arXiv subjects
Publications and source records attributed to Da Yan.
Graphs are by nature unifying abstractions that can leverage interconnectedness to represent, explore, predict, and explain real- and digital-world phenomena. Although real users and consumers of graph instances and graph workloads understand these abstractions, future problems will require new abstractions and systems. What needs to happen in the next decade for big graph processing to continue to succeed?
We build random forests models to predict elastic properties and mechanical hardness of a compound, using only its chemical formula as input. The model training uses over 10,000 target compounds and 60 features based on stoichiometric attributes, elemental properties, orbital occupations, and ionic bonding levels. Using the models, we construct triangular graphs for B-C-N compounds to map out their bulk and shear moduli, as well as hardness values. The graphs indicate that a 1:1 B-N ratio can lead to various superhard compositions. We also validate the machine learning results by evolutionary structure prediction and density functional theory. Our study shows that BC$_{10}$N, B$_4$C$_5$N$_3$, and B$_2$C$_3$N exhibit dynamically stable phases with hardness values $>40$GPa, which are potentially new superhard materials that could be synthesized by low-temperature plasma methods.
Given a 3D surface defined by an elevation function on a 2D grid as well as non-spatial features observed at each pixel, the problem of surface segmentation aims to classify pixels into contiguous classes based on both non-spatial features and surface topology. The problem has important applications in hydrology, planetary science, and biochemistry but is uniquely challenging for several reasons. First, the spatial extent of class segments follows surface contours in the topological space, regardless of their spatial shapes and directions. Second, the topological structure exists in multiple spatial scales based on different surface resolutions. Existing widely successful deep learning models for image segmentation are often not applicable due to their reliance on convolution and pooling operations to learn regular structural patterns on a grid. In contrast, we propose to represent surface topological structure by a contour tree skeleton, which is a polytree capturing the evolution of surface contours at different elevation levels. We further design a graph neural network based on the contour tree hierarchy to model surface topological structure at different spatial scales. Experimental evaluations based on real-world hydrological datasets show that our model outperforms several baseline methods in classification accuracy.
Spatial classification with limited feature observations has been a challenging problem in machine learning. The problem exists in applications where only a subset of sensors are deployed at certain spots or partial responses are collected in field surveys. Existing research mostly focuses on addressing incomplete or missing data, e.g., data cleaning and imputation, classification models that allow for missing feature values or model missing features as hidden variables in the EM algorithm. These methods, however, assume that incomplete feature observations only happen on a small subset of samples, and thus cannot solve problems where the vast majority of samples have missing feature observations. To address this issue, we recently proposed a new approach that incorporates physics-aware structural constraint into the model representation. Our approach assumes that a spatial contextual feature is observed for all sample locations and establishes spatial structural constraint from the underlying spatial contextual feature map. We design efficient algorithms for model parameter learning and class inference. This paper extends our recent approach by allowing feature values of samples in each class to follow a multi-modal distribution. We propose learning algorithms for the extended model with multi-modal distribution. Evaluations on real-world hydrological applications show that our approach significantly outperforms baseline methods in classification accuracy, and the multi-modal extension is more robust than our early single-modal version especially when feature distribution in training samples is multi-modal. Computational experiments show that the proposed solution is computationally efficient on large datasets.
We propose a block coordinate descent type algorithm for estimating the rank of a given tensor. In addition, the algorithm provides the canonical polyadic decomposition of a tensor. In order to estimate the tensor rank we use sparse optimization method using $\ell_1$ norm. The algorithm is implemented on single moving object videos and color images for approximating the rank.
Shrinking transistors, which powered the advancement of computing in the past half century, has stalled due to power wall; now extreme heterogeneity is promised to be the next driving force to feed the needs of ever-increasingly diverse scientific domains. To unlock the potentials of such supercomputers, we identify eight potential challenges in three categories: First, one needs fast data movement since extreme heterogeneity will inevitably complicate the communication circuits -- thus hampering the data movement. Second, we need to intelligently schedule suitable hardware for corresponding applications/stages. Third, we have to lower the programming complexity in order to encourage the adoption of heterogeneous computing.
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of new genomes. In this paper, we present a toolkit, called PPA-assembler, for de novo genome assembly in a distributed setting. The operations in our toolkit provide strong performance guarantees, and can be assembled to implement various sequencing strategies. PPA-assembler adopts the popular {\em de Bruijn graph} based approach for sequencing, and each operation is implemented as a program in Google's Pregel framework for big graph processing. Experiments on large real and simulated datasets demonstrate that PPA-assembler is much more efficient than the state-of-the-arts and provides good sequencing quality.
This paper proposes a general system for compute-intensive graph mining tasks that find from a big graph all subgraphs that satisfy certain requirements (e.g., graph matching and community detection). Due to the broad range of applications of such tasks, many single-threaded algorithms have been proposed. However, graphs such as online social networks and knowledge graphs often have billions of vertices and edges, which require distributed processing in order to scale. Unfortunately, existing distributed graph processing systems such as Pregel and GraphLab are designed for data-intensive analytics, and are inefficient for compute-intensive graph mining tasks since computation over any data is coupled with the data's access that involves network transmission. We propose a distributed graph mining framework, called G-thinker, which is designed for compute-intensive graph mining workloads. G-thinker provides an intuitive graph-exploration API for the convenient implementation of various graph mining algorithms, and the runtime engine provides efficient execution with bounded memory consumption, light network communication, and parallelism between computation and communication. Extensive experiments were conducted, which demonstrate that G-thinker is orders of magnitude faster than existing solution, and can scale to graphs that are two orders of magnitude larger given the same hardware resources.
The success of Google's Pregel framework in distributed graph processing has inspired a surging interest in developing Pregel-like platforms featuring a user-friendly "think like a vertex" programming model. Existing Pregel-like systems support a fault tolerance mechanism called checkpointing, which periodically saves computation states as checkpoints to HDFS, so that when a failure happens, computation rolls back to the latest checkpoint. However, a checkpoint in existing systems stores a huge amount of data, including vertex states, edges, and messages sent by vertices, which significantly degrades the failure-free performance. Moreover, the high checkpointing cost prevents frequent checkpointing, and thus recovery has to replay all the computations from a state checkpointed some time ago. In this paper, we propose a novel checkpointing approach which only stores vertex states and incremental edge updates to HDFS as a lightweight checkpoint (LWCP), so that writing an LWCP is typically tens of times faster than writing a conventional checkpoint. To recover from the latest LWCP, messages are generated from the vertex states, and graph topology is recovered by replaying incremental edge updates. We show how to realize lightweight checkpointing with minor modifications of the vertex-centric programming interface. We also apply the same idea to a recently-proposed log-based approach for fast recovery, to make it work efficiently in practice by significantly reducing the cost of garbage collection of logs. Extensive experiments on large real graphs verified the effectiveness of LWCP in improving both failure-free performance and the performance of recovery.
Pioneered by Google's Pregel, many distributed systems have been developed for large-scale graph analytics. These systems expose the user-friendly "think like a vertex" programming interface to users, and exhibit good horizontal scalability. However, these systems are designed for tasks where the majority of graph vertices participate in computation, but are not suitable for processing light-workload graph queries where only a small fraction of vertices need to be accessed. The programming paradigm adopted by these systems can seriously under-utilize the resources in a cluster for graph query processing. In this work, we develop a new open-source system, called Quegel, for querying big graphs, which treats queries as first-class citizens in the design of its computing model. Users only need to specify the Pregel-like algorithm for a generic query, and Quegel processes light-workload graph queries on demand using a novel superstep-sharing execution model to effectively utilize the cluster resources. Quegel further provides a convenient interface for constructing graph indexes, which significantly improve query performance but are not supported by existing graph-parallel systems. Our experiments verified that Quegel is highly efficient in answering various types of graph queries and is up to orders of magnitude faster than existing systems.
Inspired by the success of Google's Pregel, many systems have been developed recently for iterative computation over big graphs. These systems provide a user-friendly vertex-centric programming interface, where a programmer only needs to specify the behavior of one generic vertex when developing a parallel graph algorithm. However, most existing systems require the input graph to reside in memories of the machines in a cluster, and the few out-of-core systems suffer from problems such as poor efficiency for sparse computation workload, high demand on network bandwidth, and expensive cost incurred by external-memory join and group-by. In this paper, we introduce the GraphD system for a user to process very large graphs with ordinary computing resources. GraphD fully overlaps computation with communication, by streaming edges and messages on local disks, while transmitting messages in parallel. For a broad class of Pregel algorithms where message combiner is applicable, GraphD eliminates the need of any expensive external-memory join or group-by. These key techniques allow GraphD to achieve comparable performance to in-memory Pregel-like systems without keeping edges and messages in memories. We prove that to process a graph G=(V, E) with n machines using GraphD, each machine only requires O(|V|/n) memory space, allowing GraphD to scale to very large graphs with a small cluster. Extensive experiments show that GraphD beats existing out-of-core systems by orders of magnitude, and achieves comparable performance to in-memory systems running with enough memories.
Massive graphs, such as online social networks and communication networks, have become common today. To efficiently analyze such large graphs, many distributed graph computing systems have been developed. These systems employ the "think like a vertex" programming paradigm, where a program proceeds in iterations and at each iteration, vertices exchange messages with each other. However, using Pregel's simple message passing mechanism, some vertices may send/receive significantly more messages than others due to either the high degree of these vertices or the logic of the algorithm used. This forms the communication bottleneck and leads to imbalanced workload among machines in the cluster. In this paper, we propose two effective message reduction techniques: (1)vertex mirroring with message combining, and (2)an additional request-respond API. These techniques not only reduce the total number of messages exchanged through the network, but also bound the number of messages sent/received by any single vertex. We theoretically analyze the effectiveness of our techniques, and implement them on top of our open-source Pregel implementation called Pregel+. Our experiments on various large real graphs demonstrate that our message reduction techniques significantly improve the performance of distributed graph computation.