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In this paper, we propose a data-driven method to learn interpretable topological features of biomolecular data and demonstrate the efficacy of parsimonious models trained on topological features in predicting the stability of synthetic mini proteins. We compare models that leverage automatically-learned structural features against models trained on a large set of biophysical features determined by subject-matter experts (SME). Our models, based only on topological features of the protein structures, achieved 92%-99% of the performance of SME-based models in terms of the average precision score. By interrogating model performance and feature importance metrics, we extract numerous insights that uncover high correlations between topological features and SME features. We further showcase how combining topological features and SME features can lead to improved model performance over either feature set used in isolation, suggesting that, in some settings, topological features may provide new discriminating information not captured in existing SME features that are useful for protein stability prediction.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · 代碼 · MoDELS · 數據集 · Python ·
2024 年 10 月 3 日

In this paper, we consider contamination by code generation test sets, in particular in their use in modern large language models. We discuss three possible sources of such contamination and show findings supporting each of them: (i) direct data leakage, (ii) indirect data leakage through the use of synthetic data and (iii) overfitting to evaluation sets during model selection. To address this, we release Less Basic Python Problems (LBPP): an uncontaminated new benchmark of 161 prompts with their associated Python solutions. LBPP is released at //huggingface.co/datasets/CohereForAI/lbpp .

In this paper, we explore different approaches to anomaly detection on dynamic knowledge graphs, specifically in a microservices environment for Kubernetes applications. Our approach explores three dynamic knowledge graph representations: sequential data, one-hop graph structure, and two-hop graph structure, with each representation incorporating increasingly complex structural information. Each phase includes different machine learning and deep learning models. We empirically analyse their performance and propose an approach based on ensemble learning of these models. Our approach significantly outperforms the baseline on the ISWC 2024 Dynamic Knowledge Graph Anomaly Detection dataset, providing a robust solution for anomaly detection in dynamic complex data.

In this paper, we propose a generalized shift-splitting (GSS) preconditioner, along with its two relaxed variants to solve the double saddle point problem (DSPP). The convergence of the associated GSS iterative method is analyzed, and sufficient conditions for its convergence are established. Spectral analyses are performed to derive sharp bounds for the eigenvalues of the preconditioned matrices. Numerical experiments based on examples arising from the PDE-constrained optimization problems demonstrate the effectiveness and robustness of the proposed preconditioners compared with existing state-of-the-art preconditioners.

Neural operators serve as universal approximators for general continuous operators. In this paper, we derive the approximation rate of solution operators for the nonlinear parabolic partial differential equations (PDEs), contributing to the quantitative approximation theorem for solution operators of nonlinear PDEs. Our results show that neural operators can efficiently approximate these solution operators without the exponential growth in model complexity, thus strengthening the theoretical foundation of neural operators. A key insight in our proof is to transfer PDEs into the corresponding integral equations via Duahamel's principle, and to leverage the similarity between neural operators and Picard's iteration, a classical algorithm for solving PDEs. This approach is potentially generalizable beyond parabolic PDEs to a range of other equations, including the Navier-Stokes equation, nonlinear Schr\"odinger equations and nonlinear wave equations, which can be solved by Picard's iteration.

In this paper, we consider joint antenna allocation and transmit beamforming design in secure integrated sensing and communication (ISAC) systems. A dual-function base station (DFBS) aims to securely deliver messages to a single-antenna receiver while detecting potential eavesdroppers. To prevent eavesdropping, we incorporate specialized sensing signals, intentionally reducing communication signal power toward suspicious targets to improve sensing. We prioritize minimizing the matching error between the transmitting and required beampatterns for sensing and communication. Our design optimizes antenna allocation and beamforming at the DFBS, meeting minimum secrecy rate and power constraints. We propose solvers based on alternating optimization for the non-convex design problem. Simulations show that the antenna allocation scheme significantly improves safety performance.

In this paper, we demonstrate how to enhance the validity of causal inference with unstructured high-dimensional treatments like texts, by leveraging the power of generative Artificial Intelligence. Specifically, we propose to use a deep generative model such as large language models (LLMs) to efficiently generate treatments and use their internal representation for subsequent causal effect estimation. We show that the knowledge of this true internal representation helps separate the treatment features of interest, such as specific sentiments and certain topics, from other possibly unknown confounding features. Unlike the existing methods, our proposed approach eliminates the need to learn causal representation from the data and hence produces more accurate and efficient estimates. We formally establish the conditions required for the nonparametric identification of the average treatment effect, propose an estimation strategy that avoids the violation of the overlap assumption, and derive the asymptotic properties of the proposed estimator through the application of double machine learning. Finally, using an instrumental variables approach, we extend the proposed methodology to the settings, in which the treatment feature is based on human perception rather than is assumed to be fixed given the treatment object. We conduct simulation studies using the generated text data with an open-source LLM, Llama3, to illustrate the advantages of our estimator over the state-of-the-art causal representation learning algorithms.

In this paper, we introduce a novel training method for making any monocular depth network learn absolute scale and estimate metric road-scene depth just from regular training data, i.e., driving videos. We refer to this training framework as FUMET. The key idea is to leverage cars found on the road as sources of scale supervision and to incorporate them in network training robustly. FUMET detects and estimates the sizes of cars in a frame and aggregates scale information extracted from them into an estimate of the camera height whose consistency across the entire video sequence is enforced as scale supervision. This realizes robust unsupervised training of any, otherwise scale-oblivious, monocular depth network so that they become not only scale-aware but also metric-accurate without the need for auxiliary sensors and extra supervision. Extensive experiments on the KITTI and the Cityscapes datasets show the effectiveness of FUMET, which achieves state-of-the-art accuracy. We also show that FUMET enables training on mixed datasets of different camera heights, which leads to larger-scale training and better generalization. Metric depth reconstruction is essential in any road-scene visual modeling, and FUMET democratizes its deployment by establishing the means to convert any model into a metric depth estimator.

In this study, we consider the problem of predicting task success for open-vocabulary manipulation by a manipulator, based on instruction sentences and egocentric images before and after manipulation. Conventional approaches, including multimodal large language models (MLLMs), often fail to appropriately understand detailed characteristics of objects and/or subtle changes in the position of objects. We propose Contrastive $\lambda$-Repformer, which predicts task success for table-top manipulation tasks by aligning images with instruction sentences. Our method integrates the following three key types of features into a multi-level aligned representation: features that preserve local image information; features aligned with natural language; and features structured through natural language. This allows the model to focus on important changes by looking at the differences in the representation between two images. We evaluate Contrastive $\lambda$-Repformer on a dataset based on a large-scale standard dataset, the RT-1 dataset, and on a physical robot platform. The results show that our approach outperformed existing approaches including MLLMs. Our best model achieved an improvement of 8.66 points in accuracy compared to the representative MLLM-based model.

In this paper, we propose a novel Feature Decomposition and Reconstruction Learning (FDRL) method for effective facial expression recognition. We view the expression information as the combination of the shared information (expression similarities) across different expressions and the unique information (expression-specific variations) for each expression. More specifically, FDRL mainly consists of two crucial networks: a Feature Decomposition Network (FDN) and a Feature Reconstruction Network (FRN). In particular, FDN first decomposes the basic features extracted from a backbone network into a set of facial action-aware latent features to model expression similarities. Then, FRN captures the intra-feature and inter-feature relationships for latent features to characterize expression-specific variations, and reconstructs the expression feature. To this end, two modules including an intra-feature relation modeling module and an inter-feature relation modeling module are developed in FRN. Experimental results on both the in-the-lab databases (including CK+, MMI, and Oulu-CASIA) and the in-the-wild databases (including RAF-DB and SFEW) show that the proposed FDRL method consistently achieves higher recognition accuracy than several state-of-the-art methods. This clearly highlights the benefit of feature decomposition and reconstruction for classifying expressions.

In this paper, we propose the joint learning attention and recurrent neural network (RNN) models for multi-label classification. While approaches based on the use of either model exist (e.g., for the task of image captioning), training such existing network architectures typically require pre-defined label sequences. For multi-label classification, it would be desirable to have a robust inference process, so that the prediction error would not propagate and thus affect the performance. Our proposed model uniquely integrates attention and Long Short Term Memory (LSTM) models, which not only addresses the above problem but also allows one to identify visual objects of interests with varying sizes without the prior knowledge of particular label ordering. More importantly, label co-occurrence information can be jointly exploited by our LSTM model. Finally, by advancing the technique of beam search, prediction of multiple labels can be efficiently achieved by our proposed network model.

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