Jinbo Bi

Hongwu Peng, Shaoyi Huang, Shiyang Chen et al. · deepmind

Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm-hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 $\times$ and 2.6 $\times$ speedup compared to CPU and GPU implementation, and 4 $\times$ higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.

Chandan Chunduru, Chun Jiang Zhu, Blake Gains et al.

Graph sparsification is a powerful tool to approximate an arbitrary graph and has been used in machine learning over homogeneous graphs. In heterogeneous graphs such as knowledge graphs, however, sparsification has not been systematically exploited to improve efficiency of learning tasks. In this work, we initiate the study on heterogeneous graph sparsification and develop sampling-based algorithms for constructing sparsifiers that are provably sparse and preserve important information in the original graphs. We have performed extensive experiments to confirm that the proposed method can improve time and space complexities of representation learning while achieving comparable, or even better performance in subsequent graph learning tasks based on the learned embedding.

Aaron Palmer, Zhiyi Chi, Derek Aguiar et al.

We develop a new type of generative autoencoder called the Goodness-of-Fit Autoencoder (GoFAE), which incorporates GoF tests at two levels. At the minibatch level, it uses GoF test statistics as regularization objectives. At a more global level, it selects a regularization coefficient based on higher criticism, i.e., a test on the uniformity of the local GoF p-values. We justify the use of GoF tests by providing a relaxed $L_2$-Wasserstein bound on the distance between the latent distribution and a distribution class. We prove that optimization based on these tests can be done with stochastic gradient descent on a compact Riemannian manifold. Empirically, we show that our higher criticism parameter selection procedure balances reconstruction and generation using mutual information and uniformity of p-values respectively. Finally, we show that GoFAE achieves comparable FID scores and mean squared errors with competing deep generative models while retaining statistical indistinguishability from Gaussian in the latent space based on a variety of hypothesis tests.

Xinyu Wang, Fei Dou, Jinbo Bi et al.

Linearized string representations serve as the foundation of scalable autoregressive molecular generation; however, they introduce a fundamental modality mismatch where a single molecular graph maps to multiple distinct sequences. This ambiguity leads to \textit{trajectory divergence}, where the latent representations of structurally equivalent partial graphs drift apart due to differences in linearization history. To resolve this without abandoning the efficient string formulation, we propose Structure-Invariant Generative Molecular Alignment (SIGMA). Rather than altering the linear representation, SIGMA enables the model to strictly recognize geometric symmetries via a token-level contrastive objective, which explicitly aligns the latent states of prefixes that share identical suffixes. Furthermore, we introduce Isomorphic Beam Search (IsoBeam) to eliminate isomorphic redundancy during inference by dynamically pruning equivalent paths. Empirical evaluations on standard benchmarks demonstrate that SIGMA bridges the gap between sequence scalability and graph fidelity, yielding superior sample efficiency and structural diversity in multi-parameter optimization compared to strong baselines.

Xinyu Wang, Ke Deng, Fei Dou et al.

Model merging aims to combine multiple fine-tuned models into a single multi-task model without access to training data. Existing task-vector merging methods such as TIES, TSV-M, and Iso-C/CTS differ in their aggregation rules but treat all layers nearly uniformly. This assumption overlooks the strong layer-wise heterogeneity in large vision transformers, where shallow layers are sensitive to interference while deeper layers encode stable task-specific features. We introduce LARV, a training-free, data-free, merger-agnostic Layer-wise Adaptive Rescaling Veneer that plugs into any task-vector merger and assigns a per-layer scale to each task vector before aggregation, and show it consistently boosts diverse merging rules. LARV adaptively suppresses shallow-layer interference and amplifies deeper-layer alignment using a simple deterministic schedule, requiring no retraining or modification to existing mergers. To our knowledge, this is the first work to perform layer-aware scaling for task-vector merging. LARV computes simple data-free layer proxies and turns them into scales through a lightweight rule; we study several instantiations within one framework (e.g., tiered two/three-level scaling with fixed values, or continuous mappings) and show that tiered choices offer the best robustness, while continuous mappings remain an ablation. LARV is orthogonal to the base merger and adds negligible cost. On FusionBench with Vision Transformers, LARV consistently improves all task-vector baselines across 8/14/20-task settings; for example, Iso-C + LARV reaches 85.9% on ViT-B/32, 89.2% on ViT-B/16, and 92.6% on ViT-L/14. Layerwise analysis and corruption tests further indicate that LARV suppresses shallow-layer interference while modestly amplifying deeper, task-stable features, turning model merging into a robust, layer-aware procedure rather than a uniform one.

Qianqian Tong, Guannan Liang, Jinbo Bi

Adaptive gradient methods (AGMs) have become popular in optimizing the nonconvex problems in deep learning area. We revisit AGMs and identify that the adaptive learning rate (A-LR) used by AGMs varies significantly across the dimensions of the problem over epochs (i.e., anisotropic scale), which may lead to issues in convergence and generalization. All existing modified AGMs actually represent efforts in revising the A-LR. Theoretically, we provide a new way to analyze the convergence of AGMs and prove that the convergence rate of \textsc{Adam} also depends on its hyper-parameter $ε$, which has been overlooked previously. Based on these two facts, we propose a new AGM by calibrating the A-LR with an activation ({\em softplus}) function, resulting in the \textsc{Sadam} and \textsc{SAMSGrad} methods \footnote{Code is available at https://github.com/neilliang90/Sadam.git.}. We further prove that these algorithms enjoy better convergence speed under nonconvex, non-strongly convex, and Polyak-Łojasiewicz conditions compared with \textsc{Adam}. Empirical studies support our observation of the anisotropic A-LR and show that the proposed methods outperform existing AGMs and generalize even better than S-Momentum in multiple deep learning tasks.

Peining Zhang, Jinbo Bi, Minghu Song

Diffusion models show promise for 3D molecular generation, but face a fundamental trade-off between sampling efficiency and conformational accuracy. While flow-based models are fast, they often produce geometrically inaccurate structures, as they have difficulty capturing the multimodal distributions of molecular conformations. In contrast, denoising diffusion models are more accurate but suffer from slow sampling, a limitation attributed to sub-optimal integration between diffusion dynamics and SE(3)-equivariant architectures. To address this, we propose VEDA, a unified SE(3)-equivariant framework that combines variance-exploding diffusion with annealing to efficiently generate conformationally accurate 3D molecular structures. Specifically, our key technical contributions include: (1) a VE schedule that enables noise injection functionally analogous to simulated annealing, improving 3D accuracy and reducing relaxation energy; (2) a novel preconditioning scheme that reconciles the coordinate-predicting nature of SE(3)-equivariant networks with a residual-based diffusion objective, and (3) a new arcsin-based scheduler that concentrates sampling in critical intervals of the logarithmic signal-to-noise ratio. On the QM9 and GEOM-DRUGS datasets, VEDA matches the sampling efficiency of flow-based models, achieving state-of-the-art valency stability and validity with only 100 sampling steps. More importantly, VEDA's generated structures are remarkably stable, as measured by their relaxation energy during GFN2-xTB optimization. The median energy change is only 1.72 kcal/mol, significantly lower than the 32.3 kcal/mol from its architectural baseline, SemlaFlow. Our framework demonstrates that principled integration of VE diffusion with SE(3)-equivariant architectures can achieve both high chemical accuracy and computational efficiency.

Binghao Lu, Caiwen Ding, Jinbo Bi et al.

Change detection, which aims to detect spatial changes from a pair of multi-temporal images due to natural or man-made causes, has been widely applied in remote sensing, disaster management, urban management, etc. Most existing change detection approaches, however, are fully supervised and require labor-intensive pixel-level labels. To address this, we develop a novel weakly supervised change detection technique via Knowledge Distillation and Multiscale Sigmoid Inference (KD-MSI) that leverages image-level labels. In our approach, the Class Activation Maps (CAM) are utilized not only to derive a change probability map but also to serve as a foundation for the knowledge distillation process. This is done through a joint training strategy of the teacher and student networks, enabling the student network to highlight potential change areas more accurately than teacher network based on image-level labels. Moreover, we designed a Multiscale Sigmoid Inference (MSI) module as a post processing step to further refine the change probability map from the trained student network. Empirical results on three public datasets, i.e., WHU-CD, DSIFN-CD, and LEVIR-CD, demonstrate that our proposed technique, with its integrated training strategy, significantly outperforms the state-of-the-art.

Peining Zhang, Daniel Baker, Minghu Song et al.

Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently attracted great attention in drug R\&D. This paper comprehensively reviews the latest advancements and applications of DMs in molecular generation. It begins by introducing the theoretical principles of DMs. Subsequently, it categorizes various DM-based molecular generation methods according to their mathematical and chemical applications. The review further examines the performance of these models on benchmark datasets, with a particular focus on comparing the generation performance of existing 3D methods. Finally, it concludes by emphasizing current challenges and suggesting future research directions to fully exploit the potential of DMs in drug discovery.

Jieren Deng, Aaron Palmer, Rigel Mahmood et al.

Achieving resiliency against adversarial attacks is necessary prior to deploying neural network classifiers in domains where misclassification incurs substantial costs, e.g., self-driving cars or medical imaging. Recent work has demonstrated that robustness can be transferred from an adversarially trained teacher to a student model using knowledge distillation. However, current methods perform distillation using a single adversarial and vanilla teacher and consider homogeneous architectures (i.e., residual networks) that are susceptible to misclassify examples from similar adversarial subspaces. In this work, we develop a defense framework against adversarial attacks by distilling adversarial robustness using heterogeneous teachers (DARHT). In DARHT, the student model explicitly represents teacher logits in a student-teacher feature map and leverages multiple teachers that exhibit low adversarial example transferability (i.e., exhibit high performance on dissimilar adversarial examples). Experiments on classification tasks in both white-box and black-box scenarios demonstrate that DARHT achieves state-of-the-art clean and robust accuracies when compared to competing adversarial training and distillation methods in the CIFAR-10, CIFAR-100, and Tiny ImageNet datasets. Comparisons with homogeneous and heterogeneous teacher sets suggest that leveraging teachers with low adversarial example transferability increases student model robustness.

Soumyashree Sahoo, Chinmaey Shende, Md. Zakir Hossain et al.

Currently, depression treatment relies on closely monitoring patients response to treatment and adjusting the treatment as needed. Using self-reported or physician-administrated questionnaires to monitor treatment response is, however, burdensome, costly and suffers from recall bias. In this paper, we explore using location sensory data collected passively on smartphones to predict treatment outcome. To address heterogeneous data collection on Android and iOS phones, the two predominant smartphone platforms, we explore using domain adaptation techniques to map their data to a common feature space, and then use the data jointly to train machine learning models. Our results show that this domain adaptation approach can lead to significantly better prediction than that with no domain adaptation. In addition, our results show that using location features and baseline self-reported questionnaire score can lead to F1 score up to 0.67, comparable to that obtained using periodic self-reported questionnaires, indicating that using location data is a promising direction for predicting depression treatment outcome.

Peining Zhang, Hongchen Qin, Haochen Zhang et al.

This work investigates the zero-shot forecasting capability of time series foundation models for Leaf Area Index (LAI) forecasting in agricultural monitoring. Using the HiQ dataset (U.S., 2000-2022), we systematically compare statistical baselines, a fully supervised LSTM, and the Sundial foundation model under multiple evaluation protocols. We find that Sundial, in the zero-shot setting, can outperform a fully trained LSTM provided that the input context window is sufficiently long-specifically, when covering more than one or two full seasonal cycles. We show that a general-purpose foundation model can surpass specialized supervised models on remote-sensing time series prediction without any task-specific tuning. These results highlight the strong potential of pretrained time series foundation models to serve as effective plug-and-play forecasters in agricultural and environmental applications.

Xinyu Wang, Jinbo Bi, Minghu Song

SMILES-based molecule generation has emerged as a powerful approach in drug discovery. Deep reinforcement learning (RL) using large language model (LLM) has been incorporated into the molecule generation process to achieve high matching score in term of likelihood of desired molecule candidates. However, a critical challenge in this approach is catastrophic forgetting during the RL phase, where knowledge such as molecule validity, which often exceeds 99\% during pretraining, significantly deteriorates. Current RL algorithms applied in drug discovery, such as REINVENT, use prior models as anchors to retian pretraining knowledge, but these methods lack robust exploration mechanisms. To address these issues, we propose Partial SMILES Validation-PPO (PSV-PPO), a novel RL algorithm that incorporates real-time partial SMILES validation to prevent catastrophic forgetting while encouraging exploration. Unlike traditional RL approaches that validate molecule structures only after generating entire sequences, PSV-PPO performs stepwise validation at each auto-regressive step, evaluating not only the selected token candidate but also all potential branches stemming from the prior partial sequence. This enables early detection of invalid partial SMILES across all potential paths. As a result, PSV-PPO maintains high validity rates even during aggressive exploration of the vast chemical space. Our experiments on the PMO and GuacaMol benchmark datasets demonstrate that PSV-PPO significantly reduces the number of invalid generated structures while maintaining competitive exploration and optimization performance. While our work primarily focuses on maintaining validity, the framework of PSV-PPO can be extended in future research to incorporate additional forms of valuable domain knowledge, further enhancing reinforcement learning applications in drug discovery.

Tan Zhu, Guannan Liang, Chunjiang Zhu et al.

In stochastic contextual bandit (SCB) problems, an agent selects an action based on certain observed context to maximize the cumulative reward over iterations. Recently there have been a few studies using a deep neural network (DNN) to predict the expected reward for an action, and the DNN is trained by a stochastic gradient based method. However, convergence analysis has been greatly ignored to examine whether and where these methods converge. In this work, we formulate the SCB that uses a DNN reward function as a non-convex stochastic optimization problem, and design a stage-wise stochastic gradient descent algorithm to optimize the problem and determine the action policy. We prove that with high probability, the action sequence chosen by this algorithm converges to a greedy action policy respecting a local optimal reward function. Extensive experiments have been performed to demonstrate the effectiveness and efficiency of the proposed algorithm on multiple real-world datasets.

Guannan Liang, Qianqian Tong, Chunjiang Zhu et al.

Stochastically controlled stochastic gradient (SCSG) methods have been proved to converge efficiently to first-order stationary points which, however, can be saddle points in nonconvex optimization. It has been observed that a stochastic gradient descent (SGD) step introduces anistropic noise around saddle points for deep learning and non-convex half space learning problems, which indicates that SGD satisfies the correlated negative curvature (CNC) condition for these problems. Therefore, we propose to use a separate SGD step to help the SCSG method escape from strict saddle points, resulting in the CNC-SCSG method. The SGD step plays a role similar to noise injection but is more stable. We prove that the resultant algorithm converges to a second-order stationary point with a convergence rate of $\tilde{O}( ε^{-2} log( 1/ε))$ where $ε$ is the pre-specified error tolerance. This convergence rate is independent of the problem dimension, and is faster than that of CNC-SGD. A more general framework is further designed to incorporate the proposed CNC-SCSG into any first-order method for the method to escape saddle points. Simulation studies illustrate that the proposed algorithm can escape saddle points in much fewer epochs than the gradient descent methods perturbed by either noise injection or a SGD step.

Chao Shang, Jie Chen, Jinbo Bi

Time series forecasting is an extensively studied subject in statistics, economics, and computer science. Exploration of the correlation and causation among the variables in a multivariate time series shows promise in enhancing the performance of a time series model. When using deep neural networks as forecasting models, we hypothesize that exploiting the pairwise information among multiple (multivariate) time series also improves their forecast. If an explicit graph structure is known, graph neural networks (GNNs) have been demonstrated as powerful tools to exploit the structure. In this work, we propose learning the structure simultaneously with the GNN if the graph is unknown. We cast the problem as learning a probabilistic graph model through optimizing the mean performance over the graph distribution. The distribution is parameterized by a neural network so that discrete graphs can be sampled differentiably through reparameterization. Empirical evaluations show that our method is simpler, more efficient, and better performing than a recently proposed bilevel learning approach for graph structure learning, as well as a broad array of forecasting models, either deep or non-deep learning based, and graph or non-graph based.

Qianqian Tong, Guannan Liang, Tan Zhu et al.

Nonconvex sparse learning plays an essential role in many areas, such as signal processing and deep network compression. Iterative hard thresholding (IHT) methods are the state-of-the-art for nonconvex sparse learning due to their capability of recovering true support and scalability with large datasets. Theoretical analysis of IHT is currently based on centralized IID data. In realistic large-scale situations, however, data are distributed, hardly IID, and private to local edge computing devices. It is thus necessary to examine the property of IHT in federated settings, which update in parallel on local devices and communicate with a central server only once in a while without sharing local data. In this paper, we propose two IHT methods: Federated Hard Thresholding (Fed-HT) and Federated Iterative Hard Thresholding (FedIter-HT). We prove that both algorithms enjoy a linear convergence rate and have strong guarantees to recover the optimal sparse estimator, similar to traditional IHT methods, but now with decentralized non-IID data. Empirical results demonstrate that the Fed-HT and FedIter-HT outperform their competitor - a distributed IHT, in terms of decreasing the objective values with lower requirements on communication rounds and bandwidth.

Guannan Liang, Qianqian Tong, Jiahao Ding et al.

Sparse learning is a very important tool for mining useful information and patterns from high dimensional data. Non-convex non-smooth regularized learning problems play essential roles in sparse learning, and have drawn extensive attentions recently. We design a family of stochastic proximal gradient methods by applying arbitrary sampling to solve the empirical risk minimization problem with a non-convex and non-smooth regularizer. These methods draw mini-batches of training examples according to an arbitrary probability distribution when computing stochastic gradients. A unified analytic approach is developed to examine the convergence and computational complexity of these methods, allowing us to compare the different sampling schemes. We show that the independent sampling scheme tends to improve performance over the commonly-used uniform sampling scheme. Our new analysis also derives a tighter bound on convergence speed for the uniform sampling than the best one available so far. Empirical evaluations demonstrate that the proposed algorithms converge faster than the state of the art.

Qianqian Tong, Guannan Liang, Jinbo Bi

Federated learning allows loads of edge computing devices to collaboratively learn a global model without data sharing. The analysis with partial device participation under non-IID and unbalanced data reflects more reality. In this work, we propose federated learning versions of adaptive gradient methods - Federated AGMs - which employ both the first-order and second-order momenta, to alleviate generalization performance deterioration caused by dissimilarity of data population among devices. To further improve the test performance, we compare several schemes of calibration for the adaptive learning rate, including the standard Adam calibrated by $ε$, $p$-Adam, and one calibrated by an activation function. Our analysis provides the first set of theoretical results that the proposed (calibrated) Federated AGMs converge to a first-order stationary point under non-IID and unbalanced data settings for nonconvex optimization. We perform extensive experiments to compare these federated learning methods with the state-of-the-art FedAvg, FedMomentum and SCAFFOLD and to assess the different calibration schemes and the advantages of AGMs over the current federated learning methods.

Yijue Wang, Chenghong Wang, Zigeng Wang et al.

The large model size, high computational operations, and vulnerability against membership inference attack (MIA) have impeded deep learning or deep neural networks (DNNs) popularity, especially on mobile devices. To address the challenge, we envision that the weight pruning technique will help DNNs against MIA while reducing model storage and computational operation. In this work, we propose a pruning algorithm, and we show that the proposed algorithm can find a subnetwork that can prevent privacy leakage from MIA and achieves competitive accuracy with the original DNNs. We also verify our theoretical insights with experiments. Our experimental results illustrate that the attack accuracy using model compression is up to 13.6% and 10% lower than that of the baseline and Min-Max game, accordingly.

Jiahao Ding, Jingyi Wang, Guannan Liang et al.

The Alternating Direction Method of Multipliers (ADMM) and its distributed version have been widely used in machine learning. In the iterations of ADMM, model updates using local private data and model exchanges among agents impose critical privacy concerns. Despite some pioneering works to relieve such concerns, differentially private ADMM still confronts many research challenges. For example, the guarantee of differential privacy (DP) relies on the premise that the optimality of each local problem can be perfectly attained in each ADMM iteration, which may never happen in practice. The model trained by DP ADMM may have low prediction accuracy. In this paper, we address these concerns by proposing a novel (Improved) Plausible differentially Private ADMM algorithm, called PP-ADMM and IPP-ADMM. In PP-ADMM, each agent approximately solves a perturbed optimization problem that is formulated from its local private data in an iteration, and then perturbs the approximate solution with Gaussian noise to provide the DP guarantee. To further improve the model accuracy and convergence, an improved version IPP-ADMM adopts sparse vector technique (SVT) to determine if an agent should update its neighbors with the current perturbed solution. The agent calculates the difference of the current solution from that in the last iteration, and if the difference is larger than a threshold, it passes the solution to neighbors; or otherwise the solution will be discarded. Moreover, we propose to track the total privacy loss under the zero-concentrated DP (zCDP) and provide a generalization performance analysis. Experiments on real-world datasets demonstrate that under the same privacy guarantee, the proposed algorithms are superior to the state of the art in terms of model accuracy and convergence rate.

Chao Shang, Yun Tang, Jing Huang et al.

Knowledge graph embedding has been an active research topic for knowledge base completion, with progressive improvement from the initial TransE, TransH, DistMult et al to the current state-of-the-art ConvE. ConvE uses 2D convolution over embeddings and multiple layers of nonlinear features to model knowledge graphs. The model can be efficiently trained and scalable to large knowledge graphs. However, there is no structure enforcement in the embedding space of ConvE. The recent graph convolutional network (GCN) provides another way of learning graph node embedding by successfully utilizing graph connectivity structure. In this work, we propose a novel end-to-end Structure-Aware Convolutional Network (SACN) that takes the benefit of GCN and ConvE together. SACN consists of an encoder of a weighted graph convolutional network (WGCN), and a decoder of a convolutional network called Conv-TransE. WGCN utilizes knowledge graph node structure, node attributes and edge relation types. It has learnable weights that adapt the amount of information from neighbors used in local aggregation, leading to more accurate embeddings of graph nodes. Node attributes in the graph are represented as additional nodes in the WGCN. The decoder Conv-TransE enables the state-of-the-art ConvE to be translational between entities and relations while keeps the same link prediction performance as ConvE. We demonstrate the effectiveness of the proposed SACN on standard FB15k-237 and WN18RR datasets, and it gives about 10% relative improvement over the state-of-the-art ConvE in terms of HITS@1, HITS@3 and HITS@10.

Chao Shang, Qinqing Liu, Ko-Shin Chen et al.

Graph convolutional network (GCN) is generalization of convolutional neural network (CNN) to work with arbitrarily structured graphs. A binary adjacency matrix is commonly used in training a GCN. Recently, the attention mechanism allows the network to learn a dynamic and adaptive aggregation of the neighborhood. We propose a new GCN model on the graphs where edges are characterized in multiple views or precisely in terms of multiple relationships. For instance, in chemical graph theory, compound structures are often represented by the hydrogen-depleted molecular graph where nodes correspond to atoms and edges correspond to chemical bonds. Multiple attributes can be important to characterize chemical bonds, such as atom pair (the types of atoms that a bond connects), aromaticity, and whether a bond is in a ring. The different attributes lead to different graph representations for the same molecule. There is growing interests in both chemistry and machine learning fields to directly learn molecular properties of compounds from the molecular graph, instead of from fingerprints predefined by chemists. The proposed GCN model, which we call edge attention-based multi-relational GCN (EAGCN), jointly learns attention weights and node features in graph convolution. For each bond attribute, a real-valued attention matrix is used to replace the binary adjacency matrix. By designing a dictionary for the edge attention, and forming the attention matrix of each molecule by looking up the dictionary, the EAGCN exploits correspondence between bonds in different molecules. The prediction of compound properties is based on the aggregated node features, which is independent of the varying molecule (graph) size. We demonstrate the efficacy of the EAGCN on multiple chemical datasets: Tox21, HIV, Freesolv, and Lipophilicity, and interpret the resultant attention weights.

Guoqing Chao, Shiliang Sun, Jinbo Bi

With advances in information acquisition technologies, multi-view data become ubiquitous. Multi-view learning has thus become more and more popular in machine learning and data mining fields. Multi-view unsupervised or semi-supervised learning, such as co-training, co-regularization has gained considerable attention. Although recently, multi-view clustering (MVC) methods have been developed rapidly, there has not been a survey to summarize and analyze the current progress. Therefore, this paper reviews the common strategies for combining multiple views of data and based on this summary we propose a novel taxonomy of the MVC approaches. We further discuss the relationships between MVC and multi-view representation, ensemble clustering, multi-task clustering, multi-view supervised and semi-supervised learning. Several representative real-world applications are elaborated. To promote future development of MVC, we envision several open problems that may require further investigation and thorough examination.

Chao Shang, Aaron Palmer, Jiangwen Sun et al.

In an era when big data are becoming the norm, there is less concern with the quantity but more with the quality and completeness of the data. In many disciplines, data are collected from heterogeneous sources, resulting in multi-view or multi-modal datasets. The missing data problem has been challenging to address in multi-view data analysis. Especially, when certain samples miss an entire view of data, it creates the missing view problem. Classic multiple imputations or matrix completion methods are hardly effective here when no information can be based on in the specific view to impute data for such samples. The commonly-used simple method of removing samples with a missing view can dramatically reduce sample size, thus diminishing the statistical power of a subsequent analysis. In this paper, we propose a novel approach for view imputation via generative adversarial networks (GANs), which we name by VIGAN. This approach first treats each view as a separate domain and identifies domain-to-domain mappings via a GAN using randomly-sampled data from each view, and then employs a multi-modal denoising autoencoder (DAE) to reconstruct the missing view from the GAN outputs based on paired data across the views. Then, by optimizing the GAN and DAE jointly, our model enables the knowledge integration for domain mappings and view correspondences to effectively recover the missing view. Empirical results on benchmark datasets validate the VIGAN approach by comparing against the state of the art. The evaluation of VIGAN in a genetic study of substance use disorders further proves the effectiveness and usability of this approach in life science.

Ioannis Papavasileiou, Wenlong Zhang, Xin Wang et al.

As our population ages, neurological impairments and degeneration of the musculoskeletal system yield gait abnormalities, which can significantly reduce quality of life. Gait rehabilitative therapy has been widely adopted to help patients maximize community participation and living independence. To further improve the precision and efficiency of rehabilitative therapy, more objective methods need to be developed based on sensory data. In this paper, an algorithmic framework is proposed to provide classification of gait disorders caused by two common neurological diseases, stroke and Parkinson's Disease (PD), from ground contact force (GCF) data. An advanced machine learning method, multi-task feature learning (MTFL), is used to jointly train classification models of a subject's gait in three classes, post-stroke, PD and healthy gait. Gait parameters related to mobility, balance, strength and rhythm are used as features for the classification. Out of all the features used, the MTFL models capture the more important ones per disease, which will help provide better objective assessment and therapy progress tracking. To evaluate the proposed methodology we use data from a human participant study, which includes five PD patients, three post-stroke patients, and three healthy subjects. Despite the diversity of abnormalities, the evaluation shows that the proposed approach can successfully distinguish post-stroke and PD gait from healthy gait, as well as post-stroke from PD gait, with Area Under the Curve (AUC) score of at least 0.96. Moreover, the methodology helps select important gait features to better understand the key characteristics that distinguish abnormal gaits and design personalized treatment.

Xin Wang, Jinbo Bi, Shipeng Yu et al.

We investigate a general framework of multiplicative multitask feature learning which decomposes each task's model parameters into a multiplication of two components. One of the components is used across all tasks and the other component is task-specific. Several previous methods have been proposed as special cases of our framework. We study the theoretical properties of this framework when different regularization conditions are applied to the two decomposed components. We prove that this framework is mathematically equivalent to the widely used multitask feature learning methods that are based on a joint regularization of all model parameters, but with a more general form of regularizers. Further, an analytical formula is derived for the across-task component as related to the task-specific component for all these regularizers, leading to a better understanding of the shrinkage effect. Study of this framework motivates new multitask learning algorithms. We propose two new learning formulations by varying the parameters in the proposed framework. Empirical studies have revealed the relative advantages of the two new formulations by comparing with the state of the art, which provides instructive insights into the feature learning problem with multiple tasks.