On Pre-trained Language Models for Antibody

Antibodies are vital proteins offering robust protection for the human body from pathogens. The development of general protein and antibody-specific pre-trained language models both facilitate antibody prediction tasks. However, few studies comprehensively explore the representation capability of distinct pre-trained language models on different antibody problems. Here, to investigate the problem, we aim to answer the following key questions: (1) How do pre-trained language models perform in antibody tasks with different specificity? (2) How many benefits will the model gain if we introduce the specific biological mechanism to the pre-training process? (3) Do the learned antibody pre-trained representations make sense in real-world antibody problems, like drug discovery and immune process understanding? Previously, no benchmark available largely hindered the study to answer these questions. To facilitate the investigation, we provide an AnTibody Understanding Evaluation (ATUE) benchmark. We comprehensively evaluate the performance of protein pre-trained language models by empirical study along with conclusions and new insights. Our ATUE and code are released at https://github.com/dqwang122/EATLM.

Integrating Local Real Data with Global Gradient Prototypes for Classifier Re-Balancing in Federated Long-Tailed Learning

Federated Learning (FL) has become a popular distributed learning paradigm that involves multiple clients training a global model collaboratively in a data privacy-preserving manner. However, the data samples usually follow a long-tailed distribution in the real world, and FL on the decentralized and long-tailed data yields a poorly-behaved global model severely biased to the head classes with the majority of the training samples. To alleviate this issue, decoupled training has recently been introduced to FL, considering it has achieved promising results in centralized long-tailed learning by re-balancing the biased classifier after the instance-balanced training. However, the current study restricts the capacity of decoupled training in federated long-tailed learning with a sub-optimal classifier re-trained on a set of pseudo features, due to the unavailability of a global balanced dataset in FL. In this work, in order to re-balance the classifier more effectively, we integrate the local real data with the global gradient prototypes to form the local balanced datasets, and thus re-balance the classifier during the local training. Furthermore, we introduce an extra classifier in the training phase to help model the global data distribution, which addresses the problem of contradictory optimization goals caused by performing classifier re-balancing locally. Extensive experiments show that our method consistently outperforms the existing state-of-the-art methods in various settings.

Graph Contrastive Learning for Skeleton-based Action Recognition

In the field of skeleton-based action recognition, current top-performing graph convolutional networks (GCNs) exploit intra-sequence context to construct adaptive graphs for feature aggregation. However, we argue that such context is still \textit{local} since the rich cross-sequence relations have not been explicitly investigated. In this paper, we propose a graph contrastive learning framework for skeleton-based action recognition (\textit{SkeletonGCL}) to explore the \textit{global} context across all sequences. In specific, SkeletonGCL associates graph learning across sequences by enforcing graphs to be class-discriminative, \emph{i.e.,} intra-class compact and inter-class dispersed, which improves the GCN capacity to distinguish various action patterns. Besides, two memory banks are designed to enrich cross-sequence context from two complementary levels, \emph{i.e.,} instance and semantic levels, enabling graph contrastive learning in multiple context scales. Consequently, SkeletonGCL establishes a new training paradigm, and it can be seamlessly incorporated into current GCNs. Without loss of generality, we combine SkeletonGCL with three GCNs (2S-ACGN, CTR-GCN, and InfoGCN), and achieve consistent improvements on NTU60, NTU120, and NW-UCLA benchmarks. The source code will be available at \url{https://github.com/OliverHxh/SkeletonGCL}.

Hierarchical Reinforcement Learning for RIS-Assisted Energy-Efficient RAN

Reconfigurable intelligent surface (RIS) is emerging as a promising technology to boost the energy efficiency (EE) of 5G beyond and 6G networks. Inspired by this potential, in this paper, we investigate the RIS-assisted energy-efficient radio access networks (RAN). In particular, we combine RIS with sleep control techniques, and develop a hierarchical reinforcement learning (HRL) algorithm for network management. In HRL, the meta-controller decides the on/off status of the small base stations (SBSs) in heterogeneous networks, while the sub-controller can change the transmission power levels of SBSs to save energy. The simulations show that the RIS-assisted sleep control can achieve significantly lower energy consumption, higher throughput, and more than doubled energy efficiency than no-RIS conditions.

Diff-Glat: Diffusion Glancing Transformer for Parallel Sequence to Sequence Learning

For sequence generation, both autoregressive models and non-autoregressive models have been developed in recent years. Autoregressive models can achieve high generation quality, but the sequential decoding scheme causes slow decoding speed. Non-autoregressive models accelerate the inference speed with parallel decoding, while their generation quality still needs to be improved due to the difficulty of modeling multi-modalities in data. To address the multi-modality issue, we propose Diff-Glat, a non-autoregressive model featured with a modality diffusion process and residual glancing training. The modality diffusion process decomposes the modalities and reduces the modalities to learn for each transition. And the residual glancing sampling further smooths the modality learning procedures. Experiments demonstrate that, without using knowledge distillation data, Diff-Glat can achieve superior performance in both decoding efficiency and accuracy compared with the autoregressive Transformer.

Direct Heterogeneous Causal Learning for Resource Allocation Problems in Marketing

Marketing is an important mechanism to increase user engagement and improve platform revenue, and heterogeneous causal learning can help develop more effective strategies. Most decision-making problems in marketing can be formulated as resource allocation problems and have been studied for decades. Existing works usually divide the solution procedure into two fully decoupled stages, i.e., machine learning (ML) and operation research (OR) -- the first stage predicts the model parameters and they are fed to the optimization in the second stage. However, the error of the predicted parameters in ML cannot be respected and a series of complex mathematical operations in OR lead to the increased accumulative errors. Essentially, the improved precision on the prediction parameters may not have a positive correlation on the final solution due to the side-effect from the decoupled design. In this paper, we propose a novel approach for solving resource allocation problems to mitigate the side-effects. Our key intuition is that we introduce the decision factor to establish a bridge between ML and OR such that the solution can be directly obtained in OR by only performing the sorting or comparison operations on the decision factor. Furthermore, we design a customized loss function that can conduct direct heterogeneous causal learning on the decision factor, an unbiased estimation of which can be guaranteed when the loss converges. As a case study, we apply our approach to two crucial problems in marketing: the binary treatment assignment problem and the budget allocation problem with multiple treatments. Both large-scale simulations and online A/B Tests demonstrate that our approach achieves significant improvement compared with state-of-the-art.

Accelerating Antimicrobial Peptide Discovery with Latent Sequence-Structure Model

Antimicrobial peptide (AMP) is a promising therapy in the treatment of broad-spectrum antibiotics and drug-resistant infections. Recently, an increasing number of researchers have been introducing deep generative models to accelerate AMP discovery. However, current studies mainly focus on sequence attributes and ignore structure information, which is important in AMP biological functions. In this paper, we propose a latent sequence-structure model for AMPs (LSSAMP) with multi-scale VQ-VAE to incorporate secondary structures. By sampling in the latent space, LSSAMP can simultaneously generate peptides with ideal sequence attributes and secondary structures. Experimental results show that the peptides generated by LSSAMP have a high probability of AMP, and two of the 21 candidates have been verified to have good antimicrobial activity. Our model will be released to help create high-quality AMP candidates for follow-up biological experiments and accelerate the whole AMP discovery.

ROSE: Robust Selective Fine-tuning for Pre-trained Language Models

Even though the large-scale language models have achieved excellent performances, they suffer from various adversarial attacks. A large body of defense methods has been proposed. However, they are still limited due to redundant attack search spaces and the inability to defend against various types of attacks. In this work, we present a novel fine-tuning approach called \textbf{RO}bust \textbf{SE}letive fine-tuning (\textbf{ROSE}) to address this issue. ROSE conducts selective updates when adapting pre-trained models to downstream tasks, filtering out invaluable and unrobust updates of parameters. Specifically, we propose two strategies: the first-order and second-order ROSE for selecting target robust parameters. The experimental results show that ROSE achieves significant improvements in adversarial robustness on various downstream NLP tasks, and the ensemble method even surpasses both variants above. Furthermore, ROSE can be easily incorporated into existing fine-tuning methods to improve their adversarial robustness further. The empirical analysis confirms that ROSE eliminates unrobust spurious updates during fine-tuning, leading to solutions corresponding to flatter and wider optima than the conventional method. Code is available at \url{https://github.com/jiangllan/ROSE}.

Prompt-based Connective Prediction Method for Fine-grained Implicit Discourse Relation Recognition

Due to the absence of connectives, implicit discourse relation recognition (IDRR) is still a challenging and crucial task in discourse analysis. Most of the current work adopted multi-task learning to aid IDRR through explicit discourse relation recognition (EDRR) or utilized dependencies between discourse relation labels to constrain model predictions. But these methods still performed poorly on fine-grained IDRR and even utterly misidentified on most of the few-shot discourse relation classes. To address these problems, we propose a novel Prompt-based Connective Prediction (PCP) method for IDRR. Our method instructs large-scale pre-trained models to use knowledge relevant to discourse relation and utilizes the strong correlation between connectives and discourse relation to help the model recognize implicit discourse relations. Experimental results show that our method surpasses the current state-of-the-art model and achieves significant improvements on those fine-grained few-shot discourse relation. Moreover, our approach is able to be transferred to EDRR and obtain acceptable results. Our code is released in https://github.com/zh-i9/PCP-for-IDRR.

PARAGEN : A Parallel Generation Toolkit

PARAGEN is a PyTorch-based NLP toolkit for further development on parallel generation. PARAGEN provides thirteen types of customizable plugins, helping users to experiment quickly with novel ideas across model architectures, optimization, and learning strategies. We implement various features, such as unlimited data loading and automatic model selection, to enhance its industrial usage. ParaGen is now deployed to support various research and industry applications at ByteDance. PARAGEN is available at https://github.com/bytedance/ParaGen.