DNA-Encoded Library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly-efficient screening assays. These selection experiments, involving multiple stages of washing, elution, and identification of potent binders via unique DNA barcodes, often generate complex data. This complexity can potentially mask the underlying signals, necessitating the application of computational tools such as machine learning to uncover valuable insights. We introduce a compositional deep probabilistic model of DEL data, DEL-Compose, which decomposes molecular representations into their mono-synthon, di-synthon, and tri-synthon building blocks and capitalizes on the inherent hierarchical structure of these molecules by modeling latent reactions between embedded synthons. Additionally, we investigate methods to improve the observation models for DEL count data such as integrating covariate factors to more effectively account for data noise. Across two popular public benchmark datasets (CA-IX and HRP), our model demonstrates strong performance compared to count baselines, enriches the correct pharmacophores, and offers valuable insights via its intrinsic interpretable structure, thereby providing a robust tool for the analysis of DEL data.
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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。
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Masked AutoEncoder (MAE) has revolutionized the field of self-supervised learning with its simple yet effective masking and reconstruction strategies. However, despite achieving state-of-the-art performance across various downstream vision tasks, the underlying mechanisms that drive MAE's efficacy are less well-explored compared to the canonical contrastive learning paradigm. In this paper, we first propose a local perspective to explicitly extract a local contrastive form from MAE's reconstructive objective at the patch level. And then we introduce a new empirical framework, called Local Contrastive MAE (LC-MAE), to analyze both reconstructive and contrastive aspects of MAE. LC-MAE reveals that MAE learns invariance to random masking and ensures distribution consistency between the learned token embeddings and the original images. Furthermore, we dissect the contribution of the decoder and random masking to MAE's success, revealing both the decoder's learning mechanism and the dual role of random masking as data augmentation and effective receptive field restriction. Our experimental analysis sheds light on the intricacies of MAE and summarizes some useful design methodologies, which can inspire more powerful visual self-supervised methods.
Multicalibration is a notion of fairness for predictors that requires them to provide calibrated predictions across a large set of protected groups. Multicalibration is known to be a distinct goal than loss minimization, even for simple predictors such as linear functions. In this work, we consider the setting where the protected groups can be represented by neural networks of size $k$, and the predictors are neural networks of size $n > k$. We show that minimizing the squared loss over all neural nets of size $n$ implies multicalibration for all but a bounded number of unlucky values of $n$. We also give evidence that our bound on the number of unlucky values is tight, given our proof technique. Previously, results of the flavor that loss minimization yields multicalibration were known only for predictors that were near the ground truth, hence were rather limited in applicability. Unlike these, our results rely on the expressivity of neural nets and utilize the representation of the predictor.
Robust estimators for Generalized Linear Models (GLMs) are not easy to develop because of the nature of the distributions involved. Recently, there has been an increasing interest in this topic, especially in the presence of a possibly large number of explanatory variables. Transformed M-estimators (MT) are a natural way to extend the methodology of M-estimators to the class of GLMs and to obtain robust methods. We introduce a penalized version of MT-estimators in order to deal with high-dimensional data. We prove, under appropriate assumptions, consistency and asymptotic normality of this new class of estimators. The theory is developed for redescending $\rho$-functions and Elastic Net penalization. An iterative re-weighted least squares algorithm is given, together with a procedure to initialize it. The latter is of particular importance, since the estimating equations might have multiple roots. We illustrate the performance of this new method for the Poisson family under several type of contaminations in a Monte Carlo experiment and in an example based on a real dataset.
Answer Set Programming (ASP) is a widely used declarative programming paradigm that has shown great potential in solving complex computational problems. However, the inability to natively support non-integer arithmetic has been highlighted as a major drawback in real-world applications. This feature is crucial to accurately model and manage real-world data and information as emerged in various contexts, such as the smooth movement of video game characters, the 3D movement of mechanical arms, and data streamed by sensors. Nevertheless, extending ASP in this direction, without affecting its declarative nature and its well-defined semantics, poses non-trivial challenges; thus, no ASP system is able to reason natively with non-integer domains. Indeed, the widespread floating-point arithmetic is not applicable to the ASP case, as the reproducibility of results cannot be guaranteed and the semantics of an ASP program would not be uniquely and declaratively determined, regardless of the employed machine or solver. To overcome such limitations and in the realm of pure ASP, this paper proposes an extension of ASP in which non-integers are approximated to rational numbers, fully granting reproducibility and declarativity. We provide a well-defined semantics for the ASP-Core-2 standard extended with rational numbers and an implementation thereof. We hope this work could serve as a stepping stone towards a more expressive and versatile ASP language that can handle a broader range of real-world problems.
Molecular Property Prediction (MPP) task involves predicting biochemical properties based on molecular features, such as molecular graph structures, contributing to the discovery of lead compounds in drug development. To address data scarcity and imbalance in MPP, some studies have adopted Graph Neural Networks (GNN) as an encoder to extract commonalities from molecular graphs. However, these approaches often use a separate predictor for each task, neglecting the shared characteristics among predictors corresponding to different tasks. In response to this limitation, we introduce the GNN-MoCE architecture. It employs the Mixture of Collaborative Experts (MoCE) as predictors, exploiting task commonalities while confronting the homogeneity issue in the expert pool and the decision dominance dilemma within the expert group. To enhance expert diversity for collaboration among all experts, the Expert-Specific Projection method is proposed to assign a unique projection perspective to each expert. To balance decision-making influence for collaboration within the expert group, the Expert-Specific Loss is presented to integrate individual expert loss into the weighted decision loss of the group for more equitable training. Benefiting from the enhancements of MoCE in expert creation, dynamic expert group formation, and experts' collaboration, our model demonstrates superior performance over traditional methods on 24 MPP datasets, especially in tasks with limited data or high imbalance.
Large Language Models (LLMs) have shown excellent generalization capabilities that have led to the development of numerous models. These models propose various new architectures, tweaking existing architectures with refined training strategies, increasing context length, using high-quality training data, and increasing training time to outperform baselines. Analyzing new developments is crucial for identifying changes that enhance training stability and improve generalization in LLMs. This survey paper comprehensively analyses the LLMs architectures and their categorization, training strategies, training datasets, and performance evaluations and discusses future research directions. Moreover, the paper also discusses the basic building blocks and concepts behind LLMs, followed by a complete overview of LLMs, including their important features and functions. Finally, the paper summarizes significant findings from LLM research and consolidates essential architectural and training strategies for developing advanced LLMs. Given the continuous advancements in LLMs, we intend to regularly update this paper by incorporating new sections and featuring the latest LLM models.
2D-based Industrial Anomaly Detection has been widely discussed, however, multimodal industrial anomaly detection based on 3D point clouds and RGB images still has many untouched fields. Existing multimodal industrial anomaly detection methods directly concatenate the multimodal features, which leads to a strong disturbance between features and harms the detection performance. In this paper, we propose Multi-3D-Memory (M3DM), a novel multimodal anomaly detection method with hybrid fusion scheme: firstly, we design an unsupervised feature fusion with patch-wise contrastive learning to encourage the interaction of different modal features; secondly, we use a decision layer fusion with multiple memory banks to avoid loss of information and additional novelty classifiers to make the final decision. We further propose a point feature alignment operation to better align the point cloud and RGB features. Extensive experiments show that our multimodal industrial anomaly detection model outperforms the state-of-the-art (SOTA) methods on both detection and segmentation precision on MVTec-3D AD dataset. Code is available at //github.com/nomewang/M3DM.
Graph Convolutional Network (GCN) has achieved extraordinary success in learning effective task-specific representations of nodes in graphs. However, regarding Heterogeneous Information Network (HIN), existing HIN-oriented GCN methods still suffer from two deficiencies: (1) they cannot flexibly explore all possible meta-paths and extract the most useful ones for a target object, which hinders both effectiveness and interpretability; (2) they often need to generate intermediate meta-path based dense graphs, which leads to high computational complexity. To address the above issues, we propose an interpretable and efficient Heterogeneous Graph Convolutional Network (ie-HGCN) to learn the representations of objects in HINs. It is designed as a hierarchical aggregation architecture, i.e., object-level aggregation first, followed by type-level aggregation. The novel architecture can automatically extract useful meta-paths for each object from all possible meta-paths (within a length limit), which brings good model interpretability. It can also reduce the computational cost by avoiding intermediate HIN transformation and neighborhood attention. We provide theoretical analysis about the proposed ie-HGCN in terms of evaluating the usefulness of all possible meta-paths, its connection to the spectral graph convolution on HINs, and its quasi-linear time complexity. Extensive experiments on three real network datasets demonstrate the superiority of ie-HGCN over the state-of-the-art methods.
Recently, a considerable literature has grown up around the theme of Graph Convolutional Network (GCN). How to effectively leverage the rich structural information in complex graphs, such as knowledge graphs with heterogeneous types of entities and relations, is a primary open challenge in the field. Most GCN methods are either restricted to graphs with a homogeneous type of edges (e.g., citation links only), or focusing on representation learning for nodes only instead of jointly propagating and updating the embeddings of both nodes and edges for target-driven objectives. This paper addresses these limitations by proposing a novel framework, namely the Knowledge Embedding based Graph Convolutional Network (KE-GCN), which combines the power of GCNs in graph-based belief propagation and the strengths of advanced knowledge embedding (a.k.a. knowledge graph embedding) methods, and goes beyond. Our theoretical analysis shows that KE-GCN offers an elegant unification of several well-known GCN methods as specific cases, with a new perspective of graph convolution. Experimental results on benchmark datasets show the advantageous performance of KE-GCN over strong baseline methods in the tasks of knowledge graph alignment and entity classification.
Graph Neural Networks (GNN) has demonstrated the superior performance in many challenging applications, including the few-shot learning tasks. Despite its powerful capacity to learn and generalize from few samples, GNN usually suffers from severe over-fitting and over-smoothing as the model becomes deep, which limit the model scalability. In this work, we propose a novel Attentive GNN to tackle these challenges, by incorporating a triple-attention mechanism, \ie node self-attention, neighborhood attention, and layer memory attention. We explain why the proposed attentive modules can improve GNN for few-shot learning with theoretical analysis and illustrations. Extensive experiments show that the proposed Attentive GNN outperforms the state-of-the-art GNN-based methods for few-shot learning over the mini-ImageNet and Tiered-ImageNet datasets, with both inductive and transductive settings.
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