arXiv subjects

Jingbo Zhou

Publications and source records attributed to Jingbo Zhou.

At least 55 records · Page 3Linked to original sources

arXiv2024

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $π$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

q-bio.QM↗

arXiv2024

Irregular Traffic Time Series Forecasting Based on Asynchronous Spatio-Temporal Graph Convolutional Network

Accurate traffic forecasting is crucial for the development of Intelligent Transportation Systems (ITS), playing a pivotal role in modern urban traffic management. Traditional forecasting methods, however, struggle with the irregular traffic time series resulting from adaptive traffic signal controls, presenting challenges in asynchronous spatial dependency, irregular temporal dependency, and predicting variable-length sequences. To this end, we propose an Asynchronous Spatio-tEmporal graph convolutional nEtwoRk (ASeer) tailored for irregular traffic time series forecasting. Specifically, we first propose an Asynchronous Graph Diffusion Network to capture the spatial dependency between asynchronously measured traffic states regulated by adaptive traffic signals. After that, to capture the temporal dependency within irregular traffic state sequences, a personalized time encoding is devised to embed the continuous time signals. Then, we propose a Transformable Time-aware Convolution Network, which adapts meta-filters for time-aware convolution on the sequences with inconsistent temporal flow. Additionally, a Semi-Autoregressive Prediction Network, comprising a state evolution unit and a semi-autoregressive predictor, is designed to predict variable-length traffic sequences effectively and efficiently. Extensive experiments on a newly established benchmark demonstrate the superiority of ASeer compared with twelve competitive baselines across six metrics.

cs.LG↗

arXiv2024

Warming Up Cold-Start CTR Prediction by Learning Item-Specific Feature Interactions

In recommendation systems, new items are continuously introduced, initially lacking interaction records but gradually accumulating them over time. Accurately predicting the click-through rate (CTR) for these items is crucial for enhancing both revenue and user experience. While existing methods focus on enhancing item ID embeddings for new items within general CTR models, they tend to adopt a global feature interaction approach, often overshadowing new items with sparse data by those with abundant interactions. Addressing this, our work introduces EmerG, a novel approach that warms up cold-start CTR prediction by learning item-specific feature interaction patterns. EmerG utilizes hypernetworks to generate an item-specific feature graph based on item characteristics, which is then processed by a Graph Neural Network (GNN). This GNN is specially tailored to provably capture feature interactions at any order through a customized message passing mechanism. We further design a meta learning strategy that optimizes parameters of hypernetworks and GNN across various item CTR prediction tasks, while only adjusting a minimal set of item-specific parameters within each task. This strategy effectively reduces the risk of overfitting when dealing with limited data. Extensive experiments on benchmark datasets validate that EmerG consistently performs the best given no, a few and sufficient instances of new items.

cs.IR↗

arXiv2024

Unifying Sequences, Structures, and Descriptions for Any-to-Any Protein Generation with the Large Multimodal Model HelixProtX

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

cs.LG↗

arXiv2024

Robust Reward Placement under Uncertainty

We consider a problem of placing generators of rewards to be collected by randomly moving agents in a network. In many settings, the precise mobility pattern may be one of several possible, based on parameters outside our control, such as weather conditions. The placement should be robust to this uncertainty, to gain a competent total reward across possible networks. To study such scenarios, we introduce the Robust Reward Placement problem (RRP). Agents move randomly by a Markovian Mobility Model with a predetermined set of locations whose connectivity is chosen adversarially from a known set $Π$ of candidates. We aim to select a set of reward states within a budget that maximizes the minimum ratio, among all candidates in $Π$, of the collected total reward over the optimal collectable reward under the same candidate. We prove that RRP is NP-hard and inapproximable, and develop $Ψ$-Saturate, a pseudo-polynomial time algorithm that achieves an $ε$-additive approximation by exceeding the budget constraint by a factor that scales as $O(\ln |Π|/ε)$. In addition, we present several heuristics, most prominently one inspired by a dynamic programming algorithm for the max-min 0-1 KNAPSACK problem. We corroborate our theoretical analysis with an experimental evaluation on synthetic and real data.

cs.MA↗

arXiv2024

Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Models

Protein-ligand structure prediction is an essential task in drug discovery, predicting the binding interactions between small molecules (ligands) and target proteins (receptors). Recent advances have incorporated deep learning techniques to improve the accuracy of protein-ligand structure prediction. Nevertheless, the experimental validation of docking conformations remains costly, it raises concerns regarding the generalizability of these deep learning-based methods due to the limited training data. In this work, we show that by pre-training on a large-scale docking conformation generated by traditional physics-based docking tools and then fine-tuning with a limited set of experimentally validated receptor-ligand complexes, we can obtain a protein-ligand structure prediction model with outstanding performance. Specifically, this process involved the generation of 100 million docking conformations for protein-ligand pairings, an endeavor consuming roughly 1 million CPU core days. The proposed model, HelixDock, aims to acquire the physical knowledge encapsulated by the physics-based docking tools during the pre-training phase. HelixDock has been rigorously benchmarked against both physics-based and deep learning-based baselines, demonstrating its exceptional precision and robust transferability in predicting binding confirmation. In addition, our investigation reveals the scaling laws governing pre-trained protein-ligand structure prediction models, indicating a consistent enhancement in performance with increases in model parameters and the volume of pre-training data. Moreover, we applied HelixDock to several drug discovery-related tasks to validate its practical utility. HelixDock demonstrates outstanding capabilities on both cross-docking and structure-based virtual screening benchmarks.

cs.LG↗

arXiv2024

Enhancing Trust and Privacy in Distributed Networks: A Comprehensive Survey on Blockchain-based Federated Learning

While centralized servers pose a risk of being a single point of failure, decentralized approaches like blockchain offer a compelling solution by implementing a consensus mechanism among multiple entities. Merging distributed computing with cryptographic techniques, decentralized technologies introduce a novel computing paradigm. Blockchain ensures secure, transparent, and tamper-proof data management by validating and recording transactions via consensus across network nodes. Federated Learning (FL), as a distributed machine learning framework, enables participants to collaboratively train models while safeguarding data privacy by avoiding direct raw data exchange. Despite the growing interest in decentralized methods, their application in FL remains underexplored. This paper presents a thorough investigation into Blockchain-based FL (BCFL), spotlighting the synergy between blockchain's security features and FL's privacy-preserving model training capabilities. First, we present the taxonomy of BCFL from three aspects, including decentralized, separate networks, and reputation-based architectures. Then, we summarize the general architecture of BCFL systems, providing a comprehensive perspective on FL architectures informed by blockchain. Afterward, we analyze the application of BCFL in healthcare, IoT, and other privacy-sensitive areas. Finally, we identify future research directions of BCFL.

cs.CR↗

arXiv2024

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

q-bio.QM↗

arXiv2024

A Framework for Cost-Effective and Self-Adaptive LLM Shaking and Recovery Mechanism

As Large Language Models (LLMs) gain great success in real-world applications, an increasing number of users are seeking to develop and deploy their customized LLMs through cloud services. Nonetheless, in some specific domains, there are still concerns regarding cost and trade-offs between privacy issues and accuracy. In this study, we introduce a cost-effective and self-adaptive LLM shaking tuning and recovery mechanism, named CypherTalk. With carefully designed horizontal and vertical shaking operators, we can achieve comparable accuracy results with SOTA privacy-preserving LLM schemes using Cryptography-based or Differential Privacy-based methods. Experiments also show that with the CypherTalk framework, users can achieve reliable accuracy when using optimized shaking operator settings. To our best knowledge, this is the first work that considers cost, and trade-off between model utility and privacy in LLM scenarios.

cs.CR↗

arXiv2023

LLM for SoC Security: A Paradigm Shift

As the ubiquity and complexity of system-on-chip (SoC) designs increase across electronic devices, the task of incorporating security into an SoC design flow poses significant challenges. Existing security solutions are inadequate to provide effective verification of modern SoC designs due to their limitations in scalability, comprehensiveness, and adaptability. On the other hand, Large Language Models (LLMs) are celebrated for their remarkable success in natural language understanding, advanced reasoning, and program synthesis tasks. Recognizing an opportunity, our research delves into leveraging the emergent capabilities of Generative Pre-trained Transformers (GPTs) to address the existing gaps in SoC security, aiming for a more efficient, scalable, and adaptable methodology. By integrating LLMs into the SoC security verification paradigm, we open a new frontier of possibilities and challenges to ensure the security of increasingly complex SoCs. This paper offers an in-depth analysis of existing works, showcases practical case studies, demonstrates comprehensive experiments, and provides useful promoting guidelines. We also present the achievements, prospects, and challenges of employing LLM in different SoC security verification tasks.

cs.CR↗

arXiv2023

Tuning Pre-trained Model via Moment Probing

Recently, efficient fine-tuning of large-scale pre-trained models has attracted increasing research interests, where linear probing (LP) as a fundamental module is involved in exploiting the final representations for task-dependent classification. However, most of the existing methods focus on how to effectively introduce a few of learnable parameters, and little work pays attention to the commonly used LP module. In this paper, we propose a novel Moment Probing (MP) method to further explore the potential of LP. Distinguished from LP which builds a linear classification head based on the mean of final features (e.g., word tokens for ViT) or classification tokens, our MP performs a linear classifier on feature distribution, which provides the stronger representation ability by exploiting richer statistical information inherent in features. Specifically, we represent feature distribution by its characteristic function, which is efficiently approximated by using first- and second-order moments of features. Furthermore, we propose a multi-head convolutional cross-covariance (MHC$^3$) to compute second-order moments in an efficient and effective manner. By considering that MP could affect feature learning, we introduce a partially shared module to learn two recalibrating parameters (PSRP) for backbones based on MP, namely MP$_{+}$. Extensive experiments on ten benchmarks using various models show that our MP significantly outperforms LP and is competitive with counterparts at less training cost, while our MP$_{+}$ achieves state-of-the-art performance.

cs.CV↗

arXiv2023

Spatial Heterophily Aware Graph Neural Networks

Graph Neural Networks (GNNs) have been broadly applied in many urban applications upon formulating a city as an urban graph whose nodes are urban objects like regions or points of interest. Recently, a few enhanced GNN architectures have been developed to tackle heterophily graphs where connected nodes are dissimilar. However, urban graphs usually can be observed to possess a unique spatial heterophily property; that is, the dissimilarity of neighbors at different spatial distances can exhibit great diversity. This property has not been explored, while it often exists. To this end, in this paper, we propose a metric, named Spatial Diversity Score, to quantitatively measure the spatial heterophily and show how it can influence the performance of GNNs. Indeed, our experimental investigation clearly shows that existing heterophilic GNNs are still deficient in handling the urban graph with high spatial diversity score. This, in turn, may degrade their effectiveness in urban applications. Along this line, we propose a Spatial Heterophily Aware Graph Neural Network (SHGNN), to tackle the spatial diversity of heterophily of urban graphs. Based on the key observation that spatially close neighbors on the urban graph present a more similar mode of difference to the central node, we first design a rotation-scaling spatial aggregation module, whose core idea is to properly group the spatially close neighbors and separately process each group with less diversity inside. Then, a heterophily-sensitive spatial interaction module is designed to adaptively capture the commonality and diverse dissimilarity in different spatial groups. Extensive experiments on three real-world urban datasets demonstrate the superiority of our SHGNN over several its competitors.

cs.LG↗

arXiv2023

Multi-Temporal Relationship Inference in Urban Areas

Finding multiple temporal relationships among locations can benefit a bunch of urban applications, such as dynamic offline advertising and smart public transport planning. While some efforts have been made on finding static relationships among locations, little attention is focused on studying time-aware location relationships. Indeed, abundant location-based human activities are time-varying and the availability of these data enables a new paradigm for understanding the dynamic relationships in a period among connective locations. To this end, we propose to study a new problem, namely multi-Temporal relationship inference among locations (Trial for short), where the major challenge is how to integrate dynamic and geographical influence under the relationship sparsity constraint. Specifically, we propose a solution to Trial with a graph learning scheme, which includes a spatially evolving graph neural network (SEENet) with two collaborative components: spatially evolving graph convolution module (SEConv) and spatially evolving self-supervised learning strategy (SE-SSL). SEConv performs the intra-time aggregation and inter-time propagation to capture the multifaceted spatially evolving contexts from the view of location message passing. In addition, SE-SSL designs time-aware self-supervised learning tasks in a global-local manner with additional evolving constraint to enhance the location representation learning and further handle the relationship sparsity. Finally, experiments on four real-world datasets demonstrate the superiority of our method over several state-of-the-art approaches.

cs.LG↗

arXiv2023

PLM-GNN: A Webpage Classification Method based on Joint Pre-trained Language Model and Graph Neural Network

The number of web pages is growing at an exponential rate, accumulating massive amounts of data on the web. It is one of the key processes to classify webpages in web information mining. Some classical methods are based on manually building features of web pages and training classifiers based on machine learning or deep learning. However, building features manually requires specific domain knowledge and usually takes a long time to validate the validity of features. Considering webpages generated by the combination of text and HTML Document Object Model(DOM) trees, we propose a representation and classification method based on a pre-trained language model and graph neural network, named PLM-GNN. It is based on the joint encoding of text and HTML DOM trees in the web pages. It performs well on the KI-04 and SWDE datasets and on practical dataset AHS for the project of scholar's homepage crawling.

cs.CL↗

arXiv2023

Structure-aware Protein Self-supervised Learning

Protein representation learning methods have shown great potential to yield useful representation for many downstream tasks, especially on protein classification. Moreover, a few recent studies have shown great promise in addressing insufficient labels of proteins with self-supervised learning methods. However, existing protein language models are usually pretrained on protein sequences without considering the important protein structural information. To this end, we propose a novel structure-aware protein self-supervised learning method to effectively capture structural information of proteins. In particular, a well-designed graph neural network (GNN) model is pretrained to preserve the protein structural information with self-supervised tasks from a pairwise residue distance perspective and a dihedral angle perspective, respectively. Furthermore, we propose to leverage the available protein language model pretrained on protein sequences to enhance the self-supervised learning. Specifically, we identify the relation between the sequential information in the protein language model and the structural information in the specially designed GNN model via a novel pseudo bi-level optimization scheme. Experiments on several supervised downstream tasks verify the effectiveness of our proposed method.The code of the proposed method is available in \url{https://github.com/GGchen1997/STEPS_Bioinformatics}.

cs.LG↗

arXiv2023

Robust Training of Graph Neural Networks via Noise Governance

Graph Neural Networks (GNNs) have become widely-used models for semi-supervised learning. However, the robustness of GNNs in the presence of label noise remains a largely under-explored problem. In this paper, we consider an important yet challenging scenario where labels on nodes of graphs are not only noisy but also scarce. In this scenario, the performance of GNNs is prone to degrade due to label noise propagation and insufficient learning. To address these issues, we propose a novel RTGNN (Robust Training of Graph Neural Networks via Noise Governance) framework that achieves better robustness by learning to explicitly govern label noise. More specifically, we introduce self-reinforcement and consistency regularization as supplemental supervision. The self-reinforcement supervision is inspired by the memorization effects of deep neural networks and aims to correct noisy labels. Further, the consistency regularization prevents GNNs from overfitting to noisy labels via mimicry loss in both the inter-view and intra-view perspectives. To leverage such supervisions, we divide labels into clean and noisy types, rectify inaccurate labels, and further generate pseudo-labels on unlabeled nodes. Supervision for nodes with different types of labels is then chosen adaptively. This enables sufficient learning from clean labels while limiting the impact of noisy ones. We conduct extensive experiments to evaluate the effectiveness of our RTGNN framework, and the results validate its consistent superior performance over state-of-the-art methods with two types of label noises and various noise rates.

cs.LG↗

arXiv2023

Adaptive Depth Graph Attention Networks

As one of the most popular GNN architectures, the graph attention networks (GAT) is considered the most advanced learning architecture for graph representation and has been widely used in various graph mining tasks with impressive results. However, since GAT was proposed, none of the existing studies have provided systematic insight into the relationship between the performance of GAT and the number of layers, which is a critical issue in guiding model performance improvement. In this paper, we perform a systematic experimental evaluation and based on the experimental results, we find two important facts: (1) the main factor limiting the accuracy of the GAT model as the number of layers increases is the oversquashing phenomenon; (2) among the previous improvements applied to the GNN model, only the residual connection can significantly improve the GAT model performance. We combine these two important findings to provide a theoretical explanation that it is the residual connection that mitigates the loss of original feature information due to oversquashing and thus improves the deep GAT model performance. This provides empirical insights and guidelines for researchers to design the GAT variant model with appropriate depth and well performance. To demonstrate the effectiveness of our proposed guidelines, we propose a GAT variant model-ADGAT that adaptively selects the number of layers based on the sparsity of the graph, and experimentally demonstrate that the effectiveness of our model is significantly improved over the original GAT.

cs.LG↗

arXiv2023

Towards Table-to-Text Generation with Pretrained Language Model: A Table Structure Understanding and Text Deliberating Approach

Although remarkable progress on the neural table-to-text methods has been made, the generalization issues hinder the applicability of these models due to the limited source tables. Large-scale pretrained language models sound like a promising solution to tackle such issues. However, how to effectively bridge the gap between the structured table and the text input by fully leveraging table information to fuel the pretrained model is still not well explored. Besides, another challenge of integrating the deliberation mechanism into the text-to-text pretrained model for solving the table-to-text task remains seldom studied. In this paper, to implement the table-to-text generation with pretrained language model, we propose a table structure understanding and text deliberating approach, namely TASD. Specifically, we devise a three-layered multi-head attention network to realize the table-structure-aware text generation model with the help of the pretrained language model. Furthermore, a multi-pass decoder framework is adopted to enhance the capability of polishing generated text for table descriptions. The empirical studies, as well as human evaluation, on two public datasets, validate that our approach can generate faithful and fluent descriptive texts for different types of tables.

cs.CL↗