As datasets grow richer, an important challenge is to leverage the full features in the data to maximize the number of useful discoveries while controlling for false positives. We address this problem in the context of multiple hypotheses testing, where for each hypothesis, we observe a p-value along with a set of features specific to that hypothesis. For example, in genetic association studies, each hypothesis tests the correlation between a variant and the trait. We have a rich set of features for each variant (e.g. its location, conservation, epigenetics etc.) which could inform how likely the variant is to have a true association. However popular testing approaches, such as Benjamini-Hochberg's procedure (BH) and independent hypothesis weighting (IHW), either ignore these features or assume that the features are categorical. We propose a new algorithm, NeuralFDR, which automatically learns a discovery threshold as a function of all the hypothesis features. We parametrize the discovery threshold as a neural network, which enables flexible handling of multi-dimensional discrete and continuous features as well as efficient end-to-end optimization. We prove that NeuralFDR has strong false discovery rate (FDR) guarantees, and show that it makes substantially more discoveries in synthetic and real datasets. Moreover, we demonstrate that the learned discovery threshold is directly interpretable.

Brain connectivity analysis is a critical component of ongoing human connectome projects to decipher the healthy and diseased brain. Recent work has highlighted the power-law (multi-time scale) properties of brain signals; however, there remains a lack of methods to specifically quantify short- vs. long- time range brain connections. In this paper, using detrended partial cross-correlation analysis (DPCCA), we propose a novel functional connectivity measure to delineate brain interactions at multiple time scales, while controlling for covariates. We use a rich simulated fMRI dataset to validate the proposed method, and apply it to a real fMRI dataset in a cocaine dependence prediction task. We show that, compared to extant methods, the DPCCA-based approach not only distinguishes short and long memory functional connectivity but also improves feature extraction and enhances classification accuracy. Together, this paper contributes broadly to new computational methodologies in understanding neural information processing.

We propose a novel adaptive test of goodness-of-fit, with computational cost linear in the number of samples. We learn the test features that best indicate the differences between observed samples and a reference model, by minimizing the false negative rate. These features are constructed via Stein's method, meaning that it is not necessary to compute the normalising constant of the model. We analyse the asymptotic Bahadur efficiency of the new test, and prove that under a mean-shift alternative, our test always has greater relative efficiency than a previous linear-time kernel test, regardless of the choice of parameters for that test. In experiments, the performance of our method exceeds that of the earlier linear-time test, and matches or exceeds the power of a quadratic-time kernel test. In high dimensions and where model structure may be exploited, our goodness of fit test performs far better than a quadratic-time two-sample test based on the Maximum Mean Discrepancy, with samples drawn from the model.

Obtaining enough labeled data to robustly train complex discriminative models is a major bottleneck in the machine learning pipeline. A popular solution is combining multiple sources of weak supervision using generative models. The structure of these models affects the quality of the training labels, but is difficult to learn without any ground truth labels. We instead rely on weak supervision sources having some structure by virtue of being encoded programmatically. We present Coral, a paradigm that infers generative model structure by statically analyzing the code for these heuristics, thus significantly reducing the amount of data required to learn structure. We prove that Coral's sample complexity scales quasilinearly with the number of heuristics and number of relations identified, improving over the standard sample complexity, which is exponential in n for learning n-th degree relations. Empirically, Coral matches or outperforms traditional structure learning approaches by up to 3.81 F1 points. Using Coral to model dependencies instead of assuming independence results in better performance than a fully supervised model by 3.07 accuracy points when heuristics are used to label radiology data without ground truth labels.

Effective and efficient mitigation of malware is a long-time endeavor in the information security community. The development of an anti-malware system that can counteract an unknown malware is a prolific activity that may benefit several sectors. We envision an intelligent anti-malware system that utilizes the power of deep learning (DL) models. Using such models would enable the detection of newly-released malware through mathematical generalization. That is, finding the relationship between a given malware $x$ and its corresponding malware family $y$, $f: x \mapsto y$. To accomplish this feat, we used the Malimg dataset (Nataraj et al., 2011) which consists of malware images that were processed from malware binaries, and then we trained the following DL models 1 to classify each malware family: CNN-SVM (Tang, 2013), GRU-SVM (Agarap, 2017), and MLP-SVM. Empirical evidence has shown that the GRU-SVM stands out among the DL models with a predictive accuracy of ~84.92%. This stands to reason for the mentioned model had the relatively most sophisticated architecture design among the presented models. The exploration of an even more optimal DL-SVM model is the next stage towards the engineering of an intelligent anti-malware system.

We address the problem of latent truth discovery, LTD for short, where the goal is to discover the underlying true values of entity attributes in the presence of noisy, conflicting or incomplete information. Despite a multitude of algorithms to address the LTD problem that can be found in literature, only little is known about their overall performance with respect to effectiveness (in terms of truth discovery capabilities), efficiency and robustness. A practical LTD approach should satisfy all these characteristics so that it can be applied to heterogeneous datasets of varying quality and degrees of cleanliness. We propose a novel algorithm for LTD that satisfies the above requirements. The proposed model is based on Restricted Boltzmann Machines, thus coined LTD-RBM. In extensive experiments on various heterogeneous and publicly available datasets, LTD-RBM is superior to state-of-the-art LTD techniques in terms of an overall consideration of effectiveness, efficiency and robustness.

Opencv object detectors which are built using Haar feature-based cascade classifiers is at least a decade old. OpenCV framework provides a default pre-built haar and lbp based cascade classifiers for face and eye detection which are very good quality detectors. However, I had never measured the accuracy of these face and eye detectors. I recently discovered that pre-built haar/lbp cascades have a relatively higher false positive rates which might make them unsuitable for many use-cases. It's possible to build an eye detector with very high accuracy and low false positive rates for many cases with OpenCV.

Deloitte's examination of the incentive to integrate sensing, communications and analytics technologies in the oil and gas industry a couple of years ago noted that "increased data capture and analysis can likely save millions of dollars by eliminating as many as half of a company's unplanned well outages and boosting crude output by as much as 10% over a two-year period."

To assure cyber security of an enterprise, typically SIEM (Security Information and Event Management) system is in place to normalize security event from different preventive technologies and flag alerts. Analysts in the security operation center (SOC) investigate the alerts to decide if it is truly malicious or not. However, generally the number of alerts is overwhelming with majority of them being false positive and exceeding the SOC's capacity to handle all alerts. There is a great need to reduce the false positive rate as much as possible. While most previous research focused on network intrusion detection, we focus on risk detection and propose an intelligent Deep Belief Network machine learning system. The system leverages alert information, various security logs and analysts' investigation results in a real enterprise environment to flag hosts that have high likelihood of being compromised. Text mining and graph based method are used to generate targets and create features for machine learning. In the experiment, Deep Belief Network is compared with other machine learning algorithms, including multi-layer neural network, random forest, support vector machine and logistic regression. Results on real enterprise data indicate that the deep belief network machine learning system performs better than other algorithms for our problem and is six times more effective than current rule-based system. We also implement the whole system from data collection, label creation, feature engineering to host score generation in a real enterprise production environment.

The evaluation of machine learning algorithms in biomedical fields for applications involving sequential data lacks standardization. Common quantitative scalar evaluation metrics such as sensitivity and specificity can often be misleading depending on the requirements of the application. Evaluation metrics must ultimately reflect the needs of users yet be sufficiently sensitive to guide algorithm development. Feedback from critical care clinicians who use automated event detection software in clinical applications has been overwhelmingly emphatic that a low false alarm rate, typically measured in units of the number of errors per 24 hours, is the single most important criterion for user acceptance. Though using a single metric is not often as insightful as examining performance over a range of operating conditions, there is a need for a single scalar figure of merit. In this paper, we discuss the deficiencies of existing metrics for a seizure detection task and propose several new metrics that offer a more balanced view of performance. We demonstrate these metrics on a seizure detection task based on the TUH EEG Corpus. We show that two promising metrics are a measure based on a concept borrowed from the spoken term detection literature, Actual Term-Weighted Value, and a new metric, Time-Aligned Event Scoring (TAES), that accounts for the temporal alignment of the hypothesis to the reference annotation. We also demonstrate that state of the art technology based on deep learning, though impressive in its performance, still needs significant improvement before it will meet very strict user acceptance guidelines.