Computational methods for analysing multiscale 3D genome organization.

Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph learning methods to boost prediction performance. However, obtaining the geometric structure of molecules is not feasible in many real-world applications due to the high computational cost. In this work, we propose a novel 3D pre-training framework (dubbed 3D PGT), which pre-trains a model on 3D molecular graphs, and then fine-tunes it on molecular graphs without 3D structures. Based on fact that bond length, bond angle, and dihedral angle are three basic geometric descriptors corresponding to a complete molecular 3D conformer, we first develop a multi-task generative pre-train framework based on these three attributes. Next, to automatically fuse these three generative tasks, we design a surrogate metric using the \textit{total energy} to search for weight distribution of the three pretext task since total energy corresponding to the quality of 3D conformer.Extensive experiments on 2D molecular graphs are conducted to demonstrate the accuracy, efficiency and generalization ability of the proposed 3D PGT compared to various pre-training baselines.

pdf/automated-3d-pre-training-for-molecular-property-prediction-2rn22au7.pdf

Automated 3D Pre-Training for Molecular Property Prediction

We present Mask-then-Fill, a flexible and effective data augmentation framework for event extraction. Our approach allows for more flexible manipulation of text and thus can generate more diverse data while keeping the original event structure unchanged as much as possible. Specifically, it first randomly masks out an adjunct sentence fragment and then infills a variable-length text span with a fine-tuned infilling model. The main advantage lies in that it can replace a fragment of arbitrary length in the text with another fragment of variable length, compared to the existing methods which can only replace a single word or a fixed-length fragment. On trigger and argument extraction tasks, the proposed framework is more effective than baseline methods and it demonstrates particularly strong results in the low-resource setting. Our further analysis shows that it achieves a good balance between diversity and distributional similarity.

pdf/mask-then-fill-a-flexible-and-effective-data-augmentation-1g83niif.pdf

Mask-then-Fill: A Flexible and Effective Data Augmentation Framework for Event Extraction

We present Mask-then-Fill, a flexible and effective data augmentation framework for event extraction.Our approach allows for more flexible manipulation of text and thus can generate more diverse data while keeping the original event structure unchanged as much as possible.Specifically, it first randomly masks out an adjunct sentence fragment and then infills a variable-length text span with a fine-tuned infilling model.The main advantage lies in that it can replace a fragment of arbitrary length in the text with another fragment of variable length, compared to the existing methods which can only replace a single word or a fixed-length fragment.On trigger and argument extraction tasks, the proposed framework is more effective than baseline methods and it demonstrates particularly strong results in the low-resource setting.Our further analysis shows that it achieves a good balance between diversity and distributional similarity. 

pdf/mask-then-fill-a-flexible-and-effective-data-augmentation-53b1vliu73.pdf

Cancer is rarely the straightforward consequence of an abnormality in a single gene, but rather reflects a complex interplay of many genes, represented as gene modules. Here, we leverage the recent advances of model-agnostic interpretation approach and develop CGMega, an explainable and graph attention-based deep learning framework to perform cancer gene module dissection. CGMega outperforms current approaches in cancer gene prediction, and it provides a promising approach to integrate multi-omics information. We apply CGMega to breast cancer cell line and acute myeloid leukemia (AML) patients, and we uncover the high-order gene module formed by ErbB family and tumor factors NRG1, PPM1A and DLG2. We identify 396 candidate AML genes, and observe the enrichment of either known AML genes or candidate AML genes in a single gene module. We also identify patient-specific AML genes and associated gene modules. Together, these results indicate that CGMega can be used to dissect cancer gene modules, and provide high-order mechanistic insights into cancer development and heterogeneity. 

CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection

Zero-shot cross-lingual event argument extraction (EAE) is a challenging yet practical problem in Information Extraction. Most previous works heavily rely on external structured linguistic features, which are not easily accessible in real-world scenarios. This paper investigates a translation-based method to implicitly project annotations from the source language to the target language. With the use of translation-based parallel corpora, no additional linguistic features are required during training and inference. As a result, the proposed approach is more cost effective than previous works on zero-shot cross-lingual EAE. Moreover, our implicit annotation projection approach introduces less noises and hence is more effective and robust than explicit ones. Experimental results show that our model achieves the best performance, outperforming a number of competitive baselines. The thorough analysis further demonstrates the effectiveness of our model compared to explicit annotation projection approaches.

Translation-Based Implicit Annotation Projection for Zero-Shot Cross-Lingual Event Argument Extraction

DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation.Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation.Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome. 

/pdf/a-graph-neural-network-based-interpretable-framework-reveals-dikakcrc.pdf

A graph neural network-based interpretable framework reveals a novel DNA fragility–associated chromatin structural unit

Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges. Therefore, we design a graph neural network based method to predict DSBs (GraphDSB), using DNA sequence features and chromosome structure information. In order to improve the expression ability of the model, we introduce Jumping Knowledge architecture and several effective structural encoding methods. The contribution of structural information to the prediction of DSBs is verified by the experiments on datasets from normal human epidermal keratinocytes (NHEK) and chronic myeloid leukemia cell line (K562), and the ablation studies further demonstrate the effectiveness of the designed components in the proposed GraphDSB framework. Finally, we use GNNExplainer to analyze the contribution of node features and topology to DSBs prediction, and proved the high contribution of 5-mer DNA sequence features and two chromatin interaction modes.

pdf/graph-neural-networks-for-double-strand-dna-breaks-1eylar0j.pdf

Graph Neural Networks for Double-Strand DNA Breaks Prediction

In this paper, we present our solution of the ACM Multimedia 2022 pre-training for video understanding challenge. First, we pre-train the models on large-scale weakly-supervised video datasets with different temporal resolutions, then fine-tune the model for downstream application. Quantitative comparisons are conducted to evaluate the performance of different networks at multiple temporal resolutions. Moreover, we fusion different pre-trained models through weighted averaging. We achieve an accuracy of 62.39% in the testing set, which ranked as the first place in the video categorization track of this challenge.

Multiple Temporal Fusion based Weakly-supervised Pre-training Techniques for Video Categorization

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