Gene set collections are a common ground to study the enrichment of genes for specific phenotypic traits. Gene set enrichment analysis aims to identify genes that are over-represented in gene sets collections and might be associated with a specific phenotypic trait. However, as this involves a massive number of hypothesis testing, it is often questionable whether a pre-processing step to reduce gene sets collections' sizes is helpful. Moreover, the often highly overlapping gene sets and the consequent low interpretability of gene sets' collections demand for a reduction of the included gene sets. Inspired by this bioinformatics context, we propose a method to rank sets within a family of sets based on the distribution of the singletons and their size. We obtain sets' importance scores by computing Shapley values without incurring into the usual exponential number of evaluations of the value function. Moreover, we address the challenge of including a redundancy awareness in the rankings obtained where, in our case, sets are redundant if they show prominent intersections. We finally evaluate our approach for gene sets collections; the rankings obtained show low redundancy and high coverage of the genes. The unsupervised nature of the proposed ranking does not allow for an evident increase in the number of significant gene sets for specific phenotypic traits when reducing the size of the collections. However, we believe that the rankings proposed are of use in bioinformatics to increase interpretability of the gene sets collections and a step forward to include redundancy into Shapley values computations.
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The $h$-index is a metric used to measure the impact of a user in a publication setting, such as a member of a social network with many highly liked posts or a researcher in an academic domain with many highly cited publications. Specifically, the $h$-index of a user is the largest integer $h$ such that at least $h$ publications of the user have at least $h$ units of positive feedback. We design an algorithm that, given query access to the $n$ publications of a user and each publication's corresponding positive feedback number, outputs a $(1\pm \varepsilon)$-approximation of the $h$-index of this user with probability at least $1-\delta$ in time \[ O(\frac{n \cdot \ln{(1/\delta)}}{\varepsilon^2 \cdot h}), \] where $h$ is the actual $h$-index which is unknown to the algorithm a-priori. We then design a novel lower bound technique that allows us to prove that this bound is in fact asymptotically optimal for this problem in all parameters $n,h,\varepsilon,$ and $\delta$. Our work is one of the first in sublinear time algorithms that addresses obtaining asymptotically optimal bounds, especially in terms of the error and confidence parameters. As such, we focus on designing novel techniques for this task. In particular, our lower bound technique seems quite general -- to showcase this, we also use our approach to prove an asymptotically optimal lower bound for the problem of estimating the number of triangles in a graph in sublinear time, which now is also optimal in the error and confidence parameters. This result improves upon prior lower bounds of Eden, Levi, Ron, and Seshadhri (FOCS'15) for this problem, as well as multiple follow-ups that extended this lower bound to other subgraph counting problems.
The parameters of the log-logistic distribution are generally estimated based on classical methods such as maximum likelihood estimation, whereas these methods usually result in severe biased estimates when the data contain outliers. In this paper, we consider several alternative estimators, which not only have closed-form expressions, but also are quite robust to a certain level of data contamination. We investigate the robustness property of each estimator in terms of the breakdown point. The finite sample performance and effectiveness of these estimators are evaluated through Monte Carlo simulations and a real-data application. Numerical results demonstrate that the proposed estimators perform favorably in a manner that they are comparable with the maximum likelihood estimator for the data without contamination and that they provide superior performance in the presence of data contamination.
Semantic localization (SeLo) refers to the task of obtaining the most relevant locations in large-scale remote sensing (RS) images using semantic information such as text. As an emerging task based on cross-modal retrieval, SeLo achieves semantic-level retrieval with only caption-level annotation, which demonstrates its great potential in unifying downstream tasks. Although SeLo has been carried out successively, but there is currently no work has systematically explores and analyzes this urgent direction. In this paper, we thoroughly study this field and provide a complete benchmark in terms of metrics and testdata to advance the SeLo task. Firstly, based on the characteristics of this task, we propose multiple discriminative evaluation metrics to quantify the performance of the SeLo task. The devised significant area proportion, attention shift distance, and discrete attention distance are utilized to evaluate the generated SeLo map from pixel-level and region-level. Next, to provide standard evaluation data for the SeLo task, we contribute a diverse, multi-semantic, multi-objective Semantic Localization Testset (AIR-SLT). AIR-SLT consists of 22 large-scale RS images and 59 test cases with different semantics, which aims to provide a comprehensive evaluations for retrieval models. Finally, we analyze the SeLo performance of RS cross-modal retrieval models in detail, explore the impact of different variables on this task, and provide a complete benchmark for the SeLo task. We have also established a new paradigm for RS referring expression comprehension, and demonstrated the great advantage of SeLo in semantics through combining it with tasks such as detection and road extraction. The proposed evaluation metrics, semantic localization testsets, and corresponding scripts have been open to access at github.com/xiaoyuan1996/SemanticLocalizationMetrics .
Over recent years, there has been a rapid development of deep learning (DL) in both industry and academia fields. However, finding the optimal hyperparameters of a DL model often needs high computational cost and human expertise. To mitigate the above issue, evolutionary computation (EC) as a powerful heuristic search approach has shown significant merits in the automated design of DL models, so-called evolutionary deep learning (EDL). This paper aims to analyze EDL from the perspective of automated machine learning (AutoML). Specifically, we firstly illuminate EDL from machine learning and EC and regard EDL as an optimization problem. According to the DL pipeline, we systematically introduce EDL methods ranging from feature engineering, model generation, to model deployment with a new taxonomy (i.e., what and how to evolve/optimize), and focus on the discussions of solution representation and search paradigm in handling the optimization problem by EC. Finally, key applications, open issues and potentially promising lines of future research are suggested. This survey has reviewed recent developments of EDL and offers insightful guidelines for the development of EDL.
Meta-learning has gained wide popularity as a training framework that is more data-efficient than traditional machine learning methods. However, its generalization ability in complex task distributions, such as multimodal tasks, has not been thoroughly studied. Recently, some studies on multimodality-based meta-learning have emerged. This survey provides a comprehensive overview of the multimodality-based meta-learning landscape in terms of the methodologies and applications. We first formalize the definition of meta-learning and multimodality, along with the research challenges in this growing field, such as how to enrich the input in few-shot or zero-shot scenarios and how to generalize the models to new tasks. We then propose a new taxonomy to systematically discuss typical meta-learning algorithms combined with multimodal tasks. We investigate the contributions of related papers and summarize them by our taxonomy. Finally, we propose potential research directions for this promising field.
Since real-world objects and their interactions are often multi-modal and multi-typed, heterogeneous networks have been widely used as a more powerful, realistic, and generic superclass of traditional homogeneous networks (graphs). Meanwhile, representation learning (\aka~embedding) has recently been intensively studied and shown effective for various network mining and analytical tasks. In this work, we aim to provide a unified framework to deeply summarize and evaluate existing research on heterogeneous network embedding (HNE), which includes but goes beyond a normal survey. Since there has already been a broad body of HNE algorithms, as the first contribution of this work, we provide a generic paradigm for the systematic categorization and analysis over the merits of various existing HNE algorithms. Moreover, existing HNE algorithms, though mostly claimed generic, are often evaluated on different datasets. Understandable due to the application favor of HNE, such indirect comparisons largely hinder the proper attribution of improved task performance towards effective data preprocessing and novel technical design, especially considering the various ways possible to construct a heterogeneous network from real-world application data. Therefore, as the second contribution, we create four benchmark datasets with various properties regarding scale, structure, attribute/label availability, and \etc.~from different sources, towards handy and fair evaluations of HNE algorithms. As the third contribution, we carefully refactor and amend the implementations and create friendly interfaces for 13 popular HNE algorithms, and provide all-around comparisons among them over multiple tasks and experimental settings.
There has been appreciable progress in unsupervised network representation learning (UNRL) approaches over graphs recently with flexible random-walk approaches, new optimization objectives and deep architectures. However, there is no common ground for systematic comparison of embeddings to understand their behavior for different graphs and tasks. In this paper we theoretically group different approaches under a unifying framework and empirically investigate the effectiveness of different network representation methods. In particular, we argue that most of the UNRL approaches either explicitly or implicit model and exploit context information of a node. Consequently, we propose a framework that casts a variety of approaches -- random walk based, matrix factorization and deep learning based -- into a unified context-based optimization function. We systematically group the methods based on their similarities and differences. We study the differences among these methods in detail which we later use to explain their performance differences (on downstream tasks). We conduct a large-scale empirical study considering 9 popular and recent UNRL techniques and 11 real-world datasets with varying structural properties and two common tasks -- node classification and link prediction. We find that there is no single method that is a clear winner and that the choice of a suitable method is dictated by certain properties of the embedding methods, task and structural properties of the underlying graph. In addition we also report the common pitfalls in evaluation of UNRL methods and come up with suggestions for experimental design and interpretation of results.
We present a new method to learn video representations from large-scale unlabeled video data. Ideally, this representation will be generic and transferable, directly usable for new tasks such as action recognition and zero or few-shot learning. We formulate unsupervised representation learning as a multi-modal, multi-task learning problem, where the representations are shared across different modalities via distillation. Further, we introduce the concept of loss function evolution by using an evolutionary search algorithm to automatically find optimal combination of loss functions capturing many (self-supervised) tasks and modalities. Thirdly, we propose an unsupervised representation evaluation metric using distribution matching to a large unlabeled dataset as a prior constraint, based on Zipf's law. This unsupervised constraint, which is not guided by any labeling, produces similar results to weakly-supervised, task-specific ones. The proposed unsupervised representation learning results in a single RGB network and outperforms previous methods. Notably, it is also more effective than several label-based methods (e.g., ImageNet), with the exception of large, fully labeled video datasets.
Machine learning techniques have deeply rooted in our everyday life. However, since it is knowledge- and labor-intensive to pursue good learning performance, human experts are heavily involved in every aspect of machine learning. In order to make machine learning techniques easier to apply and reduce the demand for experienced human experts, automated machine learning (AutoML) has emerged as a hot topic with both industrial and academic interest. In this paper, we provide an up to date survey on AutoML. First, we introduce and define the AutoML problem, with inspiration from both realms of automation and machine learning. Then, we propose a general AutoML framework that not only covers most existing approaches to date but also can guide the design for new methods. Subsequently, we categorize and review the existing works from two aspects, i.e., the problem setup and the employed techniques. Finally, we provide a detailed analysis of AutoML approaches and explain the reasons underneath their successful applications. We hope this survey can serve as not only an insightful guideline for AutoML beginners but also an inspiration for future research.
We study the problem of named entity recognition (NER) from electronic medical records, which is one of the most fundamental and critical problems for medical text mining. Medical records which are written by clinicians from different specialties usually contain quite different terminologies and writing styles. The difference of specialties and the cost of human annotation makes it particularly difficult to train a universal medical NER system. In this paper, we propose a label-aware double transfer learning framework (La-DTL) for cross-specialty NER, so that a medical NER system designed for one specialty could be conveniently applied to another one with minimal annotation efforts. The transferability is guaranteed by two components: (i) we propose label-aware MMD for feature representation transfer, and (ii) we perform parameter transfer with a theoretical upper bound which is also label aware. We conduct extensive experiments on 12 cross-specialty NER tasks. The experimental results demonstrate that La-DTL provides consistent accuracy improvement over strong baselines. Besides, the promising experimental results on non-medical NER scenarios indicate that La-DTL is potential to be seamlessly adapted to a wide range of NER tasks.
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