Daily Papers

In-context learning allows large models to adapt to new tasks from a few demonstrations, but it has shown limited success in molecular design. Existing databases such as ChEMBL contain molecular properties spanning millions of biological assays, yet labeled data for each property remain scarce. To address this limitation, we introduce demonstration-conditioned diffusion models (DemoDiff), which define task contexts using a small set of molecule-score examples instead of text descriptions. These demonstrations guide a denoising Transformer to generate molecules aligned with target properties. For scalable pretraining, we develop a new molecular tokenizer with Node Pair Encoding that represents molecules at the motif level, requiring 5.5times fewer nodes. We curate a dataset containing millions of context tasks from multiple sources covering both drugs and materials, and pretrain a 0.7-billion-parameter model on it. Across 33 design tasks in six categories, DemoDiff matches or surpasses language models 100-1000times larger and achieves an average rank of 3.63 compared to 5.25-10.20 for domain-specific approaches. These results position DemoDiff as a molecular foundation model for in-context molecular design. Our code is available at https://github.com/liugangcode/DemoDiff.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

Predictor-based methods have substantially enhanced Neural Architecture Search (NAS) optimization. The efficacy of these predictors is largely influenced by the method of encoding neural network architectures. While traditional encodings used an adjacency matrix describing the graph structure of a neural network, novel encodings embrace a variety of approaches from unsupervised pretraining of latent representations to vectors of zero-cost proxies. In this paper, we categorize and investigate neural encodings from three main types: structural, learned, and score-based. Furthermore, we extend these encodings and introduce unified encodings, that extend NAS predictors to multiple search spaces. Our analysis draws from experiments conducted on over 1.5 million neural network architectures on NAS spaces such as NASBench-101 (NB101), NB201, NB301, Network Design Spaces (NDS), and TransNASBench-101. Building on our study, we present our predictor FLAN: Flow Attention for NAS. FLAN integrates critical insights on predictor design, transfer learning, and unified encodings to enable more than an order of magnitude cost reduction for training NAS accuracy predictors. Our implementation and encodings for all neural networks are open-sourced at https://github.com/abdelfattah-lab/flan_nas{https://github.com/abdelfattah-lab/flan\_nas}.

In this paper, we aim to do code completion based on implementing a Neural Network from Li et. al.. Our contribution is that we use an encoding that is in-between character and word encoding called Byte Pair Encoding (BPE). We use this on the source code files treating them as natural text without first going through the abstract syntax tree (AST). We have implemented two models: an attention-enhanced LSTM and a pointer network, where the pointer network was originally introduced to solve out of vocabulary problems. We are interested to see if BPE can replace the need for the pointer network for code completion.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these approaches encode, as well as performance trade-offs between them. However, the question of which structural properties yield the most effective encoding remains open. In this paper, we investigate this question from a geometric perspective. We propose a novel structural encoding based on discrete Ricci curvature (Local Curvature Profiles, short LCP) and show that it significantly outperforms existing encoding approaches. We further show that combining local structural encodings, such as LCP, with global positional encodings improves downstream performance, suggesting that they capture complementary geometric information. Finally, we compare different encoding types with (curvature-based) rewiring techniques. Rewiring has recently received a surge of interest due to its ability to improve the performance of Graph Neural Networks by mitigating over-smoothing and over-squashing effects. Our results suggest that utilizing curvature information for structural encodings delivers significantly larger performance increases than rewiring.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present IsoNet++, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an injective alignment between their nodes. Second, we update this alignment in a lazy fashion over multiple rounds. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, IsoNet++ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. In contrast, we consider node pairs (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

We present a novel edge-level ego-network encoding for learning on graphs that can boost Message Passing Graph Neural Networks (MP-GNNs) by providing additional node and edge features or extending message-passing formats. The proposed encoding is sufficient to distinguish Strongly Regular Graphs, a family of challenging 3-WL equivalent graphs. We show theoretically that such encoding is more expressive than node-based sub-graph MP-GNNs. In an empirical evaluation on four benchmarks with 10 graph datasets, our results match or improve previous baselines on expressivity, graph classification, graph regression, and proximity tasks -- while reducing memory usage by 18.1x in certain real-world settings.

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

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation z, which is then decoded back to a molecule. The encoding process is easy, but the decoding process remains challenging. In this work, we introduce a simple two-step decoding process. In a first step, a fully connected neural network uses the latent vector z to produce a molecular formula, for example CO_2 (one carbon and two oxygen atoms). In a second step, a graph convolutional neural network uses the same latent vector z to place bonds between the atoms that were produced in the first step (for example a double bond will be placed between the carbon and each of the oxygens). This two-step process, in which a bag of atoms is first generated, and then assembled, provides a simple framework that allows us to develop an efficient molecule auto-encoder. Numerical experiments on basic tasks such as novelty, uniqueness, validity and optimized chemical property for the 250k ZINC molecules demonstrate the performances of the proposed system. Particularly, we achieve the highest reconstruction rate of 90.5\%, improving the previous rate of 76.7\%. We also report the best property improvement results when optimization is constrained by the molecular distance between the original and generated molecules.

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.

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

A range of recent works addresses the problem of compression of sequence of tokens into a shorter sequence of real-valued vectors to be used as inputs instead of token embeddings or key-value cache. These approaches allow to reduce the amount of compute in existing language models. Despite relying on powerful models as encoders, the maximum attainable lossless compression ratio is typically not higher than x10. This fact is highly intriguing because, in theory, the maximum information capacity of large real-valued vectors is far beyond the presented rates even for 16-bit precision and a modest vector size. In this work, we explore the limits of compression by replacing the encoder with a per-sample optimization procedure. We show that vectors with compression ratios up to x1500 exist, which highlights two orders of magnitude gap between existing and practically attainable solutions. Furthermore, we empirically show that the compression limits are determined not by the length of the input but by the amount of uncertainty to be reduced, namely, the cross-entropy loss on this sequence without any conditioning. The obtained limits highlight the substantial gap between the theoretical capacity of input embeddings and their practical utilization, suggesting significant room for optimization in model design.

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

Neural architecture search (NAS) automates the design process of high-performing architectures, but remains bottlenecked by expensive performance evaluation. Most existing studies that achieve faster evaluation are mostly tied to cell-based search spaces and graph encodings tailored to those individual search spaces, limiting their flexibility and scalability when applied to more expressive search spaces. In this work, we aim to close the gap of individual search space restrictions and search space dependent network representations. We present ONNX-Bench, a benchmark consisting of a collection of neural networks in a unified format based on ONNX files. ONNX-Bench includes all open-source NAS-bench-based neural networks, resulting in a total size of more than 600k {architecture, accuracy} pairs. This benchmark allows creating a shared neural network representation, ONNX-Net, able to represent any neural architecture using natural language descriptions acting as an input to a performance predictor. This text-based encoding can accommodate arbitrary layer types, operation parameters, and heterogeneous topologies, enabling a single surrogate to generalise across all neural architectures rather than being confined to cell-based search spaces. Experiments show strong zero-shot performance across disparate search spaces using only a small amount of pretraining samples, enabling the unprecedented ability to evaluate any neural network architecture instantly.

Byte-Pair Encoding (BPE) is a popular algorithm used for tokenizing data in NLP, despite being devised initially as a compression method. BPE appears to be a greedy algorithm at face value, but the underlying optimization problem that BPE seeks to solve has not yet been laid down. We formalize BPE as a combinatorial optimization problem. Via submodular functions, we prove that the iterative greedy version is a 1{{sigma(mu^star)}}(1-e^{-{sigma(mu^star)}})-approximation of an optimal merge sequence, where {sigma(mu^star)} is the total backward curvature with respect to the optimal merge sequence mu^star. Empirically the lower bound of the approximation is approx 0.37. We provide a faster implementation of BPE which improves the runtime complexity from Oleft(N Mright) to Oleft(N log Mright), where N is the sequence length and M is the merge count. Finally, we optimize the brute-force algorithm for optimal BPE using memoization.

Research on parsing language to SQL has largely ignored the structure of the database (DB) schema, either because the DB was very simple, or because it was observed at both training and test time. In Spider, a recently-released text-to-SQL dataset, new and complex DBs are given at test time, and so the structure of the DB schema can inform the predicted SQL query. In this paper, we present an encoder-decoder semantic parser, where the structure of the DB schema is encoded with a graph neural network, and this representation is later used at both encoding and decoding time. Evaluation shows that encoding the schema structure improves our parser accuracy from 33.8% to 39.4%, dramatically above the current state of the art, which is at 19.7%.

We tackle NED by comparing entities in short sentences with graphs. Creating a context vector from graphs through deep learning is a challenging problem that has never been applied to NED. Our main contribution is to present an experimental study of recent neural techniques, as well as a discussion about which graph features are most important for the disambiguation task. In addition, a new dataset () is created to allow a clean and scalable evaluation of NED with entries, and to be used as a reference in future research. In the end our results show that a Bi-LSTM encoding of the graph triplets performs best, improving upon the baseline models and scoring an F1 value of 91.6% on the test set

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

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

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

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

State-of-the-art language models are autoregressive and operate on subword units known as tokens. Specifically, one must encode the conditioning string into a list of tokens before passing to the language models for next-token prediction. We show that popular encoding schemes, such as maximum prefix encoding (MPE) and byte-pair-encoding (BPE), induce a sampling bias that cannot be mitigated with more training or data. To counter this universal problem, for each encoding scheme above, we propose a novel algorithm to obtain unbiased estimates from any language model trained on tokenized data. Our methods do not require finetuning the model, and the complexity, defined as the number of model runs, scales linearly with the sequence length in the case of MPE. As a result, we show that one can simulate token-free behavior from a tokenized language model. We empirically verify the correctness of our method through a Markov-chain setup, where it accurately recovers the transition probabilities, as opposed to the conventional method of directly prompting tokens into the language model.

This article offers an empirical study on the different ways of encoding Chinese, Japanese, Korean (CJK) and English languages for text classification. Different encoding levels are studied, including UTF-8 bytes, characters, words, romanized characters and romanized words. For all encoding levels, whenever applicable, we provide comparisons with linear models, fastText and convolutional networks. For convolutional networks, we compare between encoding mechanisms using character glyph images, one-hot (or one-of-n) encoding, and embedding. In total there are 473 models, using 14 large-scale text classification datasets in 4 languages including Chinese, English, Japanese and Korean. Some conclusions from these results include that byte-level one-hot encoding based on UTF-8 consistently produces competitive results for convolutional networks, that word-level n-grams linear models are competitive even without perfect word segmentation, and that fastText provides the best result using character-level n-gram encoding but can overfit when the features are overly rich.

Despite its outstanding performance in various graph tasks, vanilla Message Passing Neural Network (MPNN) usually fails in link prediction tasks, as it only uses representations of two individual target nodes and ignores the pairwise relation between them. To capture the pairwise relations, some models add manual features to the input graph and use the output of MPNN to produce pairwise representations. In contrast, others directly use manual features as pairwise representations. Though this simplification avoids applying a GNN to each link individually and thus improves scalability, these models still have much room for performance improvement due to the hand-crafted and unlearnable pairwise features. To upgrade performance while maintaining scalability, we propose Neural Common Neighbor (NCN), which uses learnable pairwise representations. To further boost NCN, we study the unobserved link problem. The incompleteness of the graph is ubiquitous and leads to distribution shifts between the training and test set, loss of common neighbor information, and performance degradation of models. Therefore, we propose two intervention methods: common neighbor completion and target link removal. Combining the two methods with NCN, we propose Neural Common Neighbor with Completion (NCNC). NCN and NCNC outperform recent strong baselines by large margins. NCNC achieves state-of-the-art performance in link prediction tasks. Our code is available at https://github.com/GraphPKU/NeuralCommonNeighbor.

Byte Pair Encoding (BPE) tokenizers, widely used in Large Language Models, face challenges in multilingual settings, including penalization of non-Western scripts and the creation of tokens with partial UTF-8 sequences. Pretokenization, often reliant on complex regular expressions, can also introduce fragility and unexpected edge cases. We propose SCRIPT (Script Category Representation in PreTokenization), a novel encoding scheme that bypasses UTF-8 byte conversion by using initial tokens based on Unicode script and category properties. This approach enables a simple, rule-based pretokenization strategy that respects script boundaries, offering a robust alternative to pretokenization strategies based on regular expressions. We also introduce and validate a constrained BPE merging strategy that enforces character integrity, applicable to both SCRIPT-BPE and byte-based BPE. Our experiments demonstrate that SCRIPT-BPE achieves competitive compression while eliminating encoding-based penalties for non-Latin-script languages.

Tokenization is the first -- and often least scrutinized -- step of most NLP pipelines. Standard algorithms for learning tokenizers rely on frequency-based objectives, which favor languages dominant in the training data and consequently leave lower-resource languages with tokenizations that are disproportionately longer, morphologically implausible, or even riddled with <UNK> placeholders. This phenomenon ultimately amplifies computational and financial inequalities between users from different language backgrounds. To remedy this, we introduce Parity-aware Byte Pair Encoding (BPE), a variant of the widely-used BPE algorithm. At every merge step, Parity-aware BPE maximizes the compression gain of the currently worst-compressed language, trading a small amount of global compression for cross-lingual parity. We find empirically that Parity-aware BPE leads to more equitable token counts across languages, with negligible impact on global compression rate and no substantial effect on language-model performance in downstream tasks.

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

Neural sequence-to-sequence models provide a competitive approach to the task of mapping a question in natural language to an SQL query, also referred to as text-to-SQL generation. The Byte-Pair Encoding algorithm (BPE) has previously been used to improve machine translation (MT) between natural languages. In this work, we adapt BPE for text-to-SQL generation. As the datasets for this task are rather small compared to MT, we present a novel stopping criterion that prevents overfitting the BPE encoding to the training set. Additionally, we present AST BPE, which is a version of BPE that uses the Abstract Syntax Tree (AST) of the SQL statement to guide BPE merges and therefore produce BPE encodings that generalize better. We improved the accuracy of a strong attentive seq2seq baseline on five out of six English text-to-SQL tasks while reducing training time by more than 50% on four of them due to the shortened targets. Finally, on two of these tasks we exceeded previously reported accuracies.

Two main families of node feature augmentation schemes have been explored for enhancing GNNs: random features and spectral positional encoding. Surprisingly, however, there is still no clear understanding of the relation between these two augmentation schemes. Here we propose a novel family of positional encoding schemes which draws a link between the above two approaches and improves over both. The new approach, named Random Feature Propagation (RFP), is inspired by the power iteration method and its generalizations. It concatenates several intermediate steps of an iterative algorithm for computing the dominant eigenvectors of a propagation matrix, starting from random node features. Notably, these propagation steps are based on graph-dependent propagation operators that can be either predefined or learned. We explore the theoretical and empirical benefits of RFP. First, we provide theoretical justifications for using random features, for incorporating early propagation steps, and for using multiple random initializations. Then, we empirically demonstrate that RFP significantly outperforms both spectral PE and random features in multiple node classification and graph classification benchmarks.

We present models for encoding sentences into embedding vectors that specifically target transfer learning to other NLP tasks. The models are efficient and result in accurate performance on diverse transfer tasks. Two variants of the encoding models allow for trade-offs between accuracy and compute resources. For both variants, we investigate and report the relationship between model complexity, resource consumption, the availability of transfer task training data, and task performance. Comparisons are made with baselines that use word level transfer learning via pretrained word embeddings as well as baselines do not use any transfer learning. We find that transfer learning using sentence embeddings tends to outperform word level transfer. With transfer learning via sentence embeddings, we observe surprisingly good performance with minimal amounts of supervised training data for a transfer task. We obtain encouraging results on Word Embedding Association Tests (WEAT) targeted at detecting model bias. Our pre-trained sentence encoding models are made freely available for download and on TF Hub.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

It is well noted that coordinate based MLPs benefit -- in terms of preserving high-frequency information -- through the encoding of coordinate positions as an array of Fourier features. Hitherto, the rationale for the effectiveness of these positional encodings has been solely studied through a Fourier lens. In this paper, we strive to broaden this understanding by showing that alternative non-Fourier embedding functions can indeed be used for positional encoding. Moreover, we show that their performance is entirely determined by a trade-off between the stable rank of the embedded matrix and the distance preservation between embedded coordinates. We further establish that the now ubiquitous Fourier feature mapping of position is a special case that fulfills these conditions. Consequently, we present a more general theory to analyze positional encoding in terms of shifted basis functions. To this end, we develop the necessary theoretical formulae and empirically verify that our theoretical claims hold in practice. Codes available at https://github.com/osiriszjq/Rethinking-positional-encoding.

The attention mechanism is a core primitive in modern large language models (LLMs) and AI more broadly. Since attention by itself is permutation-invariant, position encoding is essential for modeling structured domains such as language. Rotary position encoding (RoPE) has emerged as the de facto standard approach for position encoding and is part of many modern LLMs. However, in RoPE the key/query transformation between two elements in a sequence is only a function of their relative position and otherwise independent of the actual input. This limits the expressivity of RoPE-based transformers. This paper describes PaTH, a flexible data-dependent position encoding scheme based on accumulated products of Householder(like) transformations, where each transformation is data-dependent, i.e., a function of the input. We derive an efficient parallel algorithm for training through exploiting a compact representation of products of Householder matrices, and implement a FlashAttention-style blockwise algorithm that minimizes I/O cost. Across both targeted synthetic benchmarks and moderate-scale real-world language modeling experiments, we find that PaTH demonstrates superior performance compared to RoPE and other recent baselines.

One of the recent best attempts at Text-to-SQL is the pre-trained language model. Due to the structural property of the SQL queries, the seq2seq model takes the responsibility of parsing both the schema items (i.e., tables and columns) and the skeleton (i.e., SQL keywords). Such coupled targets increase the difficulty of parsing the correct SQL queries especially when they involve many schema items and logic operators. This paper proposes a ranking-enhanced encoding and skeleton-aware decoding framework to decouple the schema linking and the skeleton parsing. Specifically, for a seq2seq encoder-decode model, its encoder is injected by the most relevant schema items instead of the whole unordered ones, which could alleviate the schema linking effort during SQL parsing, and its decoder first generates the skeleton and then the actual SQL query, which could implicitly constrain the SQL parsing. We evaluate our proposed framework on Spider and its three robustness variants: Spider-DK, Spider-Syn, and Spider-Realistic. The experimental results show that our framework delivers promising performance and robustness. Our code is available at https://github.com/RUCKBReasoning/RESDSQL.

Target encoding plays a central role when learning Convolutional Neural Networks. In this realm, One-hot encoding is the most prevalent strategy due to its simplicity. However, this so widespread encoding schema assumes a flat label space, thus ignoring rich relationships existing among labels that can be exploited during training. In large-scale datasets, data does not span the full label space, but instead lies in a low-dimensional output manifold. Following this observation, we embed the targets into a low-dimensional space, drastically improving convergence speed while preserving accuracy. Our contribution is two fold: (i) We show that random projections of the label space are a valid tool to find such lower dimensional embeddings, boosting dramatically convergence rates at zero computational cost; and (ii) we propose a normalized eigenrepresentation of the class manifold that encodes the targets with minimal information loss, improving the accuracy of random projections encoding while enjoying the same convergence rates. Experiments on CIFAR-100, CUB200-2011, Imagenet, and MIT Places demonstrate that the proposed approach drastically improves convergence speed while reaching very competitive accuracy rates.

Byte-pair encoding (BPE) is a ubiquitous algorithm in the subword tokenization process of language models as it provides multiple benefits. However, this process is solely based on pre-training data statistics, making it hard for the tokenizer to handle infrequent spellings. On the other hand, though robust to misspellings, pure character-level models often lead to unreasonably long sequences and make it harder for the model to learn meaningful words. To alleviate these challenges, we propose a character-based subword module (char2subword) that learns the subword embedding table in pre-trained models like BERT. Our char2subword module builds representations from characters out of the subword vocabulary, and it can be used as a drop-in replacement of the subword embedding table. The module is robust to character-level alterations such as misspellings, word inflection, casing, and punctuation. We integrate it further with BERT through pre-training while keeping BERT transformer parameters fixed--and thus, providing a practical method. Finally, we show that incorporating our module to mBERT significantly improves the performance on the social media linguistic code-switching evaluation (LinCE) benchmark.

This article proposes to auto-encode text at byte-level using convolutional networks with a recursive architecture. The motivation is to explore whether it is possible to have scalable and homogeneous text generation at byte-level in a non-sequential fashion through the simple task of auto-encoding. We show that non-sequential text generation from a fixed-length representation is not only possible, but also achieved much better auto-encoding results than recurrent networks. The proposed model is a multi-stage deep convolutional encoder-decoder framework using residual connections, containing up to 160 parameterized layers. Each encoder or decoder contains a shared group of modules that consists of either pooling or upsampling layers, making the network recursive in terms of abstraction levels in representation. Results for 6 large-scale paragraph datasets are reported, in 3 languages including Arabic, Chinese and English. Analyses are conducted to study several properties of the proposed model.

In this work, we investigate a typical scenario in code generation where a developer edits existing code in real time and requests a code assistant, e.g., a large language model, to re-predict the next token or next line on the fly. Naively, the LLM needs to re-encode the entire KV cache to provide an accurate prediction. However, this process is computationally expensive, especially when the sequence length is long. Simply encoding the edited subsequence and integrating it to the original KV cache meets the temporal confusion problem, leading to significantly worse performance. We address this efficiency and accuracy trade-off by introducing \textbf{Positional \textbf{Integrity Encoding} (PIE). Building upon the rotary positional encoding, PIE first removes the rotary matrices in the Key cache that introduce temporal confusion and then reapplies the correct rotary matrices. This process ensures that positional relationships between tokens are correct and requires only a single round of matrix multiplication. We validate the effectiveness of PIE through extensive experiments on the RepoBench-C-8k dataset, utilizing DeepSeek-Coder models with 1.3B, 6.7B, and 33B parameters. Our evaluation includes three real-world coding tasks: code insertion, code deletion, and multi-place code editing. Results demonstrate that PIE reduces computational overhead by over 85% compared to the standard full recomputation approach across all model sizes and tasks while well approximating the model performance.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

Recently, binary representation has been proposed as a novel representation that lies between continuous and discrete representations. It exhibits considerable information-preserving capability when being used to replace continuous input vectors. In this paper, we investigate the feasibility of further introducing it to the output side, aiming to allow models to output binary labels instead. To preserve the structural information on the output side along with label information, we extend the previous contrastive hashing method as structured contrastive hashing. More specifically, we upgrade CKY from label-level to bit-level, define a new similarity function with span marginal probabilities, and introduce a novel contrastive loss function with a carefully designed instance selection strategy. Our model achieves competitive performance on various structured prediction tasks, and demonstrates that binary representation can be considered a novel representation that further bridges the gap between the continuous nature of deep learning and the discrete intrinsic property of natural languages.

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns, exhibiting local node-level homophilic and heterophilic structures. However, existing works are only devoted to designing better HGNN backbones or architectures for node classification tasks on heterophilic and homophilic graph benchmarks simultaneously, and their analyses of HGNN performance with respect to nodes are only based on the determined data distribution without exploring the effect caused by this structural difference between training and testing nodes. How to learn invariant node representations on heterophilic graphs to handle this structure difference or distribution shifts remains unexplored. In this paper, we first discuss the limitations of previous graph-based invariant learning methods from the perspective of data augmentation. Then, we propose HEI, a framework capable of generating invariant node representations through incorporating heterophily information to infer latent environments without augmentation, which are then used for invariant prediction, under heterophilic graph structure distribution shifts. We theoretically show that our proposed method can achieve guaranteed performance under heterophilic graph structure distribution shifts. Extensive experiments on various benchmarks and backbones can also demonstrate the effectiveness of our method compared with existing state-of-the-art baselines.

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

Temporal Graph Neural Networks have garnered substantial attention for their capacity to model evolving structural and temporal patterns while exhibiting impressive performance. However, it is known that these architectures are encumbered by issues that constrain their performance, such as over-squashing and over-smoothing. Meanwhile, Transformers have demonstrated exceptional computational capacity to effectively address challenges related to long-range dependencies. Consequently, we introduce Todyformer-a novel Transformer-based neural network tailored for dynamic graphs. It unifies the local encoding capacity of Message-Passing Neural Networks (MPNNs) with the global encoding of Transformers through i) a novel patchifying paradigm for dynamic graphs to improve over-squashing, ii) a structure-aware parametric tokenization strategy leveraging MPNNs, iii) a Transformer with temporal positional-encoding to capture long-range dependencies, and iv) an encoding architecture that alternates between local and global contextualization, mitigating over-smoothing in MPNNs. Experimental evaluations on public benchmark datasets demonstrate that Todyformer consistently outperforms the state-of-the-art methods for downstream tasks. Furthermore, we illustrate the underlying aspects of the proposed model in effectively capturing extensive temporal dependencies in dynamic graphs.

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

We propose the neural string edit distance model for string-pair matching and string transduction based on learnable string edit distance. We modify the original expectation-maximization learned edit distance algorithm into a differentiable loss function, allowing us to integrate it into a neural network providing a contextual representation of the input. We evaluate on cognate detection, transliteration, and grapheme-to-phoneme conversion, and show that we can trade off between performance and interpretability in a single framework. Using contextual representations, which are difficult to interpret, we match the performance of state-of-the-art string-pair matching models. Using static embeddings and a slightly different loss function, we force interpretability, at the expense of an accuracy drop.

We provide a construction for categorical representation learning and introduce the foundations of "categorifier". The central theme in representation learning is the idea of everything to vector. Every object in a dataset S can be represented as a vector in R^n by an encoding map E: Obj(S)toR^n. More importantly, every morphism can be represented as a matrix E: Hom(S)toR^{n}_{n}. The encoding map E is generally modeled by a deep neural network. The goal of representation learning is to design appropriate tasks on the dataset to train the encoding map (assuming that an encoding is optimal if it universally optimizes the performance on various tasks). However, the latter is still a set-theoretic approach. The goal of the current article is to promote the representation learning to a new level via a category-theoretic approach. As a proof of concept, we provide an example of a text translator equipped with our technology, showing that our categorical learning model outperforms the current deep learning models by 17 times. The content of the current article is part of the recent US patent proposal (patent application number: 63110906).

We present a novel neural network for processing sequences. The ByteNet is a one-dimensional convolutional neural network that is composed of two parts, one to encode the source sequence and the other to decode the target sequence. The two network parts are connected by stacking the decoder on top of the encoder and preserving the temporal resolution of the sequences. To address the differing lengths of the source and the target, we introduce an efficient mechanism by which the decoder is dynamically unfolded over the representation of the encoder. The ByteNet uses dilation in the convolutional layers to increase its receptive field. The resulting network has two core properties: it runs in time that is linear in the length of the sequences and it sidesteps the need for excessive memorization. The ByteNet decoder attains state-of-the-art performance on character-level language modelling and outperforms the previous best results obtained with recurrent networks. The ByteNet also achieves state-of-the-art performance on character-to-character machine translation on the English-to-German WMT translation task, surpassing comparable neural translation models that are based on recurrent networks with attentional pooling and run in quadratic time. We find that the latent alignment structure contained in the representations reflects the expected alignment between the tokens.

Natural reading orders of words are crucial for information extraction from form-like documents. Despite recent advances in Graph Convolutional Networks (GCNs) on modeling spatial layout patterns of documents, they have limited ability to capture reading orders of given word-level node representations in a graph. We propose Reading Order Equivariant Positional Encoding (ROPE), a new positional encoding technique designed to apprehend the sequential presentation of words in documents. ROPE generates unique reading order codes for neighboring words relative to the target word given a word-level graph connectivity. We study two fundamental document entity extraction tasks including word labeling and word grouping on the public FUNSD dataset and a large-scale payment dataset. We show that ROPE consistently improves existing GCNs with a margin up to 8.4% F1-score.

The Transformer architecture has revolutionized various regions since it was proposed, and its effectiveness largely depends on the ability to encode positional information. Traditional position encoding methods exhibit significant limitations due to lack of robustness and flexibility of position. Therefore, Rotary Positional Encoding (RoPE) was proposed to alleviate these issues, which integrates positional information by rotating the embeddings in the attention mechanism. However, RoPE requires manually defined rotation matrices with limited transformation space, constraining the model's capacity. In this work, we propose ComRoPE, which generalizes RoPE by defining it in terms of trainable commuting angle matrices. Specifically, we demonstrate that pairwise commutativity of these matrices is essential for RoPE to achieve scalability and positional robustness. We formally define the RoPE Equation, which is an essential condition that ensures consistent performance with position offsets. Based on the theoretical analysis, we present two types of trainable commuting angle matrices as sufficient solutions to the RoPE equation, which significantly improve performance, surpassing the current state-of-the-art method by 1.6% at training resolution and 2.9% at higher resolution on the ImageNet-1K dataset. Furthermore, our framework shows versatility in generalizing to existing RoPE formulations and offering new insights for future positional encoding research. To ensure reproducibility, the source code and instructions are available at https://github.com/Longin-Yu/ComRoPE

Positional encoding mechanisms enable Transformers to model sequential structure and long-range dependencies in text. While absolute positional encodings struggle with extrapolation to longer sequences due to fixed positional representations, and relative approaches like Alibi exhibit performance degradation on extremely long contexts, the widely-used Rotary Positional Encoding (RoPE) introduces oscillatory attention patterns that hinder stable long-distance dependency modelling. We address these limitations through a geometric reformulation of positional encoding. Drawing inspiration from Lorentz transformations in hyperbolic geometry, we propose Hyperbolic Rotary Positional Encoding (HoPE), which leverages hyperbolic functions to implement Lorentz rotations on token representations. Theoretical analysis demonstrates that RoPE is a special case of our generalized formulation. HoPE fundamentally resolves RoPE's slation issues by enforcing monotonic decay of attention weights with increasing token distances. Extensive experimental results, including perplexity evaluations under several extended sequence benchmarks, show that HoPE consistently exceeds existing positional encoding methods. These findings underscore HoPE's enhanced capacity for representing and generalizing long-range dependencies. Data and code will be available.

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

Tables are ubiquitous across various domains for concisely representing structured information. Empowering large language models (LLMs) to reason over tabular data represents an actively explored direction. However, since typical LLMs only support one-dimensional~(1D) inputs, existing methods often flatten the two-dimensional~(2D) table structure into a sequence of tokens, which can severely disrupt the spatial relationships and result in an inevitable loss of vital contextual information. In this paper, we first empirically demonstrate the detrimental impact of such flattening operations on the performance of LLMs in capturing the spatial information of tables through two elaborate proxy tasks. Subsequently, we introduce a simple yet effective positional encoding method, termed ``2D-TPE'' (Two-Dimensional Table Positional Encoding), to address this challenge. 2D-TPE enables each attention head to dynamically select a permutation order of tokens within the context for attending to them, where each permutation represents a distinct traversal mode for the table, such as column-wise or row-wise traversal. 2D-TPE effectively mitigates the risk of losing essential spatial information while preserving computational efficiency, thus better preserving the table structure. Extensive experiments across five benchmarks demonstrate that 2D-TPE outperforms strong baselines, underscoring the importance of preserving the table structure for accurate table comprehension. Comprehensive analysis further reveals the substantially better scalability of 2D-TPE to large tables than baselines.

Neural image compression methods have seen increasingly strong performance in recent years. However, they suffer orders of magnitude higher computational complexity compared to traditional codecs, which stands in the way of real-world deployment. This paper takes a step forward in closing this gap in decoding complexity by adopting shallow or even linear decoding transforms. To compensate for the resulting drop in compression performance, we exploit the often asymmetrical computation budget between encoding and decoding, by adopting more powerful encoder networks and iterative encoding. We theoretically formalize the intuition behind, and our experimental results establish a new frontier in the trade-off between rate-distortion and decoding complexity for neural image compression. Specifically, we achieve rate-distortion performance competitive with the established mean-scale hyperprior architecture of Minnen et al. (2018), while reducing the overall decoding complexity by 80 %, or over 90 % for the synthesis transform alone. Our code can be found at https://github.com/mandt-lab/shallow-ntc.

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) Non-uniqueness: there are many different eigendecompositions of the same Laplacian, and (2) Instability: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a "hard partition" of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to "softly partition" eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods.

Tokenization is a fundamental component of language models for code. It involves breaking down the input into units that are later passed to the language model stack to learn high-dimensional representations used in various contexts, from classification to generation. However, the output of these tokenizers is often longer than that traditionally used in compilers and interpreters. This could result in undesirable effects, such as increased computational overhead. In this work, we investigate the effect of merging the hidden representations of subtokens that belong to the same semantic unit, such as subtokens that form a single identifier. We propose two strategies: one based on averaging the representations and another that leverages a learning-based approach. Both methods can be seamlessly integrated with existing language models for code. We conduct experiments using six language models for code: CodeBERT, GraphCodeBERT, UniXCoder, CdoeT5, CodeT5+ (220M), and CodeT5+ (770M), across three software engineering tasks: vulnerability detection, code classification, and code translation. Results show that these strategies can reduce the number of floating-point operations by 1% to 19%. Regarding downstream performance, the most significant degradation was observed in the vulnerability detection task, where the F1 score decreased by 1.82 points compared to the baseline. In contrast, for code translation, we observed an improvement of 2.47 points in CodeBLEU. This work contributes to the broader effort of improving language models for code across multiple dimensions, including both computational efficiency and downstream performance.

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

Despite extensive progress on image generation, common deep generative model architectures are not easily applied to lossless compression. For example, VAEs suffer from a compression cost overhead due to their latent variables. This overhead can only be partially eliminated with elaborate schemes such as bits-back coding, often resulting in poor single-sample compression rates. To overcome such problems, we establish a new class of tractable lossless compression models that permit efficient encoding and decoding: Probabilistic Circuits (PCs). These are a class of neural networks involving |p| computational units that support efficient marginalization over arbitrary subsets of the D feature dimensions, enabling efficient arithmetic coding. We derive efficient encoding and decoding schemes that both have time complexity O (log(D) cdot |p|), where a naive scheme would have linear costs in D and |p|, making the approach highly scalable. Empirically, our PC-based (de)compression algorithm runs 5-40 times faster than neural compression algorithms that achieve similar bitrates. By scaling up the traditional PC structure learning pipeline, we achieve state-of-the-art results on image datasets such as MNIST. Furthermore, PCs can be naturally integrated with existing neural compression algorithms to improve the performance of these base models on natural image datasets. Our results highlight the potential impact that non-standard learning architectures may have on neural data compression.

Data used for analytics and machine learning often take the form of tables with categorical entries. We introduce a family of lossless compression algorithms for such data that proceed in four steps: (i) Estimate latent variables associated to rows and columns; (ii) Partition the table in blocks according to the row/column latents; (iii) Apply a sequential (e.g. Lempel-Ziv) coder to each of the blocks; (iv) Append a compressed encoding of the latents. We evaluate it on several benchmark datasets, and study optimal compression in a probabilistic model for that tabular data, whereby latent values are independent and table entries are conditionally independent given the latent values. We prove that the model has a well defined entropy rate and satisfies an asymptotic equipartition property. We also prove that classical compression schemes such as Lempel-Ziv and finite-state encoders do not achieve this rate. On the other hand, the latent estimation strategy outlined above achieves the optimal rate.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular low displacement rank) for integrating tensor fields defined on weighted trees. Several applications of the resulting fast tree-field integrators (FTFIs) are presented, including (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) Topological Transformers (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as three extra learnable parameters per Transformer layer, leading to 1.0-1.5%+ accuracy gains. Importantly, most of FTFIs are exact methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide 5.7-13x speedups. We also provide an extensive theoretical analysis of our methods.

Retrieving graphs from a large corpus, that contain a subgraph isomorphic to a given query graph, is a core operation in many real-world applications. While recent multi-vector graph representations and scores based on set alignment and containment can provide accurate subgraph isomorphism tests, their use in retrieval remains limited by their need to score corpus graphs exhaustively. We introduce CORGII (Contextual Representation of Graphs for Inverted Indexing), a graph indexing framework in which, starting with a contextual dense graph representation, a differentiable discretization module computes sparse binary codes over a learned latent vocabulary. This text document-like representation allows us to leverage classic, highly optimized inverted indices, while supporting soft (vector) set containment scores. Pushing this paradigm further, we replace the classical, fixed impact weight of a `token' on a graph (such as TFIDF or BM25) with a data-driven, trainable impact weight. Finally, we explore token expansion to support multi-probing the index for smoother accuracy-efficiency tradeoffs. To our knowledge, CORGII is the first indexer of dense graph representations using discrete tokens mapping to efficient inverted lists. Extensive experiments show that CORGII provides better trade-offs between accuracy and efficiency, compared to several baselines.

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

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

Graph neural networks (GNNs) have gained significant attention in recent years for their ability to process data that may be represented as graphs. This has prompted several studies to explore their representational capability based on the graph isomorphism task. Notably, these works inherently assume a countable node feature representation, potentially limiting their applicability. Interestingly, only a few study GNNs with uncountable node feature representation. In the paper, a new perspective on the representational capability of GNNs is investigated across all levelsx2014node-level, neighborhood-level, and graph-levelx2014when the space of node feature representation is uncountable. Specifically, the injective and metric requirements of previous works are softly relaxed by employing a pseudometric distance on the space of input to create a soft-injective function such that distinct inputs may produce similar outputs if and only if the pseudometric deems the inputs to be sufficiently similar on some representation. As a consequence, a simple and computationally efficient soft-isomorphic relational graph convolution network (SIR-GCN) that emphasizes the contextualized transformation of neighborhood feature representations via anisotropic and dynamic message functions is proposed. Furthermore, a mathematical discussion on the relationship between SIR-GCN and key GNNs in literature is laid out to put the contribution into context, establishing SIR-GCN as a generalization of classical GNN methodologies. To close, experiments on synthetic and benchmark datasets demonstrate the relative superiority of SIR-GCN, outperforming comparable models in node and graph property prediction tasks.

Byte Pair Encoding (BPE) serves as a foundation method for text tokenization in the Natural Language Processing (NLP) field. Despite its wide adoption, the original BPE algorithm harbors an inherent flaw: it inadvertently introduces a frequency imbalance for tokens in the text corpus. Since BPE iteratively merges the most frequent token pair in the text corpus while keeping all tokens that have been merged in the vocabulary, it unavoidably holds tokens that primarily represent subwords of complete words and appear infrequently on their own in the text corpus. We term such tokens as Scaffold Tokens. Due to their infrequent appearance in the text corpus, Scaffold Tokens pose a learning imbalance issue for language models. To address that issue, we propose Scaffold-BPE, which incorporates a dynamic scaffold token removal mechanism by parameter-free, computation-light, and easy-to-implement modifications to the original BPE. This novel approach ensures the exclusion of low-frequency Scaffold Tokens from the token representations for the given texts, thereby mitigating the issue of frequency imbalance and facilitating model training. On extensive experiments across language modeling tasks and machine translation tasks, Scaffold-BPE consistently outperforms the original BPE, well demonstrating its effectiveness and superiority.

This article introduces byteSteady -- a fast model for classification using byte-level n-gram embeddings. byteSteady assumes that each input comes as a sequence of bytes. A representation vector is produced using the averaged embedding vectors of byte-level n-grams, with a pre-defined set of n. The hashing trick is used to reduce the number of embedding vectors. This input representation vector is then fed into a linear classifier. A straightforward application of byteSteady is text classification. We also apply byteSteady to one type of non-language data -- DNA sequences for gene classification. For both problems we achieved competitive classification results against strong baselines, suggesting that byteSteady can be applied to both language and non-language data. Furthermore, we find that simple compression using Huffman coding does not significantly impact the results, which offers an accuracy-speed trade-off previously unexplored in machine learning.

Recent studies have demonstrated the effectiveness of position encoding in transformer architectures. By incorporating positional information, this approach provides essential guidance for modeling dependencies between elements across different sequence positions. We introduce CoPE (a lightweight Complex Positional Encoding), a novel architecture that leverages complex-valued encoding to encode both content and positional information. Our approach replaces traditional positional encodings with complex embeddings where the real part captures semantic content and the imaginary part encodes positional information. We introduce phase-aware attention in the first layer of the transformer model to capture position-dependent patterns, followed by standard attention layers for higher-levels. We show that CoPE doesn't exhibit long term decay and is compatible with linear attention. Experimental evaluation on the GLUE benchmark suggest that our approach achieves superior performance with less computational complexity, compared to RoPE, Sinusoidal and Learned positional encodings.

Multimodal large language models (MLLMs) have achieved strong performance on vision-language tasks, yet often suffer from inefficiencies due to redundant visual tokens. Existing token merging methods reduce sequence length but frequently disrupt spatial layouts and temporal continuity by disregarding positional relationships. In this work, we propose a novel encoding operator dubbed as Positional Preservation Embedding (PPE), which has the main hallmark of preservation of spatiotemporal structure during visual token compression. PPE explicitly introduces the disentangled encoding of 3D positions in the token dimension, enabling each compressed token to encapsulate different positions from multiple original tokens. Furthermore, we show that PPE can effectively support cascade clustering -- a progressive token compression strategy that leads to better performance retention. PPE is a parameter-free and generic operator that can be seamlessly integrated into existing token merging methods without any adjustments. Applied to state-of-the-art token merging framework, PPE achieves consistent improvements of 2%sim5% across multiple vision-language benchmarks, including MMBench (general vision understanding), TextVQA (layout understanding) and VideoMME (temporal understanding). These results demonstrate that preserving positional cues is critical for efficient and effective MLLM reasoning.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels. However, the class space may not be expressive enough for covering numerous diverse local graph structures, thus limiting the performance of knowledge transfer from GNN to MLP. To address this issue, we propose to learn a new powerful graph representation space by directly labeling nodes' diverse local structures for GNN-to-MLP distillation. Specifically, we propose a variant of VQ-VAE to learn a structure-aware tokenizer on graph data that can encode each node's local substructure as a discrete code. The discrete codes constitute a codebook as a new graph representation space that is able to identify different local graph structures of nodes with the corresponding code indices. Then, based on the learned codebook, we propose a new distillation target, namely soft code assignments, to directly transfer the structural knowledge of each node from GNN to MLP. The resulting framework VQGraph achieves new state-of-the-art performance on GNN-to-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828x, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Code: https://github.com/YangLing0818/VQGraph.

Following the rationale of end-to-end modeling, CTC, RNN-T or encoder-decoder-attention models for automatic speech recognition (ASR) use graphemes or grapheme-based subword units based on e.g. byte-pair encoding (BPE). The mapping from pronunciation to spelling is learned completely from data. In contrast to this, classical approaches to ASR employ secondary knowledge sources in the form of phoneme lists to define phonetic output labels and pronunciation lexica. In this work, we do a systematic comparison between grapheme- and phoneme-based output labels for an encoder-decoder-attention ASR model. We investigate the use of single phonemes as well as BPE-based phoneme groups as output labels of our model. To preserve a simplified and efficient decoder design, we also extend the phoneme set by auxiliary units to be able to distinguish homophones. Experiments performed on the Switchboard 300h and LibriSpeech benchmarks show that phoneme-based modeling is competitive to grapheme-based encoder-decoder-attention modeling.

Large-scale pre-trained models (PTMs) have been widely used in document-oriented NLP tasks, such as question answering. However, the encoding-task coupling requirement results in the repeated encoding of the same documents for different tasks and queries, which is highly computationally inefficient. To this end, we target to decouple document encoding from downstream tasks, and propose to represent each document as a plug-and-play document module, i.e., a document plugin, for PTMs (PlugD). By inserting document plugins into the backbone PTM for downstream tasks, we can encode a document one time to handle multiple tasks, which is more efficient than conventional encoding-task coupling methods that simultaneously encode documents and input queries using task-specific encoders. Extensive experiments on 8 datasets of 4 typical NLP tasks show that PlugD enables models to encode documents once and for all across different scenarios. Especially, PlugD can save 69% computational costs while achieving comparable performance to state-of-the-art encoding-task coupling methods. Additionally, we show that PlugD can serve as an effective post-processing way to inject knowledge into task-specific models, improving model performance without any additional model training.

Tokenization is a foundational step in Natural Language Processing (NLP) tasks, bridging raw text and language models. Existing tokenization approaches like Byte-Pair Encoding (BPE) originate from the field of data compression, and it has been suggested that the effectiveness of BPE stems from its ability to condense text into a relatively small number of tokens. We test the hypothesis that fewer tokens lead to better downstream performance by introducing PathPiece, a new tokenizer that segments a document's text into the minimum number of tokens for a given vocabulary. Through extensive experimentation we find this hypothesis not to be the case, casting doubt on the understanding of the reasons for effective tokenization. To examine which other factors play a role, we evaluate design decisions across all three phases of tokenization: pre-tokenization, vocabulary construction, and segmentation, offering new insights into the design of effective tokenizers. Specifically, we illustrate the importance of pre-tokenization and the benefits of using BPE to initialize vocabulary construction. We train 64 language models with varying tokenization, ranging in size from 350M to 2.4B parameters, all of which are made publicly available.

Recent studies show that paddings in convolutional neural networks encode absolute position information which can negatively affect the model performance for certain tasks. However, existing metrics for quantifying the strength of positional information remain unreliable and frequently lead to erroneous results. To address this issue, we propose novel metrics for measuring (and visualizing) the encoded positional information. We formally define the encoded information as PPP (Position-information Pattern from Padding) and conduct a series of experiments to study its properties as well as its formation. The proposed metrics measure the presence of positional information more reliably than the existing metrics based on PosENet and a test in F-Conv. We also demonstrate that for any extant (and proposed) padding schemes, PPP is primarily a learning artifact and is less dependent on the characteristics of the underlying padding schemes.

We present LLM-Blender, an ensembling framework designed to attain consistently superior performance by leveraging the diverse strengths of multiple open-source large language models (LLMs). Our framework consists of two modules: PairRanker and GenFuser, addressing the observation that optimal LLMs for different examples can significantly vary. PairRanker employs a specialized pairwise comparison method to distinguish subtle differences between candidate outputs. It jointly encodes the input text and a pair of candidates, using cross-attention encoders to determine the superior one. Our results demonstrate that PairRanker exhibits the highest correlation with ChatGPT-based ranking. Then, GenFuser aims to merge the top-ranked candidates, generating an improved output by capitalizing on their strengths and mitigating their weaknesses. To facilitate large-scale evaluation, we introduce a benchmark dataset, MixInstruct, which is a mixture of multiple instruction datasets featuring oracle pairwise comparisons. Our LLM-Blender significantly outperform individual LLMs and baseline methods across various metrics, establishing a substantial performance gap.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

This paper investigates data-driven segmentation using Re-Pair or Byte Pair Encoding-techniques. In contrast to previous work which has primarily been focused on subword units for machine translation, we are interested in the general properties of such segments above the word level. We call these segments r-grams, and discuss their properties and the effect they have on the token frequency distribution. The proposed approach is evaluated by demonstrating its viability in embedding techniques, both in monolingual and multilingual test settings. We also provide a number of qualitative examples of the proposed methodology, demonstrating its viability as a language-invariant segmentation procedure.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Positional Encodings (PEs) are a critical component of Transformer-based Large Language Models (LLMs), providing the attention mechanism with important sequence-position information. One of the most popular types of encoding used today in LLMs are Rotary Positional Encodings (RoPE), that rotate the queries and keys based on their relative distance. A common belief is that RoPE is useful because it helps to decay token dependency as relative distance increases. In this work, we argue that this is unlikely to be the core reason. We study the internals of a trained Gemma 7B model to understand how RoPE is being used at a mechanical level. We find that Gemma learns to use RoPE to construct robust "positional" attention patterns by exploiting the highest frequencies. We also find that, in general, Gemma greatly prefers to use the lowest frequencies of RoPE, which we suspect are used to carry semantic information. We mathematically prove interesting behaviours of RoPE and conduct experiments to verify our findings, proposing a modification of RoPE that fixes some highlighted issues and improves performance. We believe that this work represents an interesting step in better understanding PEs in LLMs, which we believe holds crucial value for scaling LLMs to large sizes and context lengths.

Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs, in terms of the minimum-cost edit sequence that transforms one graph to the other. However, the exact computation of GED is NP-Hard, which has recently motivated the design of neural methods for GED estimation. However, they do not explicitly account for edit operations with different costs. In response, we propose GRAPHEDX, a neural GED estimator that can work with general costs specified for the four edit operations, viz., edge deletion, edge addition, node deletion and node addition. We first present GED as a quadratic assignment problem (QAP) that incorporates these four costs. Then, we represent each graph as a set of node and edge embeddings and use them to design a family of neural set divergence surrogates. We replace the QAP terms corresponding to each operation with their surrogates. Computing such neural set divergence require aligning nodes and edges of the two graphs. We learn these alignments using a Gumbel-Sinkhorn permutation generator, additionally ensuring that the node and edge alignments are consistent with each other. Moreover, these alignments are cognizant of both the presence and absence of edges between node-pairs. Experiments on several datasets, under a variety of edit cost settings, show that GRAPHEDX consistently outperforms state-of-the-art methods and heuristics in terms of prediction error.

Speculative decoding is widely adopted to reduce latency in large language model (LLM) inference by leveraging smaller draft models capable of handling diverse user tasks. However, emerging AI applications, such as LLM-based agents, present unique workload characteristics: instead of diverse independent requests, agentic frameworks typically submit repetitive inference requests, such as multi-agent pipelines performing similar subtasks or self-refinement loops iteratively enhancing outputs. These workloads result in long and highly predictable sequences, which current speculative decoding methods do not effectively exploit. To address this gap, we introduce SuffixDecoding, a novel method that utilizes efficient suffix trees to cache long token sequences from prompts and previous outputs. By adaptively speculating more tokens when acceptance likelihood is high and fewer when it is low, SuffixDecoding effectively exploits opportunities for longer speculations while conserving computation when those opportunities are limited. Evaluations on agentic benchmarks, including SWE-Bench and Text-to-SQL, demonstrate that SuffixDecoding achieves speedups of up to 5.3times, outperforming state-of-the-art methods -- 2.8times faster than model-based approaches like EAGLE-2/3 and 1.9times faster than model-free approaches such as Token Recycling. SuffixDecoding is open-sourced at https://github.com/snowflakedb/ArcticInference

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model's ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, 'target' segments selectively attend only to the KV-caches of their designated 'source' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings. Code and the Graph-KV data are publicly available.

Recently, the retrieval models based on dense representations have been gradually applied in the first stage of the document retrieval tasks, showing better performance than traditional sparse vector space models. To obtain high efficiency, the basic structure of these models is Bi-encoder in most cases. However, this simple structure may cause serious information loss during the encoding of documents since the queries are agnostic. To address this problem, we design a method to mimic the queries on each of the documents by an iterative clustering process and represent the documents by multiple pseudo queries (i.e., the cluster centroids). To boost the retrieval process using approximate nearest neighbor search library, we also optimize the matching function with a two-step score calculation procedure. Experimental results on several popular ranking and QA datasets show that our model can achieve state-of-the-art results.

Graph Contrastive Learning (GCL) has emerged as a popular training approach for learning node embeddings from augmented graphs without labels. Despite the key principle that maximizing the similarity between positive node pairs while minimizing it between negative node pairs is well established, some fundamental problems are still unclear. Considering the complex graph structure, are some nodes consistently well-trained and following this principle even with different graph augmentations? Or are there some nodes more likely to be untrained across graph augmentations and violate the principle? How to distinguish these nodes and further guide the training of GCL? To answer these questions, we first present experimental evidence showing that the training of GCL is indeed imbalanced across all nodes. To address this problem, we propose the metric "node compactness", which is the lower bound of how a node follows the GCL principle related to the range of augmentations. We further derive the form of node compactness theoretically through bound propagation, which can be integrated into binary cross-entropy as a regularization. To this end, we propose the PrOvable Training (POT) for GCL, which regularizes the training of GCL to encode node embeddings that follows the GCL principle better. Through extensive experiments on various benchmarks, POT consistently improves the existing GCL approaches, serving as a friendly plugin.

Representation learning on text-attributed graphs (TAGs) integrates structural connectivity with rich textual semantics, enabling applications in diverse domains. Current methods largely rely on contrastive learning to maximize cross-modal similarity, assuming tighter coupling between graph and text representations improves transfer performance. However, our empirical analysis reveals that both natural gap expansion and forced gap reduction result in performance degradation by disrupting pre-trained knowledge structures and impairing generalization. This arises from the geometric incompatibility between encoders, where graph encoders capture topological patterns, while text encoders capture semantic structures. Over-alignment compresses these distinct spaces into shared subspaces, causing structure collapse that diminishes both topological reasoning and semantic understanding. We propose LLM4GTA, a gap-aware alignment framework that preserves representation gaps as geometric necessities for maintaining modality-specific knowledge and improving transfer performance. LLM4GTA includes an adaptive gap preservation module to prevent over-alignment by monitoring similarity evolution and an intra-modal compensation mechanism that boosts discriminative power using auxiliary classifiers in graph space. Extensive experiments show significant improvements over existing methods in zero-shot and few-shot scenarios.

Existing cross-encoder models can be categorized as pointwise, pairwise, or listwise. Pairwise and listwise models allow passage interactions, which typically makes them more effective than pointwise models but less efficient and less robust to input passage order permutations. To enable efficient permutation-invariant passage interactions during re-ranking, we propose a new cross-encoder architecture with inter-passage attention: the Set-Encoder. In experiments on TREC Deep Learning and TIREx, the Set-Encoder is as effective as state-of-the-art listwise models while being more efficient and invariant to input passage order permutations. Compared to pointwise models, the Set-Encoder is particularly more effective when considering inter-passage information, such as novelty, and retains its advantageous properties compared to other listwise models. Our code is publicly available at https://github.com/webis-de/ECIR-25.

We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can traverse any series of modules in any order. DNAs are a natural generalization of the sparse methods such as Mixture-of-Experts, Mixture-of-Depths, parameter sharing, etc. Computation and communication patterns of DNA modules are learnt end-to-end during training and depend on the content and context of each token (or patch). These patterns can be shaped by further requirements added to the optimization objective such as compute/memory efficiency or load balancing. We empirically show that (i) trained DNAs are competitive with the dense baselines in both domains and (ii) compute efficiency/parameter sharing can be learnt from data. Next, we analyze the emergent connectivity and computation patterns in the trained DNAs. We find that the paths that tokens take through the models are themselves distributed according to a power-law. We show that some paths (or, equivalently, groups of modules) show emergent specialization. Finally, we demonstrate that models learn to allocate compute and active parameters in an interpretable way.

Current state-of-the-art machine translation systems are based on encoder-decoder architectures, that first encode the input sequence, and then generate an output sequence based on the input encoding. Both are interfaced with an attention mechanism that recombines a fixed encoding of the source tokens based on the decoder state. We propose an alternative approach which instead relies on a single 2D convolutional neural network across both sequences. Each layer of our network re-codes source tokens on the basis of the output sequence produced so far. Attention-like properties are therefore pervasive throughout the network. Our model yields excellent results, outperforming state-of-the-art encoder-decoder systems, while being conceptually simpler and having fewer parameters.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

Pre-trained language models have been successful in natural language generation (NLG) tasks. While various decoding methods have been employed, they often produce suboptimal results. We first present an empirical analysis of three NLG tasks: summarization, machine translation, and constrained text generation. We found that selecting the best output from the results of multiple decoding methods can significantly improve performance. To further improve reranking for NLG tasks, we proposed a novel method, PairReranker, which uses a single encoder and a pairwise loss function to jointly encode a source input and a pair of candidates and compare them. Experiments on three NLG tasks demonstrated the effectiveness and flexibility of PairReranker, showing strong results, compared with previous baselines. In addition, our PairReranker can generalize to significantly improve GPT-3 (text-davinci-003) results (e.g., 24.55\% on CommonGen and 11.35\% on WMT18 zh-en), even though our rerankers are not trained with any GPT-3 candidates.

Foundation models like ChatGPT and GPT-4 have revolutionized artificial intelligence, exhibiting remarkable abilities to generalize across a wide array of tasks and applications beyond their initial training objectives. However, graph learning has predominantly focused on single-graph models, tailored to specific tasks or datasets, lacking the ability to transfer learned knowledge to different domains. This limitation stems from the inherent complexity and diversity of graph structures, along with the different feature and label spaces specific to graph data. In this paper, we recognize text as an effective unifying medium and employ Text-Attributed Graphs (TAGs) to leverage this potential. We present our UniGraph framework, designed to learn a foundation model for TAGs, which is capable of generalizing to unseen graphs and tasks across diverse domains. Unlike single-graph models that use pre-computed node features of varying dimensions as input, our approach leverages textual features for unifying node representations, even for graphs such as molecular graphs that do not naturally have textual features. We propose a novel cascaded architecture of Language Models (LMs) and Graph Neural Networks (GNNs) as backbone networks. Additionally, we propose the first pre-training algorithm specifically designed for large-scale self-supervised learning on TAGs, based on Masked Graph Modeling. We introduce graph instruction tuning using Large Language Models (LLMs) to enable zero-shot prediction ability. Our comprehensive experiments across various graph learning tasks and domains demonstrate the model's effectiveness in self-supervised representation learning on unseen graphs, few-shot in-context transfer, and zero-shot transfer, even surpassing or matching the performance of GNNs that have undergone supervised training on target datasets.

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

Existing work on prompt compression for Large Language Models (LLM) focuses on lossy methods that try to maximize the retention of semantic information that is relevant to downstream tasks while significantly reducing the sequence length. In this paper, we introduce a task-agnostic lossless compression technique similar to LZ77 that makes it possible to reduce the input token sequence length on average by 27\% and 18\% for the two evaluation tasks explored here. Given that we use transformer-based LLMs, this equates to 47\% and 33\% less encoding computation, respectively, due to the quadratic nature of attention. The token sequence transformation is trivial to reverse and highlights that no semantic information is lost in the process. We evaluate our proposed approach on two tasks that require strict preservation of semantics/syntax and demonstrate that existing lossy compression methods perform poorly in this setting. We find that our lossless compression technique produces only a small gap in performance compared to using the uncompressed input and posit that larger models and an expanded computing budget would likely erase the gap entirely.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

In this paper, we give an in-depth analysis on the mathematical problem formulations and the probabilistic optimization explorations for some of the key components in Transformer model [33] in the field of generative AI. We explore and discuss some potential further enhancement for current state of the art methods for some key underlying technologies of generative AI models from algorithmic and probabilistic optimization perspective. In particular, we present an optimal solution for sub-word encoding (SWE) based on similar initial settings as that of byte-pair encoding (BPE) algorithm in [9] with similar objectives as that of WordPiece approach in [28, 31] to maximize the likelihood of the training data. We also present cross entropy optimization method to optimize hyperparameters for word2vec model [17]. In addition, we propose a factored combination of rotary positional encoding (RoPE) [32] and attention with linear biases (ALiBi) [23] with a harmonic series. We also present a probabilistic FlashAttention [6, 7] (PrFlashAttention) method with a probability distribution over block distances in the matrix to decide which block is likely to participate in a given round of attention computation while maintaining the lower triangle shape of the tensor for autoregressive language models by re-shaping the tensors. Finally, we present staircase adaptive quantization (SAQ) of key-value (KV) cache for multi-query attention (MQA) based on the framework presented in [16] to have gradual quantization degradation while achieving reasonable model quality and cost savings.

Relational pooling is a framework for building more expressive and permutation-invariant graph neural networks. However, there is limited understanding of the exact enhancement in the expressivity of RP and its connection with the Weisfeiler Lehman hierarchy. Starting from RP, we propose to explicitly assign labels to nodes as additional features to improve expressive power of message passing neural networks. The method is then extended to higher dimensional WL, leading to a novel k,l-WL algorithm, a more general framework than k-WL. Theoretically, we analyze the expressivity of k,l-WL with respect to k and l and unifies it with a great number of subgraph GNNs. Complexity reduction methods are also systematically discussed to build powerful and practical k,l-GNN instances. We theoretically and experimentally prove that our method is universally compatible and capable of improving the expressivity of any base GNN model. Our k,l-GNNs achieve superior performance on many synthetic and real-world datasets, which verifies the effectiveness of our framework.

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

Recent techniques such as retrieval-augmented generation or chain-of-thought reasoning have led to longer contexts and increased inference costs. Context compression techniques can reduce these costs, but the most effective approaches require fine-tuning the target model or even modifying its architecture. This can degrade its general abilities when not used for this specific purpose. Here we explore an alternative approach: an encoder that compresses the context into continuous representations which replace token embeddings in decoder LLMs. First, we perform a systematic study of training strategies and architecture choices for the encoder. Our findings led to the design of an Adaptable text Representations Compressor, named ARC-Encoder, which outputs x-times fewer continuous representations (typically x!in!{4,8}) than text tokens. We evaluate ARC-Encoder across a variety of LLM usage scenarios, ranging from in-context learning to context window extension, on both instruct and base decoders. Results show that ARC-Encoder achieves state-of-the-art performance on several benchmarks while improving computational efficiency at inference. Finally, we demonstrate that our models can be adapted to multiple decoders simultaneously, allowing a single encoder to generalize across different decoder LLMs. This makes ARC-Encoder a flexible and efficient solution for portable encoders that work seamlessly with multiple LLMs. We release a training code at https://github.com/kyutai-labs/ARC-Encoder , fine-tuning dataset and pretrained models are available at https://huggingface.co/collections/kyutai/arc-encoders-68ee18787301407d60a57047 .

This paper proposes a fundamentally new paradigm for image generation through set-based tokenization and distribution modeling. Unlike conventional methods that serialize images into fixed-position latent codes with a uniform compression ratio, we introduce an unordered token set representation to dynamically allocate coding capacity based on regional semantic complexity. This TokenSet enhances global context aggregation and improves robustness against local perturbations. To address the critical challenge of modeling discrete sets, we devise a dual transformation mechanism that bijectively converts sets into fixed-length integer sequences with summation constraints. Further, we propose Fixed-Sum Discrete Diffusion--the first framework to simultaneously handle discrete values, fixed sequence length, and summation invariance--enabling effective set distribution modeling. Experiments demonstrate our method's superiority in semantic-aware representation and generation quality. Our innovations, spanning novel representation and modeling strategies, advance visual generation beyond traditional sequential token paradigms. Our code and models are publicly available at https://github.com/Gengzigang/TokenSet.

Network embedding has been intensively studied in the literature and widely used in various applications, such as link prediction and node classification. While previous work focus on the design of new algorithms or are tailored for various problem settings, the discussion of initialization strategies in the learning process is often missed. In this work, we address this important issue of initialization for network embedding that could dramatically improve the performance of the algorithms on both effectiveness and efficiency. Specifically, we first exploit the graph partition technique that divides the graph into several disjoint subsets, and then construct an abstract graph based on the partitions. We obtain the initialization of the embedding for each node in the graph by computing the network embedding on the abstract graph, which is much smaller than the input graph, and then propagating the embedding among the nodes in the input graph. With extensive experiments on various datasets, we demonstrate that our initialization technique significantly improves the performance of the state-of-the-art algorithms on the evaluations of link prediction and node classification by up to 7.76% and 8.74% respectively. Besides, we show that the technique of initialization reduces the running time of the state-of-the-arts by at least 20%.

Contrastive learning has recently achieved remarkable success in many domains including graphs. However contrastive loss, especially for graphs, requires a large number of negative samples which is unscalable and computationally prohibitive with a quadratic time complexity. Sub-sampling is not optimal and incorrect negative sampling leads to sampling bias. In this work, we propose a meta-node based approximation technique that can (a) proxy all negative combinations (b) in quadratic cluster size time complexity, (c) at graph level, not node level, and (d) exploit graph sparsity. By replacing node-pairs with additive cluster-pairs, we compute the negatives in cluster-time at graph level. The resulting Proxy approximated meta-node Contrastive (PamC) loss, based on simple optimized GPU operations, captures the full set of negatives, yet is efficient with a linear time complexity. By avoiding sampling, we effectively eliminate sample bias. We meet the criterion for larger number of samples, thus achieving block-contrastiveness, which is proven to outperform pair-wise losses. We use learnt soft cluster assignments for the meta-node constriction, and avoid possible heterophily and noise added during edge creation. Theoretically, we show that real world graphs easily satisfy conditions necessary for our approximation. Empirically, we show promising accuracy gains over state-of-the-art graph clustering on 6 benchmarks. Importantly, we gain substantially in efficiency; up to 3x in training time, 1.8x in inference time and over 5x in GPU memory reduction.

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However, existing approaches either overlook the inherent permutation symmetry in the neural network or rely on intricate weight-sharing patterns to achieve equivariance, while ignoring the impact of the network architecture itself. In this work, we propose to represent neural networks as computational graphs of parameters, which allows us to harness powerful graph neural networks and transformers that preserve permutation symmetry. Consequently, our approach enables a single model to encode neural computational graphs with diverse architectures. We showcase the effectiveness of our method on a wide range of tasks, including classification and editing of implicit neural representations, predicting generalization performance, and learning to optimize, while consistently outperforming state-of-the-art methods. The source code is open-sourced at https://github.com/mkofinas/neural-graphs.

The residual vector quantization (RVQ) technique plays a central role in recent advances in neural audio codecs. These models effectively synthesize high-fidelity audio from a limited number of codes due to the hierarchical structure among quantization levels. In this paper, we propose an encoding algorithm to further enhance the synthesis quality of RVQ-based neural codecs at test-time. Firstly, we point out the suboptimal nature of quantized vectors generated by conventional methods. We demonstrate that quantization error can be mitigated by selecting a different set of codes. Subsequently, we present our encoding algorithm, designed to identify a set of discrete codes that achieve a lower quantization error. We then apply the proposed method to pre-trained models and evaluate its efficacy using diverse metrics. Our experimental findings validate that our method not only reduces quantization errors, but also improves synthesis quality.

Code classification is a difficult issue in program understanding and automatic coding. Due to the elusive syntax and complicated semantics in programs, most existing studies use techniques based on abstract syntax tree (AST) and graph neural network (GNN) to create code representations for code classification. These techniques utilize the structure and semantic information of the code, but they only take into account pairwise associations and neglect the high-order correlations that already exist between nodes in the AST, which may result in the loss of code structural information. On the other hand, while a general hypergraph can encode high-order data correlations, it is homogeneous and undirected which will result in a lack of semantic and structural information such as node types, edge types, and directions between child nodes and parent nodes when modeling AST. In this study, we propose to represent AST as a heterogeneous directed hypergraph (HDHG) and process the graph by heterogeneous directed hypergraph neural network (HDHGN) for code classification. Our method improves code understanding and can represent high-order data correlations beyond paired interactions. We assess heterogeneous directed hypergraph neural network (HDHGN) on public datasets of Python and Java programs. Our method outperforms previous AST-based and GNN-based methods, which demonstrates the capability of our model.

With the emerging of huge amount of unlabeled data, unsupervised out-of-distribution (OOD) detection is vital for ensuring the reliability of graph neural networks (GNNs) by identifying OOD samples from in-distribution (ID) ones during testing, where encountering novel or unknown data is inevitable. Existing methods often suffer from compromised performance due to redundant information in graph structures, which impairs their ability to effectively differentiate between ID and OOD data. To address this challenge, we propose SEGO, an unsupervised framework that integrates structural entropy into OOD detection regarding graph classification. Specifically, within the architecture of contrastive learning, SEGO introduces an anchor view in the form of coding tree by minimizing structural entropy. The obtained coding tree effectively removes redundant information from graphs while preserving essential structural information, enabling the capture of distinct graph patterns between ID and OOD samples. Furthermore, we present a multi-grained contrastive learning scheme at local, global, and tree levels using triplet views, where coding trees with essential information serve as the anchor view. Extensive experiments on real-world datasets validate the effectiveness of SEGO, demonstrating superior performance over state-of-the-art baselines in OOD detection. Specifically, our method achieves the best performance on 9 out of 10 dataset pairs, with an average improvement of 3.7\% on OOD detection datasets, significantly surpassing the best competitor by 10.8\% on the FreeSolv/ToxCast dataset pair.

Standard Byte-Pair Encoding (BPE) tokenization compresses text by pairing a learned token vocabulary with a detailed merge list. Recent work has shown that this merge list exposes a potential attack surface for extracting information about language model's training data. In this paper, we explore the downstream impact of BPE inference algorithms that do not rely on this merge list at all, and hence differ from the encoding process during BPE training. To address this question, we investigate two broad classes of BPE inference schemes that differ from BPE application during training: a) targeted deviation from merge-lists including random merge orders, and various corruptions of merge list involving deletion/truncation, and b) non-targeted BPE inference algorithms that do not depend on the merge list but focus on compressing the text either greedily or exactly. Extensive experiments across diverse language modeling tasks like accuracy-based QA benchmarks, machine translation, and open-ended generation reveal that while targeted deviation from the merge lists exhibits significant degradation in language model performance, the non-targeted merge-list-free inference algorithms result in minimal impact on downstream performance that is often much smaller than expected. These findings pave way for simpler and potentially more privacy-preserving tokenization schemes that do not catastrophically compromise model performance.

The prevalent use of Byte Pair Encoding (BPE) in Large Language Models (LLMs) facilitates robust handling of subword units and avoids issues of out-of-vocabulary words. Despite its success, a critical challenge persists: long tokens, rich in semantic information, have fewer occurrences in tokenized datasets compared to short tokens, which can result in imbalanced learning issue across different tokens. To address that, we propose LBPE, which prioritizes long tokens during the encoding process. LBPE generates tokens according to their reverse ranks of token length rather than their ranks in the vocabulary, granting longer tokens higher priority during the encoding process. Consequently, LBPE smooths the frequency differences between short and long tokens, and thus mitigates the learning imbalance. Extensive experiments across diverse language modeling tasks demonstrate that LBPE consistently outperforms the original BPE, well demonstrating its effectiveness.

Efficient real-world deployments of large language models (LLMs) rely on Key-Value (KV) caching for processing and generating long outputs, reducing the need for repetitive computation. For large contexts, Key-Value caches can take up tens of gigabytes of device memory, as they store vector representations for each token and layer. Recent work has shown that the cached vectors can be compressed through quantization, pruning or merging, but these techniques often compromise quality towards higher compression rates. In this work, we aim to improve Key & Value compression by exploiting two observations: 1) the inherent dependencies between keys and values across different layers, and 2) high-compression mechanisms for internal network states. We propose AQUA-KV, an adaptive quantization for Key-Value caches that relies on compact adapters to exploit existing dependencies between Keys and Values, and aims to "optimally" compress the information that cannot be predicted. AQUA-KV significantly improves compression rates, while maintaining high accuracy on state-of-the-art LLM families. On Llama 3.2 LLMs, we achieve near-lossless inference at 2-2.5 bits per value with under 1% relative error in perplexity and LongBench scores. AQUA-KV is one-shot, simple, and efficient: it can be calibrated on a single GPU within 1-6 hours, even for 70B models.

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.

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA folding model. Understanding the specific local structures (i.e., "motifs") that contribute to undesignability is crucial for refining RNA folding models and determining the limits of RNA designability. Despite its importance, this problem has received very little attention, and previous efforts are neither scalable nor interpretable. We develop a new theoretical framework for motif (un-)designability, and design scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identify 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Our source code is available at https://github.com/shanry/RNA-Undesign and our web server is available at http://linearfold.org/motifs.

Text-to-Image (T2I) models often suffer from issues such as semantic leakage, incorrect feature binding, and omissions of key concepts in the generated image. This work studies these phenomena by looking into the role of information flow between textual token representations. To this end, we generate images by applying the diffusion component on a subset of contextual token representations in a given prompt and observe several interesting phenomena. First, in many cases, a word or multiword expression is fully represented by one or two tokens, while other tokens are redundant. For example, in "San Francisco's Golden Gate Bridge", the token "gate" alone captures the full expression. We demonstrate the redundancy of these tokens by removing them after textual encoding and generating an image from the resulting representation. Surprisingly, we find that this process not only maintains image generation performance but also reduces errors by 21\% compared to standard generation. We then show that information can also flow between different expressions in a sentence, which often leads to semantic leakage. Based on this observation, we propose a simple, training-free method to mitigate semantic leakage: replacing the leaked item's representation after the textual encoding with its uncontextualized representation. Remarkably, this simple approach reduces semantic leakage by 85\%. Overall, our work provides a comprehensive analysis of information flow across textual tokens in T2I models, offering both novel insights and practical benefits.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

The rapid scaling of Large Language Models (LLMs) elevates inference costs and compounds substantial deployment barriers. While quantization to 8 or 4 bits mitigates this, sub-3-bit methods face severe accuracy, scalability, and efficiency degradation. We propose Convolutional Code Quantization (CCQ), an inference-optimized quantization approach compressing LLMs to 2.0-2.75 bits with minimal accuracy loss. Departing from error-prone scalar quantization or slow vector quantization, CCQ integrates a hardware-aware bit-shift encoding and decoding solution with Convolutional Code, Hybrid Encoding, and Code Cluster, jointly overcoming accuracy-speed bottlenecks. We construct a lookup-free encoding space, enabling a linear mapping between the codebook and weight vectors, thereby optimizing inference performance. Meanwhile, by drawing on the concept of data mapping from vector quantization, we minimize the performance degradation of the model under extremely low-bit conditions. Experiments demonstrate that CCQ achieves outstanding performance on LLMs across various benchmarks. We compress DeepSeek-V3 (671B total parameters) to 184GB and ERNIE-4.5-300B-A47B to 89GB, enabling single-GPU deployment of ERNIE 4.5 and eliminating inter-card communication. The 2-bit ERNIE-4.5-300B-A47B model and inference engine have been open-sourced.