Total: 2866
Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only utilize sequence or structure information alone, which hinders the performance in generation. In this study, we propose a Multi-Modal Contrastive Diffusion model (MMCD), fusing both sequence and structure modalities in a diffusion framework to co-generate novel peptide sequences and structures. Specifically, MMCD constructs the sequence-modal and structure-modal diffusion models, respectively, and devises a multi-modal contrastive learning strategy with inter-contrastive and intra-contrastive in each diffusion timestep, aiming to capture the consistency between two modalities and boost model performance. The inter-contrastive aligns sequences and structures of peptides by maximizing the agreement of their embeddings, while the intra-contrastive differentiates therapeutic and non-therapeutic peptides by maximizing the disagreement of their sequence/structure embeddings simultaneously. The extensive experiments demonstrate that MMCD performs better than other state-of-the-art deep generative methods in generating therapeutic peptides across various metrics, including antimicrobial/anticancer score, diversity, and peptide-docking.
Microarchitecture determines the implementation of a microprocessor. Designing a microarchitecture to achieve better performance, power, and area (PPA) trade-off has been increasingly difficult. Previous data-driven methodologies hold inappropriate assumptions and lack more tightly coupling with expert knowledge. This paper proposes a novel reinforcement learning-based (RL) solution that addresses these limitations. With the integration of microarchitecture scaling graph, PPA preference space embedding, and proposed lightweight environment in RL, experiments using commercial electronic design automation (EDA) tools show that our method achieves an average PPA trade-off improvement of 16.03% than previous state-of-the-art approaches with 4.07× higher efficiency. The solution qualities outperform human implementations by at most 2.03× in the PPA trade-off.
Large Language Models (LLMs) can be used as repositories of biological and chemical information to generate pharmacological lead compounds. However, for LLMs to focus on specific drug targets typically requires experimentation with progressively more refined prompts. Results thus become dependent not just on what is known about the target, but also on what is known about the prompt- engineering. In this paper, we separate the prompt into domain-constraints that can be written in a standard logical form and a simple text-based query. We investigate whether LLMs can be guided, not by refining prompts manually, but by refining the logical component automatically, keeping the query unchanged. We describe an iterative procedure LMLF (“Language Model with Logical Feedback”) in which the constraints are progressively refined using a logical notion of generalisation. On any iteration, newly generated instances are verified against the constraint, providing "logical-feedback" for the next iteration's refinement of the constraints. We evaluate LMLF using two well-known targets (inhibition of the Janus Kinase 2; and Dopamine Receptor D2); and two different LLMs (GPT-3 and PaLM). We show that LMLF, starting with the same logical constraints and query text, can be used to guide both LLMs to generate potential leads. We find: (a) Binding affinities of LMLF-generated molecules are skewed towards higher binding affinities than those from existing baselines; (b) LMLF results in generating molecules that are skewed towards higher binding affinities than without logical feedback; (c) Assessment by a computational chemist suggests that LMLF generated compounds may be novel inhibitors. These findings suggest that LLMs with logical feedback may provide a mechanism for generating new leads without requiring the domain-specialist to acquire sophisticated skills in prompt-engineering.
In the dynamic and rapidly evolving world of social media, detecting anomalous users has become a crucial task to address malicious activities such as misinformation and cyberbullying. As the increasing number of anomalous users improves the ability to mimic normal users and evade detection, existing methods only focusing on bot detection are ineffective in terms of capturing subtle distinctions between users. To address these challenges, we proposed SeGA, preference-aware self-contrastive learning for anomalous user detection, which leverages heterogeneous entities and their relations in the Twittersphere to detect anomalous users with different malicious strategies. SeGA utilizes the knowledge of large language models to summarize user preferences via posts. In addition, integrating user preferences with prompts as pseudo-labels for preference-aware self-contrastive learning enables the model to learn multifaceted aspects for describing the behaviors of users. Extensive experiments on the proposed TwBNT benchmark demonstrate that SeGA significantly outperforms the state-of-the-art methods (+3.5% ∼ 27.6%) and empirically validate the effectiveness of the model design and pre-training strategies. Our code and data are publicly available at https://github.com/ying0409/SeGA.
Biological sequence nearest neighbor search plays a fundamental role in bioinformatics. To alleviate the pain of quadratic complexity for conventional distance computation, neural distance embeddings, which project sequences into geometric space, have been recognized as a promising paradigm. To maintain the distance order between sequences, these models all deploy triplet loss and use intuitive methods to select a subset of triplets for training from a vast selection space. However, we observed that such training often enables models to distinguish only a fraction of distance orders, leaving others unrecognized. Moreover, naively selecting more triplets for training under the state-of-the-art network not only adds costs but also hampers model performance. In this paper, we introduce Bio-kNN: a kNN search framework for biological sequences. It includes a systematic triplet selection method and a multi-head network, enhancing the discernment of all distance orders without increasing training expenses. Initially, we propose a clustering-based approach to partition all triplets into several clusters with similar properties, and then select triplets from these clusters using an innovative strategy. Meanwhile, we noticed that simultaneously training different types of triplets in the same network cannot achieve the expected performance, thus we propose a multi-head network to tackle this. Our network employs a convolutional neural network(CNN) to extract local features shared by all clusters, and then learns a multi-layer perception(MLP) head for each cluster separately. Besides, we treat CNN as a special head, thereby integrating crucial local features which are neglected in previous models into our model for similarity recognition. Extensive experiments show that our Bio-kNN significantly outperforms the state-of-the-art methods on two large-scale datasets without increasing the training cost.
Ride-hailing platforms have been facing the challenge of balancing demand and supply. Existing vehicle reposition techniques often treat drivers as homogeneous agents and relocate them deterministically, assuming compliance with the reposition. In this paper, we consider a more realistic and driver-centric scenario where drivers have unique cruising preferences and can decide whether to take the recommendation or not on their own. We propose i-Rebalance, a personalized vehicle reposition technique with deep reinforcement learning (DRL). i-Rebalance estimates drivers' decisions on accepting reposition recommendations through an on-field user study involving 99 real drivers. To optimize supply-demand balance and enhance preference satisfaction simultaneously, i-Rebalance has a sequential reposition strategy with dual DRL agents: Grid Agent to determine the reposition order of idle vehicles, and Vehicle Agent to provide personalized recommendations to each vehicle in the pre-defined order. This sequential learning strategy facilitates more effective policy training within a smaller action space compared to traditional joint-action methods. Evaluation of real-world trajectory data shows that i-Rebalance improves driver acceptance rate by 38.07% and total driver income by 9.97%.
Source detection in graphs has demonstrated robust efficacy in the domain of rumor source identification. Although recent solutions have enhanced performance by leveraging deep neural networks, they often require complete user data. In this paper, we address a more challenging task, rumor source detection with incomplete user data, and propose a novel framework, i.e., Source Detection in Graphs with Incomplete Nodes via Positional Encoding and Attentive Fusion (GIN-SD), to tackle this challenge. Specifically, our approach utilizes a positional embedding module to distinguish nodes that are incomplete and employs a self-attention mechanism to focus on nodes with greater information transmission capacity. To mitigate the prediction bias caused by the significant disparity between the numbers of source and non-source nodes, we also introduce a class-balancing mechanism. Extensive experiments validate the effectiveness of GIN-SD and its superiority to state-of-the-art methods.
Quantum error correction codes (QECC) are a key component for realizing the potential of quantum computing. QECC, as its classical counterpart (ECC), enables the reduction of error rates, by distributing quantum logical information across redundant physical qubits, such that errors can be detected and corrected. In this work, we efficiently train novel end-to-end deep quantum error decoders. We resolve the quantum measurement collapse by augmenting syndrome decoding to predict an initial estimate of the system noise, which is then refined iteratively through a deep neural network. The logical error rates calculated over finite fields are directly optimized via a differentiable objective, enabling efficient decoding under the constraints imposed by the code. Finally, our architecture is extended to support faulty syndrome measurement, by efficient decoding of repeated syndrome sampling. The proposed method demonstrates the power of neural decoders for QECC by achieving state-of-the-art accuracy, outperforming for small distance topological codes, the existing end-to-end neural and classical decoders, which are often computationally prohibitive.
Rumor detection on social media has become increasingly important. Most existing graph-based models presume rumor propagation trees (RPTs) have deep structures and learn sequential stance features along branches. However, through statistical analysis on real-world datasets, we find RPTs exhibit wide structures, with most nodes being shallow 1-level replies. To focus learning on intensive substructures, we propose Rumor Adaptive Graph Contrastive Learning (RAGCL) method with adaptive view augmentation guided by node centralities. We summarize three principles for RPT augmentation: 1) exempt root nodes, 2) retain deep reply nodes, 3) preserve lower-level nodes in deep sections. We employ node dropping, attribute masking and edge dropping with probabilities from centrality-based importance scores to generate views. A graph contrastive objective then learns robust rumor representations. Extensive experiments on four benchmark datasets demonstrate RAGCL outperforms state-of-the-art methods. Our work reveals the wide-structure nature of RPTs and contributes an effective graph contrastive learning approach tailored for rumor detection through principled adaptive augmentation. The proposed principles and augmentation techniques can potentially benefit other applications involving tree-structured graphs.
Numerous solutions are proposed for the Traffic Signal Control (TSC) tasks aiming to provide efficient transportation and alleviate traffic congestion. Recently, promising results have been attained by Reinforcement Learning (RL) methods through trial and error in simulators, bringing confidence in solving cities' congestion problems. However, performance gaps still exist when simulator-trained policies are deployed to the real world. This issue is mainly introduced by the system dynamic difference between the training simulators and the real-world environments. In this work, we leverage the knowledge of Large Language Models (LLMs) to understand and profile the system dynamics by a prompt-based grounded action transformation to bridge the performance gap. Specifically, this paper exploits the pre-trained LLM's inference ability to understand how traffic dynamics change with weather conditions, traffic states, and road types. Being aware of the changes, the policies' action is taken and grounded based on realistic dynamics, thus helping the agent learn a more realistic policy. We conduct experiments on four different scenarios to show the effectiveness of the proposed PromptGAT's ability to mitigate the performance gap of reinforcement learning from simulation to reality (sim-to-real).
Device-free localization (DFL) using easily-obtained Wi-Fi received signal strength (RSS) has wide real-world applications for not requiring people to carry trackable devices. However, accurate multitarget DFL remains challenging due to the unknown number of targets, multipath interference (MPI), especially between nearby targets, and limited real-world data. In this study, we pioneeringly propose a transformer-based learning method with Wi-Fi RSS as input, and an attentional prior fusion module, to simultaneously locate an unknown number of people at random positions. To overcome the multitarget data collection challenges, we contribute a large-scale cross-domain real-simulation-augmentation training dataset with one and two real-world nearby non-person objects at limited positions and up to five simulated and augmented randomly distributed targets. Experimental results demonstrate our method's improved accuracy, generalization ability, and robustness with fewer Wi-Fi nodes than previous methods.
Fact checking aims to predict claim veracity by reasoning over multiple evidence pieces. It usually involves evidence retrieval and veracity reasoning. In this paper, we focus on the latter, reasoning over unstructured text and structured table information. Previous works have primarily relied on fine-tuning pretrained language models or training homogeneous-graph-based models. Despite their effectiveness, we argue that they fail to explore the rich semantic information underlying the evidence with different structures. To address this, we propose a novel word-level Heterogeneous-graph-based model for Fact Checking over unstructured and structured information, namely HeterFC. Our approach leverages a heterogeneous evidence graph, with words as nodes and thoughtfully designed edges representing different evidence properties. We perform information propagation via a relational graph neural network, facilitating interactions between claims and evidence. An attention-based method is utilized to integrate information, combined with a language model for generating predictions. We introduce a multitask loss function to account for potential inaccuracies in evidence retrieval. Comprehensive experiments on the large fact checking dataset FEVEROUS demonstrate the effectiveness of HeterFC. Code will be released at: https://github.com/Deno-V/HeterFC.
Text-guided molecule generation is a task where molecules are generated to match specific textual descriptions. Recently, most existing SMILES-based molecule generation methods rely on an autoregressive architecture. In this work, we propose the Text-Guided Molecule Generation with Diffusion Language Model (TGM-DLM), a novel approach that leverages diffusion models to address the limitations of autoregressive methods. TGM-DLM updates token embeddings within the SMILES string collectively and iteratively, using a two-phase diffusion generation process. The first phase optimizes embeddings from random noise, guided by the text description, while the second phase corrects invalid SMILES strings to form valid molecular representations. We demonstrate that TGM-DLM outperforms MolT5-Base, an autoregressive model, without the need for additional data resources. Our findings underscore the remarkable effectiveness of TGM-DLM in generating coherent and precise molecules with specific properties, opening new avenues in drug discovery and related scientific domains. Code will be released at: https://github.com/Deno-V/tgm-dlm.
The non-consensual exploitation of facial manipulation has emerged as a pressing societal concern. In tandem with the identification of such fake content, recent research endeavors have advocated countering manipulation techniques through proactive interventions, specifically the incorporation of adversarial noise to impede the manipulation in advance. Nevertheless, with insufficient consideration of robustness, we show that current methods falter in providing protection after simple perturbations, e.g., blur. In addition, traditional optimization-based methods face limitations in scalability as they struggle to accommodate the substantial expansion of data volume, a consequence of the time-intensive iterative pipeline. To solve these challenges, we propose a learning-based model, Adversarial Robust Safeguard (ARS), to generate desirable protection noise in a single forward process, concurrently exhibiting a heightened resistance against prevalent perturbations. Specifically, our method involves a two-way protection design, characterized by a basic protection component responsible for generating efficacious noise features, coupled with robust protection for further enhancement. In robust protection, we first fuse image features with spatially duplicated noise embedding, thereby accounting for inherent information redundancy. Subsequently, a combination comprising a differentiable perturbation module and an adversarial network is devised to simulate potential information degradation during the training process. To evaluate it, we conduct experiments on four manipulation methods and compare recent works comprehensively. The results of our method exhibit good visual effects with pronounced robustness against varied perturbations at different levels.
Flight Trajectory Prediction (FTP) is an essential task in Air Traffic Control (ATC), which can assist air traffic controllers in managing airspace more safely and efficiently. Existing approaches generally perform multi-horizon FTP tasks in an autoregressive manner, thereby suffering from error accumulation and low-efficiency problems. In this paper, a novel framework, called FlightBERT++, is proposed to i) forecast multi-horizon flight trajectories directly in a non-autoregressive way, and ii) improve the limitation of the binary encoding (BE) representation in the FlightBERT. Specifically, the FlightBERT++ is implemented by a generalized encoder-decoder architecture, in which the encoder learns the temporal-spatial patterns from historical observations and the decoder predicts the flight status for the future horizons. Compared with conventional architecture, an innovative horizon-aware contexts generator is dedicatedly designed to consider the prior horizon information, which further enables non-autoregressive multi-horizon prediction. Moreover, a differential prompted decoder is proposed to enhance the capability of the differential predictions by leveraging the stationarity of the differential sequence. The experimental results on a real-world dataset demonstrated that the FlightBERT++ outperformed the competitive baselines in both FTP performance and computational efficiency.
Log anomaly detection is a key component in the field of artificial intelligence for IT operations (AIOps). Considering log data of variant domains, retraining the whole network for unknown domains is inefficient in real industrial scenarios. However, previous deep models merely focused on extracting the semantics of log sequences in the same domain, leading to poor generalization on multi-domain logs. To alleviate this issue, we propose a unified Transformer-based framework for Log anomaly detection (LogFormer) to improve the generalization ability across different domains, where we establish a two-stage process including the pre-training and adapter-based tuning stage. Specifically, our model is first pre-trained on the source domain to obtain shared semantic knowledge of log data. Then, we transfer such knowledge to the target domain via shared parameters. Besides, the Log-Attention module is proposed to supplement the information ignored by the log-paring. The proposed method is evaluated on three public datasets and one real-world dataset. Experimental results on multiple benchmarks demonstrate the effectiveness of our LogFormer with fewer trainable parameters and lower training costs.
De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translation task, potentially overlooking critical nuances between spectra and peptides. In our research, we present ContraNovo, a pioneering algorithm that leverages contrastive learning to extract the relationship between spectra and peptides and incorporates the mass information into peptide decoding, aiming to address these intricacies more efficiently. Through rigorous evaluations on two benchmark datasets, ContraNovo consistently outshines contemporary state-of-the-art solutions, underscoring its promising potential in enhancing de novo peptide sequencing.
Solving partial differential equations (PDEs) by learning the solution operators has emerged as an attractive alternative to traditional numerical methods. However, implementing such architectures presents two main challenges: flexibility in handling irregular and arbitrary input and output formats and scalability to large discretizations. Most existing architectures are limited by their desired structure or infeasible to scale large inputs and outputs. To address these issues, we introduce an attention-based model called an inducing point operator transformer (IPOT). Inspired by inducing points methods, IPOT is designed to handle any input function and output query while capturing global interactions in a computationally efficient way. By detaching the inputs/outputs discretizations from the processor with a smaller latent bottleneck, IPOT offers flexibility in processing arbitrary discretizations and scales linearly with the size of inputs/outputs. Our experimental results demonstrate that IPOT achieves strong performances with manageable computational complexity on an extensive range of PDE benchmarks and real-world weather forecasting scenarios, compared to state-of-the-art methods. Our code is publicly available at https://github.com/7tl7qns7ch/IPOT.
Stock price forecasting has remained an extremely challenging problem for many decades due to the high volatility of the stock market. Recent efforts have been devoted to modeling complex stock correlations toward joint stock price forecasting. Existing works share a common neural architecture that learns temporal patterns from individual stock series and then mixes up temporal representations to establish stock correlations. However, they only consider time-aligned stock correlations stemming from all the input stock features, which suffer from two limitations. First, stock correlations often occur momentarily and in a cross-time manner. Second, the feature effectiveness is dynamic with market variation, which affects both the stock sequential patterns and their correlations. To address the limitations, this paper introduces MASTER, a MArkert-guided Stock TransformER, which models the momentary and cross-time stock correlation and leverages market information for automatic feature selection. MASTER elegantly tackles the complex stock correlation by alternatively engaging in intra-stock and inter-stock information aggregation. Experiments show the superiority of MASTER compared with previous works and visualize the captured realistic stock correlation to provide valuable insights.
In the hydrology field, time series forecasting is crucial for efficient water resource management, improving flood and drought control and increasing the safety and quality of life for the general population. However, predicting long-term streamflow is a complex task due to the presence of extreme events. It requires the capture of long-range dependencies and the modeling of rare but important extreme values. Existing approaches often struggle to tackle these dual challenges simultaneously. In this paper, we specifically delve into these issues and propose Distance-weighted Auto-regularized Neural network (DAN), a novel extreme-adaptive model for long-range forecasting of stremflow enhanced by polar representation learning. DAN utilizes a distance-weighted multi-loss mechanism and stackable blocks to dynamically refine indicator sequences from exogenous data, while also being able to handle uni-variate time-series by employing Gaussian Mixture probability modeling to improve robustness to severe events. We also introduce Kruskal-Wallis sampling and gate control vectors to handle imbalanced extreme data. On four real-life hydrologic streamflow datasets, we demonstrate that DAN significantly outperforms both state-of-the-art hydrologic time series prediction methods and general methods designed for long-term time series prediction.
Consumer credit services offered by electronic commerce platforms provide customers with convenient loan access during shopping and have the potential to stimulate sales. To understand the causal impact of credit lines on spending, previous studies have employed causal estimators, (e.g., direct regression (DR), inverse propensity weighting (IPW), and double machine learning (DML)) to estimate the treatment effect. However, these estimators do not treat the spending of each individual as a distribution that can capture the range and pattern of amounts spent across different orders. By disregarding the outcome as a distribution, valuable insights embedded within the outcome distribution might be overlooked. This paper thus develops distribution valued estimators which extend from existing real valued DR, IPW, and DML estimators within Rubin’s causal framework. We establish their consistency and apply them to a real dataset from a large electronic commerce platform. Our findings reveal that credit lines generally have a positive impact on spending across all quantiles, but consumers would allocate more to luxuries (higher quantiles) than necessities (lower quantiles) as credit lines increase.
Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. Furthermore, designing a more fine-grained structure representation learning method is urgently needed as PTM is a biological event that occurs at the atom granularity. In this paper, we propose a PTM site prediction method by Coupling of Multi-Granularity structure and Multi-Scale sequence representation, PTM-CMGMS for brevity. Specifically, multigranularity structure-aware representation learning is designed to learn neighborhood structure representations at the amino acid, atom, and whole protein granularity from AlphaFold predicted structures, followed by utilizing contrastive learning to optimize the structure representations. Additionally, multi-scale sequence representation learning is used to extract context sequence information, and motif generated by aligning all context sequences of PTM sites assists the prediction. Extensive experiments on three datasets show that PTM-CMGMS outperforms the state-of-the-art methods. Source code can be found at https://github.com/LZY-HZAU/PTM-CMGMS.
Determining the types of neurons within a nervous system plays a significant role in the analysis of brain connectomics and the investigation of neurological diseases. However, the efficiency of utilizing anatomical, physiological, or molecular characteristics of neurons is relatively low and costly. With the advancements in electron microscopy imaging and analysis techniques for brain tissue, we are able to obtain whole-brain connectome consisting neuronal high-resolution morphology and connectivity information. However, few models are built based on such data for automated neuron classification. In this paper, we propose NeuNet, a framework that combines morphological information of neurons obtained from skeleton and topological information between neurons obtained from neural circuit. Specifically, NeuNet consists of three components, namely Skeleton Encoder, Connectome Encoder, and Readout Layer. Skeleton Encoder integrates the local information of neurons in a bottom-up manner, with a one-dimensional convolution in neural skeleton's point data; Connectome Encoder uses a graph neural network to capture the topological information of neural circuit; finally, Readout Layer fuses the above two information and outputs classification results. We reprocess and release two new datasets for neuron classification task from volume electron microscopy(VEM) images of human brain cortex and Drosophila brain. Experiments on these two datasets demonstrated the effectiveness of our model with accuracies of 0.9169 and 0.9363, respectively. Code and data are available at: https://github.com/WHUminghui/NeuNet.
In recent years, microservices have gained widespread adoption in IT operations due to their scalability, maintenance, and flexibility. However, it becomes challenging for site reliability engineers (SREs) to pinpoint the root cause due to the complex relationship in microservices when facing system malfunctions. Previous research employed structure learning methods (e.g., PC-algorithm) to establish causal relationships and derive root causes from causal graphs. Nevertheless, they ignored the temporal order of time series data and failed to leverage the rich information inherent in the temporal relationships. For instance, in cases where there is a sudden spike in CPU utilization, it can lead to an increase in latency for other microservices. However, in this scenario, the anomaly in CPU utilization occurs before the latency increases, rather than simultaneously. As a result, the PC-algorithm fails to capture such characteristics. To address these challenges, we propose RUN, a novel approach for root cause analysis using neural Granger causal discovery with contrastive learning. RUN enhances the backbone encoder by integrating contextual information from time series and leverages a time series forecasting model to conduct neural Granger causal discovery. In addition, RUN incorporates Pagerank with a personalization vector to efficiently recommend the top-k root causes. Extensive experiments conducted on the synthetic and real-world microservice-based datasets demonstrate that RUN noticeably outperforms the state-of-the-art root cause analysis methods. Moreover, we provide an analysis scenario for the sock-shop case to showcase the practicality and efficacy of RUN in microservice-based applications. Our code is publicly available at https://github.com/zmlin1998/RUN.
High-accuracy positioning has become a fundamental enabler for intelligent connected devices. Nevertheless, the present wireless networks still rely on model-driven approaches to achieve positioning functionality, which are susceptible to performance degradation in practical scenarios, primarily due to hardware impairments. Integrating artificial intelligence into the positioning framework presents a promising solution to revolutionize the accuracy and robustness of location-based services. In this study, we address this challenge by reformulating the problem of angle-of-arrival (AoA) estimation into image reconstruction of spatial spectrum. To this end, we design a model-driven deep neural network (MoD-DNN), which can automatically calibrate the angular-dependent phase error. The proposed MoD-DNN approach employs an iterative optimization scheme between a convolutional neural network and a sparse conjugate gradient algorithm. Simulation and experimental results are presented to demonstrate the effectiveness of the proposed method in enhancing spectrum calibration and AoA estimation.