Daily Papers

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.

Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret because current benchmarks may overestimate generalization across RNA families. We present the Comprehensive Hierarchical Annotation of Non-coding RNA Groups (CHANRG), a benchmark of 170{,}083 structurally non-redundant RNAs curated from more than 10 million sequences in Rfam~15.0 using structure-aware deduplication, genome-aware split design and multiscale structural evaluation. Across 29 predictors, foundation-model methods achieved the highest held-out accuracy but lost most of that advantage out of distribution, whereas structured decoders and direct neural predictors remained markedly more robust. This gap persisted after controlling for sequence length and reflected both loss of structural coverage and incorrect higher-order wiring. Together, CHANRG and a padding-free, symmetry-aware evaluation stack provide a stricter and batch-invariant framework for developing RNA structure predictors with demonstrable out-of-distribution robustness.

Modern model hubs, such as Hugging Face, store tens of petabytes of LLMs, with fine-tuned variants vastly outnumbering base models and dominating storage consumption. Existing storage reduction techniques -- such as deduplication and compression -- are either LLM-oblivious or not compatible with each other, limiting data reduction effectiveness. Our large-scale characterization study across all publicly available Hugging Face LLM repositories reveals several key insights: (1) fine-tuned models within the same family exhibit highly structured, sparse parameter differences suitable for delta compression; (2) bitwise similarity enables LLM family clustering; and (3) tensor-level deduplication is better aligned with model storage workloads, achieving high data reduction with low metadata overhead. Building on these insights, we design BitX, an effective, fast, lossless delta compression algorithm that compresses XORed difference between fine-tuned and base LLMs. We build ZipLLM, a model storage reduction pipeline that unifies tensor-level deduplication and lossless BitX compression. By synergizing deduplication and compression around LLM family clustering, ZipLLM reduces model storage consumption by 54%, over 20% higher than state-of-the-art deduplication and compression approaches.

Deduplication is a major focus for assembling and curating training datasets for large language models (LLM) -- detecting and eliminating additional instances of the same content -- in large collections of technical documents. Unrestrained, duplicates in the training dataset increase training costs and lead to undesirable properties such as memorization in trained models or cheating on evaluation. Contemporary approaches to document-level deduplication are often extremely expensive in both runtime and memory. We propose LSHBloom, an extension to MinhashLSH, which replaces the expensive LSHIndex with lightweight Bloom filters. LSHBloom demonstrates the same deduplication performance as MinhashLSH with only a marginal increase in false positives (as low as 1e-5 in our experiments); demonstrates competitive runtime (270\% faster than MinhashLSH on peS2o); and, crucially, uses just 0.6\% of the disk space required by MinhashLSH to deduplicate peS2o. We demonstrate that this space advantage scales with increased dataset size -- at the extreme scale of several billion documents, LSHBloom promises a 250\% speedup and a 54times space advantage over traditional MinHashLSH scaling deduplication of text datasets to many billions of documents.

Generative models, such as DALL-E, Midjourney, and Stable Diffusion, have societal implications that extend beyond the field of computer science. These models require large image databases like LAION-2B, which contain two billion images. At this scale, manual inspection is difficult and automated analysis is challenging. In addition, recent studies show that duplicated images pose copyright problems for models trained on LAION2B, which hinders its usability. This paper proposes an algorithmic chain that runs with modest compute, that compresses CLIP features to enable efficient duplicate detection, even for vast image volumes. Our approach demonstrates that roughly 700 million images, or about 30\%, of LAION-2B's images are likely duplicated. Our method also provides the histograms of duplication on this dataset, which we use to reveal more examples of verbatim copies by Stable Diffusion and further justify the approach. The current version of the de-duplicated set will be distributed online.

The effectiveness of large language models (LLMs) is often hindered by duplicated data in their extensive pre-training datasets. Current approaches primarily focus on detecting and removing duplicates, which risks the loss of valuable information and neglects the varying degrees of duplication. To address this, we propose a soft deduplication method that maintains dataset integrity while selectively reducing the sampling weight of data with high commonness. Central to our approach is the concept of "data commonness", a metric we introduce to quantify the degree of duplication by measuring the occurrence probabilities of samples using an n-gram model. Empirical analysis shows that this method significantly improves training efficiency, achieving comparable perplexity scores with at least a 26% reduction in required training steps. Additionally, it enhances average few-shot downstream accuracy by 1.77% when trained for an equivalent duration. Importantly, this approach consistently improves performance, even on rigorously deduplicated datasets, indicating its potential to complement existing methods and become a standard pre-training process for LLMs.

We find that existing language modeling datasets contain many near-duplicate examples and long repetitive substrings. As a result, over 1% of the unprompted output of language models trained on these datasets is copied verbatim from the training data. We develop two tools that allow us to deduplicate training datasets -- for example removing from C4 a single 61 word English sentence that is repeated over 60,000 times. Deduplication allows us to train models that emit memorized text ten times less frequently and require fewer train steps to achieve the same or better accuracy. We can also reduce train-test overlap, which affects over 4% of the validation set of standard datasets, thus allowing for more accurate evaluation. We release code for reproducing our work and performing dataset deduplication at https://github.com/google-research/deduplicate-text-datasets.

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

Progress in machine learning has been driven in large part by massive increases in data. However, large web-scale datasets such as LAION are largely uncurated beyond searches for exact duplicates, potentially leaving much redundancy. Here, we introduce SemDeDup, a method which leverages embeddings from pre-trained models to identify and remove semantic duplicates: data pairs which are semantically similar, but not exactly identical. Removing semantic duplicates preserves performance and speeds up learning. Analyzing a subset of LAION, we show that SemDeDup can remove 50% of the data with minimal performance loss, effectively halving training time. Moreover, performance increases out of distribution. Also, analyzing language models trained on C4, a partially curated dataset, we show that SemDeDup improves over prior approaches while providing efficiency gains. SemDeDup provides an example of how simple ways of leveraging quality embeddings can be used to make models learn faster with less data.

Large Language Models (LLMs) play an ever-increasing role in the field of Artificial Intelligence (AI)--not only for natural language processing but also for code understanding and generation. To stimulate open and responsible research on LLMs for code, we introduce The Stack, a 3.1 TB dataset consisting of permissively licensed source code in 30 programming languages. We describe how we collect the full dataset, construct a permissively licensed subset, present a data governance plan, discuss limitations, and show promising results on text2code benchmarks by training 350M-parameter decoders on different Python subsets. We find that (1) near-deduplicating the data significantly boosts performance across all experiments, and (2) it is possible to match previously reported HumanEval and MBPP performance using only permissively licensed data. We make the dataset available at https://hf.co/BigCode, provide a tool called "Am I in The Stack" (https://hf.co/spaces/bigcode/in-the-stack) for developers to search The Stack for copies of their code, and provide a process for code to be removed from the dataset by following the instructions at https://www.bigcode-project.org/docs/about/the-stack/.

Retrieval-Augmented Generation (RAG) has become essential for large-scale code generation, grounding predictions in external code corpora to improve actuality. However, a critical yet underexplored aspect of RAG pipelines is chunking -- the process of dividing documents into retrievable units. Existing line-based chunking heuristics often break semantic structures, splitting functions or merging unrelated code, which can degrade generation quality. We propose chunking via Abstract Syntax Trees (\ourwork), a structure-aware method that recursively breaks large AST nodes into smaller chunks and merges sibling nodes while respecting size limits. This approach generates self-contained, semantically coherent units across programming languages and tasks, improving performance on diverse code generation tasks, e.g., boosting Recall@5 by 4.3 points on RepoEval retrieval and Pass@1 by 2.67 points on SWE-bench generation. Our work highlights the importance of structure-aware chunking for scaling retrieval-enhanced code intelligence.

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.

This paper aims to understand the impacts of various data combinations (e.g., web text, wikipedia, github, books) on the training of large language models using SlimPajama. SlimPajama is a rigorously deduplicated, multi-source dataset, which has been refined and further deduplicated to 627B tokens from the extensive 1.2T tokens RedPajama dataset contributed by Together. We've termed our research as SlimPajama-DC, an empirical analysis designed to uncover fundamental characteristics and best practices associated with employing SlimPajama in the training of large language models. During our research with SlimPajama, two pivotal observations emerged: (1) Global deduplication vs. local deduplication. We analyze and discuss how global (across different sources of datasets) and local (within the single source of dataset) deduplications affect the performance of trained models. (2) Proportions of high-quality/highly-deduplicated multi-source datasets in the combination. To study this, we construct six configurations of SlimPajama dataset and train individual ones using 1.3B Cerebras-GPT model with Alibi and SwiGLU. Our best configuration outperforms the 1.3B model trained on RedPajama using the same number of training tokens by a significant margin. All our 1.3B models are trained on Cerebras 16times CS-2 cluster with a total of 80 PFLOP/s in bf16 mixed precision. We further extend our discoveries (such as increasing data diversity is crucial after global deduplication) on a 7B model with large batch-size training. Our models and the separate SlimPajama-DC datasets are available at: https://huggingface.co/MBZUAI-LLM and https://huggingface.co/datasets/cerebras/SlimPajama-627B.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

Distributional discrepancy between training and test data can lead models to make inaccurate predictions when encountering out-of-distribution (OOD) samples in real-world applications. Although existing graph OOD detection methods leverage data-centric techniques to extract effective representations, their performance remains compromised by structural redundancy that induces semantic shifts. To address this dilemma, we propose RedOUT, an unsupervised framework that integrates structural entropy into test-time OOD detection for graph classification. Concretely, we introduce the Redundancy-aware Graph Information Bottleneck (ReGIB) and decompose the objective into essential information and irrelevant redundancy. By minimizing structural entropy, the decoupled redundancy is reduced, and theoretically grounded upper and lower bounds are proposed for optimization. Extensive experiments on real-world datasets demonstrate the superior performance of RedOUT on OOD detection. Specifically, our method achieves an average improvement of 6.7%, significantly surpassing the best competitor by 17.3% on the ClinTox/LIPO dataset pair.

Data is one of the most critical elements in building a large language model. However, existing systems either fail to customize a corpus curation pipeline or neglect to leverage comprehensive corpus assessment for iterative optimization of the curation. To this end, we present a pretraining corpus curation and assessment platform called Oasis -- a one-stop system for data quality improvement and quantification with user-friendly interactive interfaces. Specifically, the interactive modular rule filter module can devise customized rules according to explicit feedback. The debiased neural filter module builds the quality classification dataset in a negative-centric manner to remove the undesired bias. The adaptive document deduplication module could execute large-scale deduplication with limited memory resources. These three parts constitute the customized data curation module. And in the holistic data assessment module, a corpus can be assessed in local and global views, with three evaluation means including human, GPT-4, and heuristic metrics. We exhibit a complete process to use Oasis for the curation and assessment of pretraining data. In addition, an 800GB bilingual corpus curated by Oasis is publicly released.

With the advent of neural language models, the performance of code generation has been significantly boosted. However, the problem of repetitions during the generation process continues to linger. Previous work has primarily focused on content repetition, which is merely a fraction of the broader repetition problem in code generation. A more prevalent and challenging problem is structural repetition. In structural repetition, the repeated code appears in various patterns but possesses a fixed structure, which can be inherently reflected in grammar. In this paper, we formally define structural repetition and propose an efficient decoding approach called RPG, which stands for Repetition Penalization based on Grammar, to alleviate the repetition problems in code generation for LLMs. Specifically, RPG first leverages grammar rules to identify repetition problems during code generation, and then strategically decays the likelihood of critical tokens that contribute to repetitions, thereby mitigating them in code generation. To facilitate this study, we construct a new dataset CodeRepetEval to comprehensively evaluate approaches for mitigating the repetition problems in code generation. Extensive experimental results demonstrate that RPG substantially outperforms the best-performing baselines on CodeRepetEval dataset as well as HumanEval and MBPP benchmarks, effectively reducing repetitions and enhancing the quality of generated code.

The rapid scaling of large language models necessitates more lightweight finetuning methods to reduce the explosive GPU memory overhead when numerous customized models are served simultaneously. Targeting more parameter-efficient low-rank adaptation (LoRA), parameter sharing presents a promising solution. Empirically, our research into high-level sharing principles highlights the indispensable role of differentiation in reversing the detrimental effects of pure sharing. Guided by this finding, we propose Mixture of Shards (MoS), incorporating both inter-layer and intra-layer sharing schemes, and integrating four nearly cost-free differentiation strategies, namely subset selection, pair dissociation, vector sharding, and shard privatization. Briefly, it selects a designated number of shards from global pools with a Mixture-of-Experts (MoE)-like routing mechanism before sequentially concatenating them to low-rank matrices. Hence, it retains all the advantages of LoRA while offering enhanced parameter efficiency, and effectively circumvents the drawbacks of peer parameter-sharing methods. Our empirical experiments demonstrate approximately 8x parameter savings in a standard LoRA setting. The ablation study confirms the significance of each component. Our insights into parameter sharing and MoS method may illuminate future developments of more parameter-efficient finetuning methods.

Code clone detection is a critical task in software engineering, aimed at identifying duplicated or similar code fragments within or across software systems. Traditional methods often fail to capture functional equivalence, particularly for semantic clones (Type 4), where code fragments implement identical functionality despite differing syntactic structures. Recent advances in large language models (LLMs) have shown promise in understanding code semantics. However, directly applying LLMs to code clone detection yields suboptimal results due to their sensitivity to syntactic differences. To address these challenges, we propose a novel two-stage framework that combines LLM-based screening with execution-based validation for detecting semantic clones in Python programs. In the first stage, an LLM evaluates code pairs to filter out obvious non-clones based on semantic analysis. For pairs not identified as clones, the second stage employs an execution-based validation approach, utilizing LLM-generated test inputs to assess functional equivalence through cross-execution validation. Our experimental evaluation demonstrates significant improvements in precision, recall, and F1-score compared to direct LLM-based detection, highlighting the framework's effectiveness in identifying semantic clones. Future work includes exploring cross-language clone detection and optimizing the framework for large-scale applications.

Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods. However, they suffer from exponential computational costs or searching the matching without theoretical guarantees. In this paper, we develop D2Match by leveraging the efficiency of Deep learning and Degeneracy for subgraph matching. More specifically, we first prove that subgraph matching can degenerate to subtree matching, and subsequently is equivalent to finding a perfect matching on a bipartite graph. We can then yield an implementation of linear time complexity by the built-in tree-structured aggregation mechanism on graph neural networks. Moreover, circle structures and node attributes can be easily incorporated in D2Match to boost the matching performance. Finally, we conduct extensive experiments to show the superior performance of our D2Match and confirm that our D2Match indeed exploits the subtrees and differs from existing GNNs-based subgraph matching methods that depend on memorizing the data distribution divergence

In Open Source Software, the source code and any other resources available in a project can be viewed or reused by anyone subject to often permissive licensing restrictions. In contrast to some studies of dependency-based reuse supported via package managers, no studies of OSS-wide copy-based reuse exist. This dataset seeks to encourage the studies of OSS-wide copy-based reuse by providing copying activity data that captures whole-file reuse in nearly all OSS. To accomplish that, we develop approaches to detect copy-based reuse by developing an efficient algorithm that exploits World of Code infrastructure: a curated and cross referenced collection of nearly all open source repositories. We expect this data to enable future research and tool development that support such reuse and minimize associated risks.

As the demand for comprehensive evaluations of diverse model capabilities steadily increases, benchmark suites have correspondingly grown significantly in scale. Despite notable advances in redundancy reduction and subset-level performance prediction, a systematic framework that effectively integrates these methods to ensure both prediction accuracy and ranking consistency is still largely elusive. In this paper, we first perform a sample-level analysis of benchmark redundancy and identify several highly similar samples that can be eliminated. Besides, we frame benchmark compression as an optimization problem with the aim of score reconstruction. Building on these, we then propose EssenceBench, a coarse-to-fine framework utilizing an iterative Genetic Algorithm (GA), which takes the advantages of fitness-based subset search and attribution-based sample search. Compared to previous methods, our approach yields superior compression results with lower reconstruction error and markedly higher efficiency. In particular, on the HellaSwag benchmark (10K samples), our method preserves the ranking of all models shifting within 5% using 25x fewer samples, and achieves 95% ranking preservation shifting within 5% using only 200x fewer samples.

Given a database of bit strings A_1,ldots,A_min {0,1}^n, a fundamental data structure task is to estimate the distances between a given query Bin {0,1}^n with all the strings in the database. In addition, one might further want to ensure the integrity of the database by releasing these distance statistics in a secure manner. In this work, we propose differentially private (DP) data structures for this type of tasks, with a focus on Hamming and edit distance. On top of the strong privacy guarantees, our data structures are also time- and space-efficient. In particular, our data structure is epsilon-DP against any sequence of queries of arbitrary length, and for any query B such that the maximum distance to any string in the database is at most k, we output m distance estimates. Moreover, - For Hamming distance, our data structure answers any query in widetilde O(mk+n) time and each estimate deviates from the true distance by at most widetilde O(k/e^{epsilon/log k}); - For edit distance, our data structure answers any query in widetilde O(mk^2+n) time and each estimate deviates from the true distance by at most widetilde O(k/e^{epsilon/(log k log n)}). For moderate k, both data structures support sublinear query operations. We obtain these results via a novel adaptation of the randomized response technique as a bit flipping procedure, applied to the sketched strings.

This paper presents VLCache, a cache reuse framework that exploits both Key-Value (KV) cache and encoder cache from prior multimodal inputs to eliminate costly recomputation when the same multimodal inputs recur. Unlike previous heuristic approaches, we formally identify the cumulative reuse error effect and demonstrate how to minimize the non-prefix cache reuse error effectively. We further analyze the varying importance of model layers and propose a dynamic, layer-aware recomputation strategy to balance accuracy and efficiency. Experimental results show that VLCache achieves an accuracy on par with full recomputation, while requiring only 2-5% of the tokens to compute, yielding 1.2x-16x TTFT speedups. The proposed VLCache pipeline has been integrated into SGLang, enabling significantly faster inference in practical deployments.

Engineering efficient implementations of compact and succinct structures is a time-consuming and challenging task, since there is no standard library of easy-to- use, highly optimized, and composable components. One consequence is that measuring the practical impact of new theoretical proposals is a difficult task, since older base- line implementations may not rely on the same basic components, and reimplementing from scratch can be very time-consuming. In this paper we present a framework for experimentation with succinct data structures, providing a large set of configurable components, together with tests, benchmarks, and tools to analyze resource requirements. We demonstrate the functionality of the framework by recomposing succinct solutions for document retrieval.

Code-LLMs, LLMs pre-trained on large code corpora, have shown great progress in learning rich representations of the structure and syntax of code, successfully using it to generate or classify code fragments. At the same time, understanding if they are able to do so because they capture code semantics, and how well, is still an open question. In this paper, we tackle this problem by introducing SeqCoBench, a benchmark for systematically assessing how Code-LLMs can capture code functional equivalence. SeqCoBench contains over 20 code transformations that either preserve or alter the semantics of Python programs. We conduct extensive evaluations in different settings, including zero-shot and parameter-efficient finetuning methods on state-of-the-art (Code)-LLMs to see if they can discern semantically equivalent or different pairs of programs in SeqCoBench. We find that the performance gap between these LLMs and classical match-based retrieval scores is minimal, with both approaches showing a concerning lack of depth in understanding code semantics.

Information extraction from copy-heavy documents, characterized by massive volumes of structurally similar content, represents a critical yet understudied challenge in enterprise document processing. We present a systematic framework that strategically combines OCR engines with Large Language Models (LLMs) to optimize the accuracy-efficiency trade-off inherent in repetitive document extraction tasks. Unlike existing approaches that pursue universal solutions, our method exploits document-specific characteristics through intelligent strategy selection. We implement and evaluate 25 configurations across three extraction paradigms (direct, replacement, and table-based) on identity documents spanning four formats (PNG, DOCX, XLSX, PDF). Through table-based extraction methods, our adaptive framework delivers outstanding results: F1=1.0 accuracy with 0.97s latency for structured documents, and F1=0.997 accuracy with 0.6 s for challenging image inputs when integrated with PaddleOCR, all while maintaining sub-second processing speeds. The 54 times performance improvement compared with multimodal methods over naive approaches, coupled with format-aware routing, enables processing of heterogeneous document streams at production scale. Beyond the specific application to identity extraction, this work establishes a general principle: the repetitive nature of copy-heavy tasks can be transformed from a computational burden into an optimization opportunity through structure-aware method selection.

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

BigCloneBench is a well-known and widely used large-scale dataset for the evaluation of recall of clone detection tools. It has been beneficial for research on clone detection and has become a standard in evaluating the performance of clone detection tools. More recently, it has also been widely used as a dataset to evaluate machine learning approaches to semantic clone detection or code similarity detection for functional or semantic similarity. This paper demonstrates that BigCloneBench is problematic to use as ground truth for learning or evaluating semantic code similarity, and highlights the aspects of BigCloneBench that affect the ground truth quality. A manual investigation of a statistically significant random sample of 406 Weak Type-3/Type-4 clone pairs revealed that 93% of them do not have a similar functionality and are therefore mislabelled. In a literature review of 179 papers that use BigCloneBench as a dataset, we found 139 papers that used BigCloneBench to evaluate semantic clone detection and where the results are threatened in their validity by the mislabelling. As such, these papers often report high F1 scores (e.g., above 0.9), which indicates overfitting to dataset-specific artefacts rather than genuine semantic similarity detection. We emphasise that using BigCloneBench remains valid for the intended purpose of evaluating syntactic or textual clone detection of Type-1, Type-2, and Type-3 clones. We acknowledge the important contributions of BigCloneBench to two decades of traditional clone detection research. However, the usage of BigCloneBench beyond the intended purpose without careful consideration of its limitations has led to misleading results and conclusions, and potentially harmed the field of semantic clone detection.

The improvement of LLMs' instruction-following capabilities depends critically on the availability of high-quality instruction-response pairs. While existing automatic data synthetic methods alleviate the burden of manual curation, they often rely heavily on either the quality of seed data or strong assumptions about the structure and content of web documents. To tackle these challenges, we propose Web Reconstruction (WebR), a fully automated framework for synthesizing high-quality instruction-tuning (IT) data directly from raw web documents with minimal assumptions. Leveraging the inherent diversity of raw web content, we conceptualize web reconstruction as an instruction-tuning data synthesis task via a novel dual-perspective paradigm--Web as Instruction and Web as Response--where each web document is designated as either an instruction or a response to trigger the reconstruction process. Comprehensive experiments show that datasets generated by WebR outperform state-of-the-art baselines by up to 16.65% across four instruction-following benchmarks. Notably, WebR demonstrates superior compatibility, data efficiency, and scalability, enabling enhanced domain adaptation with minimal effort. The data and code are publicly available at https://github.com/YJiangcm/WebR.

We propose LGGPT, an LLM-based model tailored for unified layout generation. First, we propose Arbitrary Layout Instruction (ALI) and Universal Layout Response (ULR) as the uniform I/O template. ALI accommodates arbitrary layout generation task inputs across multiple layout domains, enabling LGGPT to unify both task-generic and domain-generic layout generation hitherto unexplored. Collectively, ALI and ULR boast a succinct structure that forgoes superfluous tokens typically found in existing HTML-based formats, facilitating efficient instruction tuning and boosting unified generation performance. In addition, we propose an Interval Quantization Encoding (IQE) strategy that compresses ALI into a more condensed structure. IQE precisely preserves valid layout clues while eliminating the less informative placeholders, facilitating LGGPT to capture complex and variable layout generation conditions during the unified training process. Experimental results demonstrate that LGGPT achieves superior or on par performance compared to existing methods. Notably, LGGPT strikes a prominent balance between proficiency and efficiency with a compact 1.5B parameter LLM, which beats prior 7B or 175B models even in the most extensive and challenging unified scenario. Furthermore, we underscore the necessity of employing LLMs for unified layout generation and suggest that 1.5B could be an optimal parameter size by comparing LLMs of varying scales. Code is available at https://github.com/NiceRingNode/LGGPT.

The increased model capacity of Diffusion Transformers (DiTs) and the demand for generating higher resolutions of images and videos have led to a significant rise in inference latency, impacting real-time performance adversely. While prior research has highlighted the presence of high similarity in activation values between adjacent diffusion steps (referred to as redundancy) and proposed various caching mechanisms to mitigate computational overhead, the exploration of redundancy in existing literature remains limited, with findings often not generalizable across different DiT models. This study aims to address this gap by conducting a comprehensive investigation into redundancy across a broad spectrum of mainstream DiT models. Our experimental analysis reveals substantial variations in the distribution of redundancy across diffusion steps among different DiT models. Interestingly, within a single model, the redundancy distribution remains stable regardless of variations in input prompts, step counts, or scheduling strategies. Given the lack of a consistent pattern across diverse models, caching strategies designed for a specific group of models may not easily transfer to others. To overcome this challenge, we introduce a tool for analyzing the redundancy of individual models, enabling subsequent research to develop tailored caching strategies for specific model architectures. The project is publicly available at https://github.com/xdit-project/DiTCacheAnalysis.

We consider the clone detection and information retrieval problems for source code, well-known tasks important for any programming language. Although it is also an important and interesting problem to find code snippets that operate identically but are written in different programming languages, to the best of our knowledge multilingual clone detection has not been studied in literature. In this work, we formulate the multilingual clone detection problem and present XCD, a new benchmark dataset produced from the CodeForces submissions dataset. Moreover, we present a novel training procedure, called cross-consistency training (CCT), that we apply to train language models on source code in different programming languages. The resulting CCT-LM model, initialized with GraphCodeBERT and fine-tuned with CCT, achieves new state of the art, outperforming existing approaches on the POJ-104 clone detection benchmark with 95.67\% MAP and AdvTest code search benchmark with 47.18\% MRR; it also shows the best results on the newly created multilingual clone detection benchmark XCD across all programming languages.

This paper presents a new approach for code similarity on High Level programs. Our technique is based on Fast Dynamic Time Warping, that builds a warp path or points relation with local restrictions. The source code is represented into Time Series using the operators inside programming languages that makes possible the comparison. This makes possible subsequence detection that represent similar code instructions. In contrast with other code similarity algorithms, we do not make features extraction. The experiments show that two source codes are similar when their respective Time Series are similar.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

This paper introduces RETSim (Resilient and Efficient Text Similarity), a lightweight, multilingual deep learning model trained to produce robust metric embeddings for near-duplicate text retrieval, clustering, and dataset deduplication tasks. We demonstrate that RETSim is significantly more robust and accurate than MinHash and neural text embeddings, achieving new state-of-the-art performance on dataset deduplication, adversarial text retrieval benchmarks, and spam clustering tasks. We also introduce the W4NT3D benchmark (Wiki-40B 4dversarial Near-T3xt Dataset) for evaluating multilingual, near-duplicate text retrieval capabilities under adversarial settings. RETSim and the W4NT3D benchmark are open-sourced under the MIT License at https://github.com/google/unisim.

Recent advances in LLM-based decompilers have been shown effective to convert low-level binaries into human-readable source code. However, there still lacks a comprehensive benchmark that provides large-scale binary-source function pairs, which is critical for advancing the LLM decompilation technology. Creating accurate binary-source mappings incurs severe issues caused by complex compilation settings and widespread function inlining that obscure the correspondence between binaries and their original source code. Previous efforts have either relied on used contest-style benchmarks, synthetic binary-source mappings that diverge significantly from the mappings in real world, or partially matched binaries with only code lines or variable names, compromising the effectiveness of analyzing the binary functionality. To alleviate these issues, we introduce Decompile-Bench, the first open-source dataset comprising two million binary-source function pairs condensed from 100 million collected function pairs, i.e., 450GB of binaries compiled from permissively licensed GitHub projects. For the evaluation purposes, we also developed a benchmark Decompile-Bench-Eval including manually crafted binaries from the well-established HumanEval and MBPP, alongside the compiled GitHub repositories released after 2025 to mitigate data leakage issues. We further explore commonly-used evaluation metrics to provide a thorough assessment of the studied LLM decompilers and find that fine-tuning with Decompile-Bench causes a 20% improvement over previous benchmarks in terms of the re-executability rate. Our code and data has been released in HuggingFace and Github. https://github.com/albertan017/LLM4Decompile

Detecting code clones is relevant to software maintenance and code refactoring. This challenge still presents unresolved cases, mainly when structural similarity does not reflect functional equivalence, though recent code models show promise. Therefore, this research aims to systematically measure the performance of several newly introduced small code models in classifying code pairs as clones or non-clones. The evaluation is based on five datasets: BigCloneBench, CodeJam, Karnalim, POJ104, and PoolC, as well as six code models: CodeBERT, GraphCodeBERT, Salesforce T5, UniXCoder, PLBART, and Polycoder. Most models performed well across standard metrics, including accuracy, precision, recall, and F1-score. However, a marginal fraction of clones remains challenging to detect, especially when the code looks similar but performs different operations. The source code that illustrates our approach is available at: https://github.com/jorge-martinez-gil/small-code-models

Disassembly is a crucial yet challenging step in binary analysis. While emerging neural disassemblers show promise for efficiency and accuracy, they frequently generate outputs violating fundamental structural constraints, which significantly compromise their practical usability. To address this critical problem, we regularize the disassembly solution space by formalizing and applying key structural constraints based on post-dominance relations. This approach systematically detects widespread errors in existing neural disassemblers' outputs. These errors often originate from models' limited context modeling and instruction-level decoding that neglect global structural integrity. We introduce Tady, a novel neural disassembler featuring an improved model architecture and a dedicated post-processing algorithm, specifically engineered to address these deficiencies. Comprehensive evaluations on diverse binaries demonstrate that Tady effectively eliminates structural constraint violations and functions with high efficiency, while maintaining instruction-level accuracy.

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

A growing body of research has demonstrated the inability of NLP models to generalize compositionally and has tried to alleviate it through specialized architectures, training schemes, and data augmentation, among other approaches. In this work, we study a different approach: training on instances with diverse structures. We propose a model-agnostic algorithm for subsampling such sets of instances from a labeled instance pool with structured outputs. Evaluating on both compositional template splits and traditional IID splits of 5 semantic parsing datasets of varying complexity, we show that structurally diverse training using our algorithm leads to comparable or better generalization than prior algorithms in 9 out of 10 dataset-split type pairs. In general, we find structural diversity to consistently improve sample efficiency compared to random train sets. Moreover, we show that structurally diverse sampling yields comprehensive test sets that are a lot more challenging than IID test sets. Finally, we provide two explanations for improved generalization from diverse train sets: 1) improved coverage of output substructures, and 2) a reduction in spurious correlations between these substructures.

Locality-sensitive hashing (LSH) is a fundamental algorithmic technique widely employed in large-scale data processing applications, such as nearest-neighbor search, entity resolution, and clustering. However, its applicability in some real-world scenarios is limited due to the need for careful design of hashing functions that align with specific metrics. Existing LSH-based Entity Blocking solutions primarily rely on generic similarity metrics such as Jaccard similarity, whereas practical use cases often demand complex and customized similarity rules surpassing the capabilities of generic similarity metrics. Consequently, designing LSH functions for these customized similarity rules presents considerable challenges. In this research, we propose a neuralization approach to enhance locality-sensitive hashing by training deep neural networks to serve as hashing functions for complex metrics. We assess the effectiveness of this approach within the context of the entity resolution problem, which frequently involves the use of task-specific metrics in real-world applications. Specifically, we introduce NLSHBlock (Neural-LSH Block), a novel blocking methodology that leverages pre-trained language models, fine-tuned with a novel LSH-based loss function. Through extensive evaluations conducted on a diverse range of real-world datasets, we demonstrate the superiority of NLSHBlock over existing methods, exhibiting significant performance improvements. Furthermore, we showcase the efficacy of NLSHBlock in enhancing the performance of the entity matching phase, particularly within the semi-supervised setting.

The demand for deploying large language models(LLMs) on mobile devices continues to increase, driven by escalating data security concerns and cloud costs. However, network bandwidth and memory limitations pose challenges for deploying billion-level models on mobile devices. In this study, we investigate the outputs of different layers across various scales of LLMs and found that the outputs of most layers exhibit significant similarity. Moreover, this similarity becomes more pronounced as the model size increases, indicating substantial redundancy in the depth direction of the LLMs. Based on this observation, we propose an efficient model volume compression strategy, termed FoldGPT, which combines block removal and block parameter sharing.This strategy consists of three parts: (1) Based on the learnable gating parameters, we determine the block importance ranking while modeling the coupling effect between blocks. Then we delete some redundant layers based on the given removal rate. (2) For the retained blocks, we apply a specially designed group parameter sharing strategy, where blocks within the same group share identical weights, significantly compressing the number of parameters and slightly reducing latency overhead. (3) After sharing these Blocks, we "cure" the mismatch caused by sparsity with a minor amount of fine-tuning and introduce a tail-layer distillation strategy to improve the performance. Experiments demonstrate that FoldGPT outperforms previous state-of-the-art(SOTA) methods in efficient model compression, demonstrating the feasibility of achieving model lightweighting through straightforward block removal and parameter sharing.

Code cloning, the duplication of code fragments, is common in software development. While some reuse aids productivity, excessive cloning hurts maintainability and introduces bugs. Hence, automatic code clone detection is vital. Meanwhile, large language models (LLMs) possess diverse code-related knowledge, making them versatile for various software engineering challenges. However, LLMs' performance in code clone detection is unclear and needs more study for accurate assessment. In this paper, we provide the first comprehensive evaluation of LLMs for clone detection, covering different clone types, languages, and prompts. We find advanced LLMs excel in detecting complex semantic clones, surpassing existing methods. Adding intermediate reasoning steps via chain-of-thought prompts noticeably enhances performance. Additionally, representing code as vector embeddings, especially with text encoders, effectively aids clone detection.Lastly, the ability of LLMs to detect code clones differs among various programming languages. Our study suggests that LLMs have potential for clone detection due to their language capabilities, offering insights for developing robust LLM-based methods to enhance software engineering.

Large language models are commonly trained on a mixture of filtered web data and curated high-quality corpora, such as social media conversations, books, or technical papers. This curation process is believed to be necessary to produce performant models with broad zero-shot generalization abilities. However, as larger models requiring pretraining on trillions of tokens are considered, it is unclear how scalable is curation and whether we will run out of unique high-quality data soon. At variance with previous beliefs, we show that properly filtered and deduplicated web data alone can lead to powerful models; even significantly outperforming models from the state-of-the-art trained on The Pile. Despite extensive filtering, the high-quality data we extract from the web is still plentiful, and we are able to obtain five trillion tokens from CommonCrawl. We publicly release an extract of 600 billion tokens from our RefinedWeb dataset, and 1.3/7.5B parameters language models trained on it.

A critical part of creating code suggestion systems is the pre-training of Large Language Models on vast amounts of source code and natural language text, often of questionable origin or quality. This may contribute to the presence of bugs and vulnerabilities in code generated by LLMs. While efforts to identify bugs at or after code generation exist, it is preferable to pre-train or fine-tune LLMs on curated, high-quality, and compliant datasets. The need for vast amounts of training data necessitates that such curation be automated, minimizing human intervention. We propose an automated source code autocuration technique that leverages the complete version history of open-source software projects to improve the quality of training data. This approach leverages the version history of all OSS projects to identify training data samples that have been modified or have undergone changes in at least one OSS project, and pinpoint a subset of samples that include fixes for bugs or vulnerabilities. We evaluate this method using The Stack v2 dataset, and find that 17% of the code versions in the dataset have newer versions, with 17% of those representing bug fixes, including 2.36% addressing known CVEs. The deduplicated version of Stack v2 still includes blobs vulnerable to 6,947 known CVEs. Furthermore, 58% of the blobs in the dataset were never modified after creation, suggesting they likely represent software with minimal or no use. Misidentified blob origins present an additional challenge, as they lead to the inclusion of non-permissively licensed code, raising serious compliance concerns. By addressing these issues, the training of new models can avoid perpetuating buggy code patterns or license violations. We expect our results to inspire process improvements for automated data curation, with the potential to enhance the reliability of outputs generated by AI tools.

Tensor network (TN) is a powerful framework in machine learning, but selecting a good TN model, known as TN structure search (TN-SS), is a challenging and computationally intensive task. The recent approach TNLS~li2022permutation showed promising results for this task, however, its computational efficiency is still unaffordable, requiring too many evaluations of the objective function. We propose TnALE, a new algorithm that updates each structure-related variable alternately by local enumeration, greatly reducing the number of evaluations compared to TNLS. We theoretically investigate the descent steps for TNLS and TnALE, proving that both algorithms can achieve linear convergence up to a constant if a sufficient reduction of the objective is reached in each neighborhood. We also compare the evaluation efficiency of TNLS and TnALE, revealing that Omega(2^N) evaluations are typically required in TNLS for reaching the objective reduction in the neighborhood, while ideally O(N^2R) evaluations are sufficient in TnALE, where N denotes the tensor order and R reflects the ``low-rankness'' of the neighborhood. Experimental results verify that TnALE can find practically good TN-ranks and permutations with vastly fewer evaluations than the state-of-the-art algorithms.

Past work has shown that large language models are susceptible to privacy attacks, where adversaries generate sequences from a trained model and detect which sequences are memorized from the training set. In this work, we show that the success of these attacks is largely due to duplication in commonly used web-scraped training sets. We first show that the rate at which language models regenerate training sequences is superlinearly related to a sequence's count in the training set. For instance, a sequence that is present 10 times in the training data is on average generated ~1000 times more often than a sequence that is present only once. We next show that existing methods for detecting memorized sequences have near-chance accuracy on non-duplicated training sequences. Finally, we find that after applying methods to deduplicate training data, language models are considerably more secure against these types of privacy attacks. Taken together, our results motivate an increased focus on deduplication in privacy-sensitive applications and a reevaluation of the practicality of existing privacy attacks.

Variable names are critical for conveying intended program behavior. Machine learning-based program analysis methods use variable name representations for a wide range of tasks, such as suggesting new variable names and bug detection. Ideally, such methods could capture semantic relationships between names beyond syntactic similarity, e.g., the fact that the names average and mean are similar. Unfortunately, previous work has found that even the best of previous representation approaches primarily capture relatedness (whether two variables are linked at all), rather than similarity (whether they actually have the same meaning). We propose VarCLR, a new approach for learning semantic representations of variable names that effectively captures variable similarity in this stricter sense. We observe that this problem is an excellent fit for contrastive learning, which aims to minimize the distance between explicitly similar inputs, while maximizing the distance between dissimilar inputs. This requires labeled training data, and thus we construct a novel, weakly-supervised variable renaming dataset mined from GitHub edits. We show that VarCLR enables the effective application of sophisticated, general-purpose language models like BERT, to variable name representation and thus also to related downstream tasks like variable name similarity search or spelling correction. VarCLR produces models that significantly outperform the state-of-the-art on IdBench, an existing benchmark that explicitly captures variable similarity (as distinct from relatedness). Finally, we contribute a release of all data, code, and pre-trained models, aiming to provide a drop-in replacement for variable representations used in either existing or future program analyses that rely on variable names.

The goal of decompilation is to convert compiled low-level code (e.g., assembly code) back into high-level programming languages, enabling analysis in scenarios where source code is unavailable. This task supports various reverse engineering applications, such as vulnerability identification, malware analysis, and legacy software migration. The end-to-end decompile method based on large langauge models (LLMs) reduces reliance on additional tools and minimizes manual intervention due to its inherent properties. However, previous end-to-end methods often lose critical information necessary for reconstructing control flow structures and variables when processing binary files, making it challenging to accurately recover the program's logic. To address these issues, we propose the ReF Decompile method, which incorporates the following innovations: (1) The Relabelling strategy replaces jump target addresses with labels, preserving control flow clarity. (2) The Function Call strategy infers variable types and retrieves missing variable information from binary files. Experimental results on the Humaneval-Decompile Benchmark demonstrate that ReF Decompile surpasses comparable baselines and achieves state-of-the-art (SOTA) performance of 61.43%.

Decompilers are important tools for reverse engineers that help them analyze software at a higher level of abstraction than assembly. Unfortunately, because compilation is lossy, deterministic decompilers produce code that is missing many of the details that make source code readable in the first place, like variable names and types. Neural decompilers, on the other hand, offer the ability to statistically fill in these details. Existing work in neural decompilation, however, suffers from substantial drawbacks that limits its ability to handle real code: it is unable to handle user-defined composite types, which are essential to fully specifying many functions' semantics, or require test cases. In this work, we introduce a new training process to finetune any LLM into a neural decompiler capable of generating the appropriate user-defined types alongside the decompilation. We introduce a new dataset, Realtype, that includes substantially more complicated and realistic types than existing neural decompilation benchmarks. Motivated by the intuition that different parts of data structures can be operated upon by different parts of the program, we show that interprocedural context can help improve neural decompilers' ability to handle user-defined types. We show that our training process yields state-of-the-art results in neural decompilation. We also publicly release the Idioms series of finetuned neural decompilation models in support of open science. In summary, we identify the need for joint code and type prediction, show that it is a hard problem, and take the first steps towards solving it.

As the adoption of large language models increases and the need for per-user or per-task model customization grows, the parameter-efficient fine-tuning (PEFT) methods, such as low-rank adaptation (LoRA) and its variants, incur substantial storage and transmission costs. To further reduce stored parameters, we introduce a "divide-and-share" paradigm that breaks the barriers of low-rank decomposition across matrix dimensions, modules and layers by sharing parameters globally via a vector bank. As an instantiation of the paradigm to LoRA, our proposed VB-LoRA composites all the low-rank matrices of LoRA from a shared vector bank with a differentiable top-k admixture module. VB-LoRA achieves extreme parameter efficiency while maintaining comparable or better performance compared to state-of-the-art PEFT methods. Extensive experiments demonstrate the effectiveness of VB-LoRA on natural language understanding, natural language generation, and instruction tuning tasks. When fine-tuning the Llama2-13B model, VB-LoRA only uses 0.4% of LoRA's stored parameters, yet achieves superior results. Our source code is available at https://github.com/leo-yangli/VB-LoRA.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

When considering a model architecture, there are several ways to reduce its memory footprint. Historically, popular approaches included selecting smaller architectures and creating sparse networks through pruning. More recently, randomized parameter-sharing (RPS) methods have gained traction for model compression at start of training. In this paper, we comprehensively assess the trade-off between memory and accuracy across RPS, pruning techniques, and building smaller models. Our findings demonstrate that RPS, which is both data and model-agnostic, consistently outperforms/matches smaller models and all moderately informed pruning strategies, such as MAG, SNIP, SYNFLOW, and GRASP, across the entire compression range. This advantage becomes particularly pronounced in higher compression scenarios. Notably, even when compared to highly informed pruning techniques like Lottery Ticket Rewinding (LTR), RPS exhibits superior performance in high compression settings. This points out inherent capacity advantage that RPS enjoys over sparse models. Theoretically, we establish RPS as a superior technique in terms of memory-efficient representation when compared to pruning for linear models. This paper argues in favor of paradigm shift towards RPS based models. During our rigorous evaluation of RPS, we identified issues in the state-of-the-art RPS technique ROAST, specifically regarding stability (ROAST's sensitivity to initialization hyperparameters, often leading to divergence) and Pareto-continuity (ROAST's inability to recover the accuracy of the original model at zero compression). We provably address both of these issues. We refer to the modified RPS, which incorporates our improvements, as STABLE-RPS.

Protein inverse folding, the design of an amino acid sequence based on a target 3D structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external knowledge or relying on protein language models (PLMs). The former omits the evolutionary information stored in protein databases, while the latter is parameter-inefficient and inflexible to adapt to ever-growing protein data. To overcome the above drawbacks, in this paper we propose a novel method, called retrieval-augmented denoising diffusion (RadDiff), for protein inverse folding. Given the target protein backbone, RadDiff uses a hierarchical search strategy to efficiently retrieve structurally similar proteins from large protein databases. The retrieved structures are then aligned residue-by-residue to the target to construct a position-specific amino acid profile, which serves as an evolutionary-informed prior that conditions the denoising process. A lightweight integration module is further designed to incorporate this prior effectively. Experimental results on the CATH, PDB, and TS50 datasets show that RadDiff consistently outperforms existing methods, improving sequence recovery rate by up to 19%. Experimental results also demonstrate that RadDiff generates highly foldable sequences and scales effectively with database size.

Effective instruction tuning is indispensable for optimizing code LLMs, aligning model behavior with user expectations and enhancing model performance in real-world applications. However, most existing methods focus on code snippets, which are limited to specific functionalities and rigid structures, restricting the complexity and diversity of the synthesized data. To address these limitations, we introduce a novel feature tree-based synthesis framework inspired by Abstract Syntax Trees (AST). Unlike AST, which captures syntactic structure of code, our framework models semantic relationships between code elements, enabling the generation of more nuanced and diverse data. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features. This process enables the identification of more complex patterns and relationships within the code. By sampling subtrees with controlled depth and breadth, our framework allows precise adjustments to the complexity of the generated code, supporting a wide range of tasks from simple function-level operations to intricate multi-file scenarios. We fine-tuned widely-used base models to create the EpiCoder series, achieving state-of-the-art performance at both the function and file levels across multiple benchmarks. Notably, empirical evidence indicates that our approach shows significant potential in synthesizing highly complex repository-level code data. Further analysis elucidates the merits of this approach by rigorously assessing data complexity and diversity through software engineering principles and LLM-as-a-judge method.

Recent efforts in fine-tuning language models often rely on automatic data selection, commonly using Nearest Neighbors retrieval from large datasets. However, we theoretically show that this approach tends to select redundant data, limiting its effectiveness or even hurting performance. To address this, we introduce SIFT, a data selection algorithm designed to reduce uncertainty about the model's response given a prompt, which unifies ideas from retrieval and active learning. Whereas Nearest Neighbor retrieval typically fails in the presence of information duplication, SIFT accounts for information duplication and optimizes the overall information gain of the selected examples. We focus our evaluations on fine-tuning at test-time for prompt-specific language modeling on the Pile dataset, and show that SIFT consistently outperforms Nearest Neighbor retrieval, with minimal computational overhead. Moreover, we show that our uncertainty estimates can predict the performance gain of test-time fine-tuning, and use this to develop an adaptive algorithm that invests test-time compute proportional to realized performance gains. We provide the activeft (Active Fine-Tuning) library which can be used as a drop-in replacement for Nearest Neighbor retrieval.

LLM serving systems typically treat user prompts as monolithic inputs, optimizing inference through decoding tricks or inter-query batching. However, many real-world prompts contain latent semantic parallelism--decomposable structures where subtasks can be executed independently to reduce latency while preserving meaning. We introduce PARALLELPROMPT, the first benchmark for measuring intra-query parallelism in natural user prompts. Our dataset comprises over 37,000 real-world prompts from public LLM chat logs, each annotated with a structured schema capturing task templates, shared context, and iteration inputs. These schemas are extracted using LLM-assisted prompting with rule-based multilingual validation. To evaluate the benefits of decomposition, we provide an execution suite that benchmarks serial vs. parallel strategies, measuring latency, structural adherence, and semantic fidelity. Our results show that intra-query parallelism can be successfully parsed in over 75% of curated datasets, unlocking up to 5x speedups on tasks like translation, comprehension, and comparative analysis, with minimal quality degradation. By releasing this benchmark, curation pipeline, and evaluation suite, we provide the first standardized testbed for studying structure-aware execution in LLM serving pipelines.

Directed acyclic graphs (DAGs) encode a lot of information about a particular distribution in their structure. However, compute required to infer these structures is typically super-exponential in the number of variables, as inference requires a sweep of a combinatorially large space of potential structures. That is, until recent advances made it possible to search this space using a differentiable metric, drastically reducing search time. While this technique -- named NOTEARS -- is widely considered a seminal work in DAG-discovery, it concedes an important property in favour of differentiability: transportability. To be transportable, the structures discovered on one dataset must apply to another dataset from the same domain. We introduce D-Struct which recovers transportability in the discovered structures through a novel architecture and loss function while remaining fully differentiable. Because D-Struct remains differentiable, our method can be easily adopted in existing differentiable architectures, as was previously done with NOTEARS. In our experiments, we empirically validate D-Struct with respect to edge accuracy and structural Hamming distance in a variety of settings.

Decompilation aims to restore compiled code to human-readable source code, but struggles with details like names and structure. Large language models (LLMs) show promise for programming tasks, motivating their application to decompilation. However, there does not exist any open-source LLM for decompilation. Moreover, existing decompilation evaluation systems mainly consider token-level accuracy and largely ignore code executability, which is the most important feature of any program. Therefore, we release the first open-access decompilation LLMs ranging from 1B to 33B pre-trained on 4 billion tokens of C source code and the corresponding assembly code. The open-source LLMs can serve as baselines for further development in the field. To ensure practical program evaluation, we introduce Decompile-Eval, the first dataset that considers re-compilability and re-executability for decompilation. The benchmark emphasizes the importance of evaluating the decompilation model from the perspective of program semantics. Experiments indicate that our LLM4Decompile has demonstrated the capability to accurately decompile 21% of the assembly code, which achieves a 50% improvement over GPT-4. Our code, dataset, and models are released at https://github.com/albertan017/LLM4Decompile

With the rapid increase in the amount of public code repositories, developers maintain a great desire to retrieve precise code snippets by using natural language. Despite existing deep learning based approaches(e.g., DeepCS and MMAN) have provided the end-to-end solutions (i.e., accepts natural language as queries and shows related code fragments retrieved directly from code corpus), the accuracy of code search in the large-scale repositories is still limited by the code representation (e.g., AST) and modeling (e.g., directly fusing the features in the attention stage). In this paper, we propose a novel learnable deep Graph for Code Search (calleddeGraphCS), to transfer source code into variable-based flow graphs based on the intermediate representation technique, which can model code semantics more precisely compared to process the code as text directly or use the syntactic tree representation. Furthermore, we propose a well-designed graph optimization mechanism to refine the code representation, and apply an improved gated graph neural network to model variable-based flow graphs. To evaluate the effectiveness of deGraphCS, we collect a large-scale dataset from GitHub containing 41,152 code snippets written in C language, and reproduce several typical deep code search methods for comparison. Besides, we design a qualitative user study to verify the practical value of our approach. The experimental results have shown that deGraphCS can achieve state-of-the-art performances, and accurately retrieve code snippets satisfying the needs of the users.

Reverse-mode differentiation is used for optimization, but it introduces references, which break the purity of the underlying programs, making them notoriously harder to optimize. We present a reverse-mode differentiation on a purely functional language with array operations. It is the first one to deliver a provably efficient, purely functional, and denotationally correct reverse-mode differentiation. We show that our transformation is semantically correct and verifies the cheap gradient principle. Inspired by PROPs and compilation to categories, we introduce a novel intermediate representation that we call 'unary form'. Our reverse-mode transformation is factored as a compilation scheme through this intermediate representation. We obtain provably efficient gradients by performing general partial evaluation optimizations after our reverse-mode transformation, as opposed to manually derived ones. For simple first-order programs, the obtained output programs resemble static-single-assignment (SSA) code. We emphasize the modularity of our approach and show how our language can easily be enriched with more optimized primitives, as required for some speed-ups in practice.

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.

Diffusion models deliver high-fidelity synthesis but remain slow due to iterative sampling. We empirically observe there exists feature invariance in deterministic sampling, and present InvarDiff, a training-free acceleration method that exploits the relative temporal invariance across timestep-scale and layer-scale. From a few deterministic runs, we compute a per-timestep, per-layer, per-module binary cache plan matrix and use a re-sampling correction to avoid drift when consecutive caches occur. Using quantile-based change metrics, this matrix specifies which module at which step is reused rather than recomputed. The same invariance criterion is applied at the step scale to enable cross-timestep caching, deciding whether an entire step can reuse cached results. During inference, InvarDiff performs step-first and layer-wise caching guided by this matrix. When applied to DiT and FLUX, our approach reduces redundant compute while preserving fidelity. Experiments show that InvarDiff achieves 2-3times end-to-end speed-ups with minimal impact on standard quality metrics. Qualitatively, we observe almost no degradation in visual quality compared with full computations.

Released Large Language Models (LLMs) are often paired with a claimed knowledge cutoff date, or the dates at which training data was gathered. Such information is crucial for applications where the LLM must provide up to date information. However, this statement only scratches the surface: do all resources in the training data share the same knowledge cutoff date? Does the model's demonstrated knowledge for these subsets closely align to their cutoff dates? In this work, we define the notion of an effective cutoff. This is distinct from the LLM designer reported cutoff and applies separately to sub-resources and topics. We propose a simple approach to estimate effective cutoffs on the resource-level temporal alignment of an LLM by probing across versions of the data. Using this analysis, we find that effective cutoffs often differ from reported cutoffs. To understand the root cause of this observation, we conduct a direct large-scale analysis on open pre-training datasets. Our analysis reveals two reasons for these inconsistencies: (1) temporal biases of CommonCrawl data due to non-trivial amounts of old data in new dumps and (2) complications in LLM deduplication schemes involving semantic duplicates and lexical near-duplicates. Overall, our results show that knowledge cutoffs are not as simple as they have seemed and that care must be taken both by LLM dataset curators as well as practitioners who seek to use information from these models.

Recently similarity graphs became the leading paradigm for efficient nearest neighbor search, outperforming traditional tree-based and LSH-based methods. Similarity graphs perform the search via greedy routing: a query traverses the graph and in each vertex moves to the adjacent vertex that is the closest to this query. In practice, similarity graphs are often susceptible to local minima, when queries do not reach its nearest neighbors, getting stuck in suboptimal vertices. In this paper we propose to learn the routing function that overcomes local minima via incorporating information about the graph global structure. In particular, we augment the vertices of a given graph with additional representations that are learned to provide the optimal routing from the start vertex to the query nearest neighbor. By thorough experiments, we demonstrate that the proposed learnable routing successfully diminishes the local minima problem and significantly improves the overall search performance.

Parallel scaling has emerged as a powerful paradigm to enhance reasoning capabilities in large language models (LLMs) by generating multiple Chain-of-Thought (CoT) traces simultaneously. However, this approach introduces significant computational inefficiency due to inter-trace redundancy -- our analysis reveals that over 80% of parallel reasoning traces yield identical final answers, representing substantial wasted computation. To address this critical efficiency bottleneck, we propose DeepPrune, a novel framework that enables efficient parallel scaling through dynamic pruning. Our method features a specialized judge model trained with focal loss and oversampling techniques to accurately predict answer equivalence from partial reasoning traces which realizes 0.87 AUROC on equivalence prediction, combined with an online greedy clustering algorithm that dynamically prunes redundant paths while preserving answer diversity. Comprehensive evaluations across three challenging benchmarks (AIME 2024, AIME 2025, and GPQA) and multiple reasoning models demonstrate that DeepPrune achieves remarkable token reduction by over 80% compared to conventional consensus sampling on most cases, while maintaining competitive accuracy within 3 percentage points. Our work establishes a new standard for efficient parallel reasoning, making high-performance reasoning more efficient. Our code and data are here: https://deepprune.github.io/

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

Instruction-following has emerged as a crucial capability for large language models (LLMs). However, existing approaches often rely on pre-existing documents or external resources to synthesize instruction-following data, which limits their flexibility and generalizability. In this paper, we introduce DecIF, a fully autonomous, meta-decomposition guided framework that generates diverse and high-quality instruction-following data using only LLMs. DecIF is grounded in the principle of decomposition. For instruction generation, we guide LLMs to iteratively produce various types of meta-information, which are then combined with response constraints to form well-structured and semantically rich instructions. We further utilize LLMs to detect and resolve potential inconsistencies within the generated instructions. Regarding response generation, we decompose each instruction into atomic-level evaluation criteria, enabling rigorous validation and the elimination of inaccurate instruction-response pairs. Extensive experiments across a wide range of scenarios and settings demonstrate DecIF's superior performance on instruction-following tasks. Further analysis highlights its strong flexibility, scalability, and generalizability in automatically synthesizing high-quality instruction data.

Decompilation transforms compiled code back into a high-level programming language for analysis when source code is unavailable. Previous work has primarily focused on enhancing decompilation performance by increasing the scale of model parameters or training data for pre-training. Based on the characteristics of the decompilation task, we propose two methods: (1) Without fine-tuning, the Self-Constructed Context Decompilation (sc^2dec) method recompiles the LLM's decompilation results to construct pairs for in-context learning, helping the model improve decompilation performance. (2) Fine-grained Alignment Enhancement (FAE), which meticulously aligns assembly code with source code at the statement level by leveraging debugging information, is employed during the fine-tuning phase to achieve further improvements in decompilation. By integrating these two methods, we achieved a Re-Executability performance improvement of approximately 7.35\% on the Decompile-Eval benchmark, establishing a new state-of-the-art performance of 55.03\%.

Extended-connectivity fingerprints (ECFPs) are a ubiquitous tool in current cheminformatics and molecular machine learning, and one of the most prevalent molecular feature extraction techniques used for chemical prediction. Atom features learned by graph neural networks can be aggregated to compound-level representations using a large spectrum of graph pooling methods; in contrast, sets of detected ECFP substructures are by default transformed into bit vectors using only a simple hash-based folding procedure. We introduce a general mathematical framework for the vectorisation of structural fingerprints via a formal operation called substructure pooling that encompasses hash-based folding, algorithmic substructure-selection, and a wide variety of other potential techniques. We go on to describe Sort & Slice, an easy-to-implement and bit-collision-free alternative to hash-based folding for the pooling of ECFP substructures. Sort & Slice first sorts ECFP substructures according to their relative prevalence in a given set of training compounds and then slices away all but the L most frequent substructures which are subsequently used to generate a binary fingerprint of desired length, L. We computationally compare the performance of hash-based folding, Sort & Slice, and two advanced supervised substructure-selection schemes (filtering and mutual-information maximisation) for ECFP-based molecular property prediction. Our results indicate that, despite its technical simplicity, Sort & Slice robustly (and at times substantially) outperforms traditional hash-based folding as well as the other investigated methods across prediction tasks, data splitting techniques, machine-learning models and ECFP hyperparameters. We thus recommend that Sort & Slice canonically replace hash-based folding as the default substructure-pooling technique to vectorise ECFPs for supervised molecular machine learning.

The linear growth of key-value (KV) cache memory and quadratic computational complexity pose significant bottlenecks for large language models (LLMs) in long-context processing. While existing KV cache optimization methods address these challenges through token pruning or feature merging, they often suffer from irreversible information loss or require costly parameter retraining. We propose ZeroMerge, a dynamic zero-shot compression framework that achieves efficient cache management through three key innovations: (1) Fine-grained memory allocation guided by multi-dimensional token importance metrics at head-level granularity, (2) A residual merging mechanism that preserves critical context through compensated attention scoring, and (3) Parameter-free adaptation compatible with diverse LLM architectures without retraining. Comprehensive evaluations across LLaMA-2 model demonstrate that ZeroMerge maintains full-cache performance at 5\% compression ratios while doubling inference throughput at 40K token lengths. The method effectively balances memory efficiency, generation quality, and deployment flexibility, advancing practical long-context LLM applications. The code is available at https://github.com/SusCom-Lab/ZeroMerge.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Retrieval-Augmented Generation (RAG) is often used with Large Language Models (LLMs) to infuse domain knowledge or user-specific information. In RAG, given a user query, a retriever extracts chunks of relevant text from a knowledge base. These chunks are sent to an LLM as part of the input prompt. Typically, any given chunk is repeatedly retrieved across user questions. However, currently, for every question, attention-layers in LLMs fully compute the key values (KVs) repeatedly for the input chunks, as state-of-the-art methods cannot reuse KV-caches when chunks appear at arbitrary locations with arbitrary contexts. Naive reuse leads to output quality degradation. This leads to potentially redundant computations on expensive GPUs and increases latency. In this work, we propose Cache-Craft, a system for managing and reusing precomputed KVs corresponding to the text chunks (we call chunk-caches) in RAG-based systems. We present how to identify chunk-caches that are reusable, how to efficiently perform a small fraction of recomputation to fix the cache to maintain output quality, and how to efficiently store and evict chunk-caches in the hardware for maximizing reuse while masking any overheads. With real production workloads as well as synthetic datasets, we show that Cache-Craft reduces redundant computation by 51% over SOTA prefix-caching and 75% over full recomputation. Additionally, with continuous batching on a real production workload, we get a 1.6X speed up in throughput and a 2X reduction in end-to-end response latency over prefix-caching while maintaining quality, for both the LLaMA-3-8B and LLaMA-3-70B models.

Code clones are semantically similar code fragments pairs that are syntactically similar or different. Detection of code clones can help to reduce the cost of software maintenance and prevent bugs. Numerous approaches of detecting code clones have been proposed previously, but most of them focus on detecting syntactic clones and do not work well on semantic clones with different syntactic features. To detect semantic clones, researchers have tried to adopt deep learning for code clone detection to automatically learn latent semantic features from data. Especially, to leverage grammar information, several approaches used abstract syntax trees (AST) as input and achieved significant progress on code clone benchmarks in various programming languages. However, these AST-based approaches still can not fully leverage the structural information of code fragments, especially semantic information such as control flow and data flow. To leverage control and data flow information, in this paper, we build a graph representation of programs called flow-augmented abstract syntax tree (FA-AST). We construct FA-AST by augmenting original ASTs with explicit control and data flow edges. Then we apply two different types of graph neural networks (GNN) on FA-AST to measure the similarity of code pairs. As far as we have concerned, we are the first to apply graph neural networks on the domain of code clone detection. We apply our FA-AST and graph neural networks on two Java datasets: Google Code Jam and BigCloneBench. Our approach outperforms the state-of-the-art approaches on both Google Code Jam and BigCloneBench tasks.

We introduce HoloClean, a framework for holistic data repairing driven by probabilistic inference. HoloClean unifies existing qualitative data repairing approaches, which rely on integrity constraints or external data sources, with quantitative data repairing methods, which leverage statistical properties of the input data. Given an inconsistent dataset as input, HoloClean automatically generates a probabilistic program that performs data repairing. Inspired by recent theoretical advances in probabilistic inference, we introduce a series of optimizations which ensure that inference over HoloClean's probabilistic model scales to instances with millions of tuples. We show that HoloClean scales to instances with millions of tuples and find data repairs with an average precision of ~90% and an average recall of above ~76% across a diverse array of datasets exhibiting different types of errors. This yields an average F1 improvement of more than 2x against state-of-the-art methods.

Assessing similarity in source code has gained significant attention in recent years due to its importance in software engineering tasks such as clone detection and code search and recommendation. This work presents a comparative analysis of unsupervised similarity measures for identifying source code clone detection. The goal is to overview the current state-of-the-art techniques, their strengths, and weaknesses. To do that, we compile the existing unsupervised strategies and evaluate their performance on a benchmark dataset to guide software engineers in selecting appropriate methods for their specific use cases. The source code of this study is available at https://github.com/jorge-martinez-gil/codesim

Multimodal models have demonstrated powerful capabilities in complex tasks requiring multimodal alignment including zero-shot classification and cross-modal retrieval. However, existing models typically rely on millions of paired multimodal samples, which are prohibitively expensive or infeasible to obtain in many domains. In this work, we explore the feasibility of building multimodal models with limited amount of paired data by aligning pretrained unimodal foundation models. We show that high-quality alignment is possible with as few as tens of thousands of paired samplesx2013less than 1% of the data typically used in the field. To achieve this, we introduce STRUCTURE, an effective regularization technique that preserves the neighborhood geometry of the latent space of unimodal encoders. Additionally, we show that aligning last layers is often suboptimal and demonstrate the benefits of aligning the layers with the highest representational similarity across modalities. These two components can be readily incorporated into existing alignment methods, yielding substantial gains across 24 zero-shot image classification and retrieval benchmarks, with average relative improvement of 51.6% in classification and 91.8% in retrieval tasks. Our results highlight the effectiveness and broad applicability of our framework for limited-sample multimodal learning and offer a promising path forward for resource-constrained domains.

Establishing precise traceability between embedded systems datasheets and their corresponding code implementations remains a fundamental challenge in systems engineering, particularly for low-level software where manual mapping between specification documents and large code repositories is infeasible. Existing Traceability Link Recovery approaches primarily rely on lexical similarity and information retrieval techniques, which struggle to capture the semantic, structural, and symbol level relationships prevalent in embedded systems software. We present a hierarchical datasheet-to-code mapping methodology that employs large language models for semantic analysis while explicitly structuring the traceability process across multiple abstraction levels. Rather than performing direct specification-to-code matching, the proposed approach progressively narrows the search space through repository-level structure inference, file-level relevance estimation, and fine-grained symbollevel alignment. The method extends beyond function-centric mapping by explicitly covering macros, structs, constants, configuration parameters, and register definitions commonly found in systems-level C/C++ codebases. We evaluate the approach on multiple open-source embedded systems repositories using manually curated datasheet-to-code ground truth. Experimental results show substantial improvements over traditional information-retrieval-based baselines, achieving up to 73.3% file mapping accuracy. We significantly reduce computational overhead, lowering total LLM token consumption by 84% and end-to-end runtime by approximately 80%. This methodology supports automated analysis of large embedded software systems and enables downstream applications such as training data generation for systems-aware machine learning models, standards compliance verification, and large-scale specification coverage analysis.

The Text-to-SQL task, aiming to translate the natural language of the questions into SQL queries, has drawn much attention recently. One of the most challenging problems of Text-to-SQL is how to generalize the trained model to the unseen database schemas, also known as the cross-domain Text-to-SQL task. The key lies in the generalizability of (i) the encoding method to model the question and the database schema and (ii) the question-schema linking method to learn the mapping between words in the question and tables/columns in the database schema. Focusing on the above two key issues, we propose a Structure-Aware Dual Graph Aggregation Network (SADGA) for cross-domain Text-to-SQL. In SADGA, we adopt the graph structure to provide a unified encoding model for both the natural language question and database schema. Based on the proposed unified modeling, we further devise a structure-aware aggregation method to learn the mapping between the question-graph and schema-graph. The structure-aware aggregation method is featured with Global Graph Linking, Local Graph Linking, and Dual-Graph Aggregation Mechanism. We not only study the performance of our proposal empirically but also achieved 3rd place on the challenging Text-to-SQL benchmark Spider at the time of writing.

Graph-based Retrieval-Augmented Generation (Graph-RAG) enhances large language models (LLMs) by structuring retrieval over an external corpus. However, existing approaches typically assume a static corpus, requiring expensive full-graph reconstruction whenever new documents arrive, limiting their scalability in dynamic, evolving environments. To address these limitations, we introduce EraRAG, a novel multi-layered Graph-RAG framework that supports efficient and scalable dynamic updates. Our method leverages hyperplane-based Locality-Sensitive Hashing (LSH) to partition and organize the original corpus into hierarchical graph structures, enabling efficient and localized insertions of new data without disrupting the existing topology. The design eliminates the need for retraining or costly recomputation while preserving high retrieval accuracy and low latency. Experiments on large-scale benchmarks demonstrate that EraRag achieves up to an order of magnitude reduction in update time and token consumption compared to existing Graph-RAG systems, while providing superior accuracy performance. This work offers a practical path forward for RAG systems that must operate over continually growing corpora, bridging the gap between retrieval efficiency and adaptability. Our code and data are available at https://github.com/EverM0re/EraRAG-Official.

Projection maintenance is one of the core data structure tasks. Efficient data structures for projection maintenance have led to recent breakthroughs in many convex programming algorithms. In this work, we further extend this framework to the Kronecker product structure. Given a constraint matrix {sf A} and a positive semi-definite matrix Win R^{ntimes n} with a sparse eigenbasis, we consider the task of maintaining the projection in the form of {sf B}^top({sf B}{sf B}^top)^{-1}{sf B}, where {sf B}={sf A}(Wotimes I) or {sf B}={sf A}(W^{1/2}otimes W^{1/2}). At each iteration, the weight matrix W receives a low rank change and we receive a new vector h. The goal is to maintain the projection matrix and answer the query {sf B}^top({sf B}{sf B}^top)^{-1}{sf B}h with good approximation guarantees. We design a fast dynamic data structure for this task and it is robust against an adaptive adversary. Following the beautiful and pioneering work of [Beimel, Kaplan, Mansour, Nissim, Saranurak and Stemmer, STOC'22], we use tools from differential privacy to reduce the randomness required by the data structure and further improve the running time.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Recently, deep learning techniques have shown great success in automatic code generation. Inspired by the code reuse, some researchers propose copy-based approaches that can copy the content from similar code snippets to obtain better performance. Practically, human developers recognize the content in the similar code that is relevant to their needs, which can be viewed as a code sketch. The sketch is further edited to the desired code. However, existing copy-based approaches ignore the code sketches and tend to repeat the similar code without necessary modifications, which leads to generating wrong results. In this paper, we propose a sketch-based code generation approach named SkCoder to mimic developers' code reuse behavior. Given a natural language requirement, SkCoder retrieves a similar code snippet, extracts relevant parts as a code sketch, and edits the sketch into the desired code. Our motivations are that the extracted sketch provides a well-formed pattern for telling models "how to write". The post-editing further adds requirement-specific details to the sketch and outputs the complete code. We conduct experiments on two public datasets and a new dataset collected by this work. We compare our approach to 20 baselines using 5 widely used metrics. Experimental results show that (1) SkCoder can generate more correct programs, and outperforms the state-of-the-art - CodeT5-base by 30.30%, 35.39%, and 29.62% on three datasets. (2) Our approach is effective to multiple code generation models and improves them by up to 120.1% in Pass@1. (3) We investigate three plausible code sketches and discuss the importance of sketches. (4) We manually evaluate the generated code and prove the superiority of our SkCoder in three aspects.

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.

Non-exemplar class-incremental learning is to recognize both the old and new classes when old class samples cannot be saved. It is a challenging task since representation optimization and feature retention can only be achieved under supervision from new classes. To address this problem, we propose a novel self-sustaining representation expansion scheme. Our scheme consists of a structure reorganization strategy that fuses main-branch expansion and side-branch updating to maintain the old features, and a main-branch distillation scheme to transfer the invariant knowledge. Furthermore, a prototype selection mechanism is proposed to enhance the discrimination between the old and new classes by selectively incorporating new samples into the distillation process. Extensive experiments on three benchmarks demonstrate significant incremental performance, outperforming the state-of-the-art methods by a margin of 3%, 3% and 6%, respectively.

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

Evolutionary model merging enables the creation of high-performing multi-task models but remains computationally prohibitive for consumer hardware. We introduce MERGE^3, an efficient framework that makes evolutionary merging feasible on a single GPU by reducing fitness computation costs 50times while preserving performance. MERGE^3 achieves this by Extracting a reduced dataset for evaluation, Estimating model abilities using Item Response Theory (IRT), and Evolving optimal merges via IRT-based performance estimators. Our method enables state-of-the-art multilingual and cross-lingual merging, transferring knowledge across languages with significantly lower computational overhead. We provide theoretical guarantees and an open-source library, democratizing high-quality model merging.

We present a static token lookup methodology for text embedding generation that achieves 1.12 ms p50 latency for single text embeddings while maintaining 60.6 MTEB average score across 8 representative tasks, corresponding to 89% of contextual model quality. The Rust implementation delivers 50,000 requests per second throughput through static embedding lookup, optimized mean pooling, and zero-copy IEEE754 binary serialization. Evaluation demonstrates exceptional duplicate detection performance (90.1% AP), strong semantic similarity (76.1% Spearman correlation), and domain-specific performance ranging from 75% to 131% of baseline across specialized domains. The system enables real-time embedding applications where sub-5ms latency is critica

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

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

The size of large language models (LLMs) has scaled dramatically in recent years and their computational and data requirements have surged correspondingly. State-of-the-art language models, even at relatively smaller sizes, typically require training on at least a trillion tokens. This rapid advancement has eclipsed the growth of open-source datasets available for large-scale LLM pretraining. In this paper, we introduce Zyda (Zyphra Dataset), a dataset under a permissive license comprising 1.3 trillion tokens, assembled by integrating several major respected open-source datasets into a single, high-quality corpus. We apply rigorous filtering and deduplication processes, both within and across datasets, to maintain and enhance the quality derived from the original datasets. Our evaluations show that Zyda not only competes favorably with other open datasets like Dolma, FineWeb, and RefinedWeb, but also substantially improves the performance of comparable models from the Pythia suite. Our rigorous data processing methods significantly enhance Zyda's effectiveness, outperforming even the best of its constituent datasets when used independently.

It has been observed that representations learned by distinct neural networks conceal structural similarities when the models are trained under similar inductive biases. From a geometric perspective, identifying the classes of transformations and the related invariances that connect these representations is fundamental to unlocking applications, such as merging, stitching, and reusing different neural modules. However, estimating task-specific transformations a priori can be challenging and expensive due to several factors (e.g., weights initialization, training hyperparameters, or data modality). To this end, we introduce a versatile method to directly incorporate a set of invariances into the representations, constructing a product space of invariant components on top of the latent representations without requiring prior knowledge about the optimal invariance to infuse. We validate our solution on classification and reconstruction tasks, observing consistent latent similarity and downstream performance improvements in a zero-shot stitching setting. The experimental analysis comprises three modalities (vision, text, and graphs), twelve pretrained foundational models, nine benchmarks, and several architectures trained from scratch.

Text-driven image editing has achieved remarkable success in following single instructions. However, real-world scenarios often involve complex, multi-step instructions, particularly ``chain'' instructions where operations are interdependent. Current models struggle with these intricate directives, and existing benchmarks inadequately evaluate such capabilities. Specifically, they often overlook multi-instruction and chain-instruction complexities, and common consistency metrics are flawed. To address this, we introduce ComplexBench-Edit, a novel benchmark designed to systematically assess model performance on complex, multi-instruction, and chain-dependent image editing tasks. ComplexBench-Edit also features a new vision consistency evaluation method that accurately assesses non-modified regions by excluding edited areas. Furthermore, we propose a simple yet powerful Chain-of-Thought (CoT)-based approach that significantly enhances the ability of existing models to follow complex instructions. Our extensive experiments demonstrate ComplexBench-Edit's efficacy in differentiating model capabilities and highlight the superior performance of our CoT-based method in handling complex edits. The data and code are released at https://github.com/llllly26/ComplexBench-Edit.

Instruction tuning has recently been recognized as an effective way of aligning Large Language Models (LLMs) to enhance their generalization ability across various tasks. However, when tuning publicly accessible, centralized LLMs with private instruction data, privacy concerns are inevitable. While direct transfer of parameterized modules between models is a plausible approach to address this, its implications and effectiveness need further exploration. This paper focuses on Offsite-Tuning (OFT), a representative technique that transfers transformer blocks between centralized LLMs and downstream emulators. Given the limited understanding of the underlying mechanism of OFT, we perform an empirical analysis on LLMs from the perspectives of representation and functional similarity. Interestingly, our findings reveal a unique modular structure within the layers of LLMs that appears to emerge as the model size expands. Simultaneously, we note subtle but potentially significant changes in representation and intermediate predictions across the layers. Inspired by these observations, we propose CRaSh, involving Clustering, Removing, and Sharing, a training-free strategy to derive improved emulators from LLMs. CRaSh significantly boosts performance of OFT with billions of parameters. Furthermore, we investigate the optimal solutions yielded by fine-tuning with and without full model through the lens of loss landscape. Our findings demonstrate a linear connectivity among these optima falling over the same basin, thereby highlighting the effectiveness of CRaSh and OFT. The source code is publicly available at https://github.com/TsinghuaC3I/CRaSh.

Parameter-efficient transfer learning (PETL) aims to reduce the scales of pretrained models for multiple downstream tasks. However, as the models keep scaling up, the memory footprint of existing PETL methods is not significantly reduced compared to the reduction of learnable parameters. This limitation hinders the practical deployment of PETL methods on memory-constrained devices. To this end, we proposed a new PETL framework, called Structure to Activation (S2A), to reduce the memory footprint of activation during fine-tuning. Specifically, our framework consists of: 1) Activation modules design(i.e., bias, prompt and side modules) in the parametric model structure, which results in a significant reduction of adjustable parameters and activation memory; 2) 4-bit quantization of activations based on their derivatives for non-parametric structures (e.g., nonlinear functions), which maintains accuracy while significantly reducing memory usage. Our S2A method consequently offers a lightweight solution in terms of both parameters and memory footprint. We evaluated S2A with different backbones and performed extensive experiments on various datasets to evaluate the effectiveness. The results show that our methods not only outperform existing PETL techniques, achieving a fourfold reduction in GPU memory footprint on average, but also shows competitive performance in accuracy with fewer tunable parameters. These demonstrate that our method is highly suitable for practical transfer learning on hardware-constrained devices.

Structural pruning enhances hardware-agnostic inference efficiency for large language models (LLMs) yet often fails to maintain comparable performance. Local pruning performs efficient layer-by-layer compression but ignores global topology. Although global pruning aims to identify an optimal sparse model, intuitive methods typically adopt a two-stage paradigm that first evaluates substructure saliency and then applies global pruning, which ignores inter-structure dependencies and fails to achieve end-to-end optimization. To address these limitations, we propose T\'yr-the-Pruner, an efficient end-to-end search-based global structural pruning framework. This framework constructs a supernet by repeatedly applying local pruning across a range of sparsity ratios to each layer in an LLM, with the core goal of determining the optimal sparsity distribution under a target overall sparsity ratio. Concretely, we introduce an effective local pruning and an expectation error accumulation approach to improve supernet construction. Furthermore, we employ an iterative prune-and-search strategy with coarse-to-fine sparsity granularity to ensure efficient search convergence. Experimental results show that T\'yr-the-Pruner achieves state-of-the-art structural pruning, retaining 97% of the dense model's performance while removing a challenging 50% of Llama-3.1-70B's parameters. Code will be available at https://github.com/AMD-AGI/Tyr-the-Pruner.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

How to efficiently serve Large Language Models (LLMs) has become a pressing issue because of their huge computational cost in their autoregressive generation process. To mitigate computational costs, LLMs often employ the KV Cache technique to improve the generation speed. While improving the computational efficiency, the storage requirements of the KV cache are substantial, particularly in long-context scenarios, leading to significant memory consumption. Existing KV cache eviction methods often degrade the performance of LLMs in long-context scenarios due to the information loss introduced by eviction. In this paper, we propose a novel KV cache merging approach, called KVMerger, to achieve adaptive KV cache compression for long-context tasks without significant performance degradation under constrained memory budgets. Our approach is inspired by the intriguing observation that key states exhibit high similarity at the token level within a single sequence. To facilitate merging, we develop an effective yet straightforward merging set identification algorithm to identify suitable KV states for merging. Our merging set identification algorithm stimulates the second observation that KV cache sparsity, from similarity perspective, is independent of the dataset and remains persistent at the model level. Subsequently, we propose a Gaussian kernel weighted merging algorithm to selectively merge all states within each merging set. We conduct extensive experiments to demonstrate the effectiveness of KVMerger for long-context tasks under constrained memory budgets, applying it to models including Llama2-7B-chat and Llama2-13B-chat. Using the LongBench and ZeroScroll benchmarks, we compare our method with other KV cache compression techniques, including H2O and CaM, showing that our method achieves superior performance across tasks with both 50% and 35% KV cache budgets.

Differentially private (DP) synthetic data generation is a promising technique for utilizing private datasets that otherwise cannot be exposed for model training or other analytics. While much research literature has focused on generating private unstructured text and image data, in enterprise settings, structured data (e.g., tabular) is more common, often including natural language fields or components. Existing synthetic data evaluation techniques (e.g., FID) struggle to capture the structural properties and correlations of such datasets. In this work, we propose Struct-Bench, a framework and benchmark for evaluating synthetic datasets derived from structured datasets that contain natural language data. The Struct-Bench framework requires users to provide a representation of their dataset structure as a Context-Free Grammar (CFG). Our benchmark comprises 5 real-world and 2 synthetically generated datasets, each annotated with CFGs. We show that these datasets demonstrably present a great challenge even for state-of-the-art DP synthetic data generation methods. Struct-Bench also includes reference implementations of different metrics and a leaderboard, thereby providing researchers a standardized evaluation platform to benchmark and investigate privacy-preserving synthetic data generation methods. Further, we also present a case study showing how to use Struct-Bench to improve the synthetic data quality of Private Evolution (PE) on structured data. The benchmark and the leaderboard have been publicly made available at https://struct-bench.github.io.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

We introduce CopySpec, an innovative technique designed to tackle the inefficiencies LLMs face when generating responses that closely resemble previous outputs. CopySpec identifies repeated sequences in the model's chat history and speculates that the same tokens will follow, enabling seamless copying without compromising output quality or requiring additional GPU memory. To evaluate the effectiveness of our approach, we conducted experiments using five LLMs and five datasets: MT-Bench, CNN/DM, GSM-8K, HumanEval, and our newly created dataset, MT-Redundant. MT-Redundant, introduced in this paper, transforms the second turn of MT-Bench into a request for variations of the first turn's answer, simulating real-world scenarios where users request modifications to prior responses. Our results demonstrate significant speed-ups: up to 2.35x on CNN/DM, 3.08x on the second turn of select MT-Redundant categories, and 2.66x on the third turn of GSM-8K's self-correction tasks. Moreover, we show that CopySpec integrates seamlessly with speculative decoding, yielding an average 49% additional speed-up over speculative decoding for the second turn of MT-Redundant across all eight categories. While LLMs, even with speculative decoding, suffer from slower inference as context sizes grow, CopySpec leverages the expanded context to accelerate inference, making it faster as the context size increases. Our code and dataset are publicly available at https://github.com/RazvanDu/CopySpec.

Large language models store all learned knowledge in a single, fixed weight vector. Teaching a model new capabilities requires modifying those same weights, inevitably degrading previously acquired knowledge. This fundamental limitation, known as catastrophic forgetting, has resisted principled solutions for decades. Existing approaches treat weights as immutable artifacts that must be protected through techniques like regularization heuristics, replay buffers, or isolated adapter modules. The problem is none of these provide a structural guarantee against forgetting. In this work, we propose Non-Interfering Weight Fields (NIWF), a framework that replaces the fixed weight paradigm with a learned function that generates weight configurations on demand from a continuous capability coordinate space. After training on a task, we commit the occupied coordinate region by snapshotting the fields outputs on anchor points to enforce a functional lock during all future training. We validate NIWF on sequential instructionfollowing and code generation tasks using Mistral-7B, demonstrating zero forgetting on committed tasks with competitive perplexity on new tasks. The framework introduces the notion of software-like versioning for neural network intelligence, where capabilities can be committed, extended, composed, and rolled back without retraining.

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

Data quality and diversity are key to the construction of effective instruction-tuning datasets. % With the increasing availability of open-source instruction-tuning datasets, it is advantageous to automatically select high-quality and diverse subsets from a vast amount of data. % Existing methods typically prioritize instance quality and use heuristic rules to maintain diversity. % However, this absence of a comprehensive view of the entire collection often leads to suboptimal results. % Moreover, heuristic rules generally focus on distance or clustering within the embedding space, which fails to accurately capture the intent of complex instructions in the semantic space. % To bridge this gap, we propose a unified method for quantifying the information content of datasets. This method models the semantic space by constructing a label graph and quantifies diversity based on the distribution of information within the graph. % Based on such a measurement, we further introduce an efficient sampling method that selects data samples iteratively to Maximize the Information Gain (MIG) in semantic space. % Experiments on various datasets and base models demonstrate that MIG consistently outperforms state-of-the-art methods. % Notably, the model fine-tuned with 5\% Tulu3 data sampled by MIG achieves comparable performance to the official SFT model trained on the full dataset, with improvements of +5.73\% on AlpacaEval and +6.89\% on Wildbench.

Recent advances in retrieval-augmented generation (RAG) have initiated a new era in repository-level code completion. However, the invariable use of retrieval in existing methods exposes issues in both efficiency and robustness, with a large proportion of the retrieved contexts proving unhelpful or harmful to code language models (code LMs). In this paper, we propose a selective RAG framework to avoid retrieval when unnecessary. To power this framework, we design a self-supervised learning approach to enable a code LM to accurately self-evaluate whether retrieval can improve its output quality and robustly leverage the potentially noisy retrieved contexts. Using this LM as both the selective RAG policy and the generation model, our framework achieves state-of-the-art repository-level code completion performance on diverse benchmarks including RepoEval, CrossCodeEval, and CrossCodeLongEval, a new long-form code completion benchmark. Meanwhile, our analyses show that selectively retrieving brings as much as 70% inference speedup in the online serving setting without harming the performance. We further demonstrate that our framework is able to accommodate different generation models, retrievers, and programming languages. These advancements position our framework as an important step towards more accurate and efficient repository-level code completion.

As large language models (LLMs) continue to scale, the memory footprint of key-value (KV) caches during inference has become a significant bottleneck. Existing approaches primarily focus on compressing KV caches within a single prompt or reusing shared prefixes or frequently ocurred text segments across prompts. However, such strategies are limited in scenarios where prompts are semantically similar but lexically different, which frequently occurs in tasks such as multi-document summarization and conversational agents. We propose SemShareKV, a KV cache sharing and compression framework that accelerates LLM inference by reusing KVCache in semantically similar prompts. Instead of relying on exact token matches, SemShareKV applies fuzzy token matching using locality-sensitive hashing (LSH) on token embeddings and incorporates Rotary Position Embedding (RoPE) to better preserve positional information. By selectively reusing relevant key-value pairs from a reference prompt's cache, SemShareKV reduces redundant computation while maintaining output quality. Experiments on diverse summarization datasets show up to 6.25times speedup and 42\% lower GPU memory usage with 5k tokens input, with negligible quality degradation. These results highlight the potential of semantic-aware cache sharing for efficient LLM inference.

Machine unlearning aims to remove specific content from trained models while preserving overall performance. However, the phenomenon of benign relearning, in which forgotten information reemerges even from benign fine-tuning data, reveals that existing unlearning methods remain fundamentally fragile. A common explanation attributes this effect to topical relevance, but we find this account insufficient. Through systematic analysis, we demonstrate that syntactic similarity, rather than topicality, is the primary driver: across benchmarks, syntactically similar data consistently trigger recovery even without topical overlap, due to their alignment in representations and gradients with the forgotten content. Motivated by this insight, we introduce syntactic diversification, which paraphrases the original forget queries into heterogeneous structures prior to unlearning. This approach effectively suppresses benign relearning, accelerates forgetting, and substantially alleviates the trade-off between unlearning efficacy and model utility.

The BigCode project is an open-scientific collaboration working on the responsible development of large language models for code. This tech report describes the progress of the collaboration until December 2022, outlining the current state of the Personally Identifiable Information (PII) redaction pipeline, the experiments conducted to de-risk the model architecture, and the experiments investigating better preprocessing methods for the training data. We train 1.1B parameter models on the Java, JavaScript, and Python subsets of The Stack and evaluate them on the MultiPL-E text-to-code benchmark. We find that more aggressive filtering of near-duplicates can further boost performance and, surprisingly, that selecting files from repositories with 5+ GitHub stars deteriorates performance significantly. Our best model outperforms previous open-source multilingual code generation models (InCoder-6.7B and CodeGen-Multi-2.7B) in both left-to-right generation and infilling on the Java, JavaScript, and Python portions of MultiPL-E, despite being a substantially smaller model. All models are released under an OpenRAIL license at https://hf.co/bigcode.

In the era of large-scale training, model merging has evolved into a tool for creating multitasking models efficiently. It enables the knowledge of models to be fused, without the need for heavy computation as required in traditional multitask learning. Existing merging methods often assume that entries at identical positions in weight matrices serve the same function, enabling straightforward entry-wise comparison and merging. However, this assumption overlooks the complexity of finetuned neural networks, where neurons may develop distinct feature compositions, making direct entry-wise merging problematic. We present Decom-Renorm-Merge (DRM), a simple yet effective approach that leverages Singular Value Decomposition to decompose and coordinate weight matrices into an aligned joint space, where entry-wise merging becomes possible. We showcase the effectiveness of DRM across various settings ranging from smaller encoder-based such as ViT and DeBERTa, encoder-decoder-based such as T5, and larger decoder-based such as Llama3.1-8B. Our experimental results show that DRM outperforms several state-of-the-art merging techniques across full finetuning and low-rank adaptation settings. Moreover, our analysis reveals renormalization as the crucial component for creating a robust and even joint space for merging, significantly contributing to the method's performance.

Deep ensemble methods often improve predictive performance, yet they suffer from three practical limitations: redundancy among base models that inflates computational cost and degrades conditioning, unstable weighting under multicollinearity, and overfitting in meta-learning pipelines. We propose a regularized meta-learning framework that addresses these challenges through a four-stage pipeline combining redundancy-aware projection, statistical meta-feature augmentation, and cross-validated regularized meta-models (Ridge, Lasso, and ElasticNet). Our multi-metric de-duplication strategy removes near-collinear predictors using correlation and MSE thresholds (τ_{corr}=0.95), reducing the effective condition number of the meta-design matrix while preserving predictive diversity. Engineered ensemble statistics and interaction terms recover higher-order structure unavailable to raw prediction columns. A final inverse-RMSE blending stage mitigates regularizer-selection variance. On the Playground Series S6E1 benchmark (100K samples, 72 base models), the proposed framework achieves an out-of-fold RMSE of 8.582, improving over simple averaging (8.894) and conventional Ridge stacking (8.627), while matching greedy hill climbing (8.603) with substantially lower runtime (4 times faster). Conditioning analysis shows a 53.7\% reduction in effective matrix condition number after redundancy projection. Comprehensive ablations demonstrate consistent contributions from de-duplication, statistical meta-features, and meta-ensemble blending. These results position regularized meta-learning as a stable and deployment-efficient stacking strategy for high-dimensional ensemble systems.

Existing Text-to-SQL generators require the entire schema to be encoded with the user text. This is expensive or impractical for large databases with tens of thousands of columns. Standard dense retrieval techniques are inadequate for schema subsetting of a large structured database, where the correct semantics of retrieval demands that we rank sets of schema elements rather than individual elements. In response, we propose a two-stage process for effective coverage during retrieval. First, we instruct an LLM to hallucinate a minimal DB schema deemed adequate to answer the query. We use the hallucinated schema to retrieve a subset of the actual schema, by composing the results from multiple dense retrievals. Remarkably, hallucination x2013 generally considered a nuisance x2013 turns out to be actually useful as a bridging mechanism. Since no existing benchmarks exist for schema subsetting on large databases, we introduce three benchmarks. Two semi-synthetic datasets are derived from the union of schemas in two well-known datasets, SPIDER and BIRD, resulting in 4502 and 798 schema elements respectively. A real-life benchmark called SocialDB is sourced from an actual large data warehouse comprising 17844 schema elements. We show that our method1 leads to significantly higher recall than SOTA retrieval-based augmentation methods.

Structured pruning is one of the most popular approaches to effectively compress the heavy deep neural networks (DNNs) into compact sub-networks while retaining performance. The existing methods suffer from multi-stage procedures along with significant engineering efforts and human expertise. The Only-Train-Once (OTO) series has been recently proposed to resolve the many pain points by streamlining the workflow by automatically conducting (i) search space generation, (ii) structured sparse optimization, and (iii) sub-network construction. However, the built-in sparse optimizers in the OTO series, i.e., the Half-Space Projected Gradient (HSPG) family, have limitations that require hyper-parameter tuning and the implicit controls of the sparsity exploration, consequently requires intervening by human expertise. To address such limitations, we propose a Hybrid Efficient Structured Sparse Optimizer (HESSO). HESSO could automatically and efficiently train a DNN to produce a high-performing subnetwork. Meanwhile, it is almost tuning-free and enjoys user-friendly integration for generic training applications. To address another common issue of irreversible performance collapse observed in pruning DNNs, we further propose a Corrective Redundant Identification Cycle (CRIC) for reliably identifying indispensable structures. We numerically demonstrate the efficacy of HESSO and its enhanced version HESSO-CRIC on a variety of applications ranging from computer vision to natural language processing, including large language model. The numerical results showcase that HESSO can achieve competitive even superior performance to varying state-of-the-arts and support most DNN architectures. Meanwhile, CRIC can effectively prevent the irreversible performance collapse and further enhance the performance of HESSO on certain applications. The code is available at https://github.com/microsoft/only_train_once.

Evaluating tabular generators remains a challenging problem, as the unique causal structural prior of heterogeneous tabular data does not lend itself to intuitive human inspection. Recent work has introduced structural fidelity as a tabular-specific evaluation dimension to assess whether synthetic data complies with the causal structures of real data. However, existing benchmarks often neglect the interplay between structural fidelity and conventional evaluation dimensions, thus failing to provide a holistic understanding of model performance. Moreover, they are typically limited to toy datasets, as quantifying existing structural fidelity metrics requires access to ground-truth causal structures, which are rarely available for real-world datasets. In this paper, we propose a novel evaluation framework that jointly considers structural fidelity and conventional evaluation dimensions. We introduce a new evaluation metric, global utility, which enables the assessment of structural fidelity even in the absence of ground-truth causal structures. In addition, we present TabStruct, a comprehensive evaluation benchmark offering large-scale quantitative analysis on 13 tabular generators from nine distinct categories, across 29 datasets. Our results demonstrate that global utility provides a task-independent, domain-agnostic lens for tabular generator performance. We release the TabStruct benchmark suite, including all datasets, evaluation pipelines, and raw results. Code is available at https://github.com/SilenceX12138/TabStruct.

The statistical distribution of content uploaded and searched on media sharing sites changes over time due to seasonal, sociological and technical factors. We investigate the impact of this "content drift" for large-scale similarity search tools, based on nearest neighbor search in embedding space. Unless a costly index reconstruction is performed frequently, content drift degrades the search accuracy and efficiency. The degradation is especially severe since, in general, both the query and database distributions change. We introduce and analyze real-world image and video datasets for which temporal information is available over a long time period. Based on the learnings, we devise DeDrift, a method that updates embedding quantizers to continuously adapt large-scale indexing structures on-the-fly. DeDrift almost eliminates the accuracy degradation due to the query and database content drift while being up to 100x faster than a full index reconstruction.

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.

Recently, Test-Time Scaling (TTS) has gained increasing attention for improving LLM reasoning performance at test time without retraining the model. A notable TTS technique is Self-Consistency (SC), which generates multiple reasoning chains in parallel and selects the final answer via majority voting. While effective, the order-of-magnitude computational overhead limits its broad deployment. Prior attempts to accelerate SC mainly rely on model-based confidence scores or heuristics with limited empirical support. For the first time, we theoretically and empirically analyze the inefficiencies of SC and reveal actionable opportunities for improvement. Building on these insights, we propose Slim-SC, a step-wise pruning strategy that identifies and removes redundant chains using inter-chain similarity at the thought level. Experiments on three STEM reasoning datasets and two recent LLM architectures show that Slim-SC reduces inference latency and KVC usage by up to 45% and 26%, respectively, with R1-Distill, while maintaining or improving accuracy, thus offering a simple yet efficient TTS alternative for SC.

Current language models tailored for code tasks often adopt the pre-training-then-fine-tuning paradigm from natural language processing, modeling source code as plain text. This approach, however, overlooks the unambiguous structures inherent in programming languages. In this work, we explore data-efficient adaptation of pre-trained code models by further pre-training and fine-tuning them with program structures. Specifically, we represent programs as parse trees -- also known as concrete syntax trees (CSTs) -- and adapt pre-trained models on serialized CSTs. Although the models that we adapt have been pre-trained only on the surface form of programs, we find that a small amount of continual pre-training and fine-tuning on CSTs without changing the model architecture yields improvements over the baseline approach across various code tasks. The improvements are found to be particularly significant when there are limited training examples, demonstrating the effectiveness of integrating program structures with plain-text representation even when working with backbone models that have not been pre-trained with structures.