With the advent of large language models (LLMs), there is a growing interest in applying LLMs to scientific tasks. In this work, we conduct an experimental study to explore applicability of LLMs for configuring, annotating, translating, explaining, and generating scientific workflows. We use 5 different workflow specific experiments and evaluate several open- and closed-source language models using state-of-the-art workflow systems. Our studies reveal that LLMs often struggle with workflow related tasks due to their lack of knowledge of scientific workflows. We further observe that the performance of LLMs varies across experiments and workflow systems. Our findings can help workflow developers and users in understanding LLMs capabilities in scientific workflows, and motivate further research applying LLMs to workflows.
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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.
The aim of this work is to develop a fully-distributed algorithmic framework for training graph convolutional networks (GCNs). The proposed method is able to exploit the meaningful relational structure of the input data, which are collected by a set of agents that communicate over a sparse network topology. After formulating the centralized GCN training problem, we first show how to make inference in a distributed scenario where the underlying data graph is split among different agents. Then, we propose a distributed gradient descent procedure to solve the GCN training problem. The resulting model distributes computation along three lines: during inference, during back-propagation, and during optimization. Convergence to stationary solutions of the GCN training problem is also established under mild conditions. Finally, we propose an optimization criterion to design the communication topology between agents in order to match with the graph describing data relationships. A wide set of numerical results validate our proposal. To the best of our knowledge, this is the first work combining graph convolutional neural networks with distributed optimization.
Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different learning objectives. Experiments are conducted on three real-world uncertain KGs via three tasks, i.e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results on these tasks, and consistently outperforms baselines on these 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 introduce an approach for deep reinforcement learning (RL) that improves upon the efficiency, generalization capacity, and interpretability of conventional approaches through structured perception and relational reasoning. It uses self-attention to iteratively reason about the relations between entities in a scene and to guide a model-free policy. Our results show that in a novel navigation and planning task called Box-World, our agent finds interpretable solutions that improve upon baselines in terms of sample complexity, ability to generalize to more complex scenes than experienced during training, and overall performance. In the StarCraft II Learning Environment, our agent achieves state-of-the-art performance on six mini-games -- surpassing human grandmaster performance on four. By considering architectural inductive biases, our work opens new directions for overcoming important, but stubborn, challenges in deep RL.
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.
Link prediction for knowledge graphs is the task of predicting missing relationships between entities. Previous work on link prediction has focused on shallow, fast models which can scale to large knowledge graphs. However, these models learn less expressive features than deep, multi-layer models -- which potentially limits performance. In this work, we introduce ConvE, a multi-layer convolutional network model for link prediction, and report state-of-the-art results for several established datasets. We also show that the model is highly parameter efficient, yielding the same performance as DistMult and R-GCN with 8x and 17x fewer parameters. Analysis of our model suggests that it is particularly effective at modelling nodes with high indegree -- which are common in highly-connected, complex knowledge graphs such as Freebase and YAGO3. In addition, it has been noted that the WN18 and FB15k datasets suffer from test set leakage, due to inverse relations from the training set being present in the test set -- however, the extent of this issue has so far not been quantified. We find this problem to be severe: a simple rule-based model can achieve state-of-the-art results on both WN18 and FB15k. To ensure that models are evaluated on datasets where simply exploiting inverse relations cannot yield competitive results, we investigate and validate several commonly used datasets -- deriving robust variants where necessary. We then perform experiments on these robust datasets for our own and several previously proposed models, and find that ConvE achieves state-of-the-art Mean Reciprocal Rank across all datasets.
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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