The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter learning capabilities of a dynamic Bayesian network (DBN) peptide-scoring algorithm, Didea, by deriving emission distributions for which its conditional log-likelihood scoring function remains concave. We show that this class of emission distributions, called Convex Virtual Emissions (CVEs), naturally generalizes the log-sum-exp function while rendering both maximum likelihood estimation and conditional maximum likelihood estimation concave for a wide range of Bayesian networks. Utilizing CVEs in Didea allows efficient learning of a large number of parameters while ensuring global convergence, in stark contrast to Didea's previous parameter learning framework (which could only learn a single parameter using a costly grid search) and other trainable models (which only ensure convergence to local optima). The newly trained scoring function substantially outperforms the state-of-the-art in both scoring function accuracy and downstream Fisher kernel analysis. Furthermore, we significantly improve Didea's runtime performance through successive optimizations to its message passing schedule and derive explicit connections between Didea's new concave score and related MS/MS scoring functions.

We address the problem of learning accurate 3D shape and camera pose from a collection of unlabeled category-specific images. We train a convolutional network to predict both the shape and the pose from a single image by minimizing the reprojection error: given several views of an object, the projections of the predicted shapes to the predicted camera poses should match the provided views. To deal with pose ambiguity, we introduce an ensemble of pose predictors which we then distill to a single student model. To allow for efficient learning of high-fidelity shapes, we represent the shapes by point clouds and devise a formulation allowing for differentiable projection of these. Our experiments show that the distilled ensemble of pose predictors learns to estimate the pose accurately, while the point cloud representation allows to predict detailed shape models.

We use differential equations based approaches to provide some {\it \textbf{physics}} insights into analyzing the dynamics of popular optimization algorithms in machine learning. In particular, we study gradient descent, proximal gradient descent, coordinate gradient descent, proximal coordinate gradient, and Newton's methods as well as their Nesterov's accelerated variants in a unified framework motivated by a natural connection of optimization algorithms to physical systems. Our analysis is applicable to more general algorithms and optimization problems {\it \textbf{beyond}} convexity and strong convexity, e.g. Polyak-\L ojasiewicz and error bound conditions (possibly nonconvex).

In this paper, we propose a conceptually simple and general framework called MetaGAN for few-shot learning problems. Most state-of-the-art few-shot classification models can be integrated with MetaGAN in a principled and straightforward way. By introducing an adversarial generator conditioned on tasks, we augment vanilla few-shot classification models with the ability to discriminate between real and fake data. We argue that this GAN-based approach can help few-shot classifiers to learn sharper decision boundary, which could generalize better. We show that with our MetaGAN framework, we can extend supervised few-shot learning models to naturally cope with unsupervised data. Different from previous work in semi-supervised few-shot learning, our algorithms can deal with semi-supervision at both sample-level and task-level. We give theoretical justifications of the strength of MetaGAN, and validate the effectiveness of MetaGAN on challenging few-shot image classification benchmarks.

Risk management in dynamic decision problems is a primary concern in many fields, including financial investment, autonomous driving, and healthcare. The mean-variance function is one of the most widely used objective functions in risk management due to its simplicity and interpretability. Existing algorithms for mean-variance optimization are based on multi-time-scale stochastic approximation, whose learning rate schedules are often hard to tune, and have only asymptotic convergence proof. In this paper, we develop a model-free policy search framework for mean-variance optimization with finite-sample error bound analysis (to local optima). Our starting point is a reformulation of the original mean-variance function with its Fenchel dual, from which we propose a stochastic block coordinate ascent policy search algorithm. Both the asymptotic convergence guarantee of the last iteration's solution and the convergence rate of the randomly picked solution are provided, and their applicability is demonstrated on several benchmark domains.

A conjugate Gamma-Poisson model for Dynamic Matrix Factorization incorporated with metadata influence (mGDMF for short) is proposed to effectively and efficiently model massive, sparse and dynamic data in recommendations. Modeling recommendation problems with a massive number of ratings and very sparse or even no ratings on some users/items in a dynamic setting is very demanding and poses critical challenges to well-studied matrix factorization models due to the large-scale, sparse and dynamic nature of the data. Our proposed mGDMF tackles these challenges by introducing three strategies: (1) constructing a stable Gamma-Markov chain model that smoothly drifts over time by combining both static and dynamic latent features of data; (2) incorporating the user/item metadata into the model to tackle sparse ratings; and (3) undertaking stochastic variational inference to efficiently handle massive data.

Exploration is a fundamental challenge in reinforcement learning (RL). Many current exploration methods for deep RL use task-agnostic objectives, such as information gain or bonuses based on state visitation. However, many practical applications of RL involve learning more than a single task, and prior tasks can be used to inform how exploration should be performed in new tasks. In this work, we study how prior tasks can inform an agent about how to explore effectively in new situations. We introduce a novel gradient-based fast adaptation algorithm - model agnostic exploration with structured noise (MAESN) - to learn exploration strategies from prior experience. The prior experience is used both to initialize a policy and to acquire a latent exploration space that can inject structured stochasticity into a policy, producing exploration strategies that are informed by prior knowledge and are more effective than random action-space noise. We show that MAESN is more effective at learning exploration strategies when compared to prior meta-RL methods, RL without learned exploration strategies, and task-agnostic exploration methods. We evaluate our method on a variety of simulated tasks: locomotion with a wheeled robot, locomotion with a quadrupedal walker, and object manipulation.

Convolutional Neural Networks(CNNs) are both computation and memory inten-sive which hindered their deployment in mobile devices. Inspired by the relevantconcept in neural science literature, we propose Synaptic Pruning: a data-drivenmethod to prune connections between input and output feature maps with a newlyproposed class of parameters called Synaptic Strength. Synaptic Strength is de-signed to capture the importance of a connection based on the amount of informa-tion it transports. Experiment results show the effectiveness of our approach. OnCIFAR-10, we prune connections for various CNN models with up to96%, whichresults in significant size reduction and computation saving. Further evaluation onImageNet demonstrates that synaptic pruning is able to discover efficient modelswhich is competitive to state-of-the-art compact CNNs such as MobileNet-V2andNasNet-Mobile. Our contribution is summarized as following: (1) We introduceSynaptic Strength, a new class of parameters for CNNs to indicate the importanceof each connections.

In order for machine learning to garner widespread public adoption, models must be able to provide interpretable and robust explanations for their decisions, as well as learn from human-provided explanations at train time. In this work, we extend the Stanford Natural Language Inference dataset with an additional layer of human-annotated natural language explanations of the entailment relations. We further implement models that incorporate these explanations into their training process and output them at test time. We show how our corpus of explanations, which we call e-SNLI, can be used for various goals, such as obtaining full sentence justifications of a model's decisions, improving universal sentence representations and transferring to out-of-domain NLI datasets.

By converting dense models into sparse ones, pruning appears to be a promising solution to reducing the computation/memory cost. This paper studies classification models, especially DNN-based ones, to demonstrate that there exists intrinsic relationships between their sparsity and adversarial robustness. Our analyses reveal, both theoretically and empirically, that nonlinear DNN-based classifiers behave differently under $l_2$ attacks from some linear ones. We further demonstrate that an appropriately higher model sparsity implies better robustness of nonlinear DNNs, whereas over-sparsified models can be more difficult to resist adversarial examples.