Entries by NEC Labs America

Prediction of Early Recurrence of Hepatocellular Carcinoma after Resection using Digital Pathology Images Assessed by Machine Learning

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Hepatocellular carcinoma (HCC) is a representative primary liver cancer caused by long-term and repetitive liver injury. Surgical resection is generally selected as the radical cure treatment. Because the early recurrence of HCC after resection is associated with low overall survival, the prediction of recurrence after resection is clinically important. However, the pathological characteristics of the early recurrence of HCC have not yet been elucidated. We attempted to predict the early recurrence of HCC after resection based on digital pathologic images of hematoxylin and eosin-stained specimens and machine learning applying a support vector machine (SVM). The 158 HCC patients meeting the Milan criteria who underwent surgical resection were included in this study. The patients were categorized into three groups: Group I, patients with HCC recurrence within 1 year after resection (16 for training and 23 for test), Group II, patients with HCC recurrence between 1 and 2 years after resection (22 and 28), and Group III, patients with no HCC recurrence within 4 years after resection (31 and 38). The SVM-based prediction method separated the three groups with 89.9% (80/89) accuracy. Prediction of Groups I was consistent for all cases, while Group II was predicted to be Group III in one case, and Group III was predicted to be Group II in 8 cases. The use of digital pathology and machine learning could be used for highly accurate prediction of HCC recurrence after surgical resection, especially that for early recurrence. Currently, in most cases after HCC resection, regular blood tests and diagnostic imaging are used for follow-up observation, however, the use of digital pathology coupled with machine learning offers potential as a method for objective postoprative follow-up observation.

Node Classification in Temporal Graphs through Stochastic Sparsification and Temporal Structural Convolution

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Node classification in temporal graphs aims to predict node labels based on historical observations. In real-world applications, temporal graphs are complex with both graph topology and node attributes evolving rapidly, which poses a high overfitting risk to existing graph learning approaches. In this paper, we propose a novel Temporal Structural Network (TSNet) model, which jointly learns temporal and structural features for node classification from the sparsified temporal graphs. We show that the proposed TSNet learns how to sparsify temporal graphs to favor the subsequent classification tasks and prevent overfitting from complex neighborhood structures. The effective local features are then extracted by simultaneous convolutions in temporal and spatial domains. Using the standard stochastic gradient descent and backpropagation techniques, TSNet iteratively optimizes sparsification and node representations for subsequent classification tasks. Experimental study on public benchmark datasets demonstrates the competitive performance of the proposed model in node classification. Besides, TSNet has the potential to help domain experts to interpret and visualize the learned models.

Model-Based Autoencoders for Imputing Discrete single-cell RNA-seq Data

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Deep neural networks have been widely applied for missing data imputation. However, most existing studies have been focused on imputing continuous data, while discrete data imputation is under-explored. Discrete data is common in real world, especially in research areas of bioinformatics, genetics, and biochemistry. In particular, large amounts of recent genomic data are discrete count data generated from single-cell RNA sequencing (scRNA-seq) technology. Most scRNA-seq studies produce a discrete matrix with prevailing ‘false’ zero count observations (missing values). To make downstream analyses more effective, imputation, which recovers the missing values, is often conducted as the first step in pre-processing scRNA-seq data. In this paper, we propose a novel Zero-Inflated Negative Binomial (ZINB) model-based autoencoder for imputing discrete scRNA-seq data. The novelties of our method are twofold. First, in addition to optimizing the ZINB likelihood, we propose to explicitly model the dropout events that cause missing values by using the Gumbel-Softmax distribution. Second, the zero-inflated reconstruction is further optimized with respect to the raw count matrix. Extensive experiments on simulation datasets demonstrate that the zero-inflated reconstruction significantly improves imputation accuracy. Real data experiments show that the proposed imputation can enhance separating different cell types and improve the accuracy of differential expression analysis.

Tripping Through Time: Efficient Localization of Activities in Videos

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Localizing moments in untrimmed videos via language queries is a new and interesting task that requires the ability to accurately ground language into video. Previous works have approached this task by processing the entire video, often more than once, to localize relevant activities. In the real world applications of this approach, such as video surveillance, efficiency is a key system requirement. In this paper, we present TripNet, an end-to-end system that uses a gated attention architecture to model fine-grained textual and visual representations in order to align text and video content. Furthermore, TripNet uses reinforcement learning to efficiently localize relevant activity clips in long videos, by learning how to intelligently skip around the video. It extracts visual features for few frames to perform activity classification. In our evaluation over Charades-STA [14], ActivityNet Captions [26] and the TACoS dataset [36], we find that TripNet achieves high accuracy and saves processing time by only looking at 32-41% of the entire video.

Adaptation Across Extreme Variations using Unlabeled Bridges

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We tackle an unsupervised domain adaptation problem for which the domain discrepancy between labeled source and unlabeled target domains is large, due to many factors of inter- and intra-domain variation. While deep domain adaptation methods have been realized by reducing the domain discrepancy, these are difficult to apply when domains are significantly different. We propose to decompose domain discrepancy into multiple but smaller, and thus easier to minimize, discrepancies by introducing unlabeled bridging domains that connect the source and target domains. We realize our proposed approach through an extension of the domain adversarial neural network with multiple discriminators, each of which accounts for reducing discrepancies between unlabeled (bridge, target) domains and a mix of all precedent domains including source. We validate the effectiveness of our method on several adaptation tasks including object recognition and semantic segmentation.

Pseudo RGB-D for Self-Improving Monocular SLAM and Depth Prediction

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Classical monocular Simultaneous Localization And Mapping (SLAM) and the recently emerging convolutional neural networks (CNNs) for monocular depth prediction represent two largely disjoint approaches towards building a 3D map of the surrounding environment. In this paper, we demonstrate that the coupling of these two by leveraging the strengths of each mitigates the other’s shortcomings. Specifically, we propose a joint narrow and wide baseline based self-improving framework, where on the one hand the CNN-predicted depth is leveraged to perform $ extit(Unknown sysvar: (pseudo))$ RGB-D feature-based SLAM, leading to better accuracy and robustness than the monocular RGB SLAM baseline. On the other hand, the bundle-adjusted 3D scene structures and camera poses from the more principled geometric SLAM are injected back into the depth network through novel wide baseline losses proposed for improving the depth prediction network, which then continues to contribute towards better pose and 3D structure estimation in the next iteration. We emphasize that our framework only requires $ extit(Unknown sysvar: ( unlabeled monocular))$ videos in both training and inference stages, and yet is able to outperform state-of-the-art self-supervised $ extit(Unknown sysvar: (monocular))$ and $ extit(Unknown sysvar: (stereo))$ depth prediction networks (e.g, Monodepth2) and feature based monocular SLAM system (i.e, ORB-SLAM). Extensive experiments on KITTI and TUM RGB-D datasets verify the superiority of our self-improving geometry-CNN framework.

SMART: Simultaneous Multi-Agent Recurrent Trajectory Prediction

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We propose advances that address two key challenges in future trajectory prediction: (i) multimodality in both training data and predictions and (ii) constant time inference regardless of number of agents. Existing trajectory predictions are fundamentally limited by lack of diversity in training data, which is difficult to acquire with sufficient coverage of possible modes. Our first contribution is an automatic method to simulate diverse trajectories in the top-view. It uses pre-existing datasets and maps as initialization, mines existing trajectories to represent realistic driving behaviors and uses a multi-agent vehicle dynamics simulator to generate diverse new trajectories that cover various modes and are consistent with scene layout constraints. Our second contribution is a novel method that generates diverse predictions while accounting for scene semantics and multi-agent interactions, with constant-time inference independent of the number of agents. We propose a convLSTM with novel state pooling operations and losses to predict scene-consistent states of multiple agents in a single forward pass, along with a CVAE for diversity. We validate our proposed multi-agent trajectory prediction approach by training and testing on the proposed simulated dataset and existing real datasets of traffic scenes. In both cases, our approach outperforms SOTA methods by a large margin, highlighting the benefits of both our diverse dataset simulation and constant-time diverse trajectory prediction methods.”

Shuffle and Attend: Video Domain Adaptation

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We address the problem of domain adaptation in videos for the task of human action recognition. Inspired by image-based domain adaptation, we can perform video adaptation by aligning the features of frames or clips of source and target videos. However, equally aligning all clips is sub-optimal as not all clips are informative for the task. As the first novelty, we propose an attention mechanism which focuses on more discriminative clips and directly optimizes for video-level (cf. clip-level) alignment. As the backgrounds are often very different between source and target, the source background-corrupted model adapts poorly to target domain videos. To alleviate this, as a second novelty, we propose to use the clip order prediction as an auxiliary task. The clip order prediction loss, when combined with domain adversarial loss, encourages learning of representations which focus on the humans and objects involved in the actions, rather than the uninformative and widely differing (between source and target) backgrounds. We empirically show that both components contribute positively towards adaptation performance. We report state-of-the-art performances on two out of three challenging public benchmarks, two based on the UCF and HMDB datasets, and one on Kinetics to NEC-Drone datasets. We also support the intuitions and the results with qualitative results.

Object Detection with a Unified Label Space from Multiple Datasets

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Given multiple datasets with different label spaces, the goal of this work is to train a single object detector predicting over the union of all the label spaces. The practical benefits of such an object detector are obvious and significant—application-relevant categories can be picked and merged form arbitrary existing datasets. However, naive merging of datasets is not possible in this case, due to inconsistent object annotations. Consider an object category like faces that is annotated in one dataset, but is not annotated in another dataset, although the object itself appears in the later’s images. Some categories, like face here, would thus be considered foreground in one dataset, but background in another. To address this challenge, we design a framework which works with such partial annotations, and we exploit a pseudo labeling approach that we adapt for our specific case. We propose loss functions that carefully integrate partial but correct annotations with complementary but noisy pseudo labels. Evaluation in the proposed novel setting requires full annotation on the test set. We collect the required annotations and define a new challenging experimental setup for this task based on existing public datasets. We show improved performances compared to competitive baselines and appropriate adaptations of existing work