arXiv subjects

Tao Shen

Publications and source records attributed to Tao Shen.

At least 73 records · Page 4Linked to original sources

arXiv2023

Enhancing Secrecy Capacity in PLS Communication with NORAN based on Pilot Information Codebooks

In recent research, non-orthogonal artificial noise (NORAN) has been proposed as an alternative to orthogonal artificial noise (AN). However, NORAN introduces additional noise into the channel, which reduces the capacity of the legitimate channel (LC). At the same time, selecting a NORAN design with ideal security performance from a large number of design options is also a challenging problem. To address these two issues, a novel NORAN based on a pilot information codebook is proposed in this letter. The codebook associates different suboptimal NORANs with pilot information as the key under different channel state information (CSI). The receiver interrogates the codebook using the pilot information to obtain the NORAN that the transmitter will transmit in the next moment, in order to eliminate the NORAN when receiving information. Therefore, NORAN based on pilot information codebooks can improve the secrecy capacity (SC) of the communication system by directly using suboptimal NORAN design schemes without increasing the noise in the LC. Numerical simulations and analyses show that the introduction of NORAN with a novel design using pilot information codebooks significantly enhances the security and improves the SC of the communication system.

eess.SP↗

arXiv2023

Accurate Prediction of Antibody Function and Structure Using Bio-Inspired Antibody Language Model

In recent decades, antibodies have emerged as indispensable therapeutics for combating diseases, particularly viral infections. However, their development has been hindered by limited structural information and labor-intensive engineering processes. Fortunately, significant advancements in deep learning methods have facilitated the precise prediction of protein structure and function by leveraging co-evolution information from homologous proteins. Despite these advances, predicting the conformation of antibodies remains challenging due to their unique evolution and the high flexibility of their antigen-binding regions. Here, to address this challenge, we present the Bio-inspired Antibody Language Model (BALM). This model is trained on a vast dataset comprising 336 million 40% non-redundant unlabeled antibody sequences, capturing both unique and conserved properties specific to antibodies. Notably, BALM showcases exceptional performance across four antigen-binding prediction tasks. Moreover, we introduce BALMFold, an end-to-end method derived from BALM, capable of swiftly predicting full atomic antibody structures from individual sequences. Remarkably, BALMFold outperforms those well-established methods like AlphaFold2, IgFold, ESMFold, and OmegaFold in the antibody benchmark, demonstrating significant potential to advance innovative engineering and streamline therapeutic antibody development by reducing the need for unnecessary trials.

q-bio.BM↗

arXiv2023

Large Language Models are Strong Zero-Shot Retriever

In this work, we propose a simple method that applies a large language model (LLM) to large-scale retrieval in zero-shot scenarios. Our method, the Language language model as Retriever (LameR), is built upon no other neural models but an LLM, while breaking brute-force combinations of retrievers with LLMs and lifting the performance of zero-shot retrieval to be very competitive on benchmark datasets. Essentially, we propose to augment a query with its potential answers by prompting LLMs with a composition of the query and the query's in-domain candidates. The candidates, regardless of correct or wrong, are obtained by a vanilla retrieval procedure on the target collection. As a part of the prompts, they are likely to help LLM generate more precise answers by pattern imitation or candidate summarization. Even if all the candidates are wrong, the prompts at least make LLM aware of in-collection patterns and genres. Moreover, due to the low performance of a self-supervised retriever, the LLM-based query augmentation becomes less effective as the retriever bottlenecks the whole pipeline. Therefore, we propose to leverage a non-parametric lexicon-based method (e.g., BM25) as the retrieval module to capture query-document overlap in a literal fashion. As such, LameR makes the retrieval procedure transparent to the LLM, thus circumventing the performance bottleneck.

cs.CL↗

arXiv2023

UnifieR: A Unified Retriever for Large-Scale Retrieval

Large-scale retrieval is to recall relevant documents from a huge collection given a query. It relies on representation learning to embed documents and queries into a common semantic encoding space. According to the encoding space, recent retrieval methods based on pre-trained language models (PLM) can be coarsely categorized into either dense-vector or lexicon-based paradigms. These two paradigms unveil the PLMs' representation capability in different granularities, i.e., global sequence-level compression and local word-level contexts, respectively. Inspired by their complementary global-local contextualization and distinct representing views, we propose a new learning framework, UnifieR which unifies dense-vector and lexicon-based retrieval in one model with a dual-representing capability. Experiments on passage retrieval benchmarks verify its effectiveness in both paradigms. A uni-retrieval scheme is further presented with even better retrieval quality. We lastly evaluate the model on BEIR benchmark to verify its transferability.

cs.IR↗

arXiv2023

LexMAE: Lexicon-Bottlenecked Pretraining for Large-Scale Retrieval

In large-scale retrieval, the lexicon-weighting paradigm, learning weighted sparse representations in vocabulary space, has shown promising results with high quality and low latency. Despite it deeply exploiting the lexicon-representing capability of pre-trained language models, a crucial gap remains between language modeling and lexicon-weighting retrieval -- the former preferring certain or low-entropy words whereas the latter favoring pivot or high-entropy words -- becoming the main barrier to lexicon-weighting performance for large-scale retrieval. To bridge this gap, we propose a brand-new pre-training framework, lexicon-bottlenecked masked autoencoder (LexMAE), to learn importance-aware lexicon representations. Essentially, we present a lexicon-bottlenecked module between a normal language modeling encoder and a weakened decoder, where a continuous bag-of-words bottleneck is constructed to learn a lexicon-importance distribution in an unsupervised fashion. The pre-trained LexMAE is readily transferred to the lexicon-weighting retrieval via fine-tuning. On the ad-hoc retrieval benchmark, MS-Marco, it achieves 42.6% MRR@10 with 45.8 QPS for the passage dataset and 44.4% MRR@100 with 134.8 QPS for the document dataset, by a CPU machine. And LexMAE shows state-of-the-art zero-shot transfer capability on BEIR benchmark with 12 datasets.

cs.IR↗

arXiv2023

Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation

The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is significantly influenced by the depth of multiple sequence alignment (MSA), which requires extensive exploration of a large protein database for similar sequences. However, not all protein sequences possess abundant homologous families, and consequently, AF2's performance can degrade on such queries, at times failing to produce meaningful results. To address this, we introduce a novel generative language model, MSA-Augmenter, which leverages protein-specific attention mechanisms and large-scale MSAs to generate useful, novel protein sequences not currently found in databases. These sequences supplement shallow MSAs, enhancing the accuracy of structural property predictions. Our experiments on CASP14 demonstrate that MSA-Augmenter can generate de novo sequences that retain co-evolutionary information from inferior MSAs, thereby improving protein structure prediction quality on top of strong AF2.

q-bio.QM↗

arXiv2023

Prompt Federated Learning for Weather Forecasting: Toward Foundation Models on Meteorological Data

To tackle the global climate challenge, it urgently needs to develop a collaborative platform for comprehensive weather forecasting on large-scale meteorological data. Despite urgency, heterogeneous meteorological sensors across countries and regions, inevitably causing multivariate heterogeneity and data exposure, become the main barrier. This paper develops a foundation model across regions capable of understanding complex meteorological data and providing weather forecasting. To relieve the data exposure concern across regions, a novel federated learning approach has been proposed to collaboratively learn a brand-new spatio-temporal Transformer-based foundation model across participants with heterogeneous meteorological data. Moreover, a novel prompt learning mechanism has been adopted to satisfy low-resourced sensors' communication and computational constraints. The effectiveness of the proposed method has been demonstrated on classical weather forecasting tasks using three meteorological datasets with multivariate time series.

cs.LG↗

arXiv2023

AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction

Deep learning-based approaches, such as AlphaFold2 (AF2), have significantly advanced protein tertiary structure prediction, achieving results comparable to real biological experimental methods. While AF2 has shown limitations in predicting the effects of mutations, its robustness against sequence mutations remains to be determined. Starting with the wild-type (WT) sequence, we investigate adversarial sequences generated via an evolutionary approach, which AF2 predicts to be substantially different from WT. Our experiments on CASP14 reveal that by modifying merely three residues in the protein sequence using a combination of replacement, deletion, and insertion strategies, the alteration in AF2's predictions, as measured by the Local Distance Difference Test (lDDT), reaches 46.61. Moreover, when applied to a specific protein, SPNS2, our proposed algorithm successfully identifies biologically meaningful residues critical to protein structure determination and potentially indicates alternative conformations, thus significantly expediting the experimental process.

q-bio.BM↗

arXiv2023

LED: Lexicon-Enlightened Dense Retriever for Large-Scale Retrieval

Retrieval models based on dense representations in semantic space have become an indispensable branch for first-stage retrieval. These retrievers benefit from surging advances in representation learning towards compressive global sequence-level embeddings. However, they are prone to overlook local salient phrases and entity mentions in texts, which usually play pivot roles in first-stage retrieval. To mitigate this weakness, we propose to make a dense retriever align a well-performing lexicon-aware representation model. The alignment is achieved by weakened knowledge distillations to enlighten the retriever via two aspects -- 1) a lexicon-augmented contrastive objective to challenge the dense encoder and 2) a pair-wise rank-consistent regularization to make dense model's behavior incline to the other. We evaluate our model on three public benchmarks, which shows that with a comparable lexicon-aware retriever as the teacher, our proposed dense one can bring consistent and significant improvements, and even outdo its teacher. In addition, we found our improvement on the dense retriever is complementary to the standard ranker distillation, which can further lift state-of-the-art performance.

cs.CL↗

arXiv2023

LexLIP: Lexicon-Bottlenecked Language-Image Pre-Training for Large-Scale Image-Text Retrieval

Image-text retrieval (ITR) is a task to retrieve the relevant images/texts, given the query from another modality. The conventional dense retrieval paradigm relies on encoding images and texts into dense representations using dual-stream encoders, however, it faces challenges with low retrieval speed in large-scale retrieval scenarios. In this work, we propose the lexicon-weighting paradigm, where sparse representations in vocabulary space are learned for images and texts to take advantage of the bag-of-words models and efficient inverted indexes, resulting in significantly reduced retrieval latency. A crucial gap arises from the continuous nature of image data, and the requirement for a sparse vocabulary space representation. To bridge this gap, we introduce a novel pre-training framework, Lexicon-Bottlenecked Language-Image Pre-Training (LexLIP), that learns importance-aware lexicon representations. This framework features lexicon-bottlenecked modules between the dual-stream encoders and weakened text decoders, allowing for constructing continuous bag-of-words bottlenecks to learn lexicon-importance distributions. Upon pre-training with same-scale data, our LexLIP achieves state-of-the-art performance on two benchmark ITR datasets, MSCOCO and Flickr30k. Furthermore, in large-scale retrieval scenarios, LexLIP outperforms CLIP with a 5.5 ~ 221.3X faster retrieval speed and 13.2 ~ 48.8X less index storage memory.

cs.CV↗

arXiv2023

Multi-Center Federated Learning: Clients Clustering for Better Personalization

Federated learning has received great attention for its capability to train a large-scale model in a decentralized manner without needing to access user data directly. It helps protect the users' private data from centralized collecting. Unlike distributed machine learning, federated learning aims to tackle non-IID data from heterogeneous sources in various real-world applications, such as those on smartphones. Existing federated learning approaches usually adopt a single global model to capture the shared knowledge of all users by aggregating their gradients, regardless of the discrepancy between their data distributions. However, due to the diverse nature of user behaviors, assigning users' gradients to different global models (i.e., centers) can better capture the heterogeneity of data distributions across users. Our paper proposes a novel multi-center aggregation mechanism for federated learning, which learns multiple global models from the non-IID user data and simultaneously derives the optimal matching between users and centers. We formulate the problem as a joint optimization that can be efficiently solved by a stochastic expectation maximization (EM) algorithm. Our experimental results on benchmark datasets show that our method outperforms several popular federated learning methods.

cs.LG↗

arXiv2023

KnowDA: All-in-One Knowledge Mixture Model for Data Augmentation in Low-Resource NLP

This paper focuses on the data augmentation for low-resource NLP tasks where the training set is limited. The existing solutions either leverage task-independent heuristic rules (e.g., Synonym Replacement) or fine-tune general-purpose pre-trained language models (e.g., GPT2) using the limited training instances to produce new synthetic data. Consequently, they have trivial task-specific knowledge and are limited to yielding low-quality synthetic data. To combat this issue, we propose Knowledge Mixture Data Augmentation Model (KnowDA) which is an Seq2Seq language model pre-trained on a mixture of diverse NLP tasks under a novel framework of Knowledge Mixture Training (KoMT). The goal of KoMT is to condense diverse NLP task-specific knowledge into the single KnowDA model (i.e., all-in-one) such that KnowDA could utilize these knowledge to quickly grasp the inherent synthesis law of the target task through limited training instances. Specifically, KoMT reformulates input examples from various heterogeneous NLP tasks into a unified text-to-text format, and employs denoising training objectives in different granularity to learn to reconstruct partial or complete samples. To the best of our knowledge, we are the first attempt to apply 100+ NLP multi-task training for data augmentation. Extensive experiments show that i) the synthetic data produced by KnowDA successfully improves performance of the strong pre-trained language models (i.e., Bert, ALBert and Deberta) by a large margin on the low-resource NLP benchmark FewGLUE, CoNLL'03 and WikiAnn; ii) KnowDA successfully transfers the task knowledge to NLP tasks whose types are seen and unseen in KoMT.

cs.CL↗

arXiv2022

Fine-Grained Distillation for Long Document Retrieval

Long document retrieval aims to fetch query-relevant documents from a large-scale collection, where knowledge distillation has become de facto to improve a retriever by mimicking a heterogeneous yet powerful cross-encoder. However, in contrast to passages or sentences, retrieval on long documents suffers from the scope hypothesis that a long document may cover multiple topics. This maximizes their structure heterogeneity and poses a granular-mismatch issue, leading to an inferior distillation efficacy. In this work, we propose a new learning framework, fine-grained distillation (FGD), for long-document retrievers. While preserving the conventional dense retrieval paradigm, it first produces global-consistent representations crossing different fine granularity and then applies multi-granular aligned distillation merely during training. In experiments, we evaluate our framework on two long-document retrieval benchmarks, which show state-of-the-art performance.

cs.IR↗

arXiv2022

DeepNoise: Signal and Noise Disentanglement based on Classifying Fluorescent Microscopy Images via Deep Learning

The high-content image-based assay is commonly leveraged for identifying the phenotypic impact of genetic perturbations in biology field. However, a persistent issue remains unsolved during experiments: the interferential technical noise caused by systematic errors (e.g., temperature, reagent concentration, and well location) is always mixed up with the real biological signals, leading to misinterpretation of any conclusion drawn. Here, we show a mean teacher based deep learning model (DeepNoise) that can disentangle biological signals from the experimental noise. Specifically, we aim to classify the phenotypic impact of 1,108 different genetic perturbations screened from 125,510 fluorescent microscopy images, which are totally unrecognizable by human eye. We validate our model by participating in the Recursion Cellular Image Classification Challenge, and our proposed method achieves an extremely high classification score (Acc: 99.596%), ranking the 2nd place among 866 participating groups. This promising result indicates the successful separation of biological and technical factors, which might help decrease the cost of treatment development and expedite the drug discovery process.

eess.IV↗

arXiv2022

PCL: Peer-Contrastive Learning with Diverse Augmentations for Unsupervised Sentence Embeddings

Learning sentence embeddings in an unsupervised manner is fundamental in natural language processing. Recent common practice is to couple pre-trained language models with unsupervised contrastive learning, whose success relies on augmenting a sentence with a semantically-close positive instance to construct contrastive pairs. Nonetheless, existing approaches usually depend on a mono-augmenting strategy, which causes learning shortcuts towards the augmenting biases and thus corrupts the quality of sentence embeddings. A straightforward solution is resorting to more diverse positives from a multi-augmenting strategy, while an open question remains about how to unsupervisedly learn from the diverse positives but with uneven augmenting qualities in the text field. As one answer, we propose a novel Peer-Contrastive Learning (PCL) with diverse augmentations. PCL constructs diverse contrastive positives and negatives at the group level for unsupervised sentence embeddings. PCL performs peer-positive contrast as well as peer-network cooperation, which offers an inherent anti-bias ability and an effective way to learn from diverse augmentations. Experiments on STS benchmarks verify the effectiveness of PCL against its competitors in unsupervised sentence embeddings.

cs.CL↗

arXiv2022

Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

q-bio.QM↗

arXiv2022

Towards Robust Ranker for Text Retrieval

A ranker plays an indispensable role in the de facto 'retrieval & rerank' pipeline, but its training still lags behind -- learning from moderate negatives or/and serving as an auxiliary module for a retriever. In this work, we first identify two major barriers to a robust ranker, i.e., inherent label noises caused by a well-trained retriever and non-ideal negatives sampled for a high-capable ranker. Thereby, we propose multiple retrievers as negative generators improve the ranker's robustness, where i) involving extensive out-of-distribution label noises renders the ranker against each noise distribution, and ii) diverse hard negatives from a joint distribution are relatively close to the ranker's negative distribution, leading to more challenging thus effective training. To evaluate our robust ranker (dubbed R$^2$anker), we conduct experiments in various settings on the popular passage retrieval benchmark, including BM25-reranking, full-ranking, retriever distillation, etc. The empirical results verify the new state-of-the-art effectiveness of our model.

cs.IR↗

arXiv2022

Edge-Cloud Polarization and Collaboration: A Comprehensive Survey for AI

Influenced by the great success of deep learning via cloud computing and the rapid development of edge chips, research in artificial intelligence (AI) has shifted to both of the computing paradigms, i.e., cloud computing and edge computing. In recent years, we have witnessed significant progress in developing more advanced AI models on cloud servers that surpass traditional deep learning models owing to model innovations (e.g., Transformers, Pretrained families), explosion of training data and soaring computing capabilities. However, edge computing, especially edge and cloud collaborative computing, are still in its infancy to announce their success due to the resource-constrained IoT scenarios with very limited algorithms deployed. In this survey, we conduct a systematic review for both cloud and edge AI. Specifically, we are the first to set up the collaborative learning mechanism for cloud and edge modeling with a thorough review of the architectures that enable such mechanism. We also discuss potentials and practical experiences of some on-going advanced edge AI topics including pretraining models, graph neural networks and reinforcement learning. Finally, we discuss the promising directions and challenges in this field.

cs.LG↗