Yi Liu

Limei Wang, Haoran Liu, Yi Liu et al.

We consider representation learning for proteins with 3D structures. We build 3D graphs based on protein structures and develop graph networks to learn their representations. Depending on the levels of details that we wish to capture, protein representations can be computed at different levels, \emph{e.g.}, the amino acid, backbone, or all-atom levels. Importantly, there exist hierarchical relations among different levels. In this work, we propose to develop a novel hierarchical graph network, known as ProNet, to capture the relations. Our ProNet is very flexible and can be used to compute protein representations at different levels of granularity. By treating each amino acid as a node in graph modeling as well as harnessing the inherent hierarchies, our ProNet is more effective and efficient than existing methods. We also show that, given a base 3D graph network that is complete, our ProNet representations are also complete at all levels. Experimental results show that ProNet outperforms recent methods on most datasets. In addition, results indicate that different downstream tasks may require representations at different levels. Our code is publicly available as part of the DIG library (\url{https://github.com/divelab/DIG}).

Zeyu Qin, Yanbo Fan, Yi Liu et al.

Deep neural networks (DNNs) have been shown to be vulnerable to adversarial examples, which can produce erroneous predictions by injecting imperceptible perturbations. In this work, we study the transferability of adversarial examples, which is significant due to its threat to real-world applications where model architecture or parameters are usually unknown. Many existing works reveal that the adversarial examples are likely to overfit the surrogate model that they are generated from, limiting its transfer attack performance against different target models. To mitigate the overfitting of the surrogate model, we propose a novel attack method, dubbed reverse adversarial perturbation (RAP). Specifically, instead of minimizing the loss of a single adversarial point, we advocate seeking adversarial example located at a region with unified low loss value, by injecting the worst-case perturbation (the reverse adversarial perturbation) for each step of the optimization procedure. The adversarial attack with RAP is formulated as a min-max bi-level optimization problem. By integrating RAP into the iterative process for attacks, our method can find more stable adversarial examples which are less sensitive to the changes of decision boundary, mitigating the overfitting of the surrogate model. Comprehensive experimental comparisons demonstrate that RAP can significantly boost adversarial transferability. Furthermore, RAP can be naturally combined with many existing black-box attack techniques, to further boost the transferability. When attacking a real-world image recognition system, Google Cloud Vision API, we obtain 22% performance improvement of targeted attacks over the compared method. Our codes are available at https://github.com/SCLBD/Transfer_attack_RAP.

Junyi Chai, Reid Pryzant, Victor Ye Dong et al. · amazon-science

Controllable text generation systems often leverage control codes to direct various properties of the output like style and length. Inspired by recent work on causal inference for NLP, this paper reveals a previously overlooked flaw in these control code-based conditional text generation algorithms. Spurious correlations in the training data can lead models to incorrectly rely on parts of the input other than the control code for attribute selection, significantly undermining downstream generation quality and controllability. We demonstrate the severity of this issue with a series of case studies and then propose two simple techniques to reduce these correlations in training sets. The first technique is based on resampling the data according to an example's propensity towards each linguistic attribute (IPS). The second produces multiple counterfactual versions of each example and then uses an additional feedback mechanism to remove noisy examples (feedback aware self-training, FAST). We evaluate on 3 tasks -- news headline, meta review, and search ads generation -- and demonstrate that FAST can significantly improve the controllability and language quality of generated outputs when compared to state-of-the-art controllable text generation approaches.

Oliver Lloyd, Yi Liu, Tom Gaunt

Embedding knowledge graphs into low-dimensional spaces is a popular method for applying approaches, such as link prediction or node classification, to these databases. This embedding process is very costly in terms of both computational time and space. Part of the reason for this is the optimisation of hyperparameters, which involves repeatedly sampling, by random, guided, or brute-force selection, from a large hyperparameter space and testing the resulting embeddings for their quality. However, not all hyperparameters in this search space will be equally important. In fact, with prior knowledge of the relative importance of the hyperparameters, some could be eliminated from the search altogether without significantly impacting the overall quality of the outputted embeddings. To this end, we ran a Sobol sensitivity analysis to evaluate the effects of tuning different hyperparameters on the variance of embedding quality. This was achieved by performing thousands of embedding trials, each time measuring the quality of embeddings produced by different hyperparameter configurations. We regressed the embedding quality on those hyperparameter configurations, using this model to generate Sobol sensitivity indices for each of the hyperparameters. By evaluating the correlation between Sobol indices, we find substantial variability in the hyperparameter sensitivities between knowledge graphs, with differing dataset characteristics being the probable cause of these inconsistencies. As an additional contribution of this work we identify several relations in the UMLS knowledge graph that may cause data leakage via inverse relations, and derive and present UMLS-43, a leakage-robust variant of that graph.

Ting Sun, Cheng Cui, Yuning Du et al.

Document layout analysis is a critical preprocessing step in document intelligence, enabling the detection and localization of structural elements such as titles, text blocks, tables, and formulas. Despite its importance, existing layout detection models face significant challenges in generalizing across diverse document types, handling complex layouts, and achieving real-time performance for large-scale data processing. To address these limitations, we present PP-DocLayout, which achieves high precision and efficiency in recognizing 23 types of layout regions across diverse document formats. To meet different needs, we offer three models of varying scales. PP-DocLayout-L is a high-precision model based on the RT-DETR-L detector, achieving 90.4% mAP@0.5 and an end-to-end inference time of 13.4 ms per page on a T4 GPU. PP-DocLayout-M is a balanced model, offering 75.2% mAP@0.5 with an inference time of 12.7 ms per page on a T4 GPU. PP-DocLayout-S is a high-efficiency model designed for resource-constrained environments and real-time applications, with an inference time of 8.1 ms per page on a T4 GPU and 14.5 ms on a CPU. This work not only advances the state of the art in document layout analysis but also provides a robust solution for constructing high-quality training data, enabling advancements in document intelligence and multimodal AI systems. Code and models are available at https://github.com/PaddlePaddle/PaddleX .

Ren Li, Yanan Cao, Qiannan Zhu et al.

Knowledge Graph Embedding (KGE) aims to learn representations for entities and relations. Most KGE models have gained great success, especially on extrapolation scenarios. Specifically, given an unseen triple (h, r, t), a trained model can still correctly predict t from (h, r, ?), or h from (?, r, t), such extrapolation ability is impressive. However, most existing KGE works focus on the design of delicate triple modeling function, which mainly tells us how to measure the plausibility of observed triples, but offers limited explanation of why the methods can extrapolate to unseen data, and what are the important factors to help KGE extrapolate. Therefore in this work, we attempt to study the KGE extrapolation of two problems: 1. How does KGE extrapolate to unseen data? 2. How to design the KGE model with better extrapolation ability? For the problem 1, we first discuss the impact factors for extrapolation and from relation, entity and triple level respectively, propose three Semantic Evidences (SEs), which can be observed from train set and provide important semantic information for extrapolation. Then we verify the effectiveness of SEs through extensive experiments on several typical KGE methods. For the problem 2, to make better use of the three levels of SE, we propose a novel GNN-based KGE model, called Semantic Evidence aware Graph Neural Network (SE-GNN). In SE-GNN, each level of SE is modeled explicitly by the corresponding neighbor pattern, and merged sufficiently by the multi-layer aggregation, which contributes to obtaining more extrapolative knowledge representation. Finally, through extensive experiments on FB15k-237 and WN18RR datasets, we show that SE-GNN achieves state-of-the-art performance on Knowledge Graph Completion task and performs a better extrapolation ability. Our code is available at https://github.com/renli1024/SE-GNN.

Weizhi Fei, Xueyan Niu, Guoqing Xie et al. · tsinghua

Although applications involving long-context inputs are crucial for the effective utilization of large language models (LLMs), they also result in increased computational costs and reduced performance. To address this challenge, we propose an efficient, training-free prompt compression method that retains key information within compressed prompts. We identify specific attention heads in transformer-based LLMs, which we designate as evaluator heads, that are capable of selecting tokens in long inputs that are most significant for inference. Building on this discovery, we develop EHPC, an Evaluator Head-based Prompt Compression method, which enables LLMs to rapidly "skim through" input prompts by leveraging only the first few layers with evaluator heads during the pre-filling stage, subsequently passing only the important tokens to the model for inference. EHPC achieves state-of-the-art results across two mainstream benchmarks: prompt compression and long-context inference acceleration. Consequently, it effectively reduces the complexity and costs associated with commercial API calls. We further demonstrate that EHPC attains competitive results compared to key-value cache-based acceleration methods, thereby highlighting its potential to enhance the efficiency of LLMs for long-context tasks.