Proceedings of the ... SIAM International Conference on Data Mining. SIAM International Conference on Data Mining最新文献

De novo molecular design is a key challenge in drug discovery due to the complexity of chemical space. With the availability of molecular datasets and advances in machine learning, many deep generative models are proposed for generating novel molecules with desired properties. However, most of the existing models focus only on molecular distribution learning and target-based molecular design, thereby hindering their potentials in real-world applications. In drug discovery, phenotypic molecular design has advantages over target-based molecular design, especially in first-in-class drug discovery. In this work, we propose the first deep graph generative model (FAME) targeting phenotypic molecular design, in particular gene expression-based molecular design. FAME leverages a conditional variational autoencoder framework to learn the conditional distribution generating molecules from gene expression profiles. However, this distribution is difficult to learn due to the complexity of the molecular space and the noisy phenomenon in gene expression data. To tackle these issues, a gene expression denoising (GED) model that employs contrastive objective function is first proposed to reduce noise from gene expression data. FAME is then designed to treat molecules as the sequences of fragments and learn to generate these fragments in autoregressive manner. By leveraging this fragment-based generation strategy and the denoised gene expression profiles, FAME can generate novel molecules with a high validity rate and desired biological activity. The experimental results show that FAME outperforms existing methods including both SMILES-based and graph-based deep generative models for phenotypic molecular design. Furthermore, the effective mechanism for reducing noise in gene expression data proposed in our study can be applied to omics data modeling in general for facilitating phenotypic drug discovery.

We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data structure. Importantly, we do not assume any pointwise correspondence between datasets, but instead rely on correspondence between a (possibly unknown) subset of data features. We leverage this assumption to construct an isometric alignment between the data. This alignment is obtained by relating the expansion of data features in harmonics derived from diffusion operators defined over each dataset. These expansions encode each feature as a function of the data geometry. We use this to relate the diffusion coordinates of each dataset through our assumption of partial feature correspondence. Then, a unified diffusion geometry is constructed over the aligned data, which can also be used to correct the original data measurements. We demonstrate our method on several datasets, showing in particular its effectiveness in biological applications including fusion of single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data measured on the same population of cells, and removal of batch effect between biological samples.

Integrative analysis jointly analyzes multiple data sets to overcome curse of dimensionality. It can detect important but weak signals by jointly selecting features for all data sets, but unfortunately the sets of important features are not always the same for all data sets. Variations which allows heterogeneous sparsity structure-a subset of data sets can have a zero coefficient for a selected feature-have been proposed, but it compromises the effect of integrative analysis recalling the problem of losing weak important signals. We propose a new integrative analysis approach which not only aggregates weak important signals well in homogeneity setting but also substantially alleviates the problem of losing weak important signals in heterogeneity setting. Our approach exploits a priori known graphical structure of features by forcing joint selection of adjacent features, and integrating such information over multiple data sets can increase the power while taking into account the heterogeneity across data sets. We confirm the problem of existing approaches and demonstrate the superiority of our method through a simulation study and an application to gene expression data from ADNI.

Learning of classification models in practice often relies on human annotation effort in which humans assign class labels to data instances. As this process can be very time-consuming and costly, finding effective ways to reduce the annotation cost becomes critical for building such models. To solve this problem, instead of soliciting instance-based annotation we explore region-based annotation as the human feedback. A region is defined as a hyper-cubic subspace of the input space X and it covers a subpopulation of data instances that fall into this region. Each region is labeled with a number in [0,1] (in binary classification setting), representing a human estimate of the positive (or negative) class proportion in the subpopulation. To quickly discover pure regions (in terms of class proportion) in the data, we have developed a novel active learning framework that constructs regions in a hierarchical and adaptive way. Hierarchical means that regions are incrementally built into a hierarchical tree, which is done by repeatedly splitting the input space. Adaptive means that our framework can adaptively choose the best heuristic for each of the region splits. Through experiments on numerous datasets we demonstrate that our framework can identify pure regions in very few region queries. Thus our approach is shown to be effective in learning classification models from very limited human feedback.

Tensor factorization is a methodology that is applied in a variety of fields, ranging from climate modeling to medical informatics. A tensor is an n-way array that captures the relationship between n objects. These multiway arrays can be factored to study the underlying bases present in the data. Two challenges arising in tensor factorization are 1) the resulting factors can be noisy and highly overlapping with one another and 2) they may not map to insights within a domain. However, incorporating supervision to increase the number of insightful factors can be costly in terms of the time and domain expertise necessary for gathering labels or domain-specific constraints. To meet these challenges, we introduce CANDECOMP/PARAFAC (CP) tensor factorization with Cannot-Link Intermode Constraints (CP-CLIC), a framework that achieves succinct, diverse, interpretable factors. This is accomplished by gradually learning constraints that are verified with auxiliary information during the decomposition process. We demonstrate CP-CLIC's potential to extract sparse, diverse, and interpretable factors through experiments on simulated data and a real-world application in medical informatics.

Heterogeneous information networks (HINs) are ubiquitous in real-world applications. Due to the heterogeneity in HINs, the typed edges may not fully align with each other. In order to capture the semantic subtlety, we propose the concept of aspects with each aspect being a unit representing one underlying semantic facet. Meanwhile, network embedding has emerged as a powerful method for learning network representation, where the learned embedding can be used as features in various downstream applications. Therefore, we are motivated to propose a novel embedding learning framework-ASPEM-to preserve the semantic information in HINs based on multiple aspects. Instead of preserving information of the network in one semantic space, ASPEM encapsulates information regarding each aspect individually. In order to select aspects for embedding purpose, we further devise a solution for ASPEM based on dataset-wide statistics. To corroborate the efficacy of ASPEM, we conducted experiments on two real-words datasets with two types of applications-classification and link prediction. Experiment results demonstrate that ASPEM can outperform baseline network embedding learning methods by considering multiple aspects, where the aspects can be selected from the given HIN in an unsupervised manner.

Annotation of classification data by humans can be a time-consuming and tedious process. Finding ways of reducing the annotation effort is critical for building the classification models in practice and for applying them to a variety of classification tasks. In this paper, we develop a new active learning framework that combines two strategies to reduce the annotation effort. First, it relies on label uncertainty information obtained from the human in terms of the Likert-scale feedback. Second, it uses active learning to annotate examples with the greatest expected change. We propose a Bayesian approach to calculate the expectation and an incremental SVM solver to reduce the time complexity of the solvers. We show the combination of our active learning strategy and the Likert-scale feedback can learn classification models more rapidly and with a smaller number of labeled instances than methods that rely on either Likert-scale labels or active learning alone.

Consecutive pattern mining aiming at finding sequential patterns substrings, is a special case of frequent pattern mining and has been played a crucial role in many real world applications, especially in biological sequence analysis, time series analysis, and network log mining. Approximations, including insertions, deletions, and substitutions, between strings are widely used in biological sequence comparisons. However, most existing string pattern mining methods only consider hamming distance without insertions/deletions (indels). Little attention has been paid to the general approximate consecutive frequent pattern mining under edit distance, potentially due to the high computational complexity, particularly on DNA sequences with billions of base pairs. In this paper, we introduce an efficient solution to this problem. We first formulate the Maximal Approximate Consecutive Frequent Pattern Mining (MACFP) problem that identifies substring patterns under edit distance in a long query sequence. Then, we propose a novel algorithm with linear time complexity to check whether the support of a substring pattern is above a predefined threshold in the query sequence, thus greatly reducing the computational complexity of MACFP. With this fast decision algorithm, we can efficiently solve the original pattern discovery problem with several indexing and searching techniques. Comprehensive experiments on sequence pattern analysis and a study on cancer genomics application demonstrate the effectiveness and efficiency of our algorithm, compared to several existing methods.

Learning accurate probabilistic models from data is crucial in many practical tasks in data mining. In this paper we present a new non-parametric calibration method called ensemble of linear trend estimation (ELiTE). ELiTE utilizes the recently proposed ℓ₁ trend ltering signal approximation method [22] to find the mapping from uncalibrated classification scores to the calibrated probability estimates. ELiTE is designed to address the key limitations of the histogram binning-based calibration methods which are (1) the use of a piecewise constant form of the calibration mapping using bins, and (2) the assumption of independence of predicted probabilities for the instances that are located in different bins. The method post-processes the output of a binary classifier to obtain calibrated probabilities. Thus, it can be applied with many existing classification models. We demonstrate the performance of ELiTE on real datasets for commonly used binary classification models. Experimental results show that the method outperforms several common binary-classifier calibration methods. In particular, ELiTE commonly performs statistically significantly better than the other methods, and never worse. Moreover, it is able to improve the calibration power of classifiers, while retaining their discrimination power. The method is also computationally tractable for large scale datasets, as it is practically O(N log N) time, where N is the number of samples.