Yixin Chen

Wenjie Xuan, Shanshan Zhao, Yu Yao et al.

Relying on large-scale training data with pixel-level labels, previous edge detection methods have achieved high performance. However, it is hard to manually label edges accurately, especially for large datasets, and thus the datasets inevitably contain noisy labels. This label-noise issue has been studied extensively for classification, while still remaining under-explored for edge detection. To address the label-noise issue for edge detection, this paper proposes to learn Pixel-level NoiseTransitions to model the label-corruption process. To achieve it, we develop a novel Pixel-wise Shift Learning (PSL) module to estimate the transition from clean to noisy labels as a displacement field. Exploiting the estimated noise transitions, our model, named PNT-Edge, is able to fit the prediction to clean labels. In addition, a local edge density regularization term is devised to exploit local structure information for better transition learning. This term encourages learning large shifts for the edges with complex local structures. Experiments on SBD and Cityscapes demonstrate the effectiveness of our method in relieving the impact of label noise. Codes are available at https://github.com/DREAMXFAR/PNT-Edge.

Haibo Qiu, Baosheng Yu, Yixin Chen et al.

Significant progress has been made recently in point cloud segmentation utilizing an encoder-decoder framework, which initially encodes point clouds into low-resolution representations and subsequently decodes high-resolution predictions. Inspired by the success of high-resolution architectures in image dense prediction, which always maintains a high-resolution representation throughout the entire learning process, we consider it also highly important for 3D dense point cloud analysis. Therefore, in this paper, we explore high-resolution architectures for 3D point cloud segmentation. Specifically, we generalize high-resolution architectures using a unified pipeline named PointHR, which includes a knn-based sequence operator for feature extraction and a differential resampling operator to efficiently communicate different resolutions. Additionally, we propose to avoid numerous on-the-fly computations of high-resolution architectures by pre-computing the indices for both sequence and resampling operators. By doing so, we deliver highly competitive high-resolution architectures while capitalizing on the benefits of well-designed point cloud blocks without additional effort. To evaluate these architectures for dense point cloud analysis, we conduct thorough experiments using S3DIS and ScanNetV2 datasets, where the proposed PointHR outperforms recent state-of-the-art methods without any bells and whistles. The source code is available at \url{https://github.com/haibo-qiu/PointHR}.

Zehao Dong, Heming Zhang, Yixin Chen et al.

Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal disease signaling pathways. Though various deep learning (AI) models have been proposed to quantitatively predict the synergism of drug combinations, the major limitation of existing deep learning methods is that they are inherently not interpretable, which makes the conclusions of AI models untransparent to human experts, henceforth limiting the robustness of the model conclusion and the implementation ability of these models in real-world human--AI healthcare. In this paper, we develop an interpretable graph neural network (GNN) that reveals the underlying essential therapeutic targets and the mechanism of the synergy (MoS) by mining the sub-molecular network of great importance. The key point of the interpretable GNN prediction model is a novel graph pooling layer, a self-attention-based node and edge pool (henceforth SANEpool), that can compute the attention score (importance) of genes and connections based on the genomic features and topology. As such, the proposed GNN model provides a systematic way to predict and interpret the drug combination synergism based on the detected crucial sub-molecular network. Experiments on various well-adopted drug-synergy-prediction datasets demonstrate that (1) the SANEpool model has superior predictive ability to generate accurate synergy score prediction, and (2) the sub-molecular networks detected by the SANEpool are self-explainable and salient for identifying synergistic drug combinations.

Sandhya Tripathi, Bradley A. Fritz, Mohamed Abdelhack et al.

An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable algorithms, especially in health care. We approach this issue in the common but difficult case of numeric features such as nearly Gaussian and binary features, where unit changes and variable shift make simple matching of univariate summaries unsuccessful. We develop two novel procedures to address this problem. First, we demonstrate multiple methods of "fingerprinting" a feature based on its associations to other features. In the setting of even modest prior information, this allows most shared features to be accurately identified. Second, we demonstrate a deep learning algorithm for translation between databases. Unlike prior approaches, our algorithm takes advantage of discovered mappings while identifying surrogates for unshared features and learning transformations. In synthetic and real-world experiments using two electronic health record databases, our algorithms outperform existing baselines for matching variable sets, while jointly learning to impute unshared or transformed variables.

Hao Zhou, Yixin Chen, David Troendle et al.

An automated and accurate fabric defect inspection system is in high demand as a replacement for slow, inconsistent, error-prone, and expensive human operators in the textile industry. Previous efforts focused on certain types of fabrics or defects, which is not an ideal solution. In this paper, we propose a novel one-class model that is capable of detecting various defects on different fabric types. Our model takes advantage of a well-designed Gabor filter bank to analyze fabric texture. We then leverage an advanced deep learning algorithm, autoencoder, to learn general feature representations from the outputs of the Gabor filter bank. Lastly, we develop a nearest neighbor density estimator to locate potential defects and draw them on the fabric images. We demonstrate the effectiveness and robustness of the proposed model by testing it on various types of fabrics such as plain, patterned, and rotated fabrics. Our model also achieves a true positive rate (a.k.a recall) value of 0.895 with no false alarms on our dataset based upon the Standard Fabric Defect Glossary.

Shengxiang Hu, Guobing Zou, Bofeng Zhang et al.

Accurate prediction of temporal QoS is crucial for maintaining service reliability and enhancing user satisfaction in dynamic service-oriented environments. However, current methods often neglect high-order latent collaborative relationships and fail to dynamically adjust feature learning for specific user-service invocations, which are critical for precise feature extraction within each time slice. Moreover, the prevalent use of RNNs for modeling temporal feature evolution patterns is constrained by their inherent difficulty in managing long-range dependencies, thereby limiting the detection of long-term QoS trends across multiple time slices. These shortcomings dramatically degrade the performance of temporal QoS prediction. To address the two issues, we propose a novel Graph Attention Collaborative Learning (GACL) framework for temporal QoS prediction. Building on a dynamic user-service invocation graph to comprehensively model historical interactions, it designs a target-prompt graph attention network to extract deep latent features of users and services at each time slice, considering implicit target-neighboring collaborative relationships and historical QoS values. Additionally, a multi-layer Transformer encoder is introduced to uncover temporal feature evolution patterns, enhancing temporal QoS prediction. Extensive experiments on the WS-DREAM dataset demonstrate that GACL significantly outperforms state-of-the-art methods for temporal QoS prediction across multiple evaluation metrics, achieving the improvements of up to 38.80%.

Yixin Chen, Tonmoy Dey, Alan Kuhnle

Distributed maximization of a submodular function in the MapReduce (MR) model has received much attention, culminating in two frameworks that allow a centralized algorithm to be run in the MR setting without loss of approximation, as long as the centralized algorithm satisfies a certain consistency property -- which had previously only been known to be satisfied by the standard greedy and continous greedy algorithms. A separate line of work has studied parallelizability of submodular maximization in the adaptive complexity model, where each thread may have access to the entire ground set. For the size-constrained maximization of a monotone and submodular function, we show that several sublinearly adaptive (highly parallelizable) algorithms satisfy the consistency property required to work in the MR setting, which yields practical, parallelizable and distributed algorithms. Separately, we develop the first distributed algorithm with linear query complexity for this problem. Finally, we provide a method to increase the maximum cardinality constraint for MR algorithms at the cost of additional MR rounds.

Heming Zhang, Tim Xu, Dekang Cao et al.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

Jiarui Feng, Donghong Cai, Yixin Chen et al.

Large Language Models (LLMs) have demonstrated remarkable capabilities in modeling sequential textual data and generalizing across diverse tasks. However, adapting LLMs to effectively handle structural data, such as knowledge graphs or web data, remains a challenging problem. Some approaches adopt complex strategies to convert graphs into text sequences, resulting in significant token overhead and rendering them impractical for large-scale graphs. Others introduce additional modules to encode graphs into fixed-size token representations for LLMs. However, these methods typically require large-scale post-training on graph-text corpus and complex alignment procedures, yet often yield sub-optimal results due to poor modality alignment. Inspired by in-parameter knowledge injection for test-time adaptation of LLMs, we propose GRIP, a novel framework that equips LLMs with the ability to internalize complex relational information from graphs through carefully designed fine-tuning tasks. This knowledge is efficiently stored within lightweight LoRA parameters, enabling the fine-tuned LLM to perform a wide range of graph-related tasks without requiring access to the original graph at inference time. Extensive experiments across multiple benchmarks validate the effectiveness and efficiency of our approach.

Quan Zhou, Wenlin Chen, Shiji Song et al.

The past years have witnessed many dedicated open-source projects that built and maintain implementations of Support Vector Machines (SVM), parallelized for GPU, multi-core CPUs and distributed systems. Up to this point, no comparable effort has been made to parallelize the Elastic Net, despite its popularity in many high impact applications, including genetics, neuroscience and systems biology. The first contribution in this paper is of theoretical nature. We establish a tight link between two seemingly different algorithms and prove that Elastic Net regression can be reduced to SVM with squared hinge loss classification. Our second contribution is to derive a practical algorithm based on this reduction. The reduction enables us to utilize prior efforts in speeding up and parallelizing SVMs to obtain a highly optimized and parallel solver for the Elastic Net and Lasso. With a simple wrapper, consisting of only 11 lines of MATLAB code, we obtain an Elastic Net implementation that naturally utilizes GPU and multi-core CPUs. We demonstrate on twelve real world data sets, that our algorithm yields identical results as the popular (and highly optimized) glmnet implementation but is one or several orders of magnitude faster.

Zan Wang, Yixin Chen, Baoxiong Jia et al.

Despite significant advancements in text-to-motion synthesis, generating language-guided human motion within 3D environments poses substantial challenges. These challenges stem primarily from (i) the absence of powerful generative models capable of jointly modeling natural language, 3D scenes, and human motion, and (ii) the generative models' intensive data requirements contrasted with the scarcity of comprehensive, high-quality, language-scene-motion datasets. To tackle these issues, we introduce a novel two-stage framework that employs scene affordance as an intermediate representation, effectively linking 3D scene grounding and conditional motion generation. Our framework comprises an Affordance Diffusion Model (ADM) for predicting explicit affordance map and an Affordance-to-Motion Diffusion Model (AMDM) for generating plausible human motions. By leveraging scene affordance maps, our method overcomes the difficulty in generating human motion under multimodal condition signals, especially when training with limited data lacking extensive language-scene-motion pairs. Our extensive experiments demonstrate that our approach consistently outperforms all baselines on established benchmarks, including HumanML3D and HUMANISE. Additionally, we validate our model's exceptional generalization capabilities on a specially curated evaluation set featuring previously unseen descriptions and scenes.

Ziyu Zhu, Xilin Wang, Yixuan Li et al.

Embodied scene understanding requires not only comprehending visual-spatial information that has been observed but also determining where to explore next in the 3D physical world. Existing 3D Vision-Language (3D-VL) models primarily focus on grounding objects in static observations from 3D reconstruction, such as meshes and point clouds, but lack the ability to actively perceive and explore their environment. To address this limitation, we introduce \underline{\textbf{M}}ove \underline{\textbf{t}}o \underline{\textbf{U}}nderstand (\textbf{\model}), a unified framework that integrates active perception with \underline{\textbf{3D}} vision-language learning, enabling embodied agents to effectively explore and understand their environment. This is achieved by three key innovations: 1) Online query-based representation learning, enabling direct spatial memory construction from RGB-D frames, eliminating the need for explicit 3D reconstruction. 2) A unified objective for grounding and exploring, which represents unexplored locations as frontier queries and jointly optimizes object grounding and frontier selection. 3) End-to-end trajectory learning that combines \textbf{V}ision-\textbf{L}anguage-\textbf{E}xploration pre-training over a million diverse trajectories collected from both simulated and real-world RGB-D sequences. Extensive evaluations across various embodied navigation and question-answering benchmarks show that MTU3D outperforms state-of-the-art reinforcement learning and modular navigation approaches by 14\%, 23\%, 9\%, and 2\% in success rate on HM3D-OVON, GOAT-Bench, SG3D, and A-EQA, respectively. \model's versatility enables navigation using diverse input modalities, including categories, language descriptions, and reference images. These findings highlight the importance of bridging visual grounding and exploration for embodied intelligence.

Zehao Dong, Qihang Zhao, Philip R. O. Payne et al.

Biomarker identification is critical for precise disease diagnosis and understanding disease pathogenesis in omics data analysis, like using fold change and regression analysis. Graph neural networks (GNNs) have been the dominant deep learning model for analyzing graph-structured data. However, we found two major limitations of existing GNNs in omics data analysis, i.e., limited-prediction (diagnosis) accuracy and limited-reproducible biomarker identification capacity across multiple datasets. The root of the challenges is the unique graph structure of biological signaling pathways, which consists of a large number of targets and intensive and complex signaling interactions among these targets. To resolve these two challenges, in this study, we presented a novel GNN model architecture, named PathFormer, which systematically integrate signaling network, priori knowledge and omics data to rank biomarkers and predict disease diagnosis. In the comparison results, PathFormer outperformed existing GNN models significantly in terms of highly accurate prediction capability ( 30% accuracy improvement in disease diagnosis compared with existing GNN models) and high reproducibility of biomarker ranking across different datasets. The improvement was confirmed using two independent Alzheimer's Disease (AD) and cancer transcriptomic datasets. The PathFormer model can be directly applied to other omics data analysis studies.

Yixin Chen, Ankur Nath, Chunli Peng et al.

For constrained, not necessarily monotone submodular maximization, all known approximation algorithms with ratio greater than $1/e$ require continuous ideas, such as queries to the multilinear extension of a submodular function and its gradient, which are typically expensive to simulate with the original set function. For combinatorial algorithms, the best known approximation ratios for both size and matroid constraint are obtained by a simple randomized greedy algorithm of Buchbinder et al. [9]: $1/e \approx 0.367$ for size constraint and $0.281$ for the matroid constraint in $\mathcal O (kn)$ queries, where $k$ is the rank of the matroid. In this work, we develop the first combinatorial algorithms to break the $1/e$ barrier: we obtain approximation ratio of $0.385$ in $\mathcal O (kn)$ queries to the submodular set function for size constraint, and $0.305$ for a general matroid constraint. These are achieved by guiding the randomized greedy algorithm with a fast local search algorithm. Further, we develop deterministic versions of these algorithms, maintaining the same ratio and asymptotic time complexity. Finally, we develop a deterministic, nearly linear time algorithm with ratio $0.377$.

Heming Zhang, Wenyu Li, Di Huang et al.

Named Entity Recognition (NER) is a fundamental task in Natural Language Processing (NLP) that plays a crucial role in information extraction, question answering, and knowledge-based systems. Traditional deep learning-based NER models often struggle with domain-specific generalization and suffer from data sparsity issues. In this work, we introduce Knowledge Graph distilled for Named Entity Recognition (KoGNER), a novel approach that integrates Knowledge Graph (KG) distillation into NER models to enhance entity recognition performance. Our framework leverages structured knowledge representations from KGs to enrich contextual embeddings, thereby improving entity classification and reducing ambiguity in entity detection. KoGNER employs a two-step process: (1) Knowledge Distillation, where external knowledge sources are distilled into a lightweight representation for seamless integration with NER models, and (2) Entity-Aware Augmentation, which integrates contextual embeddings that have been enriched with knowledge graph information directly into GNN, thereby improving the model's ability to understand and represent entity relationships. Experimental results on benchmark datasets demonstrate that KoGNER achieves state-of-the-art performance, outperforming finetuned NER models and LLMs by a significant margin. These findings suggest that leveraging knowledge graphs as auxiliary information can significantly improve NER accuracy, making KoGNER a promising direction for future research in knowledge-aware NLP.

Heming Zhang, Di Huang, Yixin Chen et al.

The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations in expressivity when capturing intricate biological relationships. To address this, we propose Graph Sequence Language Model (GraphSeqLM), a framework that enhances GNNs with biological sequence embeddings generated by Large Language Models (LLMs). These embeddings encode structural and biological properties of DNA, RNA, and proteins, augmenting GNNs with enriched features for analyzing sample-specific multi-omic data. By integrating topological, sequence-derived, and biological information, GraphSeqLM demonstrates superior predictive accuracy and outperforms existing methods, paving the way for more effective multi-omic data integration in precision medicine.

Sicong Cao, Xiaobing Sun, Ratnadira Widyasari et al.

The remarkable achievements of Artificial Intelligence (AI) algorithms, particularly in Machine Learning (ML) and Deep Learning (DL), have fueled their extensive deployment across multiple sectors, including Software Engineering (SE). However, due to their black-box nature, these promising AI-driven SE models are still far from being deployed in practice. This lack of explainability poses unwanted risks for their applications in critical tasks, such as vulnerability detection, where decision-making transparency is of paramount importance. This paper endeavors to elucidate this interdisciplinary domain by presenting a systematic literature review of approaches that aim to improve the explainability of AI models within the context of SE. The review canvasses work appearing in the most prominent SE & AI conferences and journals, and spans 108 papers across 23 unique SE tasks. Based on three key Research Questions (RQs), we aim to (1) summarize the SE tasks where XAI techniques have shown success to date; (2) classify and analyze different XAI techniques; and (3) investigate existing evaluation approaches. Based on our findings, we identified a set of challenges remaining to be addressed in existing studies, together with a set of guidelines highlighting potential opportunities we deemed appropriate and important for future work.

Xikun Zhang, Dongjin Song, Yixin Chen et al.

Memory replay based techniques have shown great success for continual learning with incrementally accumulated Euclidean data. Directly applying them to continually expanding networks, however, leads to the potential memory explosion problem due to the need to buffer representative nodes and their associated topological neighborhood structures. To this end, we systematically analyze the key challenges in the memory explosion problem, and present a general framework, \textit{i.e.}, Parameter Decoupled Graph Neural Networks (PDGNNs) with Topology-aware Embedding Memory (TEM), to tackle this issue. The proposed framework not only reduces the memory space complexity from $\mathcal{O}(nd^L)$ to $\mathcal{O}(n)$~\footnote{$n$: memory budget, $d$: average node degree, $L$: the radius of the GNN receptive field}, but also fully utilizes the topological information for memory replay. Specifically, PDGNNs decouple trainable parameters from the computation ego-subnetwork via \textit{Topology-aware Embeddings} (TEs), which compress ego-subnetworks into compact vectors (\textit{i.e.}, TEs) to reduce the memory consumption. Based on this framework, we discover a unique \textit{pseudo-training effect} in continual learning on expanding networks and this effect motivates us to develop a novel \textit{coverage maximization sampling} strategy that can enhance the performance with a tight memory budget. Thorough empirical studies demonstrate that, by tackling the memory explosion problem and incorporating topological information into memory replay, PDGNNs with TEM significantly outperform state-of-the-art techniques, especially in the challenging class-incremental setting.

Yixin Chen, Tonmoy Dey, Alan Kuhnle

For the problem of maximizing a monotone, submodular function with respect to a cardinality constraint $k$ on a ground set of size $n$, we provide an algorithm that achieves the state-of-the-art in both its empirical performance and its theoretical properties, in terms of adaptive complexity, query complexity, and approximation ratio; that is, it obtains, with high probability, query complexity of $O(n)$ in expectation, adaptivity of $O(\log(n))$, and approximation ratio of nearly $1-1/e$. The main algorithm is assembled from two components which may be of independent interest. The first component of our algorithm, LINEARSEQ, is useful as a preprocessing algorithm to improve the query complexity of many algorithms. Moreover, a variant of LINEARSEQ is shown to have adaptive complexity of $O( \log (n / k) )$ which is smaller than that of any previous algorithm in the literature. The second component is a parallelizable thresholding procedure THRESHOLDSEQ for adding elements with gain above a constant threshold. Finally, we demonstrate that our main algorithm empirically outperforms, in terms of runtime, adaptive rounds, total queries, and objective values, the previous state-of-the-art algorithm FAST in a comprehensive evaluation with six submodular objective functions.

Zehao Dong, Heming Zhang, Yixin Chen et al.

We investigate molecular mechanisms of resistant or sensitive response of cancer drug combination therapies in an inductive and interpretable manner. Though deep learning algorithms are widely used in the drug synergy prediction problem, it is still an open problem to formulate the prediction model with biological meaning to investigate the mysterious mechanisms of synergy (MoS) for the human-AI collaboration in healthcare systems. To address the challenges, we propose a deep graph neural network, IDSP (Interpretable Deep Signaling Pathways), to incorporate the gene-gene as well as gene-drug regulatory relationships in synergic drug combination predictions. IDSP automatically learns weights of edges based on the gene and drug node relations, i.e., signaling interactions, by a multi-layer perceptron (MLP) and aggregates information in an inductive manner. The proposed architecture generates interpretable drug synergy prediction by detecting important signaling interactions, and can be implemented when the underlying molecular mechanism encounters unseen genes or signaling pathways. We test IDWSP on signaling networks formulated by genes from 46 core cancer signaling pathways and drug combinations from NCI ALMANAC drug combination screening data. The experimental results demonstrated that 1) IDSP can learn from the underlying molecular mechanism to make prediction without additional drug chemical information while achieving highly comparable performance with current state-of-art methods; 2) IDSP show superior generality and flexibility to implement the synergy prediction task on both transductive tasks and inductive tasks. 3) IDSP can generate interpretable results by detecting different salient signaling patterns (i.e. MoS) for different cell lines.

Yixin Chen, Alan Kuhnle

We present combinatorial and parallelizable algorithms for maximization of a submodular function, not necessarily monotone, with respect to a size constraint. We improve the best approximation factor achieved by an algorithm that has optimal adaptivity and nearly optimal query complexity to $0.193 - \varepsilon$. The conference version of this work mistakenly employed a subroutine that does not work for non-monotone, submodular functions. In this version, we propose a fixed and improved subroutine to add a set with high average marginal gain, ThreshSeq, which returns a solution in $O( \log(n) )$ adaptive rounds with high probability. Moreover, we provide two approximation algorithms. The first has approximation ratio $1/6 - \varepsilon$, adaptivity $O( \log (n) )$, and query complexity $O( n \log (k) )$, while the second has approximation ratio $0.193 - \varepsilon$, adaptivity $O( \log^2 (n) )$, and query complexity $O(n \log (k))$. Our algorithms are empirically validated to use a low number of adaptive rounds and total queries while obtaining solutions with high objective value in comparison with state-of-the-art approximation algorithms, including continuous algorithms that use the multilinear extension.

Zhicheng Cui, Bradley A Fritz, Christopher R King et al.

Logistic regression (LR) is widely used in clinical prediction because it is simple to deploy and easy to interpret. Nevertheless, being a linear model, LR has limited expressive capability and often has unsatisfactory performance. Generalized additive models (GAMs) extend the linear model with transformations of input features, though feature interaction is not allowed for all GAM variants. In this paper, we propose a factored generalized additive model (F-GAM) to preserve the model interpretability for targeted features while allowing a rich model for interaction with features fixed within the individual. We evaluate F-GAM on prediction of two targets, postoperative acute kidney injury and acute respiratory failure, from a single-center database. We find superior model performance of F-GAM in terms of AUPRC and AUROC compared to several other GAM implementations, random forests, support vector machine, and a deep neural network. We find that the model interpretability is good with results with high face validity.

Muhan Zhang, Yixin Chen

We propose an inductive matrix completion model without using side information. By factorizing the (rating) matrix into the product of low-dimensional latent embeddings of rows (users) and columns (items), a majority of existing matrix completion methods are transductive, since the learned embeddings cannot generalize to unseen rows/columns or to new matrices. To make matrix completion inductive, most previous works use content (side information), such as user's age or movie's genre, to make predictions. However, high-quality content is not always available, and can be hard to extract. Under the extreme setting where not any side information is available other than the matrix to complete, can we still learn an inductive matrix completion model? In this paper, we propose an Inductive Graph-based Matrix Completion (IGMC) model to address this problem. IGMC trains a graph neural network (GNN) based purely on 1-hop subgraphs around (user, item) pairs generated from the rating matrix and maps these subgraphs to their corresponding ratings. It achieves highly competitive performance with state-of-the-art transductive baselines. In addition, IGMC is inductive -- it can generalize to users/items unseen during the training (given that their interactions exist), and can even transfer to new tasks. Our transfer learning experiments show that a model trained out of the MovieLens dataset can be directly used to predict Douban movie ratings with surprisingly good performance. Our work demonstrates that: 1) it is possible to train inductive matrix completion models without using side information while achieving similar or better performances than state-of-the-art transductive methods; 2) local graph patterns around a (user, item) pair are effective predictors of the rating this user gives to the item; and 3) Long-range dependencies might not be necessary for modeling recommender systems.

Muhan Zhang, Shali Jiang, Zhicheng Cui et al.

Graph structured data are abundant in the real world. Among different graph types, directed acyclic graphs (DAGs) are of particular interest to machine learning researchers, as many machine learning models are realized as computations on DAGs, including neural networks and Bayesian networks. In this paper, we study deep generative models for DAGs, and propose a novel DAG variational autoencoder (D-VAE). To encode DAGs into the latent space, we leverage graph neural networks. We propose an asynchronous message passing scheme that allows encoding the computations on DAGs, rather than using existing simultaneous message passing schemes to encode local graph structures. We demonstrate the effectiveness of our proposed DVAE through two tasks: neural architecture search and Bayesian network structure learning. Experiments show that our model not only generates novel and valid DAGs, but also produces a smooth latent space that facilitates searching for DAGs with better performance through Bayesian optimization.

Zhicheng Cui, Wenlin Chen, Yixin Chen

Time series classification (TSC), the problem of predicting class labels of time series, has been around for decades within the community of data mining and machine learning, and found many important applications such as biomedical engineering and clinical prediction. However, it still remains challenging and falls short of classification accuracy and efficiency. Traditional approaches typically involve extracting discriminative features from the original time series using dynamic time warping (DTW) or shapelet transformation, based on which an off-the-shelf classifier can be applied. These methods are ad-hoc and separate the feature extraction part with the classification part, which limits their accuracy performance. Plus, most existing methods fail to take into account the fact that time series often have features at different time scales. To address these problems, we propose a novel end-to-end neural network model, Multi-Scale Convolutional Neural Networks (MCNN), which incorporates feature extraction and classification in a single framework. Leveraging a novel multi-branch layer and learnable convolutional layers, MCNN automatically extracts features at different scales and frequencies, leading to superior feature representation. MCNN is also computationally efficient, as it naturally leverages GPU computing. We conduct comprehensive empirical evaluation with various existing methods on a large number of benchmark datasets, and show that MCNN advances the state-of-the-art by achieving superior accuracy performance than other leading methods.

Wenlin Chen, James T. Wilson, Stephen Tyree et al.

As deep nets are increasingly used in applications suited for mobile devices, a fundamental dilemma becomes apparent: the trend in deep learning is to grow models to absorb ever-increasing data set sizes; however mobile devices are designed with very little memory and cannot store such large models. We present a novel network architecture, HashedNets, that exploits inherent redundancy in neural networks to achieve drastic reductions in model sizes. HashedNets uses a low-cost hash function to randomly group connection weights into hash buckets, and all connections within the same hash bucket share a single parameter value. These parameters are tuned to adjust to the HashedNets weight sharing architecture with standard backprop during training. Our hashing procedure introduces no additional memory overhead, and we demonstrate on several benchmark data sets that HashedNets shrink the storage requirements of neural networks substantially while mostly preserving generalization performance.