Le Song

Yuchen Zhuang, Yinghao Li, Jerry Junyang Cheung et al. · gatech

We study the problem of extracting N-ary relation tuples from scientific articles. This task is challenging because the target knowledge tuples can reside in multiple parts and modalities of the document. Our proposed method ReSel decomposes this task into a two-stage procedure that first retrieves the most relevant paragraph/table and then selects the target entity from the retrieved component. For the high-level retrieval stage, ReSel designs a simple and effective feature set, which captures multi-level lexical and semantic similarities between the query and components. For the low-level selection stage, ReSel designs a cross-modal entity correlation graph along with a multi-view architecture, which models both semantic and document-structural relations between entities. Our experiments on three scientific information extraction datasets show that ReSel outperforms state-of-the-art baselines significantly.

Rongzhi Zhang, Yue Yu, Pranav Shetty et al.

Weakly-supervised learning (WSL) has shown promising results in addressing label scarcity on many NLP tasks, but manually designing a comprehensive, high-quality labeling rule set is tedious and difficult. We study interactive weakly-supervised learning -- the problem of iteratively and automatically discovering novel labeling rules from data to improve the WSL model. Our proposed model, named PRBoost, achieves this goal via iterative prompt-based rule discovery and model boosting. It uses boosting to identify large-error instances and then discovers candidate rules from them by prompting pre-trained LMs with rule templates. The candidate rules are judged by human experts, and the accepted rules are used to generate complementary weak labels and strengthen the current model. Experiments on four tasks show PRBoost outperforms state-of-the-art WSL baselines up to 7.1% and bridges the gaps with fully supervised models. Our Implementation is available at \url{https://github.com/rz-zhang/PRBoost}.

Dingmin Wang, Shengchao Liu, Hanchen Wang et al. · stanford

Graph Neural Networks (GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the first-order Weisfeiler-Lehman test (1-WL). An effective approach to this challenge is to explicitly retrieve some annotated examples used to enhance GNN models. While retrieval-enhanced models have been proved to be effective in many language and vision domains, it remains an open question how effective retrieval-enhanced GNNs are when applied to graph datasets. Motivated by this, we want to explore how the retrieval idea can help augment the useful information learned in the graph neural networks, and we design a retrieval-enhanced scheme called GRAPHRETRIEVAL, which is agnostic to the choice of graph neural network models. In GRAPHRETRIEVAL, for each input graph, similar graphs together with their ground-true labels are retrieved from an existing database. Thus they can act as a potential enhancement to complete various graph property predictive tasks. We conduct comprehensive experiments over 13 datasets, and we observe that GRAPHRETRIEVAL is able to reach substantial improvements over existing GNNs. Moreover, our empirical study also illustrates that retrieval enhancement is a promising remedy for alleviating the long-tailed label distribution problem.

Ruijia Wang, Xiao Wang, Chuan Shi et al.

Recent studies show that graph convolutional network (GCN) often performs worse for low-degree nodes, exhibiting the so-called structural unfairness for graphs with long-tailed degree distributions prevalent in the real world. Graph contrastive learning (GCL), which marries the power of GCN and contrastive learning, has emerged as a promising self-supervised approach for learning node representations. How does GCL behave in terms of structural fairness? Surprisingly, we find that representations obtained by GCL methods are already fairer to degree bias than those learned by GCN. We theoretically show that this fairness stems from intra-community concentration and inter-community scatter properties of GCL, resulting in a much clear community structure to drive low-degree nodes away from the community boundary. Based on our theoretical analysis, we further devise a novel graph augmentation method, called GRAph contrastive learning for DEgree bias (GRADE), which applies different strategies to low- and high-degree nodes. Extensive experiments on various benchmarks and evaluation protocols validate the effectiveness of the proposed method.

Zhihang Hu, Qinze Yu, Yucheng Guo et al.

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the vast combinatorial search space. Recently, computational approaches, specifically deep learning models have emerged as an efficient way to discover synergistic combinations. While previous methods reported fair performance, their models usually do not take advantage of multi-modal data and they are unable to handle new drugs or cell lines. In this study, we collected data from various datasets covering various drug-related aspects. Then, we take advantage of large-scale pre-training models to generate informative representations and features for drugs, proteins, and diseases. Based on that, a message-passing graph is built on top to propagate information together with graph structure learning flexibility. This is first introduced in the biological networks and enables us to generate pseudo-relations in the graph. Our framework achieves state-of-the-art results in comparison with other deep learning-based methods on synergistic prediction benchmark datasets. We are also capable of inferencing new drug combination data in a test on an independent set released by AstraZeneca, where 10% of improvement over previous methods is observed. In addition, we're robust against unseen drugs and surpass almost 15% AU ROC compared to the second-best model. We believe our framework contributes to both the future wet-lab discovery of novel drugs and the building of promising guidance for precise combination medicine.

Mengyang Liu, Shanchuan Li, Xinshi Chen et al.

Graph neural networks (GNNs) enable the analysis of graphs using deep learning, with promising results in capturing structured information in graphs. This paper focuses on creating a small graph to represent the original graph, so that GNNs trained on the size-reduced graph can make accurate predictions. We view the original graph as a distribution of receptive fields and aim to synthesize a small graph whose receptive fields share a similar distribution. Thus, we propose Graph Condesation via Receptive Field Distribution Matching (GCDM), which is accomplished by optimizing the synthetic graph through the use of a distribution matching loss quantified by maximum mean discrepancy (MMD). Additionally, we demonstrate that the synthetic graph generated by GCDM is highly generalizable to a variety of models in evaluation phase and that the condensing speed is significantly improved using this framework.

Yining Wang, Xumeng Gong, Shaochuan Li et al.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

Mengyang Liu, Haozheng Luo, Leonard Thong et al.

Weak labeling is a popular weak supervision strategy for Named Entity Recognition (NER) tasks, with the goal of reducing the necessity for hand-crafted annotations. Although there are numerous remarkable annotation tools for NER labeling, the subject of integrating weak labeling sources is still unexplored. We introduce a web-based tool for text annotation called SciAnnotate, which stands for scientific annotation tool. Compared to frequently used text annotation tools, our annotation tool allows for the development of weak labels in addition to providing a manual annotation experience. Our tool provides users with multiple user-friendly interfaces for creating weak labels. SciAnnotate additionally allows users to incorporate their own language models and visualize the output of their model for evaluation. In this study, we take multi-source weak label denoising as an example, we utilized a Bertifying Conditional Hidden Markov Model to denoise the weak label generated by our tool. We also evaluate our annotation tool against the dataset provided by Mysore which contains 230 annotated materials synthesis procedures. The results shows that a 53.7% reduction in annotation time obtained AND a 1.6\% increase in recall using weak label denoising. Online demo is available at https://sciannotate.azurewebsites.net/(demo account can be found in README), but we don't host a model server with it, please check the README in supplementary material for model server usage.

Min Zhao, Xin Guo, Le Song et al.

The environment of most real-world scenarios such as malls and supermarkets changes at all times. A pre-built map that does not account for these changes becomes out-of-date easily. Therefore, it is necessary to have an up-to-date model of the environment to facilitate long-term operation of a robot. To this end, this paper presents a general lifelong simultaneous localization and mapping (SLAM) framework. Our framework uses a multiple session map representation, and exploits an efficient map updating strategy that includes map building, pose graph refinement and sparsification. To mitigate the unbounded increase of memory usage, we propose a map-trimming method based on the Chow-Liu maximum-mutual-information spanning tree. The proposed SLAM framework has been comprehensively validated by over a month of robot deployment in real supermarket environment. Furthermore, we release the dataset collected from the indoor and outdoor changing environment with the hope to accelerate lifelong SLAM research in the community. Our dataset is available at https://github.com/sanduan168/lifelong-SLAM-dataset.

Karan Samel, Zelin Zhao, Binghong Chen et al.

Events across a timeline are a common data representation, seen in different temporal modalities. Individual atomic events can occur in a certain temporal ordering to compose higher level composite events. Examples of a composite event are a patient's medical symptom or a baseball player hitting a home run, caused distinct temporal orderings of patient vitals and player movements respectively. Such salient composite events are provided as labels in temporal datasets and most works optimize models to predict these composite event labels directly. We focus on uncovering the underlying atomic events and their relations that lead to the composite events within a noisy temporal data setting. We propose Neural Temporal Logic Programming (Neural TLP) which first learns implicit temporal relations between atomic events and then lifts logic rules for composite events, given only the composite events labels for supervision. This is done through efficiently searching through the combinatorial space of all temporal logic rules in an end-to-end differentiable manner. We evaluate our method on video and healthcare datasets where it outperforms the baseline methods for rule discovery.

Xinshi Chen, Yan Zhu, Haowen Xu et al.

Dynamic graphs with ordered sequences of events between nodes are prevalent in real-world industrial applications such as e-commerce and social platforms. However, representation learning for dynamic graphs has posed great computational challenges due to the time and structure dependency and irregular nature of the data, preventing such models from being deployed to real-world applications. To tackle this challenge, we propose an efficient algorithm, Efficient Dynamic Graph lEarning (EDGE), which selectively expresses certain temporal dependency via training loss to improve the parallelism in computations. We show that EDGE can scale to dynamic graphs with millions of nodes and hundreds of millions of temporal events and achieve new state-of-the-art (SOTA) performance.

James Fox, Bo Zhao, Sivasankaran Rajamanickam et al.

Learning 3D representations that generalize well to arbitrarily oriented inputs is a challenge of practical importance in applications varying from computer vision to physics and chemistry. We propose a novel multi-resolution convolutional architecture for learning over concentric spherical feature maps, of which the single sphere representation is a special case. Our hierarchical architecture is based on alternatively learning to incorporate both intra-sphere and inter-sphere information. We show the applicability of our method for two different types of 3D inputs, mesh objects, which can be regularly sampled, and point clouds, which are irregularly distributed. We also propose an efficient mapping of point clouds to concentric spherical images, thereby bridging spherical convolutions on grids with general point clouds. We demonstrate the effectiveness of our approach in improving state-of-the-art performance on 3D classification tasks with rotated data.

Rohit Batra, Hanjun Dai, Tran Doan Huan et al.

The design/discovery of new materials is highly non-trivial owing to the near-infinite possibilities of material candidates, and multiple required property/performance objectives. Thus, machine learning tools are now commonly employed to virtually screen material candidates with desired properties by learning a theoretical mapping from material-to-property space, referred to as the \emph{forward} problem. However, this approach is inefficient, and severely constrained by the candidates that human imagination can conceive. Thus, in this work on polymers, we tackle the materials discovery challenge by solving the \emph{inverse} problem: directly generating candidates that satisfy desired property/performance objectives. We utilize syntax-directed variational autoencoders (VAE) in tandem with Gaussian process regression (GPR) models to discover polymers expected to be robust under three extreme conditions: (1) high temperatures, (2) high electric field, and (3) high temperature \emph{and} high electric field, useful for critical structural, electrical and energy storage applications. This approach to learn from (and augment) human ingenuity is general, and can be extended to discover polymers with other targeted properties and performance measures.

Chao Qu, Hui Li, Chang Liu et al.

We propose a \emph{collaborative} multi-agent reinforcement learning algorithm named variational policy propagation (VPP) to learn a \emph{joint} policy through the interactions over agents. We prove that the joint policy is a Markov Random Field under some mild conditions, which in turn reduces the policy space effectively. We integrate the variational inference as special differentiable layers in policy such that the actions can be efficiently sampled from the Markov Random Field and the overall policy is differentiable. We evaluate our algorithm on several large scale challenging tasks and demonstrate that it outperforms previous state-of-the-arts.

Jianbo Chen, Le Song, Martin J. Wainwright et al.

We study instancewise feature importance scoring as a method for model interpretation. Any such method yields, for each predicted instance, a vector of importance scores associated with the feature vector. Methods based on the Shapley score have been proposed as a fair way of computing feature attributions of this kind, but incur an exponential complexity in the number of features. This combinatorial explosion arises from the definition of the Shapley value and prevents these methods from being scalable to large data sets and complex models. We focus on settings in which the data have a graph structure, and the contribution of features to the target variable is well-approximated by a graph-structured factorization. In such settings, we develop two algorithms with linear complexity for instancewise feature importance scoring. We establish the relationship of our methods to the Shapley value and another closely related concept known as the Myerson value from cooperative game theory. We demonstrate on both language and image data that our algorithms compare favorably with other methods for model interpretation.