In hospitals, data are siloed to specific information systems that make the same information available under different modalities such as the different medical imaging exams the patient undergoes (CT scans, MRI, PET, Ultrasound, etc.) and their associated radiology reports. This offers unique opportunities to obtain and use at train-time those multiple views of the same information that might not always be available at test-time. In this paper, we propose an innovative framework that makes the most of available data by learning good representations of a multi-modal input that are resilient to modality dropping at test-time, using recent advances in mutual information maximization. By maximizing cross-modal information at train time, we are able to outperform several state-of-the-art baselines in two different settings, medical image classification, and segmentation. In particular, our method is shown to have a strong impact on the inference-time performance of weaker modalities.

In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, in a reference-free fashion. We report that our model captures information of both DNA sequence similarity as well as DNA sequence abundance in the embedding latent space. We confirm the quality of these vectors by comparing them to known gene sub-structures and report that the latent space recovers exon information from raw RNA-Seq data from acute myeloid leukemia patients. Furthermore we show that this latent space allows the detection of genomic abnormalities such as translocations as well as patient-specific mutations, making this representation space both useful for visualization as well as analysis.

We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep model similar to the spatial bias imposed by convolutions on an image. We explore the usage of Graph Convolutional Neural Networks coupled with dropout and gene embeddings to utilize the graph information. We find this approach provides an advantage for particular tasks in a low data regime but is very dependent on the quality of the graph used. We conclude that more work should be done in this direction. We design experiments that show why existing methods fail to capture signal that is present in the data when features are added which clearly isolates the problem that needs to be addressed.

We investigate the integration of a planning mechanism into sequence-to-sequence models using attention. We develop a model which can plan ahead in the future when it computes its alignments between input and output sequences, constructing a matrix of proposed future alignments and a commitment vector that governs whether to follow or recompute the plan. This mechanism is inspired by the recently proposed strategic attentive reader and writer (STRAW) model for Reinforcement Learning. Our proposed model is end-to-end trainable using primarily differentiable operations. We show that it outperforms a strong baseline on character-level translation tasks from WMT'15, the algorithmic task of finding Eulerian circuits of graphs, and question generation from the text. Our analysis demonstrates that the model computes qualitatively intuitive alignments, converges faster than the baselines, and achieves superior performance with fewer parameters.

We investigate the integration of a planning mechanism into sequence-to-sequence models using attention. We develop a model which can plan ahead in the future when it computes its alignments between input and output sequences, constructing a matrix of proposed future alignments and a commitment vector that governs whether to follow or recompute the plan. This mechanism is inspired by the recently proposed strategic attentive reader and writer (STRAW) model for Reinforcement Learning. Our proposed model is end-to-end trainable using primarily differentiable operations. We show that it outperforms a strong baseline on character-level translation tasks from WMT'15, the algorithmic task of finding Eulerian circuits of graphs, and question generation from the text. Our analysis demonstrates that the model computes qualitatively intuitive alignments, converges faster than the baselines, and achieves superior performance with fewer parameters.

Generative Adversarial Networks (GANs) have gathered a lot of attention from the computer vision community, yielding impressive results for image generation. Advances in the adversarial generation of natural language from noise however are not commensurate with the progress made in generating images, and still lag far behind likelihood based methods. In this paper, we take a step towards generating natural language with a GAN objective alone. We introduce a simple baseline that addresses the discrete output space problem without relying on gradient estimators and show that it is able to achieve state-of-the-art results on a Chinese poem generation dataset. We present quantitative results on generating sentences from context-free and probabilistic context-free grammars, and qualitative language modeling results. A conditional version is also described that can generate sequences conditioned on sentence characteristics.