skip to main content


Title: Structure Meets Sequences: Predicting Network of Co-evolving Sequences
Co-evolving sequences are ubiquitous in a variety of applications, where different sequences are often inherently inter-connected with each other. We refer to such sequences, together with their inherent connections modeled as a structured network, as network of co-evolving sequences (NoCES). Typical NoCES applications in- clude road traffic monitoring, company revenue prediction, motion capture, etc. To date, it remains a daunting challenge to accurately model NoCES due to the coupling between network structure and sequences. In this paper, we propose to modeling NoCES with the aim of simultaneously capturing both the dynamics and the inter- play between network structure and sequences. Specifically, we propose a joint learning framework to alternatively update the network representations and sequence representations as the se- quences evolve over time. A unique feature of our framework lies in that it can deal with the case when there are co-evolving sequences on both network nodes and edges. Experimental evaluations on four real datasets demonstrate that the proposed approach (1) out- performs the existing competitors in terms of prediction accuracy, and (2) scales linearly w.r.t. the sequence length and the network size.  more » « less
Award ID(s):
1939725 1947135 2134079
NSF-PAR ID:
10332503
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
WSDM
Page Range / eLocation ID:
1090 to 1098
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Motivation

    Alternative splicing generates multiple isoforms from a single gene, greatly increasing the functional diversity of a genome. Although gene functions have been well studied, little is known about the specific functions of isoforms, making accurate prediction of isoform functions highly desirable. However, the existing approaches to predicting isoform functions are far from satisfactory due to at least two reasons: (i) unlike genes, isoform-level functional annotations are scarce. (ii) The information of isoform functions is concealed in various types of data including isoform sequences, co-expression relationship among isoforms, etc.

    Results

    In this study, we present a novel approach, DIFFUSE (Deep learning-based prediction of IsoForm FUnctions from Sequences and Expression), to predict isoform functions. To integrate various types of data, our approach adopts a hybrid framework by first using a deep neural network (DNN) to predict the functions of isoforms from their genomic sequences and then refining the prediction using a conditional random field (CRF) based on co-expression relationship. To overcome the lack of isoform-level ground truth labels, we further propose an iterative semi-supervised learning algorithm to train both the DNN and CRF together. Our extensive computational experiments demonstrate that DIFFUSE could effectively predict the functions of isoforms and genes. It achieves an average area under the receiver operating characteristics curve of 0.840 and area under the precision–recall curve of 0.581 over 4184 GO functional categories, which are significantly higher than the state-of-the-art methods. We further validate the prediction results by analyzing the correlation between functional similarity, sequence similarity, expression similarity and structural similarity, as well as the consistency between the predicted functions and some well-studied functional features of isoform sequences.

    Availability and implementation

    https://github.com/haochenucr/DIFFUSE.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
    more » « less
  2. According to the National Academies, a week long forecast of velocity, vertical structure, and duration of the Loop Current (LC) and its eddies at a given location is a critical step toward understanding their effects on the gulf ecosystems as well as toward anticipating and mitigating the outcomes of anthropogenic and natural disasters in the Gulf of Mexico (GoM). However, creating such a forecast has remained a challenging problem since LC behavior is dominated by dynamic processes across multiple time and spatial scales not resolved at once by conventional numerical models. In this paper, building on the foundation of spatiotemporal predictive learning in video prediction, we develop a physics informed deep learning based prediction model called—Physics-informed Tensor-train ConvLSTM (PITT-ConvLSTM)—for forecasting 3D geo-spatiotemporal sequences. Specifically, we propose (1) a novel 4D higher-order recurrent neural network with empirical orthogonal function analysis to capture the hidden uncorrelated patterns of each hierarchy, (2) a convolutional tensor-train decomposition to capture higher-order space-time correlations, and (3) a mechanism that incorporates prior physics from domain experts by informing the learning in latent space. The advantage of our proposed approach is clear: constrained by the law of physics, the prediction model simultaneously learns good representations for frame dependencies (both short-term and long-term high-level dependency) and inter-hierarchical relations within each time frame. Experiments on geo-spatiotemporal data collected from the GoM demonstrate that the PITT-ConvLSTM model can successfully forecast the volumetric velocity of the LC and its eddies for a period greater than 1 week. 
    more » « less
  3. A real-world text corpus sometimes comprises not only text documents, but also semantic links between them (e.g., academic papers in a bibliographic network are linked by citations and co-authorships). Text documents and semantic connections form a text-rich network, which empowers a wide range of downstream tasks such as classification and retrieval. However, pretraining methods for such structures are still lacking, making it difficult to build one generic model that can be adapted to various tasks on text-rich networks. Current pretraining objectives, such as masked language modeling, purely model texts and do not take inter-document structure information into consideration. To this end, we propose our PretrAining on TexT-Rich NetwOrk framework PATTON. PATTON1 includes two pretraining strategies: network-contextualized masked language modeling and masked node prediction, to capture the inherent dependency between textual attributes and network structure. We conduct experiments on four downstream tasks in five datasets from both academic and e-commerce domains, where PATTON outperforms baselines significantly and consistently. 
    more » « less
  4. Citations of scientific papers and patents reveal the knowledge flow and usually serve as the metric for evaluating their novelty and impacts in the field. Citation Forecasting thus has various applications in the real world. Existing works on citation forecasting typically exploit the sequential properties of citation events, without exploring the citation network. In this paper, we propose to explore both the citation network and the related citation event sequences which provide valuable information for future citation forecasting. We propose a novel Citation Network and Event Sequence (CINES) Model to encode signals in the citation network and related citation event sequences into various types of embeddings for decoding to the arrivals of future citations. Moreover, we propose a temporal network attention and three alternative designs of bidirectional feature propagation to aggregate the retrospective and prospective aspects of publications in the citation network, coupled with the citation event sequence embeddings learned by a two-level attention mechanism for the citation forecasting. We evaluate our models and baselines on both a U.S. patent dataset and a DBLP dataset. Experimental results show that our models outperform the state-of-the-art methods, i.e., RMTPP, CYAN-RNN, Intensity-RNN, and PC-RNN, reducing the forecasting error by 37.76% - 75.32%. 
    more » « less
  5. Abstract Motivation

    Template-based modeling, including homology modeling and protein threading, is a popular method for protein 3D structure prediction. However, alignment generation and template selection for protein sequences without close templates remain very challenging.

    Results

    We present a new method called DeepThreader to improve protein threading, including both alignment generation and template selection, by making use of deep learning (DL) and residue co-variation information. Our method first employs DL to predict inter-residue distance distribution from residue co-variation and sequential information (e.g. sequence profile and predicted secondary structure), and then builds sequence-template alignment by integrating predicted distance information and sequential features through an ADMM algorithm. Experimental results suggest that predicted inter-residue distance is helpful to both protein alignment and template selection especially for protein sequences without very close templates, and that our method outperforms currently popular homology modeling method HHpred and threading method CNFpred by a large margin and greatly outperforms the latest contact-assisted protein threading method EigenTHREADER.

    Availability and implementation

    http://raptorx.uchicago.edu/

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
    more » « less