The answers to many unsolved problems lie in the intractable chemical space of molecules and materials. Machine learning techniques are rapidly growing in popularity as a way to compress and explore chemical space efficiently. One of the most important aspects of machine learning techniques is representation through the feature vector, which should contain the most important descriptors necessary to make accurate predictions, not least of which is the atomic species in the molecule or material. In this work we introduce a compressed representation of physical properties for atomic species we call the elemental modes. The elemental modes provide an excellent representation by capturing many of the nuances of the periodic table and the similarity of atomic species. We apply the elemental modes to several different tasks for machine learning algorithms and show that they enable us to make improvements to these tasks even beyond simply achieving higher accuracy predictions.

DBSCAN is a classical density-based clustering procedure which has had tremendous practical relevance. However, it implicitly needs to compute the empirical density for each sample point, leading to a quadratic worst-case time complexity, which may be too slow on large datasets. We propose DBSCAN++, a simple modification of DBSCAN which only requires computing the densities for a subset of the points. We show empirically that, compared to traditional DBSCAN, DBSCAN++ can provide not only competitive performance but also added robustness in the bandwidth hyperparameter while taking a fraction of the runtime. We also present statistical consistency guarantees showing the trade-off between computational cost and estimation rates. Surprisingly, up to a certain point, we can enjoy the same estimation rates while lowering computational cost, showing that DBSCAN++ is a sub-quadratic algorithm that attains minimax optimal rates for level-set estimation, a quality that may be of independent interest.

Exploiting low-rank structure of the user-item rating matrix has been the crux of many recommendation engines. However, existing recommendation engines force raters with heterogeneous behavior profiles to map their intrinsic rating scales to a common rating scale (e.g. 1-5). This non-linear transformation of the rating scale shatters the low-rank structure of the rating matrix, therefore resulting in a poor fit and consequentially, poor recommendations. In this paper, we propose Clustered Monotone Transforms for Rating Factorization (CMTRF), a novel approach to perform regression up to unknown monotonic transforms over unknown population segments. Essentially, for recommendation systems, the technique searches for monotonic transformations of the rating scales resulting in a better fit. This is combined with an underlying matrix factorization regression model that couples the user-wise ratings to exploit shared low dimensional structure. The rating scale transformations can be generated for each user, for a cluster of users, or for all the users at once, forming the basis of three simple and efficient algorithms proposed in this paper, all of which alternate between transformation of the rating scales and matrix factorization regression. Despite the non-convexity, CMTRF is theoretically shown to recover a unique solution under mild conditions. Experimental results on two synthetic and seven real-world datasets show that CMTRF outperforms other state-of-the-art baselines.

Generative Adversarial Networks have surprising ability for generating sharp and realistic images, though they are known to suffer from the so-called mode collapse problem. In this paper, we propose a new GAN variant called Mixture Density GAN that while being capable of generating high-quality images, overcomes this problem by encouraging the Discriminator to form clusters in its embedding space, which in turn leads the Generator to exploit these and discover different modes in the data. This is achieved by positioning Gaussian density functions in the corners of a simplex, using the resulting Gaussian mixture as a likelihood function over discriminator embeddings, and formulating an objective function for GAN training that is based on these likelihoods. We show that the optimum of our training objective is attained if and only if the generated and the real distribution match exactly. We further support our theoretical results with empirical evaluations on one synthetic and several real image datasets (CIFAR-10, CelebA, MNIST, and FashionMNIST). We demonstrate empirically (1) the quality of the generated images in Mixture Density GAN and their strong similarity to real images, as measured by the Fr\'echet Inception Distance (FID), which compares very favourably with state-of-the-art methods, and (2) the ability to avoid mode collapse and discover all data modes.

In this paper, we investigate Dimensionality reduction (DR) maps in an information retrieval setting from a quantitative topology point of view. In particular, we show that no DR maps can achieve perfect precision and perfect recall simultaneously. Thus a continuous DR map must have imperfect precision. We further prove an upper bound on the precision of Lipschitz continuous DR maps. While precision is a natural measure in an information retrieval setting, it does not measure `how' wrong the retrieved data is. We therefore propose a new measure based on Wasserstein distance that comes with similar theoretical guarantee. A key technical step in our proofs is a particular optimization problem of the $L_2$-Wasserstein distance over a constrained set of distributions. We provide a complete solution to this optimization problem, which can be of independent interest on the technical side.

We investigate whether the standard dimensionality reduction technique of PCA inadvertently produces data representations with different fidelity for two different populations. We show on several real-world data sets, PCA has higher reconstruction error on population A than on B (for example, women versus men or lower- versus higher-educated individuals). This can happen even when the data set has a similar number of samples from A and B. This motivates our study of dimensionality reduction techniques which maintain similar fidelity for A and B. We define the notion of Fair PCA and give a polynomial-time algorithm for finding a low dimensional representation of the data which is nearly-optimal with respect to this measure. Finally, we show on real-world data sets that our algorithm can be used to efficiently generate a fair low dimensional representation of the data.

The expectation-maximization (EM) algorithm is almost ubiquitous for parameter estimation in model-based clustering problems; however, it can become stuck at local maxima, due to its single path, monotonic nature. Rather than using an EM algorithm, an evolutionary algorithm (EA) is developed. This EA facilitates a different search of the fitness landscape, i.e., the likelihood surface, utilizing both crossover and mutation. Furthermore, this EA represents an efficient approach to "hard" model-based clustering and so it can be viewed as a sort of generalization of the k-means algorithm, which is itself equivalent to a classification EM algorithm for a Gaussian mixture model with spherical component covariances. The EA is illustrated on several data sets, and its performance is compared to k-means clustering as well as model-based clustering with an EM algorithm.

While deep representation learning has become increasingly capable of separating task-relevant representations from other confounding factors in the data, two significant challenges remain. First, there is often an unknown and potentially infinite number of confounding factors coinciding in the data. Second, not all of these factors are readily observable. In this paper, we present a deep conditional generative model that learns to disentangle a task-relevant representation from an unknown number of confounding factors that may grow infinitely. This is achieved by marrying the representational power of deep generative models with Bayesian non-parametric factor models, where a supervised deterministic encoder learns task-related representation and a probabilistic encoder with an Indian Buffet Process (IBP) learns the unknown number of unobservable confounding factors. We tested the presented model in two datasets: a handwritten digit dataset (MNIST) augmented with colored digits and a clinical ECG dataset with significant inter-subject variations and augmented with signal artifacts. These diverse data sets highlighted the ability of the presented model to grow with the complexity of the data and identify the absence or presence of unobserved confounding factors.

Unsupervised dimension selection is an important problem that seeks to reduce dimensionality of data, while preserving the most useful characteristics. While dimensionality reduction is commonly utilized to construct low-dimensional embeddings, they produce feature spaces that are hard to interpret. Further, in applications such as sensor design, one needs to perform reduction directly in the input domain, instead of constructing transformed spaces. Consequently, dimension selection (DS) aims to solve the combinatorial problem of identifying the top-$k$ dimensions, which is required for effective experiment design, reducing data while keeping it interpretable, and designing better sensing mechanisms. In this paper, we develop a novel approach for DS based on graph signal analysis to measure feature influence. By analyzing synthetic graph signals with a blue noise spectrum, we show that we can measure the importance of each dimension. Using experiments in supervised learning and image masking, we demonstrate the superiority of the proposed approach over existing techniques in capturing crucial characteristics of high dimensional spaces, using only a small subset of the original features.

This study presents a multimodal machine learning model to predict ICD-10 diagnostic codes. We developed separate machine learning models that can handle data from different modalities, including unstructured text, semi-structured text and structured tabular data. We further employed an ensemble method to integrate all modality-specific models to generate ICD-10 codes. Key evidence was also extracted to make our prediction more convincing and explainable. We used the Medical Information Mart for Intensive Care III (MIMIC -III) dataset to validate our approach. For ICD code prediction, our best-performing model (micro-F1 = 0.7633, micro-AUC = 0.9541) significantly outperforms other baseline models including TF-IDF (micro-F1 = 0.6721, micro-AUC = 0.7879) and Text-CNN model (micro-F1 = 0.6569, micro-AUC = 0.9235). For interpretability, our approach achieves a Jaccard Similarity Coefficient (JSC) of 0.1806 on text data and 0.3105 on tabular data, where well-trained physicians achieve 0.2780 and 0.5002 respectively.