BackgroundThis paper introduces and applies a genome wide predictive study to learn a model that predicts whether a new subject will develop breast cancer or not, based on her SNP profile.ResultsWe first genotyped 696 female subjects (348 breast cancer cases and 348 apparently healthy controls), predominantly of Caucasian origin from Alberta, Canada using Affymetrix Human SNP 6.0 arrays. Then, we applied EIGENSTRAT population stratification correction method to remove 73 subjects not belonging to the Caucasian population. Then, we filtered any SNP that had any missing calls, whose genotype frequency was deviated from Hardy-Weinberg equilibrium, or whose minor allele frequency was less than 5%. Finally, we applied a combination of MeanDiff feature selection method and KNN learning method to this filtered dataset to produce a breast cancer prediction model. LOOCV accuracy of this classifier is 59.55%. Random permutation tests show that this result is significantly better than the baseline accuracy of 51.52%. Sensitivity analysis shows that the classifier is fairly robust to the number of MeanDiff-selected SNPs. External validation on the CGEMS breast cancer dataset, the only other publicly available breast cancer dataset, shows that this combination of MeanDiff and KNN leads to a LOOCV accuracy of 60.25%, which is significantly better than its baseline of 50.06%. We then considered a dozen different combinations of feature selection and learning method, but found that none of these combinations produces a better predictive model than our model. We also considered various biological feature selection methods like selecting SNPs reported in recent genome wide association studies to be associated with breast cancer, selecting SNPs in genes associated with KEGG cancer pathways, or selecting SNPs associated with breast cancer in the F-SNP database to produce predictive models, but again found that none of these models achieved accuracy better than baseline.ConclusionsWe anticipate producing more accurate breast cancer prediction models by recruiting more study subjects, providing more accurate labelling of phenotypes (to accommodate the heterogeneity of breast cancer), measuring other genomic alterations such as point mutations and copy number variations, and incorporating non-genetic information about subjects such as environmental and lifestyle factors.

Next generation task-oriented dialog systems need to understand conversational contexts with their perceived surroundings, to effectively help users in the real-world multimodal environment. Existing task-oriented dialog datasets aimed towards virtual assistance fall short and do not situate the dialog in the user's multimodal context. To overcome, we present a new dataset for Situated and Interactive Multimodal Conversations, SIMMC 2.0, which includes 11K taskoriented user$assistant dialogs (117K utterances) in the shopping domain, grounded in immersive and photo-realistic scenes.The dialogs are collected using a two-phase pipeline: (1) A novel multimodal dialog simulator generates simulated dialog flows, with an emphasis on diversity and richness of interactions, (2) Manual paraphrasing of the generated utterances to collect diverse referring expressions. We provide an in-depth analysis of the collected dataset, and describe in detail the four main benchmark tasks we propose. Our baseline model, powered by the state-of-theart language model, shows promising results, and highlights new challenges and directions for the community to study 1 .

We introduce a unified framework to jointly model images, text, and human attention traces. Our work is built on top of the recent Localized Narratives annotation framework [30], where each word of a given caption is paired with a mouse trace segment. We propose two novel tasks:(1) predict a trace given an image and caption (i.e., visual grounding), and (2) predict a caption and a trace given only an image. Learning the grounding of each word is challenging, due to noise in the human-provided traces and the presence of words that cannot be meaningfully visually grounded. We present a novel model architecture that is jointly trained on dual tasks (controlled trace generation and controlled caption generation). To evaluate the quality of the generated traces, we propose a local bipartite matching (LBM) distance metric which allows the comparison of two traces of different lengths. Extensive experiments show our model is robust to the imperfect training data and outperforms the baselines by a clear margin. Moreover, we demonstrate that our model pre-trained on the proposed tasks can be also beneficial to the downstream task of COCO's guided image captioning. Our code 1 and project page 2 are publicly available.

We present NN-grams, a novel, hybrid language model integrating n-grams and neural networks (NN) for speech recognition. The model takes as input both word histories as well as n-gram counts. Thus, it combines the memorization capacity and scalability of an n-gram model with the generalization ability of neural networks. We report experiments where the model is trained on 26B words. NN-grams are efficient at runtime since they do not include an output soft-max layer. The model is trained using noise contrastive estimation (NCE), an approach that transforms the estimation problem of neural networks into one of binary classification between data samples and noise samples. We present results with noise samples derived from either an n-gram distribution or from speech recognition lattices. NN-grams outperforms an n-gram model on an Italian speech recognition dictation task.