In practice, there are often explicit constraints on what representations or decisions are acceptable in an application of machine learning. For example it may be a legal requirement that a decision must not favour a particular group. Alternatively it can be that that representation of data must not have identifying information. We address these two related issues by learning flexible representations that minimize the capability of an adversarial critic. This adversary is trying to predict the relevant sensitive variable from the representation, and so minimizing the performance of the adversary ensures there is little or no information in the representation about the sensitive variable. We demonstrate this adversarial approach on two problems: making decisions free from discrimination and removing private information from images. We formulate the adversarial model as a minimax problem, and optimize that minimax objective using a stochastic gradient alternate min-max optimizer. We demonstrate the ability to provide discriminant free representations for standard test problems, and compare with previous state of the art methods for fairness, showing statistically significant improvement across most cases. The flexibility of this method is shown via a novel problem: removing annotations from images, from unaligned training examples of annotated and unannotated images, and with no a priori knowledge of the form of annotation provided to the model.

The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their literatures and data are consequently fragmented, distributed and sometimes--at least apparently--inconsistent. This makes it extremely difficult to build significant explanatory models with the result that effects in these systems that are brought about by many interacting factors are poorly understood. The rule-based approach to modelling has shown some promise for the representation of the highly combinatorial systems typically found in signalling where many of the proteins are composed of multiple binding domains, capable of simultaneous interactions, and/or peptide motifs controlled by post-translational modifications. However, the rule-based approach requires highly detailed information about the precise conditions for each and every interaction which is rarely available from any one single source. Rather, these conditions must be painstakingly inferred and curated, by hand, from information contained in many papers--each of which contains only part of the story. In this paper, we introduce a graph-based meta-model, attuned to the representation of cellular signalling networks, which aims to ease this massive cognitive burden on the rule-based curation process. This meta-model is a generalization of that used by Kappa and BNGL which allows for the flexible representation of knowledge at various levels of granularity. In particular, it allows us to deal with information which has either too little, or too much, detail with respect to the strict rule-based meta-model. Our approach provides a basis for the gradual aggregation of fragmented biological knowledge extracted from the literature into an instance of the meta-model from which we can define an automated translation into executable Kappa programs.

We introduce overdispersed black-box variational inference, a method to reduce the variance of the Monte Carlo estimator of the gradient in black-box variational inference. Instead of taking samples from the variational distribution, we use importance sampling to take samples from an overdispersed distribution in the same exponential family as the variational approximation. Our approach is general since it can be readily applied to any exponential family distribution, which is the typical choice for the variational approximation. We run experiments on two non-conjugate probabilistic models to show that our method effectively reduces the variance, and the overhead introduced by the computation of the proposal parameters and the importance weights is negligible. We find that our overdispersed importance sampling scheme provides lower variance than black-box variational inference, even when the latter uses twice the number of samples.

Tackling pattern recognition problems in areas such as computer vision, bioinformatics, speech or text recognition is often done best by taking into account task-specific statistical relations between output variables. In structured prediction, this internal structure is used to predict multiple outputs simultaneously, leading to more accurate and coherent predictions. Structural support vector machines (SSVMs) are nonprobabilistic models that optimize a joint input-output function through margin-based learning. Because SSVMs generally disregard the interplay between unary and interaction factors during the training phase, final parameters are suboptimal. Moreover, its factors are often restricted to linear combinations of input features, limiting its generalization power. To improve prediction accuracy, this paper proposes: (i) Joint inference and learning by integration of back-propagation and loss-augmented inference in SSVM subgradient descent; (ii) Extending SSVM factors to neural networks that form highly nonlinear functions of input features. Image segmentation benchmark results demonstrate improvements over conventional SSVM training methods in terms of accuracy, highlighting the feasibility of end-to-end SSVM training with neural factors.

Finding efficient and provable methods to solve non-convex optimization problems is an outstanding challenge in machine learning and optimization theory. A popular approach used to tackle non-convex problems is to use convex relaxation techniques to find a convex surrogate for the problem. Unfortunately, convex relaxations typically must be found on a problem-by-problem basis. Thus, providing a general-purpose strategy to estimate a convex relaxation would have a wide reaching impact. Here, we introduce Convex Relaxation Regression (CoRR), an approach for learning convex relaxations for a class of smooth functions. The main idea behind our approach is to estimate the convex envelope of a function $f$ by evaluating $f$ at a set of $T$ random points and then fitting a convex function to these function evaluations. We prove that with probability greater than $1-\delta$, the solution of our algorithm converges to the global optimizer of $f$ with error $\mathcal{O} \Big( \big(\frac{\log(1/\delta) }{T} \big)^{\alpha} \Big)$ for some $\alpha> 0$. Our approach enables the use of convex optimization tools to solve a class of non-convex optimization problems.

The emergence of collective dynamics in neural networks is a mechanism of the animal and human brain for information processing. In this paper, we develop a computational technique of distributed processing elements, which are called particles. We observe the collective dynamics of particles in a complex network for transductive inference on semi-supervised learning problems. Three actions govern the particles' dynamics: walking, absorption, and generation. Labeled vertices generate new particles that compete against rival particles for edge domination. Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles. The result from the model simulation consists of sets of edges sorted by the label dominance. Each set tends to form a connected subnetwork to represent a data class. Although the intrinsic dynamics of the model is a stochastic one, we prove there exists a deterministic version with largely reduced computational complexity; specifically, with subquadratic growth. Furthermore, the edge domination process corresponds to an unfolding map. Intuitively, edges "stretch" and "shrink" according to edge dynamics. Consequently, such effect summarizes the relevant relationships between vertices and uncovered data classes. The proposed model captures important details of connectivity patterns over the edge dynamics evolution, which contrasts with previous approaches focused on vertex dynamics. Computer simulations reveal that our model can identify nonlinear features in both real and artificial data, including boundaries between distinct classes and the overlapping structure of data.

We prove, using the subspace embedding guarantee in a black box way, that one can achieve the spectral norm guarantee for approximate matrix multiplication with a dimensionality-reducing map having $m = O(\tilde{r}/\varepsilon^2)$ rows. Here $\tilde{r}$ is the maximum stable rank, i.e. squared ratio of Frobenius and operator norms, of the two matrices being multiplied. This is a quantitative improvement over previous work of [MZ11, KVZ14], and is also optimal for any oblivious dimensionality-reducing map. Furthermore, due to the black box reliance on the subspace embedding property in our proofs, our theorem can be applied to a much more general class of sketching matrices than what was known before, in addition to achieving better bounds. For example, one can apply our theorem to efficient subspace embeddings such as the Subsampled Randomized Hadamard Transform or sparse subspace embeddings, or even with subspace embedding constructions that may be developed in the future. Our main theorem, via connections with spectral error matrix multiplication shown in prior work, implies quantitative improvements for approximate least squares regression and low rank approximation. Our main result has also already been applied to improve dimensionality reduction guarantees for $k$-means clustering [CEMMP14], and implies new results for nonparametric regression [YPW15]. We also separately point out that the proof of the "BSS" deterministic row-sampling result of [BSS12] can be modified to show that for any matrices $A, B$ of stable rank at most $\tilde{r}$, one can achieve the spectral norm guarantee for approximate matrix multiplication of $A^T B$ by deterministically sampling $O(\tilde{r}/\varepsilon^2)$ rows that can be found in polynomial time. The original result of [BSS12] was for rank instead of stable rank. Our observation leads to a stronger version of a main theorem of [KMST10].

Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist only provides a probabilistic model and a dataset, nothing else. ADVI automatically derives an efficient variational inference algorithm, freeing the scientist to refine and explore many models. ADVI supports a broad class of models-no conjugacy assumptions are required. We study ADVI across ten different models and apply it to a dataset with millions of observations. ADVI is integrated into Stan, a probabilistic programming system; it is available for immediate use.

Estimating the number of unseen species is an important problem in many scientific endeavors. Its most popular formulation, introduced by Fisher, uses $n$ samples to predict the number $U$ of hitherto unseen species that would be observed if $t\cdot n$ new samples were collected. Of considerable interest is the largest ratio $t$ between the number of new and existing samples for which $U$ can be accurately predicted. In seminal works, Good and Toulmin constructed an intriguing estimator that predicts $U$ for all $t\le 1$, thereby showing that the number of species can be estimated for a population twice as large as that observed. Subsequently Efron and Thisted obtained a modified estimator that empirically predicts $U$ even for some $t>1$, but without provable guarantees. We derive a class of estimators that $\textit{provably}$ predict $U$ not just for constant $t>1$, but all the way up to $t$ proportional to $\log n$. This shows that the number of species can be estimated for a population $\log n$ times larger than that observed, a factor that grows arbitrarily large as $n$ increases. We also show that this range is the best possible and that the estimators' mean-square error is optimal up to constants for any $t$. Our approach yields the first provable guarantee for the Efron-Thisted estimator and, in addition, a variant which achieves stronger theoretical and experimental performance than existing methodologies on a variety of synthetic and real datasets. The estimators we derive are simple linear estimators that are computable in time proportional to $n$. The performance guarantees hold uniformly for all distributions, and apply to all four standard sampling models commonly used across various scientific disciplines: multinomial, Poisson, hypergeometric, and Bernoulli product.

Developing efficient and scalable algorithms for Latent Dirichlet Allocation (LDA) is of wide interest for many applications. Previous work has developed an O(1) Metropolis-Hastings sampling method for each token. However, the performance is far from being optimal due to random accesses to the parameter matrices and frequent cache misses. In this paper, we first carefully analyze the memory access efficiency of existing algorithms for LDA by the scope of random access, which is the size of the memory region in which random accesses fall, within a short period of time. We then develop WarpLDA, an LDA sampler which achieves both the best O(1) time complexity per token and the best O(K) scope of random access. Our empirical results in a wide range of testing conditions demonstrate that WarpLDA is consistently 5-15x faster than the state-of-the-art Metropolis-Hastings based LightLDA, and is comparable or faster than the sparsity aware F+LDA. With WarpLDA, users can learn up to one million topics from hundreds of millions of documents in a few hours, at an unprecedentedly throughput of 11G tokens per second.