United States

RNA-binding proteins (RBPs) play a significant part in several biological processes in the living cell, such as gene regulation and mRNA localization. Several deep learning methods, especially the model based on convolutional neural network(CNN), have been used to predict the binding sites. However, previous methods fail to represent RNA secondary structure features. The traditional deep learning methods generally transform the RNA secondary structure to a regular matrix that cannot reveal the topological structure information of RNA. To effectively extract the structure features of RNA, we propose an RNA secondary structure representation network (RNASSR-Net) based on graph convolutional neural network (GCN) and convolution neural network (CNN) for RBP binding prediction. RNASSR-Net constructs the graph model derived from the RNA secondary structure to learn the topological properties of RNA. Then, it obtains the spatial importance of each base in RNA with CNN to guide the representation of the RNA secondary structure. Finally, RNASSR-Net combines the structure and sequence features to predict the binding sites. Experimental results demonstrate the proposed method outperforms a few state-of-the-art methods on the benchmark datasets and gets a higher improvement on the small-size data. Besides, the proposed RNASSR-Net is also used to detect the accurate motifs compared with the experimentally verified motifs, which reveals the binding region location and RNA structure interpretation for some biological guidance in the future.

AAAI 2021

RNA Secondary Structure Representation Network for RNA-Proteins Binding Prediction

## Welcome!
"I am excited to welcome you to this year’s edition of the Conference on Empirical Methods in Natural Language Processing! Importantly, it marks the 30th edition of EMNLP. With over 8,000 submissions, more than 3,000 accepted papers, and thousands of attendees, we have come a long way from that first
workshop, which had 14 accepted papers. As the field looks ahead, Suzhou is the fitting location for celebrating this milestone: rooted in a long literary tradition, yet modern and forward-looking, and home to a large share of the NLP community."<br>

*Message from the General Chair, Dirk Hovy*





<br>

EMNLP 2025

Celebrate 30 Years of EMNLP! 
EMNLP 2025 will be held in Suzhou, China from November 5th to November 9th, 2025.

technical paper

The purpose of the AAAI conference is to promote research in artificial intelligence (AI) and scientific exchange among AI researchers, practitioners, scientists, and engineers in affiliated disciplines. 

Sentence semantic matching is one of the fundamental tasks in natural language processing, which requires an agent to determine the semantic relation among input sentences. Recently, deep neural networks have achieved impressive performance in this area, especially BERT. Despite the effectiveness of these models, most of them treat output labels as meaningless one-hot vectors, underestimating the semantic information and guidance of relations that these labels reveal, especially for  tasks with a small number of labels. To address this problem, we propose a Relation of Relation Learning Network (R2-Net) for sentence semantic matching. Specifically, we first employ BERT to encode the input sentences from a global perspective. Then a CNN-based encoder is designed to capture keywords and phrase information from a local perspective. To fully leverage labels for better relation information extraction, we introduce a self-supervised relation of relation classification task for guiding R2-Net to consider more about labels. Meanwhile, a triplet loss is employed to distinguish the intra-class and inter-class relations in a finer granularity. Empirical experiments on two sentence semantic matching tasks demonstrate the superiority of our proposed model. As a byproduct, we have released the codes to facilitate other researches.

Making the Relation Matters: Relation of Relation Learning Network for Sentence Semantic Matching

Cross-modal retrieval has become an active study field with the expanding scale of multimodal data. To date, most existing methods transform multimodal data into a common representation space where semantic similarities between items can be directly measured across different modalities. However, these methods typically suffer from following limitations: 1) They usually attempt to bridge the modality gap by designing losses in the common representation space which may not be sufficient to eliminate potential heterogeneity of different modalities in the common space. 2) They typically treat labels as independent individuals and ignore label relationships which are important for constructing semantic links between multimodal data. In this work, we propose a novel Dual Adversarial Graph Neural Networks (DAGNN) composed of the dual generative adversarial networks and the multi-hop graph neural networks, which learn modality-invariant and discriminative common representations for cross-modal retrieval. Firstly, we construct the dual generative adversarial networks to project multimodal data into a common representation space. Secondly, we leverage the multi-hop graph neural networks, in which a layer aggregation mechanism is proposed to exploit multi-hop propagation information, to capture the label correlation dependency and learn inter-dependent classifiers. Comprehensive experiments conducted on two cross-modal retrieval benchmark datasets, NUS-WIDE and MIRFlickr, indicate the superiority of DAGNN.

Dual Adversarial Graph Neural Networks for Multi-Label Cross-Modal Retrieval

We propose a knowledge-enhanced approach, ERNIE-ViL, which incorporates structured knowledge obtained from scene graphs to learn joint representations of vision-language. ERNIE-ViL tries to build the detailed semantic connections (objects, attributes of objects and relationships between objects) across vision and language, which are essential to vision-language cross-modal tasks. Utilizing scene graphs of visual scenes, ERNIE-ViL constructs Scene Graph Prediction tasks, i.e., Object Prediction, Attribute Prediction and Relationship Prediction tasks in the pre-training phase. Specifically, these prediction tasks are implemented by predicting nodes of different types in the scene graph parsed from the sentence. Thus, ERNIE-ViL can learn the joint representations characterizing the alignments of the detailed semantics across vision and language. After pre-training on large scale image-text aligned datasets, we validate the effectiveness of ERNIE-ViL on 5 cross-modal downstream tasks. ERNIE-ViL achieves state-of-the-art performances on all these tasks and ranks the first place on the VCR leaderboard with an absolute improvement of 3.7%.

ERNIE-ViL: Knowledge Enhanced Vision-Language Representations through Scene Graphs

We consider the problem of designing policies for Markov decision processes (MDPs) with dynamic coherent risk objectives and constraints. We begin by formulating the problem in a Lagrangian framework. Under the assumption that the risk objectives and constraints can be represented by a Markov risk transition mapping, we propose an optimization-based method to synthesize Markovian policies that lower-bound the constrained risk-averse problem.  We demonstrate that the formulated optimization problems are in the form of difference convex programs (DCPs) and can be solved by the disciplined convex-concave programming (DCCP) framework. We show that these results generalize linear programs for constrained MDPs with total discounted expected costs and constraints. Finally, we illustrate the effectiveness of the proposed method with numerical experiments on a rover navigation problem involving conditional-value-at-risk (CVaR) and entropic-value-at-risk (EVaR) coherent risk measures.

Constrained Risk-Averse Markov Decision Processes

Modeling the behavior of coupled networks is challenging due to their intricate dynamics. For example in neuroscience, it is of critical importance to understand the relationship between the functional neural processes and the anatomical connectivities. Modern neuroimaging techniques allow us to separately measure functional connectivities through fMRI imaging and measure underlying white matter wirings through diffusion imaging. Previous studies have shown that structural edges in brain networks improve the inference of functional edges and vice versa. In this paper, we investigate the idea of coupled networks through an optimization framework by focusing on interactions between structural edges and functional edges of brain networks. We consider both types of edges as observed instances of random variables that represent different underlying network processes. The proposed framework does not depend on the Gaussian functional form and achieves a more robust selection on non-Gaussian data compared with existing approaches. To incorporate existing domain knowledge into such studies, we propose a novel formulation to place hard network constraints on the noise term while estimating interactions. This not only leads to a cleaner way of applying network constraints but also brings a more scalable solution when the network connectivity is sparse. We validate our method on multishell diffusion and task-evoked fMRI datasets from Human Connectome Project, leading to both important insights on structural backbones that support various types of task activities performed during the scanning sessions as well as general solutions to the study of coupled networks.

Learning Interpretable Models for Couple Networks under Domain Constraints

Tables of data are used to record vast amounts of socioeconomic, scientific, and governmental information. Although humans create tables using underlying organizational principles, unfortunately AI systems struggle to understand the contents of these tables. This paper introduces an end-to-end system for table understanding, the process of capturing the relational structure of data in tables. We introduce models that identify cell types, group these cells into blocks of data that serve a similar functional role, and predict the relationships between these blocks. We introduce a hybrid, neuro-symbolic approach, combining embedded representations learned from thousands of tables with probabilistic constraints that capture regularities in how humans organize tables. Our neuro-symbolic model is better able to capture positional invariants of headers and enforce homogeneity of data types. One limitation in this research area is the lack of rich datasets for evaluating end-to-end table understanding, so we introduce a new benchmark dataset comprised of 431 diverse tables from data.gov. The evaluation results show that our system achieves the state-of-the-art performance on cell type classification, block identification, and relationship prediction, improving over prior efforts by up to 7% of macro F1 score.

A Hybrid Probabilistic Approach for Table Understanding

Graph topological structures are crucial to distinguish different-class graphs. In this work, we propose a deep Wasserstein graph discriminant learning (WGDL) framework to learn discriminative embeddings of graphs in Wasserstein-metric (W-metric) matching space. In order to bypass the calculation of W-metric class centers in discriminant analysis, as well as better support batch process learning, we introduce a reference set of graphs (aka graph dictionary) to express those representative graph samples (aka dictionary keys).
On the bridge of graph dictionary, every input graph can be projected into the latent dictionary space through our proposed Wasserstein graph transformation (WGT). In WGT, we formulate inter-graph distance in W-metric space by virtue of the optimal transport (OT) principle, which effectively expresses the correlations of cross-graph structures.
To make WGDL better representation ability, we dynamically update graph dictionary during training by maximizing the ratio of inter-class versus intra-class Wasserstein distance. To evaluate our WGDL method, comprehensive experiments are conducted on six graph classification datasets. Experimental results demonstrate the effectiveness of our WGDL, and state-of-the-art performance.

Deep Wasserstein Graph Discriminant Learning for Graph Classification

Point processes are a useful mathematical tool for describing events over time, and so there are many recent approaches for representing and learning them. One notable open question is how to precisely describe the flexibility of point process models and whether there exists a general model that can represent all point processes. Our work bridges this gap. Focusing on the widely used event intensity function representation of point processes, we provide a proof that a class of learnable functions can universally approximate any valid intensity function. The proof connects the well known Stone-Weierstrass Theorem for function approximation, the uniform density of non-negative continuous functions using a transfer functions, the formulation of the parameters of a piece-wise continuous functions as a dynamic system, and a recurrent neural network implementation for capturing the dynamics. Using these insights, we design and implement UNIPoint, a novel neural point process model, using recurrent neural networks to parameterise sums of basis function upon each event. Evaluations on synthetic and real world datasets show that this simpler representation performs better than Hawkes process variants and more complex neural network-based approaches. We expect this result will provide a practical basis for selecting and tuning models, as well as furthering theoretical work on representational complexity and learnability.

UNIpoint: Universally Approximating Point Processes Intensities

We aim to address the problem of Natural Language Video Localization (NLVL) â€” localizing the video segment corresponding to a natural language description in a long and untrimmed video. State-of-the-art NLVL methods are almost in one-stage fashion, which can be typically grouped into two categories: 1) anchor-based approach: it first pre-defines a series of video segment candidates (e.g., by sliding window), and then does classification for each candidate; 2) anchor-free approach: it directly predicts the probabilities for each video frame as a boundary or intermediate frame inside the positive segment. However, both kinds of one-stage approaches have inherent drawbacks: the anchor-based approach is susceptible to the heuristic rules, further limiting the capability of handling videos with variant length. While the anchor-free approach fails to exploit the segment-level interaction thus achieving inferior results. In this paper, we propose a novel Boundary Proposal Network (BPNet), a universal two-stage framework that gets rid of the issues mentioned above. Specifically, in the first stage, BPNet utilizes an anchor-free model to generate a group of high-quality candidate video segments with their boundaries. In the second stage, a visual-language fusion layer is proposed to jointly model the multi-modal interaction between the candidate and the language query, followed by a matching score rating layer that outputs the alignment score for each candidate. We evaluate our BPNet on three challenging NLVL benchmarks (i.e., Charades-STA, TACoS and ActivityNet-Captions). Extensive experiments and ablative studies on these datasets demonstrate that the BPNet outperforms the state-of-the-art methods.

Boundary Proposal Network for Two-Stage Natural Language Video Localization

Recently, a zero-shot entity linking task is introduced to challenge the generalization ability of entity linking models. In this task, mentions must be linked to unseen entities and only the textual information is available. In order to make full use of the documents, previous work has proposed a BERT-based model which can only take fixed length of text as input. However, the key information for entity linking may exist in nearly everywhere of the documents thus the proposed model cannot capture them all. To leverage more textual information and enhance text understanding capability, we propose a bidirectional multi-paragraph reading model for the zero-shot entity linking task. Firstly, the model treats the mention context as a query and matches it with multiple paragraphs of the entity description documents. Then, the mention-aware entity representation obtained from the first step is used as a query to match multiple paragraphs in the document containing the mention through an entity-mention attention mechanism. In particular, a new pre-training strategy is employed to strengthen the representative ability. Experimental results show that our bidirectional model can capture long-range context dependencies and outperform the baseline model by 3-4% in terms of accuracy.

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