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George Karypis

George Karypis contributes to research discovery and scholarly infrastructure.

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Published work

29 published item(s)

preprint2026arXiv

DualKV: Shared-Prompt Flash Attention for Efficient RL Training with Large Rollouts and Long Contexts

Modern RL post-training methods such as GRPO and DAPO train on $N$ response sequences of $R$ tokens sampled from a shared prompt of $P$ tokens, but standard FlashAttention replicates all $P$ prompt tokens $N$ times across both forward and backward passes -- duplicating compute and memory on identical hidden states. In large-rollout, long-context RL training ($N{\geq}16$, $P{\geq}8\text{K}$), this redundancy dominates the policy update cost. We observe that in decoder-only models, causal masking makes prompt representations invariant across sequences at every layer, so all per-token operations (norms, projections, MLP) and attention can process the prompt once -- a property not yet exploited at the kernel level for training. We propose \textbf{DualKV}, the first FlashAttention kernel variant that eliminates shared-prompt replication during RL training, via (1)~fused CUDA forward and backward kernels that iterate over two disjoint KV regions -- shared context and per-sequence response -- in a single kernel launch, and (2)~a data-pipeline redesign in veRL that repacks $N(P{+}R)$ tokens into $P{+}NR$ tokens per micro-batch, extending the token reduction from attention to the entire model by a factor $ρ= N(P{+}R)/(P{+}NR)$. DualKV is mathematically equivalent to standard attention and introduces no approximation. On Qwen3-8B GRPO training with 8$\times$H100 GPUs ($N{=}32$, 8K-context), DualKV achieves $1.63$--$2.09\times$ policy-update speedup, enables $2\times$ larger micro-batches, and raises MFU from $36\%$ to $76\%$. Similar gains hold for DAPO ($2.47\times$ speedup, $77\%$ MFU). At 30B MoE scale on 16$\times$H100, DualKV achieves $3.82\times$ policy-update and $3.38\times$ end-to-end step speedup over FlashAttention (which requires 4-way Ulysses sequence parallelism to avoid OOM).

preprint2026arXiv

MaxCode: A Max-Reward Reinforcement Learning Framework for Automated Code Optimization

Large Language Models (LLMs) demonstrate strong capabilities in general coding tasks but encounter two key challenges when optimizing code: (i) the complexity of writing optimized code (such as performant CUDA kernels and competition-level CPU code) requires expertise in systems, algorithms and specific languages and (ii) requires interpretation of performance metrics like timing and device utilization beyond binary correctness. In this work, we explore inference-time search algorithms that guide the LLM to discover better solutions through iterative refinement based on execution feedback. Our approach, called MaxCode unifies existing search methods under a max-reward reinforcement learning framework, making the observation and action-value functions modular for modification. To enhance the observation space, we integrate a natural language critique model that converts raw execution feedback into diagnostic insights about errors and performance bottlenecks, and the best-discounted reward seen so far. Together, these provide richer input to the code proposal function. To improve exploration during search, we train a generative reward-to-go model using action values from rollouts to rerank potential solutions. Testing on the KernelBench (CUDA) and PIE (C++) optimization benchmarks shows that MaxCode improves optimized code performance compared to baselines, achieving 20.3% and 10.1% relative improvements in absolute speedup value and relative speedup ranking, respectively.

preprint2022arXiv

Coarse-to-Fine Sparse Sequential Recommendation

Sequential recommendation aims to model dynamic user behavior from historical interactions. Self-attentive methods have proven effective at capturing short-term dynamics and long-term preferences. Despite their success, these approaches still struggle to model sparse data, on which they struggle to learn high-quality item representations. We propose to model user dynamics from shopping intents and interacted items simultaneously. The learned intents are coarse-grained and work as prior knowledge for item recommendation. To this end, we present a coarse-to-fine self-attention framework, namely CaFe, which explicitly learns coarse-grained and fine-grained sequential dynamics. Specifically, CaFe first learns intents from coarse-grained sequences which are dense and hence provide high-quality user intent representations. Then, CaFe fuses intent representations into item encoder outputs to obtain improved item representations. Finally, we infer recommended items based on representations of items and corresponding intents. Experiments on sparse datasets show that CaFe outperforms state-of-the-art self-attentive recommenders by 44.03% NDCG@5 on average.

preprint2022arXiv

Distributed Hybrid CPU and GPU training for Graph Neural Networks on Billion-Scale Graphs

Graph neural networks (GNN) have shown great success in learning from graph-structured data. They are widely used in various applications, such as recommendation, fraud detection, and search. In these domains, the graphs are typically large and heterogeneous, containing many millions or billions of vertices and edges of different types. To tackle this challenge, we develop DistDGLv2, a system that extends DistDGL for training GNNs on massive heterogeneous graphs in a mini-batch fashion, using distributed hybrid CPU/GPU training. DistDGLv2 places graph data in distributed CPU memory and performs mini-batch computation in GPUs. For ease of use, DistDGLv2 adopts API compatible with Deep Graph Library (DGL)'s mini-batch training and heterogeneous graph API, which enables distributed training with almost no code modification. To ensure model accuracy, DistDGLv2 follows a synchronous training approach and allows ego-networks forming mini-batches to include non-local vertices. To ensure data locality and load balancing, DistDGLv2 partitions heterogeneous graphs by using a multi-level partitioning algorithm with min-edge cut and multiple balancing constraints. DistDGLv2 deploys an asynchronous mini-batch generation pipeline that makes computation and data access asynchronous to fully utilize all hardware (CPU, GPU, network, PCIe). The combination allows DistDGLv2 to train high-quality models while achieving high parallel efficiency and memory scalability. We demonstrate DistDGLv2 on various GNN workloads. Our results show that DistDGLv2 achieves 2-3X speedup over DistDGL and 18X speedup over Euler. It takes only 5-10 seconds to complete an epoch on graphs with hundreds of millions of vertices on a cluster with 64 GPUs.

preprint2022arXiv

Efficient and effective training of language and graph neural network models

Can we combine heterogenous graph structure with text to learn high-quality semantic and behavioural representations? Graph neural networks (GNN)s encode numerical node attributes and graph structure to achieve impressive performance in a variety of supervised learning tasks. Current GNN approaches are challenged by textual features, which typically need to be encoded to a numerical vector before provided to the GNN that may incur some information loss. In this paper, we put forth an efficient and effective framework termed language model GNN (LM-GNN) to jointly train large-scale language models and graph neural networks. The effectiveness in our framework is achieved by applying stage-wise fine-tuning of the BERT model first with heterogenous graph information and then with a GNN model. Several system and design optimizations are proposed to enable scalable and efficient training. LM-GNN accommodates node and edge classification as well as link prediction tasks. We evaluate the LM-GNN framework in different datasets performance and showcase the effectiveness of the proposed approach. LM-GNN provides competitive results in an Amazon query-purchase-product application.

preprint2022arXiv

Exploring the Role of Task Transferability in Large-Scale Multi-Task Learning

Recent work has found that multi-task training with a large number of diverse tasks can uniformly improve downstream performance on unseen target tasks. In contrast, literature on task transferability has established that the choice of intermediate tasks can heavily affect downstream task performance. In this work, we aim to disentangle the effect of scale and relatedness of tasks in multi-task representation learning. We find that, on average, increasing the scale of multi-task learning, in terms of the number of tasks, indeed results in better learned representations than smaller multi-task setups. However, if the target tasks are known ahead of time, then training on a smaller set of related tasks is competitive to the large-scale multi-task training at a reduced computational cost.

preprint2022arXiv

Joint Learning of Hierarchical Community Structure and Node Representations: An Unsupervised Approach

Graph representation learning has demonstrated improved performance in tasks such as link prediction and node classification across a range of domains. Research has shown that many natural graphs can be organized in hierarchical communities, leading to approaches that use these communities to improve the quality of node representations. However, these approaches do not take advantage of the learned representations to also improve the quality of the discovered communities and establish an iterative and joint optimization of representation learning and community discovery. In this work, we present Mazi, an algorithm that jointly learns the hierarchical community structure and the node representations of the graph in an unsupervised fashion. To account for the structure in the node representations, Mazi generates node representations at each level of the hierarchy, and utilizes them to influence the node representations of the original graph. Further, the communities at each level are discovered by simultaneously maximizing the modularity metric and minimizing the distance between the representations of a node and its community. Using multi-label node classification and link prediction tasks, we evaluate our method on a variety of synthetic and real-world graphs and demonstrate that Mazi outperforms other hierarchical and non-hierarchical methods.

preprint2022arXiv

Learning Personalized Item-to-Item Recommendation Metric via Implicit Feedback

This paper studies the item-to-item recommendation problem in recommender systems from a new perspective of metric learning via implicit feedback. We develop and investigate a personalizable deep metric model that captures both the internal contents of items and how they were interacted with by users. There are two key challenges in learning such model. First, there is no explicit similarity annotation, which deviates from the assumption of most metric learning methods. Second, these approaches ignore the fact that items are often represented by multiple sources of meta data and different users use different combinations of these sources to form their own notion of similarity. To address these challenges, we develop a new metric representation embedded as kernel parameters of a probabilistic model. This helps express the correlation between items that a user has interacted with, which can be used to predict user interaction with new items. Our approach hinges on the intuition that similar items induce similar interactions from the same user, thus fitting a metric-parameterized model to predict an implicit feedback signal could indirectly guide it towards finding the most suitable metric for each user. To this end, we also analyze how and when the proposed method is effective from a theoretical lens. Its empirical effectiveness is also demonstrated on several real-world datasets.

preprint2022arXiv

Meta-learning via Language Model In-context Tuning

The goal of meta-learning is to learn to adapt to a new task with only a few labeled examples. To tackle this problem in NLP, we propose $\textit{in-context tuning}$, which recasts adaptation and prediction as a simple sequence prediction problem: to form the input sequence, we concatenate the task instruction, the labeled examples, and the target input to predict; to meta-train the model to learn from in-context examples, we fine-tune a pre-trained language model (LM) to predict the target label from the input sequences on a collection of tasks. We benchmark our method on two collections of text classification tasks: LAMA and BinaryClfs. Compared to first-order MAML which adapts the model with gradient descent, our method better leverages the inductive bias of LMs to perform pattern matching, and outperforms MAML by an absolute $6\%$ AUC ROC score on BinaryClfs, with increasing advantage w.r.t. model size. Compared to non-fine-tuned in-context learning (i.e. prompting a raw LM), in-context tuning directly learns to learn from in-context examples. On BinaryClfs, in-context tuning improves the average AUC-ROC score by an absolute $10\%$, and reduces the variance with respect to example ordering by 6x and example choices by 2x.

preprint2022arXiv

Nimble GNN Embedding with Tensor-Train Decomposition

This paper describes a new method for representing embedding tables of graph neural networks (GNNs) more compactly via tensor-train (TT) decomposition. We consider the scenario where (a) the graph data that lack node features, thereby requiring the learning of embeddings during training; and (b) we wish to exploit GPU platforms, where smaller tables are needed to reduce host-to-GPU communication even for large-memory GPUs. The use of TT enables a compact parameterization of the embedding, rendering it small enough to fit entirely on modern GPUs even for massive graphs. When combined with judicious schemes for initialization and hierarchical graph partitioning, this approach can reduce the size of node embedding vectors by 1,659 times to 81,362 times on large publicly available benchmark datasets, achieving comparable or better accuracy and significant speedups on multi-GPU systems. In some cases, our model without explicit node features on input can even match the accuracy of models that use node features.

preprint2022arXiv

ScatterSample: Diversified Label Sampling for Data Efficient Graph Neural Network Learning

What target labels are most effective for graph neural network (GNN) training? In some applications where GNNs excel-like drug design or fraud detection, labeling new instances is expensive. We develop a data-efficient active sampling framework, ScatterSample, to train GNNs under an active learning setting. ScatterSample employs a sampling module termed DiverseUncertainty to collect instances with large uncertainty from different regions of the sample space for labeling. To ensure diversification of the selected nodes, DiverseUncertainty clusters the high uncertainty nodes and selects the representative nodes from each cluster. Our ScatterSample algorithm is further supported by rigorous theoretical analysis demonstrating its advantage compared to standard active sampling methods that aim to simply maximize the uncertainty and not diversify the samples. In particular, we show that ScatterSample is able to efficiently reduce the model uncertainty over the whole sample space. Our experiments on five datasets show that ScatterSample significantly outperforms the other GNN active learning baselines, specifically it reduces the sampling cost by up to 50% while achieving the same test accuracy.

preprint2022arXiv

TGL: A General Framework for Temporal GNN Training on Billion-Scale Graphs

Many real world graphs contain time domain information. Temporal Graph Neural Networks capture temporal information as well as structural and contextual information in the generated dynamic node embeddings. Researchers have shown that these embeddings achieve state-of-the-art performance in many different tasks. In this work, we propose TGL, a unified framework for large-scale offline Temporal Graph Neural Network training where users can compose various Temporal Graph Neural Networks with simple configuration files. TGL comprises five main components, a temporal sampler, a mailbox, a node memory module, a memory updater, and a message passing engine. We design a Temporal-CSR data structure and a parallel sampler to efficiently sample temporal neighbors to formtraining mini-batches. We propose a novel random chunk scheduling technique that mitigates the problem of obsolete node memory when training with a large batch size. To address the limitations of current TGNNs only being evaluated on small-scale datasets, we introduce two large-scale real-world datasets with 0.2 and 1.3 billion temporal edges. We evaluate the performance of TGL on four small-scale datasets with a single GPU and the two large datasets with multiple GPUs for both link prediction and node classification tasks. We compare TGL with the open-sourced code of five methods and show that TGL achieves similar or better accuracy with an average of 13x speedup. Our temporal parallel sampler achieves an average of 173x speedup on a multi-core CPU compared with the baselines. On a 4-GPU machine, TGL can train one epoch of more than one billion temporal edges within 1-10 hours. To the best of our knowledge, this is the first work that proposes a general framework for large-scale Temporal Graph Neural Networks training on multiple GPUs.

preprint2022arXiv

TraverseNet: Unifying Space and Time in Message Passing for Traffic Forecasting

This paper aims to unify spatial dependency and temporal dependency in a non-Euclidean space while capturing the inner spatial-temporal dependencies for traffic data. For spatial-temporal attribute entities with topological structure, the space-time is consecutive and unified while each node's current status is influenced by its neighbors' past states over variant periods of each neighbor. Most spatial-temporal neural networks for traffic forecasting study spatial dependency and temporal correlation separately in processing, gravely impaired the spatial-temporal integrity, and ignore the fact that the neighbors' temporal dependency period for a node can be delayed and dynamic. To model this actual condition, we propose TraverseNet, a novel spatial-temporal graph neural network, viewing space and time as an inseparable whole, to mine spatial-temporal graphs while exploiting the evolving spatial-temporal dependencies for each node via message traverse mechanisms. Experiments with ablation and parameter studies have validated the effectiveness of the proposed TraverseNet, and the detailed implementation can be found from https://github.com/nnzhan/TraverseNet.

preprint2021arXiv

An Empirical Comparison of Deep Learning Models for Knowledge Tracing on Large-Scale Dataset

Knowledge tracing (KT) is the problem of modeling each student's mastery of knowledge concepts (KCs) as (s)he engages with a sequence of learning activities. It is an active research area to help provide learners with personalized feedback and materials. Various deep learning techniques have been proposed for solving KT. Recent release of large-scale student performance dataset \cite{choi2019ednet} motivates the analysis of performance of deep learning approaches that have been proposed to solve KT. Our analysis can help understand which method to adopt when large dataset related to student performance is available. We also show that incorporating contextual information such as relation between exercises and student forget behavior further improves the performance of deep learning models.

preprint2021arXiv

Benchmarking Accuracy and Generalizability of Four Graph Neural Networks Using Large In Vitro ADME Datasets from Different Chemical Spaces

In this work, we benchmark a variety of single- and multi-task graph neural network (GNN) models against lower-bar and higher-bar traditional machine learning approaches employing human engineered molecular features. We consider four GNN variants -- Graph Convolutional Network (GCN), Graph Attention Network (GAT), Message Passing Neural Network (MPNN), and Attentive Fingerprint (AttentiveFP). So far deep learning models have been primarily benchmarked using lower-bar traditional models solely based on fingerprints, while more realistic benchmarks employing fingerprints, whole-molecule descriptors and predictions from other related endpoints (e.g., LogD7.4) appear to be scarce for industrial ADME datasets. In addition to time-split test sets based on Genentech data, this study benefits from the availability of measurements from an external chemical space (Roche data). We identify GAT as a promising approach to implementing deep learning models. While all GNN models significantly outperform lower-bar benchmark traditional models solely based on fingerprints, only GATs seem to offer a small but consistent improvement over higher-bar benchmark traditional models. Finally, the accuracy of in vitro assays from different laboratories predicting the same experimental endpoints appears to be comparable with the accuracy of GAT single-task models, suggesting that most of the observed error from the models is a function of the experimental error propagation.

preprint2021arXiv

IACN: Influence-aware and Attention-based Co-evolutionary Network for Recommendation

Recommending relevant items to users is a crucial task on online communities such as Reddit and Twitter. For recommendation system, representation learning presents a powerful technique that learns embeddings to represent user behaviors and capture item properties. However, learning embeddings on online communities is a challenging task because the user interest keep evolving. This evolution can be captured from 1) interaction between user and item, 2) influence from other users in the community. The existing dynamic embedding models only consider either of the factors to update user embeddings. However, at a given time, user interest evolves due to a combination of the two factors. To this end, we propose Influence-aware and Attention-based Co-evolutionary Network (IACN). Essentially, IACN consists of two key components: interaction modeling and influence modeling layer. The interaction modeling layer is responsible for updating the embedding of a user and an item when the user interacts with the item. The influence modeling layer captures the temporal excitation caused by interactions of other users. To integrate the signals obtained from the two layers, we design a novel fusion layer that effectively combines interaction-based and influence-based embeddings to predict final user embedding. Our model outperforms the existing state-of-the-art models from various domains.

preprint2021arXiv

Learning over Families of Sets -- Hypergraph Representation Learning for Higher Order Tasks

Graph representation learning has made major strides over the past decade. However, in many relational domains, the input data are not suited for simple graph representations as the relationships between entities go beyond pairwise interactions. In such cases, the relationships in the data are better represented as hyperedges (set of entities) of a non-uniform hypergraph. While there have been works on principled methods for learning representations of nodes of a hypergraph, these approaches are limited in their applicability to tasks on non-uniform hypergraphs (hyperedges with different cardinalities). In this work, we exploit the incidence structure to develop a hypergraph neural network to learn provably expressive representations of variable sized hyperedges which preserve local-isomorphism in the line graph of the hypergraph, while also being invariant to permutations of its constituent vertices. Specifically, for a given vertex set, we propose frameworks for (1) hyperedge classification and (2) variable sized expansion of partially observed hyperedges which captures the higher order interactions among vertices and hyperedges. We evaluate performance on multiple real-world hypergraph datasets and demonstrate consistent, significant improvement in accuracy, over state-of-the-art models.

preprint2021arXiv

Learning Student Interest Trajectory for MOOCThread Recommendation

In recent years, Massive Open Online Courses (MOOCs) have witnessed immense growth in popularity. Now, due to the recent Covid19 pandemic situation, it is important to push the limits of online education. Discussion forums are primary means of interaction among learners and instructors. However, with growing class size, students face the challenge of finding useful and informative discussion forums. This problem can be solved by matching the interest of students with thread contents. The fundamental challenge is that the student interests drift as they progress through the course, and forum contents evolve as students or instructors update them. In our paper, we propose to predict future interest trajectories of students. Our model consists of two key operations: 1) Update operation and 2) Projection operation. Update operation models the inter-dependency between the evolution of student and thread using coupled Recurrent Neural Networks when the student posts on the thread. The projection operation learns to estimate future embedding of students and threads. For students, the projection operation learns the drift in their interests caused by the change in the course topic they study. The projection operation for threads exploits how different posts induce varying interest levels in a student according to the thread structure. Extensive experimentation on three real-world MOOC datasets shows that our model significantly outperforms other baselines for thread recommendation.

preprint2021arXiv

PanRep: Graph neural networks for extracting universal node embeddings in heterogeneous graphs

Learning unsupervised node embeddings facilitates several downstream tasks such as node classification and link prediction. A node embedding is universal if it is designed to be used by and benefit various downstream tasks. This work introduces PanRep, a graph neural network (GNN) model, for unsupervised learning of universal node representations for heterogenous graphs. PanRep consists of a GNN encoder that obtains node embeddings and four decoders, each capturing different topological and node feature properties. Abiding to these properties the novel unsupervised framework learns universal embeddings applicable to different downstream tasks. PanRep can be furthered fine-tuned to account for possible limited labels. In this operational setting PanRep is considered as a pretrained model for extracting node embeddings of heterogenous graph data. PanRep outperforms all unsupervised and certain supervised methods in node classification and link prediction, especially when the labeled data for the supervised methods is small. PanRep-FT (with fine-tuning) outperforms all other supervised approaches, which corroborates the merits of pretraining models. Finally, we apply PanRep-FT for discovering novel drugs for Covid-19. We showcase the advantage of universal embeddings in drug repurposing and identify several drugs used in clinical trials as possible drug candidates.

preprint2021arXiv

Universal Representation for Code

Learning from source code usually requires a large amount of labeled data. Despite the possible scarcity of labeled data, the trained model is highly task-specific and lacks transferability to different tasks. In this work, we present effective pre-training strategies on top of a novel graph-based code representation, to produce universal representations for code. Specifically, our graph-based representation captures important semantics between code elements (e.g., control flow and data flow). We pre-train graph neural networks on the representation to extract universal code properties. The pre-trained model then enables the possibility of fine-tuning to support various downstream applications. We evaluate our model on two real-world datasets -- spanning over 30M Java methods and 770K Python methods. Through visualization, we reveal discriminative properties in our universal code representation. By comparing multiple benchmarks, we demonstrate that the proposed framework achieves state-of-the-art results on method name prediction and code graph link prediction.

preprint2020arXiv

Adaptive Matrix Completion for the Users and the Items in Tail

Recommender systems are widely used to recommend the most appealing items to users. These recommendations can be generated by applying collaborative filtering methods. The low-rank matrix completion method is the state-of-the-art collaborative filtering method. In this work, we show that the skewed distribution of ratings in the user-item rating matrix of real-world datasets affects the accuracy of matrix-completion-based approaches. Also, we show that the number of ratings that an item or a user has positively correlates with the ability of low-rank matrix-completion-based approaches to predict the ratings for the item or the user accurately. Furthermore, we use these insights to develop four matrix completion-based approaches, i.e., Frequency Adaptive Rating Prediction (FARP), Truncated Matrix Factorization (TMF), Truncated Matrix Factorization with Dropout (TMF + Dropout) and Inverse Frequency Weighted Matrix Factorization (IFWMF), that outperforms traditional matrix-completion-based approaches for the users and the items with few ratings in the user-item rating matrix.

preprint2020arXiv

Context-aware Non-linear and Neural Attentive Knowledge-based Models for Grade Prediction

Grade prediction for future courses not yet taken by students is important as it can help them and their advisers during the process of course selection as well as for designing personalized degree plans and modifying them based on their performance. One of the successful approaches for accurately predicting a student's grades in future courses is Cumulative Knowledge-based Regression Models (CKRM). CKRM learns shallow linear models that predict a student's grades as the similarity between his/her knowledge state and the target course. However, prior courses taken by a student can have \black{different contributions when estimating a student's knowledge state and towards each target course, which} cannot be captured by linear models. Moreover, CKRM and other grade prediction methods ignore the effect of concurrently-taken courses on a student's performance in a target course. In this paper, we propose context-aware non-linear and neural attentive models that can potentially better estimate a student's knowledge state from his/her prior course information, as well as model the interactions between a target course and concurrent courses. Compared to the competing methods, our experiments on a large real-world dataset consisting of more than $1.5$M grades show the effectiveness of the proposed models in accurately predicting students' grades. Moreover, the attention weights learned by the neural attentive model can be helpful in better designing their degree plans.

preprint2020arXiv

COVID-19 Knowledge Graph: Accelerating Information Retrieval and Discovery for Scientific Literature

The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID-19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduces the quality of similarity-based article recommendations for users. In this work, we present the COVID-19 Knowledge Graph (CKG), a heterogeneous graph for extracting and visualizing complex relationships between COVID-19 scientific articles. The CKG combines semantic information with document topological information for the application of similar document retrieval. The CKG is constructed using the latent schema of the data, and then enriched with biomedical entity information extracted from the unstructured text of articles using scalable AWS technologies to form relations in the graph. Finally, we propose a document similarity engine that leverages low-dimensional graph embeddings from the CKG with semantic embeddings for similar article retrieval. Analysis demonstrates the quality of relationships in the CKG and shows that it can be used to uncover meaningful information in COVID-19 scientific articles. The CKG helps power www.cord19.aws and is publicly available.

preprint2020arXiv

Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks

Advancing research in the emerging field of deep graph learning requires new tools to support tensor computation over graphs. In this paper, we present the design principles and implementation of Deep Graph Library (DGL). DGL distills the computational patterns of GNNs into a few generalized sparse tensor operations suitable for extensive parallelization. By advocating graph as the central programming abstraction, DGL can perform optimizations transparently. By cautiously adopting a framework-neutral design, DGL allows users to easily port and leverage the existing components across multiple deep learning frameworks. Our evaluation shows that DGL significantly outperforms other popular GNN-oriented frameworks in both speed and memory consumption over a variety of benchmarks and has little overhead for small scale workloads.

preprint2020arXiv

DGL-KE: Training Knowledge Graph Embeddings at Scale

Knowledge graphs have emerged as a key abstraction for organizing information in diverse domains and their embeddings are increasingly used to harness their information in various information retrieval and machine learning tasks. However, the ever growing size of knowledge graphs requires computationally efficient algorithms capable of scaling to graphs with millions of nodes and billions of edges. This paper presents DGL-KE, an open-source package to efficiently compute knowledge graph embeddings. DGL-KE introduces various novel optimizations that accelerate training on knowledge graphs with millions of nodes and billions of edges using multi-processing, multi-GPU, and distributed parallelism. These optimizations are designed to increase data locality, reduce communication overhead, overlap computations with memory accesses, and achieve high operation efficiency. Experiments on knowledge graphs consisting of over 86M nodes and 338M edges show that DGL-KE can compute embeddings in 100 minutes on an EC2 instance with 8 GPUs and 30 minutes on an EC2 cluster with 4 machines with 48 cores/machine. These results represent a 2x~5x speedup over the best competing approaches. DGL-KE is available on https://github.com/awslabs/dgl-ke.

preprint2020arXiv

Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing

Predicting interactions among heterogenous graph structured data has numerous applications such as knowledge graph completion, recommendation systems and drug discovery. Often times, the links to be predicted belong to rare types such as the case in repurposing drugs for novel diseases. This motivates the task of few-shot link prediction. Typically, GCNs are ill-equipped in learning such rare link types since the relation embedding is not learned in an inductive fashion. This paper proposes an inductive RGCN for learning informative relation embeddings even in the few-shot learning regime. The proposed inductive model significantly outperforms the RGCN and state-of-the-art KGE models in few-shot learning tasks. Furthermore, we apply our method on the drug-repurposing knowledge graph (DRKG) for discovering drugs for Covid-19. We pose the drug discovery task as link prediction and learn embeddings for the biological entities that partake in the DRKG. Our initial results corroborate that several drugs used in clinical trials were identified as possible drug candidates. The method in this paper are implemented using the efficient deep graph learning (DGL)

preprint2020arXiv

Graph InfoClust: Leveraging cluster-level node information for unsupervised graph representation learning

Unsupervised (or self-supervised) graph representation learning is essential to facilitate various graph data mining tasks when external supervision is unavailable. The challenge is to encode the information about the graph structure and the attributes associated with the nodes and edges into a low dimensional space. Most existing unsupervised methods promote similar representations across nodes that are topologically close. Recently, it was shown that leveraging additional graph-level information, e.g., information that is shared among all nodes, encourages the representations to be mindful of the global properties of the graph, which greatly improves their quality. However, in most graphs, there is significantly more structure that can be captured, e.g., nodes tend to belong to (multiple) clusters that represent structurally similar nodes. Motivated by this observation, we propose a graph representation learning method called Graph InfoClust (GIC), that seeks to additionally capture cluster-level information content. These clusters are computed by a differentiable K-means method and are jointly optimized by maximizing the mutual information between nodes of the same clusters. This optimization leads the node representations to capture richer information and nodal interactions, which improves their quality. Experiments show that GIC outperforms state-of-art methods in various downstream tasks (node classification, link prediction, and node clustering) with a 0.9% to 6.1% gain over the best competing approach, on average.

preprint2020arXiv

Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning

There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for COVID-19.

preprint2020arXiv

Scalable Label Propagation for Multi-relational Learning on the Tensor Product of Graphs

Multi-relational learning on knowledge graphs infers high-order relations among the entities across the graphs. This learning task can be solved by label propagation on the tensor product of the knowledge graphs to learn the high-order relations as a tensor. In this paper, we generalize a widely used label propagation model to the normalized tensor product graph, and propose an optimization formulation and a scalable Low-rank Tensor-based Label Propagation algorithm (LowrankTLP) to infer multi-relations for two learning tasks, hyperlink prediction and multiple graph alignment. The optimization formulation minimizes the upper bound of the noisy tensor estimation error for multiple graph alignment, by learning with a subset of the eigen-pairs in the spectrum of the normalized tensor product graph. We also provide a data-dependent transductive Rademacher bound for binary hyperlink prediction. We accelerate LowrankTLP with parallel tensor computation which enables label propagation on a tensor product of 100 graphs each of size 1000 in less than half hour in the simulation. LowrankTLP was also applied to predicting the author-paper-venue hyperlinks in publication records, alignment of segmented regions across up to 26 CT-scan images and alignment of protein-protein interaction networks across multiple species. The experiments demonstrate that LowrankTLP indeed well approximates the original label propagation with better scalability and accuracy.