Graph neural networks (GNN) are deep learning architectures for graphs. Essentially, a GNN is a distributed message passing algorithm, which is controlled by parameters learned from data. It operates on the vertices of a graph: in each iteration, vertices receive a message on each incoming edge, aggregate these messages, and then update their state based on their current state and the aggregated messages. The expressivity of GNNs can be characterised in terms of certain fragments of first-order logic with counting and the Weisfeiler-Lehman algorithm. The core GNN architecture comes in two different versions. In the first version, a message only depends on the state of the source vertex, whereas in the second version it depends on the states of the source and target vertices. In practice, both of these versions are used, but the theory of GNNs so far mostly focused on the first one. On the logical side, the two versions correspond to two fragments of first-order logic with counting that we call modal and guarded. The question whether the two versions differ in their expressivity has been mostly overlooked in the GNN literature and has only been asked recently (Grohe, LICS'23). We answer this question here. It turns out that the answer is not as straightforward as one might expect. By proving that the modal and guarded fragment of first-order logic with counting have the same expressivity over labelled undirected graphs, we show that in a non-uniform setting the two GNN versions have the same expressivity. However, we also prove that in a uniform setting the second version is strictly more expressive.
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In this work, we investigate the controllability of large language models (LLMs) on scientific summarization tasks. We identify key stylistic and content coverage factors that characterize different types of summaries such as paper reviews, abstracts, and lay summaries. By controlling stylistic features, we find that non-fine-tuned LLMs outperform humans in the MuP review generation task, both in terms of similarity to reference summaries and human preferences. Also, we show that we can improve the controllability of LLMs with keyword-based classifier-free guidance (CFG) while achieving lexical overlap comparable to strong fine-tuned baselines on arXiv and PubMed. However, our results also indicate that LLMs cannot consistently generate long summaries with more than 8 sentences. Furthermore, these models exhibit limited capacity to produce highly abstractive lay summaries. Although LLMs demonstrate strong generic summarization competency, sophisticated content control without costly fine-tuning remains an open problem for domain-specific applications.
The adoption of deep learning in ECG diagnosis is often hindered by the scarcity of large, well-labeled datasets in real-world scenarios, leading to the use of transfer learning to leverage features learned from larger datasets. Yet the prevailing assumption that transfer learning consistently outperforms training from scratch has never been systematically validated. In this study, we conduct the first extensive empirical study on the effectiveness of transfer learning in multi-label ECG classification, by investigating comparing the fine-tuning performance with that of training from scratch, covering a variety of ECG datasets and deep neural networks. We confirm that fine-tuning is the preferable choice for small downstream datasets; however, when the dataset is sufficiently large, training from scratch can achieve comparable performance, albeit requiring a longer training time to catch up. Furthermore, we find that transfer learning exhibits better compatibility with convolutional neural networks than with recurrent neural networks, which are the two most prevalent architectures for time-series ECG applications. Our results underscore the importance of transfer learning in ECG diagnosis, yet depending on the amount of available data, researchers may opt not to use it, considering the non-negligible cost associated with pre-training.
Feature attribution methods are popular in interpretable machine learning. These methods compute the attribution of each input feature to represent its importance, but there is no consensus on the definition of "attribution", leading to many competing methods with little systematic evaluation, complicated in particular by the lack of ground truth attribution. To address this, we propose a dataset modification procedure to induce such ground truth. Using this procedure, we evaluate three common methods: saliency maps, rationales, and attentions. We identify several deficiencies and add new perspectives to the growing body of evidence questioning the correctness and reliability of these methods applied on datasets in the wild. We further discuss possible avenues for remedy and recommend new attribution methods to be tested against ground truth before deployment. The code is available at \url{//github.com/YilunZhou/feature-attribution-evaluation}.
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.
Non-convex optimization is ubiquitous in modern machine learning. Researchers devise non-convex objective functions and optimize them using off-the-shelf optimizers such as stochastic gradient descent and its variants, which leverage the local geometry and update iteratively. Even though solving non-convex functions is NP-hard in the worst case, the optimization quality in practice is often not an issue -- optimizers are largely believed to find approximate global minima. Researchers hypothesize a unified explanation for this intriguing phenomenon: most of the local minima of the practically-used objectives are approximately global minima. We rigorously formalize it for concrete instances of machine learning problems.
Knowledge graph (KG) embedding encodes the entities and relations from a KG into low-dimensional vector spaces to support various applications such as KG completion, question answering, and recommender systems. In real world, knowledge graphs (KGs) are dynamic and evolve over time with addition or deletion of triples. However, most existing models focus on embedding static KGs while neglecting dynamics. To adapt to the changes in a KG, these models need to be re-trained on the whole KG with a high time cost. In this paper, to tackle the aforementioned problem, we propose a new context-aware Dynamic Knowledge Graph Embedding (DKGE) method which supports the embedding learning in an online fashion. DKGE introduces two different representations (i.e., knowledge embedding and contextual element embedding) for each entity and each relation, in the joint modeling of entities and relations as well as their contexts, by employing two attentive graph convolutional networks, a gate strategy, and translation operations. This effectively helps limit the impacts of a KG update in certain regions, not in the entire graph, so that DKGE can rapidly acquire the updated KG embedding by a proposed online learning algorithm. Furthermore, DKGE can also learn KG embedding from scratch. Experiments on the tasks of link prediction and question answering in a dynamic environment demonstrate the effectiveness and efficiency of DKGE.
Graph Convolutional Networks (GCNs) have recently become the primary choice for learning from graph-structured data, superseding hash fingerprints in representing chemical compounds. However, GCNs lack the ability to take into account the ordering of node neighbors, even when there is a geometric interpretation of the graph vertices that provides an order based on their spatial positions. To remedy this issue, we propose Geometric Graph Convolutional Network (geo-GCN) which uses spatial features to efficiently learn from graphs that can be naturally located in space. Our contribution is threefold: we propose a GCN-inspired architecture which (i) leverages node positions, (ii) is a proper generalisation of both GCNs and Convolutional Neural Networks (CNNs), (iii) benefits from augmentation which further improves the performance and assures invariance with respect to the desired properties. Empirically, geo-GCN outperforms state-of-the-art graph-based methods on image classification and chemical tasks.
Graph Neural Networks (GNNs) for representation learning of graphs broadly follow a neighborhood aggregation framework, where the representation vector of a node is computed by recursively aggregating and transforming feature vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs in capturing different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.
We investigate a lattice-structured LSTM model for Chinese NER, which encodes a sequence of input characters as well as all potential words that match a lexicon. Compared with character-based methods, our model explicitly leverages word and word sequence information. Compared with word-based methods, lattice LSTM does not suffer from segmentation errors. Gated recurrent cells allow our model to choose the most relevant characters and words from a sentence for better NER results. Experiments on various datasets show that lattice LSTM outperforms both word-based and character-based LSTM baselines, achieving the best results.
This paper proposes a method to modify traditional convolutional neural networks (CNNs) into interpretable CNNs, in order to clarify knowledge representations in high conv-layers of CNNs. In an interpretable CNN, each filter in a high conv-layer represents a certain object part. We do not need any annotations of object parts or textures to supervise the learning process. Instead, the interpretable CNN automatically assigns each filter in a high conv-layer with an object part during the learning process. Our method can be applied to different types of CNNs with different structures. The clear knowledge representation in an interpretable CNN can help people understand the logics inside a CNN, i.e., based on which patterns the CNN makes the decision. Experiments showed that filters in an interpretable CNN were more semantically meaningful than those in traditional CNNs.
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