Xinyu Yuan

Mikhail Galkin, Xinyu Yuan, Hesham Mostafa et al. · deepmind

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

Zhaocheng Zhu, Xinyu Yuan, Mikhail Galkin et al. · deepmind

Reasoning on large-scale knowledge graphs has been long dominated by embedding methods. While path-based methods possess the inductive capacity that embeddings lack, their scalability is limited by the exponential number of paths. Here we present A*Net, a scalable path-based method for knowledge graph reasoning. Inspired by the A* algorithm for shortest path problems, our A*Net learns a priority function to select important nodes and edges at each iteration, to reduce time and memory footprint for both training and inference. The ratio of selected nodes and edges can be specified to trade off between performance and efficiency. Experiments on both transductive and inductive knowledge graph reasoning benchmarks show that A*Net achieves competitive performance with existing state-of-the-art path-based methods, while merely visiting 10% nodes and 10% edges at each iteration. On a million-scale dataset ogbl-wikikg2, A*Net not only achieves a new state-of-the-art result, but also converges faster than embedding methods. A*Net is the first path-based method for knowledge graph reasoning at such scale.

Minghao Xu, Xinyu Yuan, Santiago Miret et al.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Hung-Min Hsu, Xinyu Yuan, Baohua Zhu et al.

Package theft detection has been a challenging task mainly due to lack of training data and a wide variety of package theft cases in reality. In this paper, we propose a new Global and Local Fusion Package Theft Detection Embedding (GLF-PTDE) framework to generate package theft scores for each segment within a video to fulfill the real-world requirements on package theft detection. Moreover, we construct a novel Package Theft Detection dataset to facilitate the research on this task. Our method achieves 80% AUC performance on the newly proposed dataset, showing the effectiveness of the proposed GLF-PTDE framework and its robustness in different real scenes for package theft detection.

Xinyu Yuan, Zichen Wang, Marcus Collins et al.

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

Xinyu Yuan, Yan Qiao, Meng Li et al.

Estimating the frequency of items on the high-volume, fast data stream has been extensively studied in many areas, such as database and network measurement. Traditional sketches provide only coarse estimates under strict memory constraints. Although some learning-augmented methods have emerged recently, they typically rely on offline training with real frequencies or/and labels, which are often unavailable. Moreover, these methods suffer from slow update speeds, limiting their suitability for real-time processing despite offering only marginal accuracy improvements. To overcome these challenges, we propose UCL-sketch, a practical learning-based paradigm for per-key frequency estimation. Our design introduces two key innovations: (i) an online training mechanism based on equivalent learning that requires no ground truth (GT), and (ii) a highly scalable architecture leveraging logically structured estimation buckets to scale to real-world data stream. The UCL-sketch, which utilizes compressive sensing (CS), converges to an estimator that provably yields a error bound far lower than that of prior works, without sacrificing the speed of processing. Extensive experiments on both real-world and synthetic datasets demonstrate that our approach outperforms previously proposed approaches regarding per-key accuracy and distribution. Notably, under extremely tight memory budgets, its quality almost matches that of an (infeasible) omniscient oracle. Moreover, compared to the existing equation-based sketch, UCL-sketch achieves an average decoding speedup of nearly 500 times. To help further research and development, our code is publicly available at https://github.com/Y-debug-sys/UCL-sketch.

Xinyu Yuan, Yan Qiao, Pei Zhao et al.

The traffic matrix estimation (TME) problem has been widely researched for decades of years. Recent progresses in deep generative models offer new opportunities to tackle TME problems in a more advanced way. In this paper, we leverage the powerful ability of denoising diffusion probabilistic models (DDPMs) on distribution learning, and for the first time adopt DDPM to address the TME problem. To ensure a good performance of DDPM on learning the distributions of TMs, we design a preprocessing module to reduce the dimensions of TMs while keeping the data variety of each OD flow. To improve the estimation accuracy, we parameterize the noise factors in DDPM and transform the TME problem into a gradient-descent optimization problem. Finally, we compared our method with the state-of-the-art TME methods using two real-world TM datasets, the experimental results strongly demonstrate the superiority of our method on both TM synthesis and TM estimation.

Zhaocheng Zhu, Chence Shi, Zuobai Zhang et al.

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.