In this paper we address a task of relation mention extraction from noisy data: extracting representative phrases for a particular relation from noisy sentences that are collected via distant supervision. Despite its significance and value in many downstream applications, this task is less studied on noisy data. The major challenges exists in 1) the lack of annotation on mention phrases, and more severely, 2) handling noisy sentences which do not express a relation at all. To address the two challenges, we formulate the task as a semi-Markov decision process and propose a novel hierarchical reinforcement learning model. Our model consists of a top-level sentence selector to remove noisy sentences, a low-level mention extractor to extract relation mentions, and a reward estimator to provide signals to guide data denoising and mention extraction without explicit annotations. Experimental results show that our model is effective to extract relation mentions from noisy data.

In classification, the de facto method for aggregating individual losses is the average loss. When the actual metric of interest is 0-1 loss, it is common to minimize the average surrogate loss for some well-behaved (e.g. convex) surrogate. Recently, several other aggregate losses such as the maximal loss and average top-$k$ loss were proposed as alternative objectives to address shortcomings of the average loss. However, we identify common classification settings, e.g. the data is imbalanced, has too many easy or ambiguous examples, etc., when average, maximal and average top-$k$ all suffer from suboptimal decision boundaries, even on an infinitely large training set. To address this problem, we propose a new classification objective called the close-$k$ aggregate loss, where we adaptively minimize the loss for points close to the decision boundary. We provide theoretical guarantees for the 0-1 accuracy when we optimize close-$k$ aggregate loss. We also conduct systematic experiments across the PMLB and OpenML benchmark datasets. Close-$k$ achieves significant gains in 0-1 test accuracy, improvements of $\geq 2$% and $p<0.05$, in over 25% of the datasets compared to average, maximal and average top-$k$. In contrast, the previous aggregate losses outperformed close-$k$ in less than 2% of the datasets.

We propose an algorithm for clustering high dimensional data. If $P$ features for $N$ objects are represented in an $N\times P$ matrix ${\bf X}$, where $N\ll P$, the method is based on exploiting the cluster-dependent structure of the $N\times N$ matrix ${\bf XX}^T$. Computational burden thus depends primarily on $N$, the number of objects to be clustered, rather than $P$, the number of features that are measured. This makes the method particularly useful in high dimensional settings, where it is substantially faster than a number of other popular clustering algorithms. Aside from an upper bound on the number of potential clusters, the method is independent of tuning parameters. When compared to $16$ other clustering algorithms on $32$ genomic datasets with gold standards, we show that it provides the most accurate cluster configuration more than twice as often than its closest competitors. We illustrate the method on data taken from highly cited genomic studies.

This paper considers manifold optimization problems with nonsmooth and nonconvex objective function. Existing methods for solving this kind of problems can be classified into two classes. Algorithms in the first class rely on information of the subgradients of the objective function, which leads to slow convergence rate. Algorithms in the second class are based on operator-splitting techniques, but they usually lack rigorous convergence guarantees. In this paper, we propose a retraction-based proximal gradient method for solving this class of problems. We prove that the proposed method globally converges to a stationary point. Iteration complexity for obtaining an $\epsilon$-stationary solution is also analyzed. Numerical results on solving sparse PCA and compressed modes problems are reported to demonstrate the advantages of the proposed method.

A tensor network is a diagram that specifies a way to "multiply" a collection of tensors together to produce another tensor (or matrix). Many existing algorithms for tensor problems (such as tensor decomposition and tensor PCA), although they are not presented this way, can be viewed as spectral methods on matrices built from simple tensor networks. In this work we leverage the full power of this abstraction to design new algorithms for certain continuous tensor decomposition problems. An important and challenging family of tensor problems comes from orbit recovery, a class of inference problems involving group actions (inspired by applications such as cryo-electron microscopy). Orbit recovery problems over finite groups can often be solved via standard tensor methods. However, for infinite groups, no general algorithms are known. We give a new spectral algorithm based on tensor networks for one such problem: continuous multi-reference alignment over the infinite group SO(2). Our algorithm extends to the more general heterogeneous case.

We address the classical problem of hierarchical clustering, but in a framework where one does not have access to a representation of the objects or their pairwise similarities. Instead we assume that only a set of comparisons between objects are available in terms of statements of the form "objects $i$ and $j$ are more similar than objects $k$ and $l$". Such a scenario is commonly encountered in crowdsourcing applications. The focus of this work is to develop comparison-based hierarchical clustering algorithms that do not rely on the principles of ordinal embedding. We propose comparison-based variants of average linkage clustering. We provide statistical guarantees for the proposed methods under a planted partition model for hierarchical clustering. We also empirically demonstrate the performance of the proposed methods on several datasets.

Stan is a probabilistic programming language that has been increasingly used for real-world scalable projects. However, to make practical inference possible, the language sacrifices some of its usability by adopting a block syntax, which lacks compositionality and flexible user-defined functions. Moreover, the semantics of the language has been mainly given in terms of intuition about implementation, and has not been formalised. This paper provides a formal treatment of the Stan language, and introduces the probabilistic programming language SlicStan --- a compositional, self-optimising version of Stan. Our main contributions are: (1) the formalisation of a core subset of Stan through an operational density-based semantics; (2) the design and semantics of the Stan-like language SlicStan, which facilities better code reuse and abstraction through its compositional syntax, more flexible functions, and information-flow type system; and (3) a formal, semantic-preserving procedure for translating SlicStan to Stan.

There are various algorithms and methodologies used for automated screening of cervical cancer by segmenting and classifying cervical cancer cells into different categories. This study presents a critical review of different research papers published that integrated AI methods in screening cervical cancer via different approaches analyzed in terms of typical metrics like dataset size, drawbacks, accuracy etc. An attempt has been made to furnish the reader with an insight of Machine Learning algorithms like SVM (Support Vector Machines), GLCM (Gray Level Co-occurrence Matrix), k-NN (k-Nearest Neighbours), MARS (Multivariate Adaptive Regression Splines), CNNs (Convolutional Neural Networks), spatial fuzzy clustering algorithms, PNNs (Probabilistic Neural Networks), Genetic Algorithm, RFT (Random Forest Trees), C5.0, CART (Classification and Regression Trees) and Hierarchical clustering algorithm for feature extraction, cell segmentation and classification. This paper also covers the publicly available datasets related to cervical cancer. It presents a holistic review on the computational methods that have evolved over the period of time, in chronological order in detection of malignant cells.

Identification of high affinity drug-target interactions (DTI) is a major research question in drug discovery. In this study, we propose a novel methodology to predict drug-target binding affinity using only ligand SMILES information. We represent proteins using the word-embeddings of the SMILES representations of their strong binding ligands. Each SMILES is represented in the form of a set of chemical words and a protein is described by the set of chemical words with the highest Term Frequency- Inverse Document Frequency (TF-IDF) value. We then utilize the Support Vector Regression (SVR) algorithm to predict protein - drug binding affinities in the Davis and KIBA Kinase datasets. We also compared the performance of SMILES representation with the recently proposed DeepSMILES representation and found that using DeepSMILES yields better performance in the prediction task. Using only SMILESVec, which is a strictly string based representation of the proteins based on their interacting ligands, we were able to predict drug-target binding affinity as well as or better than the KronRLS or SimBoost models that utilize protein sequence.

A clinician desires to use a risk-stratification method that achieves confident risk-stratification - the risk estimates of the different patients reflect the true risks with a high probability. This allows him/her to use these risks to make accurate predictions about prognosis and decisions about screening, treatments for the current patient. We develop Risk-stratify - a two phase algorithm that is designed to achieve confident risk-stratification. In the first phase, we grow a tree to partition the covariate space. Each node in the tree is split using statistical tests that determine if the risks of the child nodes are different or not. The choice of the statistical tests depends on whether the data is censored (Log-rank test) or not (U-test). The set of the leaves of the tree form a partition. The risk distribution of patients that belong to a leaf is different from the sibling leaf but not the rest of the leaves. Therefore, some of the leaves that have similar underlying risks are incorrectly specified to have different risks. In the second phase, we develop a novel recursive graph decomposition approach to address this problem. We merge the leaves of the tree that have similar risks to form new leaves that form the final output. We apply Risk-stratify on a cohort of patients (with no history of cardiovascular disease) from UK Biobank and assess their risk for cardiovascular disease. Risk-stratify significantly improves risk-stratification, i.e., a lower fraction of the groups have over/under estimated risks (measured in terms of false discovery rate; 33% reduction) in comparison to state-of-the-art methods for cardiovascular prediction (Random forests, Cox model, etc.). We find that the Cox model significantly over estimates the risk of 21,621 patients out of 216,211 patients. Risk-stratify can accurately categorize 2,987 of these 21,621 patients as low-risk individuals.