cost-Constrained Retrieval Optimization System for Retrieval-Augmented Generation

Large Language Models (LLMs) have demonstrated remarkable generation capabilities but often struggle to access up-to-date information, which can lead to hallucinations. Retrieval-Augmented Generation (RAG) addresses this issue by incorporating knowledge from external databases, enabling more accurate and relevant responses. Due to the context window constraints of LLMs, it is impractical to input the entire external database context directly into the model. Instead, only the most relevant information, referred to as chunks, is selectively retrieved. However, current RAG research faces three key challenges. First, existing solutions often select each chunk independently, overlooking potential correlations among them. Second, in practice the utility of chunks is non-monotonic, meaning that adding more chunks can decrease overall utility. Traditional methods emphasize maximizing the number of included chunks, which can inadvertently compromise performance. Third, each type of user query possesses unique characteristics that require tailored handling, an aspect that current approaches do not fully consider. To overcome these challenges, we propose a cost constrained retrieval optimization system CORAG for retrieval-augmented generation. We employ a Monte Carlo Tree Search (MCTS) based policy framework to find optimal chunk combinations sequentially, allowing for a comprehensive consideration of correlations among chunks. Additionally, rather than viewing budget exhaustion as a termination condition, we integrate budget constraints into the optimization of chunk combinations, effectively addressing the non-monotonicity of chunk utility.

  • 5 authors
·
Nov 1, 2024

Binary BPE: A Family of Cross-Platform Tokenizers for Binary Analysis

Sequence models for binary analysis are bottlenecked by byte-level tokenization: raw bytes waste precious context window capacity for transformers and other neural network architectures, and many existing text-oriented tokenizers fail on arbitrary 0x00--0xFF sequences. To address this issue, we introduce the Binary BPE tokenizer family, a set of cross-platform Byte Pair Encoding (BPE) tokenizers for executables trained on a large corpus of binaries spanning multiple platforms, architectures, and operating systems, including Linux, Windows, macOS, Android, and malware sources. We release trained tokenizers with vocabularies of 4K, 8K, 16K, 32K, and 64K tokens, enabling both systematic scaling studies and practical deployment from resource-constrained edge devices to high-throughput datacenters. These tokenizers discover interpretable patterns (ELF/PE headers, instruction sequences, cross-platform strings) while yielding multi-byte compression per token. On representative uncompressed executables (e.g., ELF/PE/Mach-O rather than compressed APKs), the Binary BPE tokenizers typically allow for roughly 2-3x more binary content per fixed-length transformer context window than raw bytes, enabling more efficient research and practical deployment for content identification, malware detection, reverse engineering, and optimization. We release the trained Binary BPE tokenizers on HuggingFace, providing a drop-in, open-source foundation for binary-focused language models and context-efficient agentic tools.

  • 1 authors
·
Nov 14, 2025

Evaluating the Impact of Source Code Parsers on ML4SE Models

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.

  • 4 authors
·
Jun 17, 2022

SLUGGER: Lossless Hierarchical Summarization of Massive Graphs

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.

  • 3 authors
·
Dec 10, 2021

Goose: Anisotropic Speculation Trees for Training-Free Speculative Decoding

Speculative decoding accelerates large language model inference by drafting multiple candidate tokens and verifying them in a single forward pass. Candidates are organized as a tree: deeper trees accept more tokens per step, but adding depth requires sacrificing breadth (fallback options) under a fixed verification budget. Existing training-free methods draft from a single token source and shape their trees without distinguishing candidate quality across origins. We observe that two common training-free token sources - n-gram matches copied from the input context, and statistical predictions from prior forward passes - differ dramatically in acceptance rate (~6x median gap, range 2-18x across five models and five benchmarks). We prove that when such a quality gap exists, the optimal tree is anisotropic (asymmetric): reliable tokens should form a deep chain while unreliable tokens spread as wide branches, breaking through the depth limit of balanced trees. We realize this structure in GOOSE, a training-free framework that builds an adaptive spine tree - a deep chain of high-acceptance context-matched tokens with wide branches of low-acceptance alternatives at each node. We prove that the number of tokens accepted per step is at least as large as that of either source used alone. On five LLMs (7B-33B) and five benchmarks, GOOSE achieves 1.9-4.3x lossless speedup, outperforming balanced-tree baselines by 12-33% under the same budget.

  • 3 authors
·
Apr 1

Turning Trash into Treasure: Accelerating Inference of Large Language Models with Token Recycling

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.

  • 8 authors
·
Aug 16, 2024 2

A Framework for End-to-End Learning on Semantic Tree-Structured Data

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.

  • 2 authors
·
Feb 13, 2020

Dynamic Chunking for End-to-End Hierarchical Sequence Modeling

Despite incredible progress in language models (LMs) in recent years, largely resulting from moving away from specialized models designed for specific tasks to general models based on powerful architectures (e.g. the Transformer) that learn everything from raw data, pre-processing steps such as tokenization remain a barrier to true end-to-end foundation models. We introduce a collection of new techniques that enable a dynamic chunking mechanism which automatically learns content -- and context -- dependent segmentation strategies learned jointly with the rest of the model. Incorporating this into an explicit hierarchical network (H-Net) allows replacing the (implicitly hierarchical) tokenization-LM-detokenization pipeline with a single model learned fully end-to-end. When compute- and data- matched, an H-Net with one stage of hierarchy operating at the byte level outperforms a strong Transformer language model operating over BPE tokens. Iterating the hierarchy to multiple stages further increases its performance by modeling multiple levels of abstraction, demonstrating significantly better scaling with data and matching a token-based Transformer of twice its size. H-Nets pretrained on English show significantly increased character-level robustness, and qualitatively learn meaningful data-dependent chunking strategies without any heuristics or explicit supervision. Finally, the H-Net's improvement over tokenized pipelines is further increased in languages and modalities with weaker tokenization heuristics, such as Chinese and code, or DNA sequences (nearly 4x improvement in data efficiency over baselines), showing the potential of true end-to-end models that learn and scale better from unprocessed data.

  • 3 authors
·
Jul 10, 2025 4

TreeSynth: Synthesizing Diverse Data from Scratch via Tree-Guided Subspace Partitioning

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.

  • 10 authors
·
Mar 21, 2025 1

BiBench: Benchmarking and Analyzing Network Binarization

Network binarization emerges as one of the most promising compression approaches offering extraordinary computation and memory savings by minimizing the bit-width. However, recent research has shown that applying existing binarization algorithms to diverse tasks, architectures, and hardware in realistic scenarios is still not straightforward. Common challenges of binarization, such as accuracy degradation and efficiency limitation, suggest that its attributes are not fully understood. To close this gap, we present BiBench, a rigorously designed benchmark with in-depth analysis for network binarization. We first carefully scrutinize the requirements of binarization in the actual production and define evaluation tracks and metrics for a comprehensive and fair investigation. Then, we evaluate and analyze a series of milestone binarization algorithms that function at the operator level and with extensive influence. Our benchmark reveals that 1) the binarized operator has a crucial impact on the performance and deployability of binarized networks; 2) the accuracy of binarization varies significantly across different learning tasks and neural architectures; 3) binarization has demonstrated promising efficiency potential on edge devices despite the limited hardware support. The results and analysis also lead to a promising paradigm for accurate and efficient binarization. We believe that BiBench will contribute to the broader adoption of binarization and serve as a foundation for future research. The code for our BiBench is released https://github.com/htqin/BiBench .

  • 8 authors
·
Jan 26, 2023

A Systematic Framework for Enterprise Knowledge Retrieval: Leveraging LLM-Generated Metadata to Enhance RAG Systems

In enterprise settings, efficiently retrieving relevant information from large and complex knowledge bases is essential for operational productivity and informed decision-making. This research presents a systematic framework for metadata enrichment using large language models (LLMs) to enhance document retrieval in Retrieval-Augmented Generation (RAG) systems. Our approach employs a comprehensive, structured pipeline that dynamically generates meaningful metadata for document segments, substantially improving their semantic representations and retrieval accuracy. Through extensive experiments, we compare three chunking strategies-semantic, recursive, and naive-and evaluate their effectiveness when combined with advanced embedding techniques. The results demonstrate that metadata-enriched approaches consistently outperform content-only baselines, with recursive chunking paired with TF-IDF weighted embeddings yielding an 82.5% precision rate compared to 73.3% for semantic content-only approaches. The naive chunking strategy with prefix-fusion achieved the highest Hit Rate@10 of 0.925. Our evaluation employs cross-encoder reranking for ground truth generation, enabling rigorous assessment via Hit Rate and Metadata Consistency metrics. These findings confirm that metadata enrichment enhances vector clustering quality while reducing retrieval latency, making it a key optimization for RAG systems across knowledge domains. This work offers practical insights for deploying high-performance, scalable document retrieval solutions in enterprise settings, demonstrating that metadata enrichment is a powerful approach for enhancing RAG effectiveness.

  • 5 authors
·
Dec 4, 2025

Bridging Cache-Friendliness and Concurrency: A Locality-Optimized In-Memory B-Skiplist

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

  • 5 authors
·
Jul 29, 2025

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

  • 6 authors
·
Jun 26, 2023

Assemblage: Automatic Binary Dataset Construction for Machine Learning

Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpuses of malicious binaries, obtaining high-quality corpuses of benign binaries for modern systems has proven challenging (e.g., due to licensing issues). Consequently, machine learning based pipelines for binary analysis utilize either costly commercial corpuses (e.g., VirusTotal) or open-source binaries (e.g., coreutils) available in limited quantities. To address these issues, we present Assemblage: an extensible cloud-based distributed system that crawls, configures, and builds Windows PE binaries to obtain high-quality binary corpuses suitable for training state-of-the-art models in binary analysis. We have run Assemblage on AWS over the past year, producing 890k Windows PE and 428k Linux ELF binaries across 29 configurations. Assemblage is designed to be both reproducible and extensible, enabling users to publish "recipes" for their datasets, and facilitating the extraction of a wide array of features. We evaluated Assemblage by using its data to train modern learning-based pipelines for compiler provenance and binary function similarity. Our results illustrate the practical need for robust corpuses of high-quality Windows PE binaries in training modern learning-based binary analyses. Assemblage can be downloaded from https://assemblage-dataset.net

  • 8 authors
·
May 7, 2024

MLCPD: A Unified Multi-Language Code Parsing Dataset with Universal AST Schema

We introduce the MultiLang Code Parser Dataset (MLCPD), a large-scale, language-agnostic dataset unifying syntactic and structural representations of code across ten major programming languages. MLCPD contains over seven million parsed source files normalized under our proposed universal Abstract Syntax Tree (AST) schema, enabling consistent cross-language reasoning, structural learning, and multilingual software analysis. Unlike existing corpora that focus purely on token-level code or isolated parsers, MLCPD provides both hierarchical tree representations and rich metadata for every file, ensuring lossless syntactic coverage and structural uniformity. Each entry includes a normalized schema, language-level metadata, and abstracted node semantics stored in Parquet format for scalable retrieval. Empirical analyses reveal strong cross-language structural regularities-demonstrating that syntactic graphs from languages as diverse as Python, Java, and Go can be aligned under a shared schema. We release the dataset publicly on Hugging Face and the accompanying codebase on GitHub, which includes complete pipelines for dataset reproduction, grammar compilation, and a visualization tool for exploring the unified AST across languages. Together, these resources establish MLCPD as an open, reproducible foundation for future research in cross-language representation learning and program analysis.

  • 2 authors
·
Oct 18, 2025

HEAPr: Hessian-based Efficient Atomic Expert Pruning in Output Space

Mixture-of-Experts (MoE) architectures in large language models (LLMs) deliver exceptional performance and reduced inference costs compared to dense LLMs. However, their large parameter counts result in prohibitive memory requirements, limiting practical deployment. While existing pruning methods primarily focus on expert-level pruning, this coarse granularity often leads to substantial accuracy degradation. In this work, we introduce HEAPr, a novel pruning algorithm that decomposes experts into smaller, indivisible atomic experts, enabling more precise and flexible atomic expert pruning. To measure the importance of each atomic expert, we leverage second-order information based on principles similar to Optimal Brain Surgeon (OBS) theory. To address the computational and storage challenges posed by second-order information, HEAPr exploits the inherent properties of atomic experts to transform the second-order information from expert parameters into that of atomic expert parameters, and further simplifies it to the second-order information of atomic expert outputs. This approach reduces the space complexity from O(d^4), where d is the model's dimensionality, to O(d^2). HEAPr requires only two forward passes and one backward pass on a small calibration set to compute the importance of atomic experts. Extensive experiments on MoE models, including DeepSeek MoE and Qwen MoE family, demonstrate that HEAPr outperforms existing expert-level pruning methods across a wide range of compression ratios and benchmarks. Specifically, HEAPr achieves nearly lossless compression at compression ratios of 20% ~ 25% in most models, while also reducing FLOPs nearly by 20%. The code can be found at https://github.com/LLIKKE/HEAPr{https://github.com/LLIKKE/HEAPr}.

  • 6 authors
·
Sep 26, 2025

ChunkLLM: A Lightweight Pluggable Framework for Accelerating LLMs Inference

Transformer-based large models excel in natural language processing and computer vision, but face severe computational inefficiencies due to the self-attention's quadratic complexity with input tokens. Recently, researchers have proposed a series of methods based on block selection and compression to alleviate this problem, but they either have issues with semantic incompleteness or poor training-inference efficiency. To comprehensively address these challenges, we propose ChunkLLM, a lightweight and pluggable training framework. Specifically, we introduce two components: QK Adapter (Q-Adapter and K-Adapter) and Chunk Adapter. The former is attached to each Transformer layer, serving dual purposes of feature compression and chunk attention acquisition. The latter operates at the bottommost layer of the model, functioning to detect chunk boundaries by leveraging contextual semantic information. During the training phase, the parameters of the backbone remain frozen, with only the QK Adapter and Chunk Adapter undergoing training. Notably, we design an attention distillation method for training the QK Adapter, which enhances the recall rate of key chunks. During the inference phase, chunk selection is triggered exclusively when the current token is detected as a chunk boundary, thereby accelerating model inference. Experimental evaluations are conducted on a diverse set of long-text and short-text benchmark datasets spanning multiple tasks. ChunkLLM not only attains comparable performance on short-text benchmarks but also maintains 98.64% of the performance on long-context benchmarks while preserving a 48.58% key-value cache retention rate. Particularly, ChunkLLM attains a maximum speedup of 4.48x in comparison to the vanilla Transformer in the processing of 120K long texts.

  • 6 authors
·
Sep 28, 2025

SitEmb-v1.5: Improved Context-Aware Dense Retrieval for Semantic Association and Long Story Comprehension

Retrieval-augmented generation (RAG) over long documents typically involves splitting the text into smaller chunks, which serve as the basic units for retrieval. However, due to dependencies across the original document, contextual information is often essential for accurately interpreting each chunk. To address this, prior work has explored encoding longer context windows to produce embeddings for longer chunks. Despite these efforts, gains in retrieval and downstream tasks remain limited. This is because (1) longer chunks strain the capacity of embedding models due to the increased amount of information they must encode, and (2) many real-world applications still require returning localized evidence due to constraints on model or human bandwidth. We propose an alternative approach to this challenge by representing short chunks in a way that is conditioned on a broader context window to enhance retrieval performance -- i.e., situating a chunk's meaning within its context. We further show that existing embedding models are not well-equipped to encode such situated context effectively, and thus introduce a new training paradigm and develop the situated embedding models (SitEmb). To evaluate our method, we curate a book-plot retrieval dataset specifically designed to assess situated retrieval capabilities. On this benchmark, our SitEmb-v1 model based on BGE-M3 substantially outperforms state-of-the-art embedding models, including several with up to 7-8B parameters, with only 1B parameters. Our 8B SitEmb-v1.5 model further improves performance by over 10% and shows strong results across different languages and several downstream applications.

  • 9 authors
·
Aug 3, 2025 3

SAGE: A Framework of Precise Retrieval for RAG

Retrieval-augmented generation (RAG) has demonstrated significant proficiency in conducting question-answering (QA) tasks within a specified corpus. Nonetheless, numerous failure instances of RAG in QA still exist. These failures are not solely attributable to the limitations of Large Language Models (LLMs); instead, they predominantly arise from the retrieval of inaccurate information for LLMs due to two limitations: (1) Current RAG methods segment the corpus without considering semantics, making it difficult to find relevant context due to impaired correlation between questions and the segments. (2) There is a trade-off between missing essential context with fewer context retrieved and getting irrelevant context with more context retrieved. In this paper, we introduce a RAG framework (SAGE), to overcome these limitations. First, to address the segmentation issue without considering semantics, we propose to train a semantic segmentation model. This model is trained to segment the corpus into semantically complete chunks. Second, to ensure that only the most relevant chunks are retrieved while the irrelevant ones are ignored, we design a chunk selection algorithm to dynamically select chunks based on the decreasing speed of the relevance score, leading to a more relevant selection. Third, to further ensure the precision of the retrieved chunks, we propose letting LLMs assess whether retrieved chunks are excessive or lacking and then adjust the amount of context accordingly. Experiments show that SAGE outperforms baselines by 61.25% in the quality of QA on average. Moreover, by avoiding retrieving noisy context, SAGE lowers the cost of the tokens consumed in LLM inference and achieves a 49.41% enhancement in cost efficiency on average. Additionally, our work offers valuable insights for boosting RAG.

  • 3 authors
·
Mar 3, 2025 2

Digestion Algorithm in Hierarchical Symbolic Forests: A Fast Text Normalization Algorithm and Semantic Parsing Framework for Specific Scenarios and Lightweight Deployment

Text Normalization and Semantic Parsing have numerous applications in natural language processing, such as natural language programming, paraphrasing, data augmentation, constructing expert systems, text matching, and more. Despite the prominent achievements of deep learning in Large Language Models (LLMs), the interpretability of neural network architectures is still poor, which affects their credibility and hence limits the deployments of risk-sensitive scenarios. In certain scenario-specific domains with scarce data, rapidly obtaining a large number of supervised learning labels is challenging, and the workload of manually labeling data would be enormous. Catastrophic forgetting in neural networks further leads to low data utilization rates. In situations where swift responses are vital, the density of the model makes local deployment difficult and the response time long, which is not conducive to local applications of these fields. Inspired by the multiplication rule, a principle of combinatorial mathematics, and human thinking patterns, a multilayer framework along with its algorithm, the Digestion Algorithm in Hierarchical Symbolic Forests (DAHSF), is proposed to address these above issues, combining text normalization and semantic parsing workflows. The Chinese Scripting Language "Fire Bunny Intelligent Development Platform V2.0" is an important test and application of the technology discussed in this paper. DAHSF can run locally in scenario-specific domains on little datasets, with model size and memory usage optimized by at least two orders of magnitude, thus improving the execution speed, and possessing a promising optimization outlook.

  • 1 authors
·
Dec 18, 2024

Efficient Long-Context LLM Inference via KV Cache Clustering

Large language models (LLMs) with extended context windows have become increasingly prevalent for tackling complex tasks. However, the substantial Key-Value (KV) cache required for long-context LLMs poses significant deployment challenges. Existing approaches either discard potentially critical information needed for future generations or offer limited efficiency gains due to high computational overhead. In this paper, we introduce Chelsea, a simple yet effective framework for online KV cache clustering. Our approach is based on the observation that key states exhibit high similarity along the sequence dimension. To enable efficient clustering, we divide the sequence into chunks and propose Chunked Soft Matching, which employs an alternating partition strategy within each chunk and identifies clusters based on similarity. Chelsea then merges the KV cache within each cluster into a single centroid. Additionally, we provide a theoretical analysis of the computational complexity and the optimality of the intra-chunk partitioning strategy. Extensive experiments across various models and long-context benchmarks demonstrate that Chelsea achieves up to 80% reduction in KV cache memory usage while maintaining comparable model performance. Moreover, with minimal computational overhead, Chelsea accelerates the decoding stage of inference by up to 3.19times and reduces end-to-end latency by up to 2.72times.

  • 11 authors
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Jun 12, 2025

MoDora: Tree-Based Semi-Structured Document Analysis System

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

  • 11 authors
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Feb 26 1

CompactAttention: Accelerating Chunked Prefill with Block-Union KV Selection

Chunked prefill has become a widely adopted serving strategy for long-context large language models, but efficient attention computation in this regime remains challenging. Existing sparse attention methods are primarily designed for one-shot prefill and do not translate efficiently to chunked prefill: block-sparse kernels lose efficiency when the query length is limited by the chunk size, while fine-grained pattern search becomes costly when repeated over the accumulated KV cache at every chunk. QUOKA, a recent method that directly targets chunked prefill, avoids sparse-kernel overhead but relies on query-subsampled, token-level KV selection, which can miss query-specific KV entries and introduce explicit KV-copy overhead. To address these limitations, we propose CompactAttention, a chunked-prefill attention mechanism based on Block-Union KV Selection. CompactAttention treats 2D block-sparse masks as KV-selection signals rather than direct sparse-kernel execution plans, and converts them into GQA-aware per-group KV block tables through Q-block union and intra-group union. This construction produces the minimal block tables that preserve all KV blocks selected by the input masks under paged execution constraints, enabling selected KV blocks to be accessed in place without explicit KV compaction. On LLaMA-3.1-8B-Instruct, CompactAttention maintains accuracy close to dense attention on the RULER benchmark while delivering up to 2.72times attention speedup at 128K context length under chunked prefill.

Linguistic Structure Induction from Language Models

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

  • 1 authors
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Mar 11, 2024

ToM: Leveraging Tree-oriented MapReduce for Long-Context Reasoning in Large Language Models

Large Language Models (LLMs), constrained by limited context windows, often face significant performance degradation when reasoning over long contexts. To address this, Retrieval-Augmented Generation (RAG) retrieves and reasons over chunks but frequently sacrifices logical coherence due to its reliance on similarity-based rankings. Similarly, divide-and-conquer frameworks (DCF) split documents into small chunks for independent reasoning and aggregation. While effective for local reasoning, DCF struggles to capture long-range dependencies and risks inducing conflicts by processing chunks in isolation. To overcome these limitations, we propose ToM, a novel Tree-oriented MapReduce framework for long-context reasoning. ToM leverages the inherent hierarchical structure of long documents (e.g., main headings and subheadings) by constructing a DocTree through hierarchical semantic parsing and performing bottom-up aggregation. Using a Tree MapReduce approach, ToM enables recursive reasoning: in the Map step, rationales are generated at child nodes; in the Reduce step, these rationales are aggregated across sibling nodes to resolve conflicts or reach consensus at parent nodes. Experimental results on 70B+ LLMs show that ToM significantly outperforms existing divide-and-conquer frameworks and retrieval-augmented generation methods, achieving better logical coherence and long-context reasoning. Our code is available at https://github.com/gjn12-31/ToM .

  • 8 authors
·
Nov 1, 2025

Parsed Categoric Encodings with Automunge

The Automunge open source python library platform for tabular data pre-processing automates feature engineering data transformations of numerical encoding and missing data infill to received tidy data on bases fit to properties of columns in a designated train set for consistent and efficient application to subsequent data pipelines such as for inference, where transformations may be applied to distinct columns in "family tree" sets with generations and branches of derivations. Included in the library of transformations are methods to extract structure from bounded categorical string sets by way of automated string parsing, in which comparisons between entries in the set of unique values are parsed to identify character subset overlaps which may be encoded by appended columns of boolean overlap detection activations or by replacing string entries with identified overlap partitions. Further string parsing options, which may also be applied to unbounded categoric sets, include extraction of numeric substring partitions from entries or search functions to identify presence of specified substring partitions. The aggregation of these methods into "family tree" sets of transformations are demonstrated for use to automatically extract structure from categoric string compositions in relation to the set of entries in a column, such as may be applied to prepare categoric string set encodings for machine learning without human intervention.

  • 1 authors
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Feb 18, 2022

Faster Algorithms for Text-to-Pattern Hamming Distances

We study the classic Text-to-Pattern Hamming Distances problem: given a pattern P of length m and a text T of length n, both over a polynomial-size alphabet, compute the Hamming distance between P and T[i, ., . , i+m-1] for every shift i, under the standard Word-RAM model with Theta(log n)-bit words. - We provide an O(nm) time Las Vegas randomized algorithm for this problem, beating the decades-old O(n m log m) running time [Abrahamson, SICOMP 1987]. We also obtain a deterministic algorithm, with a slightly higher O(nm(log mloglog m)^{1/4}) running time. Our randomized algorithm extends to the k-bounded setting, with running time Obig(n+nk{m}big), removing all the extra logarithmic factors from earlier algorithms [Gawrychowski and Uzna\'{n}ski, ICALP 2018; Chan, Golan, Kociumaka, Kopelowitz and Porat, STOC 2020]. - For the (1+epsilon)-approximate version of Text-to-Pattern Hamming Distances, we give an O(epsilon^{-0.93}n) time Monte Carlo randomized algorithm, beating the previous O(epsilon^{-1}n) running time [Kopelowitz and Porat, FOCS 2015; Kopelowitz and Porat, SOSA 2018]. Our approximation algorithm exploits a connection with 3SUM, and uses a combination of Fredman's trick, equality matrix product, and random sampling; in particular, we obtain new results on approximate counting versions of 3SUM and Exact Triangle, which may be of independent interest. Our exact algorithms use a novel combination of hashing, bit-packed FFT, and recursion; in particular, we obtain a faster algorithm for computing the sumset of two integer sets, in the regime when the universe size is close to quadratic in the number of elements. We also prove a fine-grained equivalence between the exact Text-to-Pattern Hamming Distances problem and a range-restricted, counting version of 3SUM.

  • 4 authors
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Oct 19, 2023

QChunker: Learning Question-Aware Text Chunking for Domain RAG via Multi-Agent Debate

The effectiveness upper bound of retrieval-augmented generation (RAG) is fundamentally constrained by the semantic integrity and information granularity of text chunks in its knowledge base. To address these challenges, this paper proposes QChunker, which restructures the RAG paradigm from retrieval-augmentation to understanding-retrieval-augmentation. Firstly, QChunker models the text chunking as a composite task of text segmentation and knowledge completion to ensure the logical coherence and integrity of text chunks. Drawing inspiration from Hal Gregersen's "Questions Are the Answer" theory, we design a multi-agent debate framework comprising four specialized components: a question outline generator, text segmenter, integrity reviewer, and knowledge completer. This framework operates on the principle that questions serve as catalysts for profound insights. Through this pipeline, we successfully construct a high-quality dataset of 45K entries and transfer this capability to small language models. Additionally, to handle long evaluation chains and low efficiency in existing chunking evaluation methods, which overly rely on downstream QA tasks, we introduce a novel direct evaluation metric, ChunkScore. Both theoretical and experimental validations demonstrate that ChunkScore can directly and efficiently discriminate the quality of text chunks. Furthermore, during the text segmentation phase, we utilize document outlines for multi-path sampling to generate multiple candidate chunks and select the optimal solution employing ChunkScore. Extensive experimental results across four heterogeneous domains exhibit that QChunker effectively resolves aforementioned issues by providing RAG with more logically coherent and information-rich text chunks.

  • 6 authors
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Mar 12

MST-compression: Compressing and Accelerating Binary Neural Networks with Minimum Spanning Tree

Binary neural networks (BNNs) have been widely adopted to reduce the computational cost and memory storage on edge-computing devices by using one-bit representation for activations and weights. However, as neural networks become wider/deeper to improve accuracy and meet practical requirements, the computational burden remains a significant challenge even on the binary version. To address these issues, this paper proposes a novel method called Minimum Spanning Tree (MST) compression that learns to compress and accelerate BNNs. The proposed architecture leverages an observation from previous works that an output channel in a binary convolution can be computed using another output channel and XNOR operations with weights that differ from the weights of the reused channel. We first construct a fully connected graph with vertices corresponding to output channels, where the distance between two vertices is the number of different values between the weight sets used for these outputs. Then, the MST of the graph with the minimum depth is proposed to reorder output calculations, aiming to reduce computational cost and latency. Moreover, we propose a new learning algorithm to reduce the total MST distance during training. Experimental results on benchmark models demonstrate that our method achieves significant compression ratios with negligible accuracy drops, making it a promising approach for resource-constrained edge-computing devices.

  • 5 authors
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Aug 25, 2023

Grounding Language Model with Chunking-Free In-Context Retrieval

This paper presents a novel Chunking-Free In-Context (CFIC) retrieval approach, specifically tailored for Retrieval-Augmented Generation (RAG) systems. Traditional RAG systems often struggle with grounding responses using precise evidence text due to the challenges of processing lengthy documents and filtering out irrelevant content. Commonly employed solutions, such as document chunking and adapting language models to handle longer contexts, have their limitations. These methods either disrupt the semantic coherence of the text or fail to effectively address the issues of noise and inaccuracy in evidence retrieval. CFIC addresses these challenges by circumventing the conventional chunking process. It utilizes the encoded hidden states of documents for in-context retrieval, employing auto-aggressive decoding to accurately identify the specific evidence text required for user queries, eliminating the need for chunking. CFIC is further enhanced by incorporating two decoding strategies, namely Constrained Sentence Prefix Decoding and Skip Decoding. These strategies not only improve the efficiency of the retrieval process but also ensure that the fidelity of the generated grounding text evidence is maintained. Our evaluations of CFIC on a range of open QA datasets demonstrate its superiority in retrieving relevant and accurate evidence, offering a significant improvement over traditional methods. By doing away with the need for document chunking, CFIC presents a more streamlined, effective, and efficient retrieval solution, making it a valuable advancement in the field of RAG systems.

  • 5 authors
·
Feb 15, 2024