Three-Dimensionally Embedded Graph Convolutional Network (3DGCN) for Molecule Interpretation

We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the vector to handle the spatial information from molecular topology. The 3DGCN model exhibits significantly higher performance on various tasks compared with other deep-learning models, and has the ability of generalizing a given conformer to targeted features regardless of its rotations in the 3D space. More significantly, our model also can distinguish the 3D rotations of a molecule and predict the target value, depending upon the rotation degree, in the protein-ligand docking problem, when trained with orientation-dependent datasets. The rotation distinguishability of 3DGCN, along with rotation equivariance, provides a key milestone in the implementation of three-dimensionality to the field of deep-learning chemistry that solves challenging biochemical problems.Comment: 39 pages, 14 figures, 5 table

LoANs: Weakly Supervised Object Detection with Localizer Assessor Networks

Recently, deep neural networks have achieved remarkable performance on the task of object detection and recognition. The reason for this success is mainly grounded in the availability of large scale, fully annotated datasets, but the creation of such a dataset is a complicated and costly task. In this paper, we propose a novel method for weakly supervised object detection that simplifies the process of gathering data for training an object detector. We train an ensemble of two models that work together in a student-teacher fashion. Our student (localizer) is a model that learns to localize an object, the teacher (assessor) assesses the quality of the localization and provides feedback to the student. The student uses this feedback to learn how to localize objects and is thus entirely supervised by the teacher, as we are using no labels for training the localizer. In our experiments, we show that our model is very robust to noise and reaches competitive performance compared to a state-of-the-art fully supervised approach. We also show the simplicity of creating a new dataset, based on a few videos (e.g. downloaded from YouTube) and artificially generated data.Comment: To appear in AMV18. Code, datasets and models available at https://github.com/Bartzi/loan

HYDRA: Hybrid Deep Magnetic Resonance Fingerprinting

Purpose: Magnetic resonance fingerprinting (MRF) methods typically rely on dictio-nary matching to map the temporal MRF signals to quantitative tissue parameters. Such approaches suffer from inherent discretization errors, as well as high computational complexity as the dictionary size grows. To alleviate these issues, we propose a HYbrid Deep magnetic ResonAnce fingerprinting approach, referred to as HYDRA. Methods: HYDRA involves two stages: a model-based signature restoration phase and a learning-based parameter restoration phase. Signal restoration is implemented using low-rank based de-aliasing techniques while parameter restoration is performed using a deep nonlocal residual convolutional neural network. The designed network is trained on synthesized MRF data simulated with the Bloch equations and fast imaging with steady state precession (FISP) sequences. In test mode, it takes a temporal MRF signal as input and produces the corresponding tissue parameters. Results: We validated our approach on both synthetic data and anatomical data generated from a healthy subject. The results demonstrate that, in contrast to conventional dictionary-matching based MRF techniques, our approach significantly improves inference speed by eliminating the time-consuming dictionary matching operation, and alleviates discretization errors by outputting continuous-valued parameters. We further avoid the need to store a large dictionary, thus reducing memory requirements. Conclusions: Our approach demonstrates advantages in terms of inference speed, accuracy and storage requirements over competing MRF method

Class reconstruction driven adversarial domain adaptation for hyperspectral image classification

We address the problem of cross-domain classification of hyperspectral image (HSI) pairs under the notion of unsupervised domain adaptation (UDA). The UDA problem aims at classifying the test samples of a target domain by exploiting the labeled training samples from a related but different source domain. In this respect, the use of adversarial training driven domain classifiers is popular which seeks to learn a shared feature space for both the domains. However, such a formalism apparently fails to ensure the (i) discriminativeness, and (ii) non-redundancy of the learned space. In general, the feature space learned by domain classifier does not convey any meaningful insight regarding the data. On the other hand, we are interested in constraining the space which is deemed to be simultaneously discriminative and reconstructive at the class-scale. In particular, the reconstructive constraint enables the learning of category-specific meaningful feature abstractions and UDA in such a latent space is expected to better associate the domains. On the other hand, we consider an orthogonality constraint to ensure non-redundancy of the learned space. Experimental results obtained on benchmark HSI datasets (Botswana and Pavia) confirm the efficacy of the proposal approach

Scanner Invariant Representations for Diffusion MRI Harmonization

Purpose: In the present work we describe the correction of diffusion-weighted MRI for site and scanner biases using a novel method based on invariant representation. Theory and Methods: Pooled imaging data from multiple sources are subject to variation between the sources. Correcting for these biases has become very important as imaging studies increase in size and multi-site cases become more common. We propose learning an intermediate representation invariant to site/protocol variables, a technique adapted from information theory-based algorithmic fairness; by leveraging the data processing inequality, such a representation can then be used to create an image reconstruction that is uninformative of its original source, yet still faithful to underlying structures. To implement this, we use a deep learning method based on variational auto-encoders (VAE) to construct scanner invariant encodings of the imaging data. Results: To evaluate our method, we use training data from the 2018 MICCAI Computational Diffusion MRI (CDMRI) Challenge Harmonization dataset. Our proposed method shows improvements on independent test data relative to a recently published baseline method on each subtask, mapping data from three different scanning contexts to and from one separate target scanning context. Conclusion: As imaging studies continue to grow, the use of pooled multi-site imaging will similarly increase. Invariant representation presents a strong candidate for the harmonization of these data

Variational Deep Semantic Hashing for Text Documents

As the amount of textual data has been rapidly increasing over the past decade, efficient similarity search methods have become a crucial component of large-scale information retrieval systems. A popular strategy is to represent original data samples by compact binary codes through hashing. A spectrum of machine learning methods have been utilized, but they often lack expressiveness and flexibility in modeling to learn effective representations. The recent advances of deep learning in a wide range of applications has demonstrated its capability to learn robust and powerful feature representations for complex data. Especially, deep generative models naturally combine the expressiveness of probabilistic generative models with the high capacity of deep neural networks, which is very suitable for text modeling. However, little work has leveraged the recent progress in deep learning for text hashing. In this paper, we propose a series of novel deep document generative models for text hashing. The first proposed model is unsupervised while the second one is supervised by utilizing document labels/tags for hashing. The third model further considers document-specific factors that affect the generation of words. The probabilistic generative formulation of the proposed models provides a principled framework for model extension, uncertainty estimation, simulation, and interpretability. Based on variational inference and reparameterization, the proposed models can be interpreted as encoder-decoder deep neural networks and thus they are capable of learning complex nonlinear distributed representations of the original documents. We conduct a comprehensive set of experiments on four public testbeds. The experimental results have demonstrated the effectiveness of the proposed supervised learning models for text hashing.Comment: 11 pages, 4 figure

Laboratory support during and after the Ebola virus endgame: Towards a sustained laboratory infrastructure

The Ebola virus epidemic in West Africa is on the brink of entering a second phase in which the (inter)national efforts to slow down virus transmission will be engaged to end the epidemic. The response community must consider the longevity of their current laboratory support, as it is essential that diagnostic capacity in the affected countries be supported beyond the end of the epidemic. The emergency laboratory response should be used to support building structural diagnostic and outbreak surveillance capacity

Iterative Segmentation from Limited Training Data: Applications to Congenital Heart Disease

We propose a new iterative segmentation model which can be accurately learned from a small dataset. A common approach is to train a model to directly segment an image, requiring a large collection of manually annotated images to capture the anatomical variability in a cohort. In contrast, we develop a segmentation model that recursively evolves a segmentation in several steps, and implement it as a recurrent neural network. We learn model parameters by optimizing the interme- diate steps of the evolution in addition to the final segmentation. To this end, we train our segmentation propagation model by presenting incom- plete and/or inaccurate input segmentations paired with a recommended next step. Our work aims to alleviate challenges in segmenting heart structures from cardiac MRI for patients with congenital heart disease (CHD), which encompasses a range of morphological deformations and topological changes. We demonstrate the advantages of this approach on a dataset of 20 images from CHD patients, learning a model that accurately segments individual heart chambers and great vessels. Com- pared to direct segmentation, the iterative method yields more accurate segmentation for patients with the most severe CHD malformations.Comment: Presented at the Deep Learning in Medical Image Analysis Workshop, MICCAI 201

HeMIS: Hetero-Modal Image Segmentation

We introduce a deep learning image segmentation framework that is extremely robust to missing imaging modalities. Instead of attempting to impute or synthesize missing data, the proposed approach learns, for each modality, an embedding of the input image into a single latent vector space for which arithmetic operations (such as taking the mean) are well defined. Points in that space, which are averaged over modalities available at inference time, can then be further processed to yield the desired segmentation. As such, any combinatorial subset of available modalities can be provided as input, without having to learn a combinatorial number of imputation models. Evaluated on two neurological MRI datasets (brain tumors and MS lesions), the approach yields state-of-the-art segmentation results when provided with all modalities; moreover, its performance degrades remarkably gracefully when modalities are removed, significantly more so than alternative mean-filling or other synthesis approaches.Comment: Accepted as an oral presentation at MICCAI 201

Dynamic clustering of time series with Echo State Networks

In this paper we introduce a novel methodology for unsupervised analysis of time series, based upon the iterative implementation of a clustering algorithm embedded into the evolution of a recurrent Echo State Network. The main features of the temporal data are captured by the dynamical evolution of the network states, which are then subject to a clustering procedure. We apply the proposed algorithm to time series coming from records of eye movements, called saccades, which are recorded for diagnosis of a neurodegenerative form of ataxia. This is a hard classification problem, since saccades from patients at an early stage of the disease are practically indistinguishable from those coming from healthy subjects. The unsupervised clustering algorithm implanted within the recurrent network produces more compact clusters, compared to conventional clustering of static data, and provides a source of information that could aid diagnosis and assessment of the disease.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec