Machine LearningRead the latest publications from our world-class team of researchers from our Machine Learning team who have been at the forefront of machine learning developments, including deep learning, support vector machines, and semantic analysis, for over a decade. We develop innovative technologies integrated into NEC’s products and services. Machine learning is the critical technology for data analytics and artificial intelligence. Recent progress in this field opens opportunities for various new applications.

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SplitBrain: Hybrid Data and Model Parallel Deep Learning

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The recent success of deep learning applications has coincided with those widely available powerful computational resources for training sophisticated machine learning models with huge datasets. Nonetheless, training large models such as convolutional neural networks using model parallelism (as opposed to data parallelism) is challenging because the complex nature of communication between model shards makes it difficult to partition the computation efficiently across multiple machines with an acceptable trade off. This paper presents SplitBrain, a high performance distributed deep learning framework supporting hybrid data and model parallelism. Specifically, SplitBrain provides layer specific partitioning that co locates compute intensive convolutional layers while sharding memory demanding layers. A novel scalable group communication is proposed to further improve the training throughput with reduced communication overhead. The results show that SplitBrain can achieve nearly linear speedup while saving up to 67% of memory consumption for data and model parallel VGG over CIFAR 10.

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A Deep Generative Model for Molecule Optimization via One Fragment Modification

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Molecule optimization is a critical step in drug development to improve the desired properties of drug candidates through chemical modification. We have developed a novel deep generative model, Modof, over molecular graphs for molecule optimization. Modof modifies a given molecule through the prediction of a single site of disconnection at the molecule and the removal and/or addition of fragments at that site. A pipeline of multiple, identical Modof models is implemented into Modof-pipe to modify an input molecule at multiple disconnection sites. Here we show that Modof-pipe is able to retain major molecular scaffolds, allow controls over intermediate optimization steps and better constrain molecule similarities. Modof-pipe outperforms the state-of-the-art methods on benchmark datasets. Without molecular similarity constraints, Modof-pipe achieves 81.2% improvement in the octanol–water partition coefficient, penalized by synthetic accessibility and ring size, and 51.2%, 25.6% and 9.2% improvement if the optimized molecules are at least 0.2, 0.4 and 0.6 similar to those before optimization, respectively. Modof-pipe is further enhanced into Modof-pipem to allow modification of one molecule to multiple optimized ones. Modof-pipem achieves additional performance improvement, at least 17.8% better than Modof-pipe.

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Retrieval, Analogy, and Composition: A framework for Compositional Generalization in Image Captioning

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Image captioning systems are expected to have the ability to combine individual concepts when describing scenes with concept combinations that are not observed during training. In spite of significant progress in image captioning with the help of the autoregressive generation framework, current approaches fail to generalize well to novel concept combinations. We propose a new framework that revolves around probing several similar image caption training instances (retrieval), performing analogical reasoning over relevant entities in retrieved prototypes (analogy), and enhancing the generation process with reasoning outcomes (composition). Our method augments the generation model by referring to the neighboring instances in the training set to produce novel concept combinations in generated captions. We perform experiments on the widely used image captioning benchmarks. The proposed models achieve substantial improvement over the compared baselines on both composition-related evaluation metrics and conventional image captioning metrics.

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Team Papelo at FEVEROUS: Multi-hop Evidence Pursuit

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We develop a system for the FEVEROUS fact extraction and verification task that ranks an initial set of potential evidence and then pursues missing evidence in subsequent hops by trying to generate it, with a “next hop prediction module” whose output is matched against page elements in a predicted article. Seeking evidence with the next hop prediction module continues to improve FEVEROUS score for up to seven hops. Label classification is trained on possibly incomplete extracted evidence chains, utilizing hints that facilitate numerical comparison. The system achieves .281 FEVEROUS score and .658 label accuracy on the development set, and finishes in second place with .259 FEVEROUS score and .576 label accuracy on the test set.

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Prediction of Non-Muscle Invasive Bladder Cancer Recurrence using Machine Learning of Quantitative Nuclear Features

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Non-muscle invasive bladder cancer (NMIBC) generally has a good prognosis, however, recurrence after transurethral resection (TUR), the standard primary treatment, is a major problem. Clinical management after TUR has been based on risk classification using clinicopathological factors, but these classifications are not complete. In this study, we attempted to predict early recurrence of NMIBC based on machine learning of quantitative morphological features. In general, structural, cellular, and nuclear atypia are evaluated to determine cancer atypia. However, since it is difficult to accurately quantify structural atypia from TUR specimens, in this study, we used only nuclear atypia and analyzed it using feature extraction followed by classification using Support Vector Machine and Random Forest machine learning algorithms. For the analysis, 125 patients diagnosed with NMIBC were used, data from 95 patients were randomly selected for the training set, and data from 30 patients were randomly selected for the test set. The results showed that the support vector machine-based model predicted recurrence within 2 years after TUR with a probability of 90% and the random forest-based model with probability of 86.7%. In the future, the system can be used to objectively predict NMIBC recurrence after TUR.

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Dual Projection Generative Adversarial Networks for Conditional Image Generation

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Conditional Generative Adversarial Networks (cGANs) extend the standard unconditional GAN framework to learning joint data-label distributions from samples, and have been established as powerful generative models capable of generating high-fidelity imagery. A challenge of training such a model lies in properly infusing class information into its generator and discriminator. For the discriminator, class conditioning can be achieved by either (1) directly incorporating labels as input or (2) involving labels in an auxiliary classification loss. In this paper, we show that the former directly aligns the class-conditioned fake-and-real data distributions P (image|class) (data matching), while the latter aligns data-conditioned class distributions P (class|image) (label matching). Although class separability does not directly translate to sample quality and becomes a burden if classification itself is intrinsically difficult, the discriminator cannot provide useful guidance for the generator if features of distinct classes are mapped to the same point and thus become inseparable. Motivated by this intuition, we propose a Dual Projection GAN (P2GAN) model that learns to balance between data matching and label matching. We then propose an improved cGAN model with Auxiliary Classification that directly aligns the fake and real conditionals P (class|image) by minimizing their f-divergence. Experiments on a synthetic Mixture of Gaussian (MoG) dataset and a variety of real-world datasets including CIFAR100, ImageNet, and VGGFace2 demonstrate the efficacy of our proposed models.

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Learning Higher-order Object Interactions for Keypoint-based Video Understanding

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Action recognition is an important problem that requires identifying actions in video by learning complex interactions across scene actors and objects. However, modern deep-learning based networks often require significant computation and may capture scene context using various modalities that further increases compute costs. Efficient methods such as those used for AR/VR often only use human-keypoint information but suffer from a loss of scene context that hurts accuracy. In this paper, we describe an action-localization method, KeyNet, that uses only the keypoint data for tracking and action recognition. Specifically, KeyNet introduces the use of object based keypoint information to capture context in the scene. Our method illustrates how to build a structured intermediate representation that allows modeling higher-order interactions in the scene from object and human keypoints without using any RGB information. We find that KeyNet is able to track and classify human actions at just 5 FPS. More importantly, we demonstrate that object keypoints can be modeled to recover any loss in context from using keypoint information over AVA action and Kinetics datasets.

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Towards Robustness of Deep Neural Networks via Networks via Regularization

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Recent studies have demonstrated the vulnerability of deep neural networks against adversarial examples. In-spired by the observation that adversarial examples often lie outside the natural image data manifold and the intrinsic dimension of image data is much smaller than its pixel space dimension, we propose to embed high-dimensional input images into a low-dimensional space and apply regularization on the embedding space to push the adversarial examples back to the manifold. The proposed framework is called Embedding Regularized Classifier (ER-Classifier), which improves the adversarial robustness of the classifier through embedding regularization. Besides improving classification accuracy against adversarial examples, the framework can be combined with detection methods to detect adversarial examples. Experimental results on several benchmark datasets show that, our proposed framework achieves good performance against strong adversarial at-tack methods.

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Overcoming Poor Word Embeddings with Word Definitions

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Modern natural language understanding models depend on pretrained subword embeddings, but applications may need to reason about words that were never or rarely seen during pretraining. We show that examples that depend critically on a rarer word are more challenging for natural language inference models. Then we explore how a model could learn to use definitions, provided in natural text, to overcome this handicap. Our model’s understanding of a definition is usually weaker than a well-modeled word embedding, but it recovers most of the performance gap from using a completely untrained word.

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DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays

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MotivationMapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods with limited training data. Moreover, past approaches have implemented enhancer discovery as a binary classification problem without accurate boundary detection, producing low-resolution annotations with superfluous regions and reducing the statistical power for downstream analyses (e.g. causal variant mapping and functional validations). Here, we addressed these challenges via a two-step model called Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays (DECODE). First, we employed direct enhancer-activity readouts from novel functional characterization assays, such as STARR-seq, to train a deep neural network for accurate cell-type-specific enhancer prediction. Second, to improve the annotation resolution, we implemented a weakly supervised object detection framework for enhancer localization with precise boundary detection (to a 10 bp resolution) using Gradient-weighted Class Activation Mapping.ResultsOur DECODE binary classifier outperformed a state-of-the-art enhancer prediction method by 24% in transgenic mouse validation. Furthermore, the object detection framework can condense enhancer annotations to only 13% of their original size, and these compact annotations have significantly higher conservation scores and genome-wide association study variant enrichments than the original predictions. Overall, DECODE is an effective tool for enhancer classification and precise localization.

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