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Genome-Wide Association Studies (GWAS) face unique challenges in the era of big genomics data, particularly when dealing with ultra-high-dimensional datasets where the number of genetic features significantly exceeds the available samples. This paper introduces an extension to the feature selection methodology proposed by Mirzaei et al. (2020), specifically tailored to tackle the intricacies associated with ultra-high-dimensional GWAS data. Our extended approach enhances the original method by introducing a Frobenius norm penalty into the student network, augmenting its capacity to adapt to scenarios characterized by a multitude of features and limited samples. Operating seamlessly in both supervised and unsupervised settings, our method employs two key neural networks. The first leverages an autoencoder or supervised autoencoder for dimension reduction, extracting salient features from the ultra-high-dimensional genomic data. The second network, a regularized feed-forward model with a single hidden layer, is designed for precise feature selection. The introduction of the Frobenius norm penalty in the student network significantly boosts the method's resilience to the challenges posed by ultra-high-dimensional GWAS datasets. Experimental results showcase the efficacy of our approach in feature selection for GWAS data. The method not only handles the inherent complexities of ultra-high-dimensional settings but also demonstrates superior adaptability to the nuanced structures present in genomics data. The flexibility and versatility of our proposed methodology are underscored by its successful performance across a spectrum of experiments.

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特(te)(te)征(zheng)(zheng)選(xuan)擇(ze)( Feature Selection )也稱(cheng)特(te)(te)征(zheng)(zheng)子集(ji)選(xuan)擇(ze)( Feature Subset Selection , FSS ),或屬性(xing)(xing)選(xuan)擇(ze)( Attribute Selection )。是(shi)(shi)指從已有的(de)(de)(de)M個特(te)(te)征(zheng)(zheng)(Feature)中選(xuan)擇(ze)N個特(te)(te)征(zheng)(zheng)使得系統(tong)的(de)(de)(de)特(te)(te)定(ding)指標(biao)最優(you)化,是(shi)(shi)從原始特(te)(te)征(zheng)(zheng)中選(xuan)擇(ze)出(chu)一些最有效特(te)(te)征(zheng)(zheng)以降(jiang)低數據(ju)集(ji)維度的(de)(de)(de)過程,是(shi)(shi)提高學習算法(fa)性(xing)(xing)能(neng)的(de)(de)(de)一個重要手段,也是(shi)(shi)模(mo)式識別(bie)中關鍵的(de)(de)(de)數據(ju)預處理步驟。對于一個學習算法(fa)來說,好(hao)的(de)(de)(de)學習樣本是(shi)(shi)訓練模(mo)型的(de)(de)(de)關鍵。

Weakly supervised instance segmentation (WSIS) using only image-level labels is a challenging task due to the difficulty of aligning coarse annotations with the finer task. However, with the advancement of deep neural networks (DNNs), WSIS has garnered significant attention. Following a proposal-based paradigm, we encounter a redundant segmentation problem resulting from a single instance being represented by multiple proposals. For example, we feed a picture of a dog and proposals into the network and expect to output only one proposal containing a dog, but the network outputs multiple proposals. To address this problem, we propose a novel approach for WSIS that focuses on the online refinement of complete instances through the use of MaskIoU heads to predict the integrity scores of proposals and a Complete Instances Mining (CIM) strategy to explicitly model the redundant segmentation problem and generate refined pseudo labels. Our approach allows the network to become aware of multiple instances and complete instances, and we further improve its robustness through the incorporation of an Anti-noise strategy. Empirical evaluations on the PASCAL VOC 2012 and MS COCO datasets demonstrate that our method achieves state-of-the-art performance with a notable margin. Our implementation will be made available at //github.com/ZechengLi19/CIM.

This study evaluates the ability of Large Language Model (LLM)-based Subpopulation Representative Models (SRMs) to generalize from empirical data, utilizing in-context learning with data from the 2016 and 2020 American National Election Studies. We explore generalization across response variables and demographic subgroups. While conditioning with empirical data improves performance on the whole, the benefit of in-context learning varies considerably across demographics, sometimes hurting performance for one demographic while helping performance for others. The inequitable benefits of in-context learning for SRM present a challenge for practitioners implementing SRMs, and for decision-makers who might come to rely on them. Our work highlights a need for fine-grained benchmarks captured from diverse subpopulations that test not only fidelity but generalization.

Large Language Models (LLMs) excel in diverse areas, yet struggle with complex scientific reasoning, especially in the field of chemistry. Different from the simple chemistry tasks (e.g., molecule classification) addressed in previous studies, complex chemistry problems require not only vast knowledge and precise calculation, but also compositional reasoning about rich dynamic interactions of different concepts (e.g., temperature changes). Our study shows that even advanced LLMs, like GPT-4, can fail easily in different ways. Interestingly, the errors often stem not from a lack of domain knowledge within the LLMs, but rather from the absence of an effective reasoning structure that guides the LLMs to elicit the right knowledge, incorporate the knowledge in step-by-step reasoning, and iteratively refine results for further improved quality. On this basis, we introduce StructChem, a simple yet effective prompting strategy that offers the desired guidance and substantially boosts the LLMs' chemical reasoning capability. Testing across four chemistry areas -- quantum chemistry, mechanics, physical chemistry, and kinetics -- StructChem substantially enhances GPT-4's performance, with up to 30\% peak improvement. Our analysis also underscores the unique difficulties of precise grounded reasoning in science with LLMs, highlighting a need for more research in this area. Code is available at \url{//github.com/ozyyshr/StructChem}.

Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information from its neighbors using a permutation-invariant aggregation function. Standard well-examined choices such as the mean or sum aggregation functions have limited capabilities, as they are not able to capture interactions among neighbors. In this work, we formalize these interactions using an information-theoretic framework that notably includes synergistic information. Driven by this definition, we introduce the Graph Ordering Attention (GOAT) layer, a novel GNN component that captures interactions between nodes in a neighborhood. This is achieved by learning local node orderings via an attention mechanism and processing the ordered representations using a recurrent neural network aggregator. This design allows us to make use of a permutation-sensitive aggregator while maintaining the permutation-equivariance of the proposed GOAT layer. The GOAT model demonstrates its increased performance in modeling graph metrics that capture complex information, such as the betweenness centrality and the effective size of a node. In practical use-cases, its superior modeling capability is confirmed through its success in several real-world node classification benchmarks.

Data in Knowledge Graphs often represents part of the current state of the real world. Thus, to stay up-to-date the graph data needs to be updated frequently. To utilize information from Knowledge Graphs, many state-of-the-art machine learning approaches use embedding techniques. These techniques typically compute an embedding, i.e., vector representations of the nodes as input for the main machine learning algorithm. If a graph update occurs later on -- specifically when nodes are added or removed -- the training has to be done all over again. This is undesirable, because of the time it takes and also because downstream models which were trained with these embeddings have to be retrained if they change significantly. In this paper, we investigate embedding updates that do not require full retraining and evaluate them in combination with various embedding models on real dynamic Knowledge Graphs covering multiple use cases. We study approaches that place newly appearing nodes optimally according to local information, but notice that this does not work well. However, we find that if we continue the training of the old embedding, interleaved with epochs during which we only optimize for the added and removed parts, we obtain good results in terms of typical metrics used in link prediction. This performance is obtained much faster than with a complete retraining and hence makes it possible to maintain embeddings for dynamic Knowledge Graphs.

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.

Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.

Relation prediction for knowledge graphs aims at predicting missing relationships between entities. Despite the importance of inductive relation prediction, most previous works are limited to a transductive setting and cannot process previously unseen entities. The recent proposed subgraph-based relation reasoning models provided alternatives to predict links from the subgraph structure surrounding a candidate triplet inductively. However, we observe that these methods often neglect the directed nature of the extracted subgraph and weaken the role of relation information in the subgraph modeling. As a result, they fail to effectively handle the asymmetric/anti-symmetric triplets and produce insufficient embeddings for the target triplets. To this end, we introduce a \textbf{C}\textbf{o}mmunicative \textbf{M}essage \textbf{P}assing neural network for \textbf{I}nductive re\textbf{L}ation r\textbf{E}asoning, \textbf{CoMPILE}, that reasons over local directed subgraph structures and has a vigorous inductive bias to process entity-independent semantic relations. In contrast to existing models, CoMPILE strengthens the message interactions between edges and entitles through a communicative kernel and enables a sufficient flow of relation information. Moreover, we demonstrate that CoMPILE can naturally handle asymmetric/anti-symmetric relations without the need for explosively increasing the number of model parameters by extracting the directed enclosing subgraphs. Extensive experiments show substantial performance gains in comparison to state-of-the-art methods on commonly used benchmark datasets with variant inductive settings.

Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

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