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.

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.

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

Molecular docking, a pivotal computational tool for drug discovery, predicts the binding interactions between small molecules (ligands) and target proteins (receptors). Conventional physics-based docking tools, though widely used, face limitations in precision due to restricted conformational sampling and imprecise scoring functions. Recent endeavors have employed deep learning techniques to enhance docking accuracy, but their generalization remains a concern due to limited training data. Leveraging the success of extensive and diverse data in other domains, we introduce HelixDock, a novel approach for site-specific molecular docking. Hundreds of millions of binding poses are generated by traditional docking tools, encompassing diverse protein targets and small molecules. Our deep learning-based docking model, a SE(3)-equivariant network, is pre-trained with this large-scale dataset and then fine-tuned with a small number of precise receptor-ligand complex structures. Comparative analyses against physics-based and deep learning-based baseline methods highlight HelixDock's superiority, especially on challenging test sets. Our study elucidates the scaling laws of the pre-trained molecular docking models, showcasing consistent improvements with increased model parameters and pre-train data quantities. Harnessing the power of extensive and diverse generated data holds promise for advancing AI-driven drug discovery.

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.

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

Accurate traffic forecasting at intersections governed by intelligent traffic signals is critical for the advancement of an effective intelligent traffic signal control system. However, due to the irregular traffic time series produced by intelligent intersections, the traffic forecasting task becomes much more intractable and imposes three major new challenges: 1) asynchronous spatial dependency, 2) irregular temporal dependency among traffic data, and 3) variable-length sequence to be predicted, which severely impede the performance of current traffic forecasting methods. To this end, we propose an Asynchronous Spatio-tEmporal graph convolutional nEtwoRk (ASeer) to predict the traffic states of the lanes entering intelligent intersections in a future time window. Specifically, by linking lanes via a traffic diffusion graph, we first propose an Asynchronous Graph Diffusion Network to model the asynchronous spatial dependency between the time-misaligned traffic state measurements of lanes. After that, to capture the temporal dependency within irregular traffic state sequence, a learnable personalized time encoding is devised to embed the continuous time for each lane. Then we propose a Transformable Time-aware Convolution Network that learns meta-filters to derive time-aware convolution filters with transformable filter sizes for efficient temporal convolution on the irregular sequence. Furthermore, a Semi-Autoregressive Prediction Network consisting of a state evolution unit and a semiautoregressive predictor is designed to effectively and efficiently predict variable-length traffic state sequences. Extensive experiments on two real-world datasets demonstrate the effectiveness of ASeer in six metrics.

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.

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.

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.

GNNs,You can be Stronger,Deeper and Faster

Graph neural networks (GNNs), a type of neural network that can learn from graph-structured data and learn the representation of nodes by aggregating their neighbors, have shown excellent performance in downstream tasks.However, it is known that the performance of graph neural networks (GNNs) degrades gradually as the number of layers increases. Based on k-hop subgraph aggregation, which is a new concept, we propose a new perspective to understand the expressive power of GNN.From this perspective, we reveal the potential causes of the performance degradation of the deep traditional GNN - aggregated subgraph overlap, and the fact that the residual-based graph neural networks in fact exploit the aggregation results of 1 to k hop subgraphs to improve the effectiveness.Further, we propose a new sampling-based node-level residual module named SDF, which is shown by theoretical derivation to obtain a superior expressive power compared to previous residual methods by using information from 1 to k hop subgraphs more flexibly. Extensive experiments show that the performance and efficiency of GNN with the SDF module outperform other methods.

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.