Deep learning has the potential to revolutionize quantum chemistry as it is ideally suited to learn representations for structured data and speed up the exploration of chemical space. While convolutional neural networks have proven to be the first choice for images, audio and video data, the atoms in molecules are not restricted to a grid. Instead, their precise locations contain essential physical information, that would get lost if discretized. Thus, we propose to use continuous-filter convolutional layers to be able to model local correlations without requiring the data to lie on a grid. We apply those layers in SchNet: a novel deep learning architecture modeling quantum interactions in molecules. We obtain a joint model for the total energy and interatomic forces that follows fundamental quantum-chemical principles. Our architecture achieves state-of-the-art performance for benchmarks of equilibrium molecules and molecular dynamics trajectories. Finally, we introduce a more challenging benchmark with chemical and structural variations that suggests the path for further work.

In this paper, we propose doubly convolutional neural networks (DCNNs), which significantly improve the performance of CNNs by further exploring this idea. In stead of allocating a set of convolutional filters that are independently learned, a DCNN maintains groups of filters where filters within each group are translated versions of each other. Practically, a DCNN can be easily implemented by a two-step convolution procedure, which is supported by most modern deep learning libraries. We perform extensive experiments on three image classification benchmarks: CIFAR-10, CIFAR-100 and ImageNet, and show that DCNNs consistently outperform other competing architectures. We have also verified that replacing a convolutional layer with a doubly convolutional layer at any depth of a CNN can improve its performance. Moreover, various design choices of DCNNs are demonstrated, which shows that DCNN can serve the dual purpose of building more accurate models and/or reducing the memory footprint without sacrificing the accuracy.

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.

Effective convolutional neural networks are trained on large sets of labeled data. However, creating large labeled datasets is a very costly and time-consuming task. Semi-supervised learning uses unlabeled data to train a model with higher accuracy when there is a limited set of labeled data available. In this paper, we consider the problem of semi-supervised learning with convolutional neural networks. Techniques such as randomized data augmentation, dropout and random max-pooling provide better generalization and stability for classifiers that are trained using gradient descent. Multiple passes of an individual sample through the network might lead to different predictions due to the non-deterministic behavior of these techniques. We propose an unsupervised loss function that takes advantage of the stochastic nature of these methods and minimizes the difference between the predictions of multiple passes of a training sample through the network. We evaluate the proposed method on several benchmark datasets.

Few ideas have enjoyed as large an impact on deep learning as convolution. For any problem involving pixels or spatial representations, common intuition holds that convolutional neural networks may be appropriate. In this paper we show a striking counterexample to this intuition via the seemingly trivial coordinate transform problem, which simply requires learning a mapping between coordinates in (x,y) Cartesian space and coordinates in one-hot pixel space. Although convolutional networks would seem appropriate for this task, we show that they fail spectacularly. We demonstrate and carefully analyze the failure first on a toy problem, at which point a simple fix becomes obvious.

A widespread folklore for explaining the success of Convolutional Neural Networks (CNNs) is that CNNs use a more compact representation than the Fully-connected Neural Network (FNN) and thus require fewer training samples to accurately estimate their parameters. We initiate the study of rigorously characterizing the sample complexity of estimating CNNs. We show that for an $m$-dimensional convolutional filter with linear activation acting on a $d$-dimensional input, the sample complexity of achieving population prediction error of $\epsilon$ is $\widetilde{O(m/\epsilon^2)$, whereas the sample-complexity for its FNN counterpart is lower bounded by $\Omega(d/\epsilon^2)$ samples. Since, in typical settings $m \ll d$, this result demonstrates the advantage of using a CNN. We further consider the sample complexity of estimating a one-hidden-layer CNN with linear activation where both the $m$-dimensional convolutional filter and the $r$-dimensional output weights are unknown. For this model, we show that the sample complexity is $\widetilde{O}\left((m+r)/\epsilon^2\right)$ when the ratio between the stride size and the filter size is a constant. For both models, we also present lower bounds showing our sample complexities are tight up to logarithmic factors. Our main tools for deriving these results are a localized empirical process analysis and a new lemma characterizing the convolutional structure. We believe that these tools may inspire further developments in understanding CNNs.