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Program performance optimization is essential for achieving high execution efficiency, yet it remains a challenging task that requires expertise in both software and hardware. Large Language Models (LLMs), trained on high-quality code from platforms like GitHub and other open-source sources, have shown promise in generating optimized code for simple snippets. However, current LLM-based solutions often fall short when tackling project-level programs due to the complexity of call graphs and the intricate interactions among functions. In this paper, we emulate the process a human expert might follow when optimizing project-level programs and introduce a three-phase framework POLO (PrOject-Level Optimizer) to address this limitation. First, we profile the program to identify performance bottlenecks using an iterative weighting algorithm. Next, we conduct structural analysis by scanning the project and generating a graph that represents the program's structure. Finally, two LLM agents collaborate in iterative cycles to rewrite and optimize the code at these hotspots, gradually improving performance. We conduct experiments on open-source and proprietary projects. The results demonstrate that POLO accurately identifies performance bottlenecks and successfully applies optimizations. Under the O3 compilation flag, the optimized programs achieved speedups ranging from 1.34x to 21.5x.
Researchers, policy makers, and engineers need to make sense of data from spreading processes as diverse as rumor spreading in social networks, viral infections, and water contamination. Classical questions include predicting infection behavior in a given network or deducing the network structure from infection data. Most of the research on network infections studies static graphs, that is, the connections in the network are assumed to not change. More recently, temporal graphs, in which connections change over time, have been used to more accurately represent real-world infections, which rarely occur in unchanging networks. We propose a model for temporal graph discovery that is consistent with previous work on static graphs and embraces the greater expressiveness of temporal graphs. For this model, we give algorithms and lower bounds which are often tight. We analyze different variations of the problem, which make our results widely applicable and it also clarifies which aspects of temporal infections make graph discovery easier or harder. We round off our analysis with an experimental evaluation of our algorithm on real-world interaction data from the Stanford Network Analysis Project and on temporal Erdős-Renyi graphs. On Erdős-Renyi graphs, we uncover a threshold behavior, which can be explained by a novel connectivity parameter that we introduce during our theoretical analysis.
Large language models (LLMs) have garnered increasing attention owing to their powerful comprehension and generation capabilities. Generally, larger LLMs (L-LLMs) that require paid interfaces exhibit significantly superior performance compared to smaller LLMs (S-LLMs) that can be deployed on a variety of devices. Knowledge distillation (KD) aims to empower S-LLMs with the capabilities of L-LLMs, while S-LLMs merely mimic the outputs of L-LLMs, failing to get the powerful decision-making capability for new situations. Consequently, S-LLMs are helpless when it comes to continuous decision-making tasks that require logical reasoning. To tackle the identified challenges, we propose a novel framework called Logic Distillation (LD). Initially, LD employs L-LLMs to instantiate complex instructions into discrete functions and illustrates their usage to establish a function base. Subsequently, LD fine-tunes S-LLMs based on the function base to learn the logic employed by L-LLMs in decision-making. During testing, S-LLMs will yield decision-making outcomes, function by function, based on current states. Experiments demonstrate that with the assistance of LD, S-LLMs can achieve outstanding results in continuous decision-making tasks, comparable to, or even surpassing, those of L-LLMs. The code and data for the proposed method are provided for research purposes https://github.com/Anfeather/Logic-Distillation.
More accurate construction of brain effective conncetivity networks remains a great challenge to achieve accurate auxiliary diagnosis of brain diseases and in-depth exploration of brain function. However, existing methods only consider higher-order or non-stationary assumptions, rather than simultaneously constructing higher-order and non-stationary networks. Among many existing methods, Bayesian network methods demonstrate superior network structure learning ability. In this work, the forward-backward search (FBS) method is optimized by using brain active information, which is improved to a higher-order network structure learning method, called TSTAI. Firstly, in the process of non-stationary network structure learning, two-stage idea is used to search the change points. Then, in the process of learning higher-order network structure, FBS method is combined with two kinds of brain active information to improve the condition set filtering process and scoring function, respectively. Finally, the pruning strategy is used to reduce the search space. Extensive experiments on simulated and real data demonstrate the effectiveness of TSTAI. Through experiments, the TSTAI is compared with state-of-the-art higher-order network construction methods, and the proposed method achieves an improvement of 3.6% and 17.4% respectively in the network construction accuracy.
Fourier Neural Operators (FNO) have emerged as promising solutions for efficiently solving partial differential equations (PDEs) by learning infinite-dimensional function mappings through frequency domain transformations. However, the sparsity of high-frequency signals limits computational efficiency for high-dimensional inputs, and fixed-pattern truncation often causes high-frequency signal loss, reducing performance in scenarios such as high-resolution inputs or long-term predictions. To address these challenges, we propose FreqMoE, an efficient and progressive training framework that exploits the dependency of high-frequency signals on low-frequency components. The model first learns low-frequency weights and then applies a sparse upward-cycling strategy to construct a mixture of experts (MoE) in the frequency domain, effectively extending the learned weights to high-frequency regions. Experiments on both regular and irregular grid PDEs demonstrate that FreqMoE achieves up to 16.6 percent accuracy improvement while using merely 2.1 percent parameters (47.32x reduction) compared to dense FNO. Furthermore, the approach demonstrates remarkable stability in long-term predictions and generalizes seamlessly to various FNO variants and grid structures, establishing a new Low frequency Pretraining, High frequency Fine-tuning'' paradigm for solving PDEs.
The bulk of the literature on opinion optimization in social networks adopts the Friedkin–Johnsen (FJ) opinion dynamics model, in which the innate opinions of all nodes are known: this is an unrealistic assumption. In this paper, we study opinion optimization under the FJ model without the full knowledge of innate opinions. Specifically, we borrow from the literature a series of objective functions, aimed at minimizing polarization and/or disagreement, and we tackle the budgeted optimization problem, where we can query the innate opinions of only a limited number of nodes. Given the complexity of our problem, we propose a framework based on three steps: (1) select the limited number of nodes we query, (2) reconstruct the innate opinions of all nodes based on those queried, and (3) optimize the objective function with the reconstructed opinions. For each step of the framework, we present and systematically evaluate several effective strategies. A key contribution of our work is a rigorous error propagation analysis that quantifies how reconstruction errors in innate opinions impact the quality of the final solutions. Our experiments on various synthetic and real-world datasets show that we can effectively minimize polarization and disagreement even if we have quite limited information about innate opinions.
Multivariate time series forecasting holds significant theoretical and practical importance in various fields, including web analytics and transportation. Recently, graph neural networks and graph differential equations have shown exceptional capabilities in modeling spatio-temporal features. However, existing methods often suffer from over-smoothing, hindering real-world problem-solving. In this work, we analyze the graph propagation process as a dynamical system and propose a novel feedback mechanism to enhance representation power, adaptively adjusting the representations to align with desired performance outcomes, thereby fundamentally mitigating the issue of over-smoothing. Moreover, we introduce an effective multivariate time series forecasting model called SF-GDE, based on the proposed graph propagation with the feedback mechanism. Intensive experiments are conducted on three real-world datasets from diverse fields. Results show that SF-GDE outperforms the state of the arts, and the feedback mechanism can serve as a universal booster to improve performance for graph propagation models.
Community detection, a vital technology for real-world applications, uncovers cohesive node groups (communities) by leveraging both topological and attribute similarities in social networks. However, existing Graph Convolutional Networks (GCNs) trained to maximize modularity often converge to suboptimal solutions. Additionally, directly using human-labeled communities for training can undermine topological cohesiveness by grouping disconnected nodes based solely on node attributes. We address these issues by proposing a novel Topological and Attributive Similarity-based Community detection (TAS-Com) method. TAS-Com introduces a novel loss function that exploits the highly effective and scalable Leiden algorithm to detect community structures with global optimal modularity. Leiden is further utilized to refine human-labeled communities to ensure connectivity within each community, enabling TAS-Com to detect community structures with desirable trade-offs between modularity and compliance with human labels. Experimental results on multiple benchmark networks confirm that TAS-Com can significantly outperform several state-of-the-art algorithms.
Single-cell sequencing technology provides deep insights into gene activity at the individual cell level, facilitating the study of gene regulatory mechanisms. However, observed gene expression are often influenced by confounding factors such as batch effects, perturbations, and spatial position, which obscure the true gene regulatory network that governs the cell’s intrinsic state. To address these challenges, we propose scConCRL, a novel conditionally causal representation learning framework designed to extract the true gene regulatory relationships independent of confounding information. By considering both fine-grained molecular gene variables and coarse-grained latent domain variables, scConCRL not only uncovers the intrinsic biological signals but also models the complex relationships between these variables. This dual function enables the separation of genuine cellular states from domain information, providing valuable insights for downstream analyses and biological discovery. We demonstrate the effectiveness of our model on multi-domain datasets from different platforms and perturbation conditions, showing its ability to accurately disentangle confounding influences and discover novel gene relationships. Extensive comparisons across various scenarios illustrate the superior performance of scConCRL in several tasks compared to existing methods.
Knowledge tracing (KT) aims to predict learners' future performance based on historical learning interactions. However, existing KT models predominantly focus on data from a single course, limiting their ability to capture a comprehensive understanding of learners' knowledge states. In this paper, we propose TransKT, a contrastive cross-course knowledge tracing method that leverages concept graph guided knowledge transfer to model the relationships between learning behaviors across different courses, thereby enhancing knowledge state estimation. Specifically, TransKT constructs a cross-course concept graph by leveraging zero-shot Large Language Model (LLM) prompts to establish implicit links between related concepts across different courses. This graph serves as the foundation for knowledge transfer, enabling the model to integrate and enhance the semantic features of learners' interactions across courses. Furthermore, TransKT includes an LLM-to-LM pipeline for incorporating summarized semantic features, which significantly improves the performance of Graph Convolutional Networks (GCNs) used for knowledge transfer. Additionally, TransKT employs a contrastive objective that aligns single-course and cross-course knowledge states, thereby refining the model's ability to provide a more robust and accurate representation of learners' overall knowledge states. Our code and datasets are available at https://github.com/DQYZHWK/TransKT/.
Recent advancements in radiology report generation have utilized deep neural networks such as CNNs and Transformers, achieving notable improvements in generating accurate and detailed reports. However, their practical adoption is hindered by the challenge of balancing global dependency modeling with computational efficiency. The state space model, particularly its enhanced variant Mamba, offers promising linear-complexity solutions for long-range dependency modeling. Despite its strengths, Mamba’s fixed positional encoding limits its ability to effectively capture complex spatial dependencies. To address this gap, we propose RRG-Mamba, an advanced framework for efficient radiology report generation. Within the RRGMamba, we enhance the vanilla Mamba by integrating rotary position encoding (RoPE), enabling dynamic modeling of relative positional information in visual feature sequences. Furthermore, we design a global dependency learning module to optimize long-range visual feature sequence modeling. Extensive experiments on publicly available datasets, including IU X-Ray and MIMIC-CXR, demonstrate that RRG-Mamba achieves a 3.7% improvement in BLEU-4 score over existing models, along with significant gains in computational and memory efficiency. Our code is available at https://github.com/Eleanorhxd/RRG-Mamba.
Generative artificial intelligence in music has made significant strides, yet it still falls short of the substantial achievements seen in natural language processing, primarily due to the limited availability of music data. Knowledge-informed approaches have been shown to enhance the performance of music generation models, even when only a few pieces of musical knowledge are integrated. This paper seeks to leverage comprehensive music theory in AI-driven music generation tasks, such as algorithmic composition and style transfer, which traditionally require significant manual effort with existing techniques. We introduce a novel automatic music lexicon construction model that generates a lexicon, named CompLex, comprising 37,432 items derived from just 9 manually input category keywords and 5 sentence prompt templates. A new multi-agent algorithm is proposed to automatically detect and mitigate hallucinations. CompLex demonstrates impressive performance improvements across three state-of-the-art text-to-music generation models, encompassing both symbolic and audio-based methods. Furthermore, we evaluate CompLex in terms of completeness, accuracy, non-redundancy, and executability, confirming that it possesses the key characteristics of an effective lexicon.
Checking the reliability of machine-learning models is a crucial, but challenging task. Nomos is an existing, automated framework for testing general, user-provided functional properties of models, including so-called hyperproperties expressed over more than one model execution. Nomos aims to find model inputs that expose ``bugs'', that is, property violations. However, performing thousands of model invocations during testing is costly both in terms of time and money (for metered APIs, such as OpenAI's). We present LaZ (pronounced ``lazy''), an extension of Nomos that automatically minimizes the number of model invocations to boost the test throughput and thereby find bugs more efficiently. During test execution, LaZ automatically identifies redundant invocations---invocations where the model output does not affect the final test outcome---and skips them, much like lazy evaluation in certain programming languages. This optimization enables a second one that dynamically reorders model invocations to skip the more expensive ones. As a result, LaZ finds the same number of bugs as Nomos, but does so median 33% and up to 60% faster.
Accurate molecular property prediction is a critical challenge with wide-ranging applications in chemistry, materials science, and drug discovery. Molecular representation methods, including fingerprints and graph neural networks (GNNs), achieve state-of-the-art results by effectively deriving features from molecular structures. However, these methods often overlook decades of accumulated semantic and contextual knowledge. Recent advancements in large language models (LLMs) demonstrate remarkable reasoning abilities and prior knowledge across scientific domains, leading us to hypothesize that LLMs can generate rich molecular representations when guided to reason in multiple perspectives. To address these gaps, we propose M^2LLM, a multi-view framework that integrates three perspectives: the molecular structure view, the molecular task view, and the molecular rules view. These views are fused dynamically to adapt to task requirements, and experiments demonstrate that M^2LLM achieves state-of-the-art performance on multiple benchmarks across classification and regression tasks. Moreover, we demonstrate that representation derived from LLM achieves exceptional performance by leveraging two core functionalities: the generation of molecular embeddings through their encoding capabilities and the curation of molecular features through advanced reasoning processes.
Although AlphaZero has achieved superhuman performance in board games, recent studies reveal its limitations in handling scenarios requiring a comprehensive understanding of the entire board, such as recognizing long-sequence patterns in Go. To address this challenge, we propose ResTNet, a network that interleaves residual and Transformer blocks to bridge local and global knowledge. ResTNet improves playing strength across multiple board games, increasing win rate from 54.6% to 60.8% in 9x9 Go, 53.6% to 60.9% in 19x19 Go, and 50.4% to 58.0% in 19x19 Hex. In addition, ResTNet effectively processes global information and tackles two long-sequence patterns in 19x19 Go, including circular pattern and ladder pattern. It reduces the mean square error for circular pattern recognition from 2.58 to 1.07 and lowers the attack probability against an adversary program from 70.44% to 23.91%. ResTNet also improves ladder pattern recognition accuracy from 59.15% to 80.01%. By visualizing attention maps, we demonstrate that ResTNet captures critical game concepts in both Go and Hex, offering insights into AlphaZero's decision-making process. Overall, ResTNet shows a promising approach to integrating local and global knowledge, paving the way for more effective AlphaZero-based algorithms in board games. Our code is available at https://rlg.iis.sinica.edu.tw/papers/restnet.
API migration is essential for software maintenance due to the rapid evolution of third-party libraries where API elements may change continuously through updates. There are two main challenges for API migration at the project level, especially across multiple versions: 1) lack of specific library evolution knowledge across multi-version; 2) difficulty in identifying the chain of changes at the project level. This paper proposes a project-level cross-multi-version API migration framework APIMig. We first construct an API evolution knowledge graph (KG) to capture changes between adjacent library versions and then derive coherent cross-version API evolution knowledge by KG reasoning. Second, we design a chain exploration algorithm to track the chain of changes and aggregate the affected code segments. Finally, a large language model is employed in completing API migration by providing the API evolution knowledge and the chain of changes. We construct an evolution KG for the Lucene library from version 4.0.0 to 10.1.0 and evaluate our approach through project migration pairs that depend on different major versions. Our framework shows improvements over the baseline in migrating projects across 7 major versions, achieving average increases of 16.52% in CodeBLEU scores and 28.49% in VCEU scores in GPT-4o.
Machine unlearning aims to eliminate the influence of a subset of training samples (i.e., unlearning samples) from a trained model. Effectively and efficiently removing the unlearning samples without negatively impacting the overall model performance is challenging. Existing works mainly exploit input and output space and classification loss, which can result in ineffective unlearning or performance loss. In addition, they utilize unlearning or remaining samples ineffectively, sacrificing either unlearning efficacy or efficiency. Our main insight is that the direct optimization on the representation space utilizing both unlearning and remaining samples can effectively remove influence of unlearning samples while maintaining representations learned from remaining samples. We propose a contrastive unlearning framework, leveraging the concept of representation learning for more effective unlearning. It removes the influence of unlearning samples by contrasting their embeddings against the remaining samples' embeddings so that their embeddings are closer to the embeddings of unseen samples. Experiments on a variety of datasets and models on both class unlearning and sample unlearning showed that contrastive unlearning achieves the best unlearning effects and efficiency with the lowest performance loss compared with the state-of-the-art algorithms. In addition, it is generalizable to different contrastive frameworks and other models such as vision-language models. Our main code is available on github.com/Emory-AIMS/Contrastive-Unlearning
Latent diffusion models have exhibited considerable potential in generative tasks. Watermarking is considered to be an alternative to safeguard the copyright of generative models and prevent their misuse. However, in the context of model distribution scenarios, the accessibility of models to large scale of model users brings new challenges to the security, efficiency and robustness of existing watermark solutions. To address these issues, we propose a secure and efficient watermarking solution. A new security mechanism is designed to prevent watermark leakage and watermark escape, which considers watermark randomness and watermark-model association as two constraints for mandatory watermark injection. To reduce the time cost of training the security module, watermark injection and the security mechanism are decoupled, ensuring that fine-tuning VAE only accomplishes the security mechanism without the burden of learning watermark patterns. A watermark distribution-based verification strategy is proposed to enhance the robustness against diverse attacks in the model distribution scenarios. Experimental results prove that our watermarking consistently outperforms existing six baselines on effectiveness and robustness against ten image processing attacks and adversarial attacks, while enhancing security in the distribution scenarios. The code is available at https://anonymous.4open.science/r/DistriMark-F11F/.
The prediction of information popularity propagation is critical for applications such as recommendation systems, targeted advertising, and social media trend analysis. Traditional approaches primarily rely on historical cascade data, often sacrificing timeliness for prediction accuracy. These methods capture aggregate diffusion patterns but fail to account for the complex temporal dynamics of early-stage propagation. In this paper, we introduce Diffusion Guided Propagation Augmentation(DGPA), a novel framework designed to improve early-stage popularity prediction. DGPA models cascade dynamics by leveraging a generative approach, where a temporal conditional interpolator serves as a noising process and forecasting as a denoising process. By iteratively generating cascade representations through a sampling procedure, DGPA effectively incorporates the evolving time steps of diffusion, significantly enhancing prediction timeliness and accuracy. Extensive experiments on benchmark datasets from Twitter, Weibo, and APS demonstrate that DGPA outperforms state-of-the-art methods in early-stage popularity prediction.
Trajectory similarity aims to identify pairs of similar trajectories, serving as a crucial operation in spatial-temporal data mining. Although several approaches have been proposed, they encounter the following two issues: 1) An overemphasis on spatial similarity in road networks while the rich semantic information embedded in trajectories is not fully exploited; 2) Dependence on Recurrent Neural Network (RNN) architectures would struggle to capture long-term dependencies. To address these limitations, we propose a Dual-branch Attention-based framework with Spatial and Semantic information (DASS) based on self-supervised learning. Specifically, DASS comprises two core components: 1) A trajectory representation module that models spatial-temporal adjacent relationships in the form of graph and converts semantics into numerical embeddings. 2) A backbone encoder with a co-attention module to independently process two features before they are integrated. Extensive experiments on real-world datasets demonstrate that DASS outperforms state-of-the-art methods, establishing itself as a novel paradigm.
Portfolio selection is a critical task in finance, involving the allocation of resources across various assets. However, current methods often struggle to maintain robust performance due to the inherent low signal-to-noise ratio in raw financial data and shifts in data distribution. We propose AlphaGAT, a novel two-stage learning approach for portfolio selection, designed to adapt to different market scenarios. Inspired by the concept of alpha factors, which transform historical market data into actionable signals, the first stage introduces an advanced model named CATimeMixer for alpha factor generation with a novel loss function to improve the effectiveness and robustness. CATimeMixer integrates TimeMixer with Conv1D (C) and cross-asset Attention (A). Specifically, Conv1D enhances TimeMixer by capturing trend and seasonal features across different scales, while cross-asset attention enables TimeMixer to extract interrelationships between different assets. The second stage applies reinforcement learning to dynamically adjust weights, integrating alpha factors into trading signals. Recognizing the varying effectiveness of alpha factors across different periods, our RL agent innovatively transforms the alpha factors into graphs and employs graph attention networks (GAT) to discern the significance of different alpha factors, enhancing policy robustness. Extensive experiments on real-world market data show that our approach outperforms state-of-the-art methods.
Single-step retrosynthesis is a crucial task in organic synthesis, where the objective is to identify the reactants needed to produce a given product. In recent years, a variety of machine learning methods have been developed to tackle retrosynthesis prediction. In our study, we introduce RetroMoE, a novel generative model designed for the single-step retrosynthesis task. We start with a non-symmetric variational autoencoder (VAE) that incorporates a graph encoder to map molecular graphs into a latent space, followed by a transformer decoder for precise prediction of molecular SMILES strings. Additionally, we implement a simple yet effective mixture-of-experts (MoE) network to translate the product latent embedding into the reactant latent embedding. To our knowledge, this is the first approach that frames single-step retrosynthesis as a latent translation problem. Extensive experiments on the USPTO-50K and USPTO-MIT datasets demonstrate the superiority of our method, which not only surpasses most semi-template-based and template-free methods but also delivers competitive results against template-based methods. Notably, under the class-known setting on the USPTO-50K, our method achieves top-1 exact match accuracy comparable to the state-of-the-art template method, RetroKNN.
Accurate prediction of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties is crucial in drug development, as these properties directly impact a drug's efficacy and safety. However, existing multi-task learning models often face challenges related to noise interference and task conflicts when dealing with complex molecular structures. To address these issues, we propose a novel multi-task Graph Neural Network (GNN) model, \textbf{MTGIB-UNet}. The model begins by encoding molecular graphs to capture intricate molecular structure information. Subsequently, based on the Graph Information Bottleneck (GIB) principle, the model compresses the information flow by extracting subgraphs, retaining task-relevant features while removing noise for each task. These embeddings are then fused through a gated network that dynamically adjusts the contribution weights of auxiliary tasks to the primary task. Specifically, an uncertainty weighting (UW) strategy is applied, with additional emphasis placed on the primary task, allowing dynamic adjustment of task weights while strengthening the influence of the primary task on model training. Experiments on standard ADMET datasets demonstrate that our model outperforms existing methods. Additionally, the model shows good interpretability by identifying key molecular substructures related to specific ADMET endpoints.
Forecasting stock prices is complex and challenging. Uncovering correlations among stocks has proven to enhance stock price forecasting. However, existing correlation discovery methods, such as concept-based methods, are slow, inaccurate, and limited by their reliance on predefined concepts and manual analysis. In this paper, we propose COGRASP, a novel approach for stock price forecasting that constructs stock co-occurrence graphs automatically by analyzing rapidly updated sources such as reports, newspapers, and social media. Besides, we aggregate forecasts across multiple timescales (i.e., long-, medium-, and short-term) to capture multi-timescale trends fluctuations, thereby enhancing price forecasting accuracy. In experiments with real-world open-source stock market data, COGRASP outperforms state-of-the-art methods.
Major Depressive Disorder (MDD) is a prevalent and severe mental disease. Functional Magnetic Resonance Imaging (fMRI)-based diagnostic methods, which analyze Functional Connectivity (FC) to identify abnormal functional connections, have shown promise as biomarker-based approaches for diagnosing depression. However, the high costs of fMRI data result in small sample sizes, hindering the effective identification of abnormal FC patterns. Moreover, existing methods often overlook the potential benefits of incorporating domain knowledge into their models. In this paper, we propose KnowMDD, a novel knowledge-guided cross contrastive learning framework for MDD diagnosis. By incorporating domain knowledge and employing data augmentation, KnowMDD addresses data sparsity while improving robustness and interpretability. Specifically, multiple atlases are used to construct complementary brain graph representations. The default mode network, closely associated with depression, is introduced into the contrastive learning paradigm for diverse subgraph augmentations, while an attention mechanism captures global semantic relationships between brain regions. Based on them, a cross contrastive learning is designed to learn robust representations for accurate diagnosis. Extensive experiments demonstrate the effectiveness, robustness, and interpretability of KnowMDD, which outperforms state-of-the-art methods. We also develop a demonstration system to show its practical application.