In recent years, the landscape of digital biomedicine and healthcare has been reshaped due to the disruptive breakthroughs in AIfacilitated by tremendous data and high-performance computers, large language models (LLMs) have transformed information technology from accessing data to performing analytical tasks.While demonstrating unprecedented capabilities, LLMs have been found unreliable in tasks requiring factual knowledge and rigorous reasoning.Biomedicine and healthcare, as an important vertical domain rapidly benefitting from progress in AI, necessitates strict requirements on the accuracy, controllability, and interpretability of analytical models, posing critical challenges for LLMs.Despite recent studies addressing the hallucination problem of LLMs, research on empowering LLMs with the ability to plan, reason, and ground with explicit knowledge has also started to prosper, especially in the biomedicine and healthcare domain.On the other hand, biomedical data are enormous and notoriously complex, coming from various sources (e.g., biomedical knowledge bases, online literature, and hospitals) and bearing various modalities (e.g., tables, texts, images and time-series).Healthcare professionals have spent decades collecting, cleaning, and curating various types of data.The processes are extremely costly, producing various datasets with different data schemas, coding systems, and quality standards, many privately

Health AI suffers from a systemic reproducibility crisis that irreparably hinders research across both academia and industry [4,5].One key tool poised to solve this crisis is the Medical Event Data Standard (MEDS), a comprehensive data format and open-source ecosystem designed to enhance reproducibility and interoperability of AI research using longitudinal Electronic Health Records (EHR) [6].Currently adopted by over 15 institutions globally, MEDS encompasses various open-source tools, published models, and data processing pipelines, enabling streamlined model development and robust benchmarking.In this tutorial, participants will gain key hands-on experience in working with the MEDS format to perform efficient, reproducible, state-of-the-art AI research over real health data.Participants will transform data into the MEDS format, preprocess data, build predictive models, and contribute to the decentralized MEDS-DEV benchmarking platform.Interactive exercises using Jupyter notebooks will provide hands-on experience and practical skills for reproducible health AI research.Attendees will leave equipped

Recently, there has been a growing interest among researchers in understanding molecules and their textual descriptions through molecule language models (MoLM). However, despite some early promising developments, the advancement of MoLM still trails significantly behind that of vision language models (VLM). This is because unique challenges exist apart from VLM in the field of MoLM due to 1) a limited amount of molecule-text paired data and 2) missing expertise that occurred due to the specialized areas of focus among the experts. To this end, we propose AMOLE, which 1) augments molecule-text pairs with structural similarity preserving loss, and 2) transfers the expertise between the molecules. Specifically, AMOLE enriches molecule-text pairs by sharing descriptions among structurally similar molecules with a novel structural similarity preserving loss. Moreover, we propose an expertise reconstruction loss to transfer knowledge from molecules that have extensive expertise to those with less expertise. Extensive experiments on various downstream tasks demonstrate the superiority of AMOLE in comprehending molecules and their descriptions, highlighting its potential for application in real-world drug discovery. The source code for AMOLE is available at https://github.com/Namkyeong/AMOLE.

Data organized in tabular format is ubiquitous in real-world applications, and users often craft tables with biased feature definitions and flexibly set prediction targets of their interests. Thus, a rapid development of a robust, effective, dataset-versatile, user-friendly tabular prediction approach is highly desired. While Gradient Boosting Decision Trees (GBDTs) and existing deep neural networks (DNNs) have been extensively utilized by professional users, they present several challenges for casual users, particularly: (i) the dilemma of model selection due to their different dataset preferences, and (ii) the need for heavy hyperparameter searching, failing which their performances are deemed inadequate. In this paper, we delve into this question: Can we develop a deep learning model that serves as a sure bet solution for a wide range of tabular prediction tasks, while also being user-friendly for casual users? We delve into three key drawbacks of deep tabular models, encompassing: (P1) lack of rotational variance property, (P2) large data demand, and (P3) over-smooth solution. We propose ExcelFormer, addressing these challenges through a semi-permeable attention module that effectively constrains the influence of less informative features to break the DNNs' rotational invariance property (for P1), data augmentation approaches tailored for tabular data (for P2), and attentive feedforward network to boost the model fitting capability (for P3). These designs collectively make ExcelFormer a sure bet solution for diverse tabular datasets. Extensive and stratified experiments conducted on real-world datasets demonstrate that our model outperforms previous approaches across diverse tabular data prediction tasks, and this framework can be friendly to casual users, offering ease of use without the heavy hyperparameter tuning. The codes are available at https://github.com/whatashot/excelformer.

Clinical trial digital twins are virtual patients that reflect personal characteristics in a high degree of granularity and can be used to simulate various patient outcomes under different conditions. With the growth of clinical trial databases captured by Electronic Data Capture (EDC) systems, there is a growing interest in using machine learning models to generate digital twins. This can benefit the drug development process by reducing the sample size required for participant recruitment, improving patient outcome predictive modeling, and mitigating privacy risks when sharing synthetic clinical trial data. However, prior research has mainly focused on generating Electronic Healthcare Records (EHRs), which often assume large training data and do not account for personalized synthetic patient record generation. In this paper, we propose a sample-efficient method TWIN for generating personalized clinical trial digital twins. TWIN can produce digital twins of patient-level clinical trial records with high fidelity to the targeting participant's record and preserves the temporal relations across visits and events. We compare our method with various baselines for generating real-world patient-level clinical trial data. The results show that TWIN generates synthetic trial data with high fidelity to facilitate patient outcome predictions in low-data scenarios and strong privacy protection against real patients from the trials.

A comprehensive patient health history is essential for patient care and healthcare research. However, due to the distributed nature of healthcare services, patient health records are often scattered across multiple systems. Existing record linkage approaches primarily rely on patient identifiers, which have inherent limitations such as privacy invasion and identifier discrepancies. To tackle this problem, we propose linking de-identified patient health records by matching health patterns without strictly relying on sensitive patient identifiers. Our model MedLink solves two challenges faced with the patient linkage task: (1) the challenge of identifying the same patients based on data collected in different timelines as disease progression makes the record matching difficult, and (2) the challenge of identifying distinct health patterns as common medical codes dominate health records and overshadow the more informative low-prevalence codes. To address these challenges, MedLink utilizes bi-directional health prediction to predict future codes forwardly and past codes backwardly, thus accounting for the health progression. MedLink also has a prevalence-aware retrieval design to focus more on the low-prevalence but informative codes during learning. MedLink can be trained end-to-end and is lightweight for efficient inference on large patient databases. We evaluate MedLink against leading baselines on real-world patient datasets, including the critical care dataset MIMIC-III and a large health claims dataset. Results show that MedLink outperforms the best baseline by 4% in top-1 accuracy with only 8% memory cost. Additionally, when combined with existing identifier-based linkage approaches, MedLink can improve their performance by up to 15%.

Deep learning (DL) has emerged as a promising tool in healthcare applications. However, the reproducibility of many studies in this field is limited by the lack of accessible code implementations and standard benchmarks. To address the issue, we create PyHealth, a comprehensive library to build, deploy, and validate DL pipelines for healthcare applications. PyHealth supports various data modalities, including electronic health records (EHRs), physiological signals, medical images, and clinical text. It offers various advanced DL models and maintains comprehensive medical knowledge systems. The library is designed to support both DL researchers and clinical data scientists. Upon the time of writing, PyHealth has received 633 stars, 130 forks, and 15k+ downloads in total on GitHub.

Protein engineering has important applications in drug discovery. Among others, inverse protein folding is a fundamental task in protein design, which aims at generating protein's amino acid sequence given a 3D graph structure. However, most existing methods for inverse protein folding are based on sequential generative models and therefore limited in uncertainty quantification and exploration ability to the entire protein space. To address the issues, we propose a sampling method for inverse protein folding (SIPF). Specifically, we formulate inverse protein folding as a sampling problem and design two pretrained neural networks as Markov Chain Monte Carlo (MCMC) proposal distribution. To ensure sampling efficiency, we further design (i) an adaptive sampling scheme to select variables for sampling and (ii) an approximate target distribution as a surrogate of the unavailable target distribution. Empirical studies have been conducted to validate the effectiveness of SIPF, achieving 7.4% relative improvement on recovery rate and 6.4% relative reduction in perplexity compared to the best baseline.

In recent years, therapeutic antibodies have become one of the fastest-growing classes of drugs and have been approved for the treatment of a wide range of indications, from cancer to autoimmune diseases. Complementarity-determining regions (CDRs) are part of the variable chains in antibodies and determine specific antibody-antigen binding. Some explorations use in silicon methods to design antibody CDR loops. However, the existing methods faced the challenges of maintaining the specific geometry shape of the CDR loops. This paper proposes a Constrained Energy Model (CEM) to address this issue. Specifically, we design a constrained manifold to characterize the geometry constraints of the CDR loops. Then we design the energy model in the constrained manifold and only depict the energy landscape of the manifold instead of the whole space in the vanilla energy model. The geometry shape of the generated CDR loops is automatically preserved. Theoretical analysis shows that learning on the constrained manifold requires less sample complexity than the unconstrained method. CEM's superiority is validated via thorough empirical studies, achieving consistent and significant improvement with up to 33.4% relative reduction in terms of 3D geometry error (Root Mean Square Deviation, RMSD) and 8.4% relative reduction in terms of amino acid sequence metric (perplexity) compared to the best baseline method. The code is publicly available at https://github.com/futianfan/energy_model4antibody_design

Population-level disease prediction estimates the number of potential patients of particular diseases in some location at a future time based on (frequently updated) historical disease statistics. Existing approaches often assume the existing disease statistics are reliable and will not change. However, in practice, data collection is often time-consuming and has time delays, with both historical and current disease statistics being updated continuously. In this work, we propose a real-time population-level disease prediction model which captures data latency (PopNet) and incorporates the updated data for improved predictions. To achieve this goal, PopNet models real-time data and updated data using two separate systems, each capturing spatial and temporal effects using hybrid graph attention networks and recurrent neural networks. PopNet then fuses the two systems using both spatial and temporal latency-aware attentions in an end-to-end manner. We evaluate PopNet on real-world disease datasets and show that PopNet consistently outperforms all baseline disease prediction and general spatial-temporal prediction models, achieving up to 47% lower root mean squared error and 24% lower mean absolute error compared with the best baselines.

The goal of molecular optimization is to generate molecules similar to a target molecule but with better chemical properties. Deep generative models have shown great success in molecule optimization. However, due to the iterative local generation process of deep generative models, the resulting molecules can significantly deviate from the input in molecular similarity and size, leading to poor chemical properties. The key issue here is that the existing deep generative models restrict their attention on substructure-level generation without considering the entire molecule as a whole. To address this challenge, we propose Molecule-Level Reward functions (MOLER) to encourage (1) the input and the generated molecule to be similar, and to ensure (2) the generated molecule has a similar size to the input. The proposed method can be combined with various deep generative models. Policy gradient technique is introduced to optimize reward-based objectives with small computational overhead. Empirical studies show that MOLER achieves up to 20.2% relative improvement in success rate over the best baseline method on several properties, including QED, DRD2 and LogP.

There is a growing interest in applying deep learning (DL) to healthcare, driven by the availability of data with multiple feature channels inrich-dataenvironments (e.g., intensive care units). However, in many other practical situations, we can only access data with much fewer feature channels in apoor-dataenvironments (e.g., at home), which often results in predictive models with poor performance. How can we boost the performance of models learned from suchpoor-dataenvironment by leveraging knowledge extracted from existing models trained usingrich datain a related environment? To address this question, we develop a knowledge infusion framework namedCHEERthat can succinctly summarize suchrich modelinto transferable representations, which can be incorporated into thepoor modelto improve its performance. The infused model is analyzed theoretically and evaluated empirically on several datasets. Our empirical results showed thatCHEERoutperformed baselines by 5.60 to 46.80 percent in terms of the macro-F1 score on multiple physiological datasets.

Class imbalance is a significant i ssue t hat causes neural networks to underfit t o t he r are c lasses. Traditional mitigation strategies include loss reshaping and data resampling which amount to increasing the loss contribution of minority classes and decreasing the loss contributed by the majority ones. However, by treating each example within a class equally, these methods lead to undesirable scenarios where hard-to-classify examples from the majority classes are down-weighted and easy-to-classify examples from the minority classes are up-weighted. We propose the Hardness Aware Reweighting (HAR) framework, which circumvents this issue by increasing the loss contribution of hard examples from both the majority and minority classes. This is achieved by augmenting a neural network with intermediate classifier b ranches t o e nable e arly-exiting d uring t raining. Experimental results on large-scale datasets demonstrate that HAR consistently improves state-of-the-art accuracy while saving up to 20% of inference FLOPS.

We propose CUP, a new method for compressing and accelerating deep neural networks. At its core, CUP achieves compression by clustering and pruning similar filters in each layer. For clustering, CUP uses hierarchical clustering which allows for an elegant parameterization of model capacity through a single hyper-parameter t. We observe that by increasing t, CUP can dynamically reduce model capacity through non-uniform layer-wise pruning leading to two advantages. First, CUP can effectively compress a model to within the desired compute budget through a simple line-search on t. Second, through a simple extension, CUP can obtain the pruned model in a single training pass leading to large savings in training time. On Imagenet, CUP leads to a 2.47× FLOPS reduction on Resnet-50 with less than 1% drop in top-5 accuracy. Notably, in the retrain-free setting, CUP-RF saves over 10 hours of training time on 3 GPUs, in comparison to state-of-the-art methods. The code for CUP is open sourced1.

Drug discovery aims at finding promising drug molecules for treating target diseases. Existing computational drug discovery methods mainly depend on molecule databases, ignoring valuable data collected from clinical trials. In this work, we propose PRIME to leverage high-quality drug molecules and drug-disease relations in historical clinical trials to narrow down the molecular search space in drug discovery. PRIME also introduces time dependency constraints to model evolving drug-disease relations using a probabilistic deep learning model that can quantify model uncertainty. We evaluated PRIME against leading models on both de novo design and drug repurposing tasks. Results show that compared with the best baselines, PRIME achieves 25.9% relative improvement (i.e., reduction) in average hit-ranking on drug repurposing and 47.6% relative improvement in success rate on de novo design.

Thanks to the explosion of heterogeneous healthcare data and advanced machine learning and data mining techniques, specifically deep learning methods, we now have an opportunity to make difference in healthcare. In this tutorial, we will present state-of-the-art deep learning methods and their real-world applications, specifically focusing on exploring the unique characteristics of different types of healthcare data. The first half will be spent on introducing recent advances in mining structured healthcare data, including computational phenotyping, disease early detection/risk prediction and treatment recommendation. In the second half, we will focus on challenges specific to the unstructured healthcare data, and introduce advanced deep learning methods in automated ICD coding, understandable medical language translation, clinical trial mining, and medical report generation. This tutorial is intended for students, engineers and researchers who are interested in applying deep learning methods to healthcare, and prerequisite knowledge will be minimal. The tutorial will be concluded with open problems and a Q&A session.

Existing tensor completion formulation mostly relies on partial observations from a single tensor. However, tensors extracted from real-world data often are more complex due to: (i) Partial observation: Only a small subset of tensor elements are available. (ii) Coarse observation: Some tensor modes only present coarse and aggregated patterns (e.g., monthly summary instead of daily reports). In this paper, we are given a subset of the tensor and some aggregated/coarse observations (along one or more modes) and seek to recover the original fine-granular tensor with low-rank factorization. We formulate a coupled tensor completion problem and propose an efficient Multi-resolution Tensor Completion model (MTC) to solve the problem. Our MTC model explores tensor mode properties and leverages the hierarchy of resolutions to recursively initialize an optimization setup, and optimizes on the coupled system using alternating least squares. MTC ensures low computational and space complexity. We evaluate our model on two COVID-19 related spatio-temporal tensors. The experiments show that MTC could provide 65.20% and 75.79% percentage of fitness (PoF) in tensor completion with only 5% fine granular observations, which is 27.96% relative improvement over the best baseline. To evaluate the learned low-rank factors, we also design a tensor prediction task for daily and cumulative disease case predictions, where MTC achieves 50% in PoF and 30% relative improvements over the best baseline.

Successful health risk prediction demands accuracy and reliability of the model. Existing predictive models mainly depend on mining electronic health records (EHR) with advanced deep learning techniques to improve model accuracy. However, they all ignore the importance of publicly available online health data, especially socioeconomic status, environmental factors, and detailed demographic information for each location, which are all strong predictive signals and can definitely augment precision medicine. To achieve model reliability, the model needs to provide accurate prediction and uncertainty score of the prediction. However, existing uncertainty estimation approaches often failed in handling high-dimensional data, which are present in multi-sourced data.

This paper presents an active distillation method for a local institution (e.g., hospital) to find the best queries within its given budget to distill an on-server black-box model’s predictive knowledge into a local surrogate with transparent parameterization. This allows local institutions to understand better the predictive reasoning of the black-box model in its own local context or to further customize the distilled knowledge with its private dataset that cannot be centralized and fed into the server model. The proposed method thus addresses several challenges of deploying machine learning (ML) in many industrial settings (e.g., healthcare analytics) with strong proprietary constraints. These include: (1) the opaqueness of the server model’s architecture which prevents local users from understanding its predictive reasoning in their local data contexts; (2) the increasing cost and risk of uploading local data on the cloud for analysis; and (3) the need to customize the server model with private onsite data. We evaluated the proposed method on both benchmark and real-world healthcare data where significant improvements over existing local distillation methods were observed. A theoretical analysis of the proposed method is also presented.

Data-driven machine learning has become ubiquitous. A marketplace for machine learning models connects data owners and model buyers, and can dramatically facilitate data-driven machine learning applications. In this paper, we take a formal data marketplace perspective and propose the first en D -to-end mod e l m a rketp l ace with diff e rential p r ivacy ( Dealer ) towards answering the following questions: How to formulate data owners' compensation functions and model buyers' price functions? How can the broker determine prices for a set of models to maximize the revenue with arbitrage-free guarantee, and train a set of models with maximum Shapley coverage given a manufacturing budget to remain competitive ? For the former, we propose compensation function for each data owner based on Shapley value and privacy sensitivity, and price function for each model buyer based on Shapley coverage sensitivity and noise sensitivity. Both privacy sensitivity and noise sensitivity are measured by the level of differential privacy. For the latter, we formulate two optimization problems for model pricing and model training, and propose efficient dynamic programming algorithms. Experiment results on the real chess dataset and synthetic datasets justify the design of Dealer and verify the efficiency and effectiveness of the proposed algorithms.

Data-driven machine learning (ML) has witnessed great success across a variety of application domains. Since ML model training relies on a large amount of data, there is a growing demand for high-quality data to be collected for ML model training. Data markets can be employed to significantly facilitate data collection. In this work, we demonstrate Dealer, an en D -to-end model m a rketp l ace with diff e rential p r ivacy. Dealer consists of three entities, data owners, the broker, and model buyers. Data owners receive compensation for their data usages allocated by the broker; The broker collects data from data owners, builds and sells models to model buyers; Model buyers buy their target models from the broker. We demonstrate the functionalities of the three participating entities and the abbreviated interactions between them. The demonstration allows the audience to understand and experience interactively the process of model trading. The audience can act as a data owner to control what and how the data would be compensated, can act as a broker to price machine learning models with maximum revenue, as well as can act as a model buyer to purchase target models that meet expectations.

Visualizing latent embeddings is a popular approach to explain classification models, including deep neural networks. However, existing visualization methods such as t-distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation Projection (UMAP) are often used as a post-processing step which is independent of the classification models. The resulting visualization can be misaligned with the classification models. In this paper, we propose ViVA, a novel method for semi-supervised Visualization via Variational Autoencoders. ViVA learns from both unlabeled and labeled data by jointly optimizing both visualization loss and classification loss. As a parameterized model using neural networks, ViVA can easily project new data to the same embedding space. Experiments show that ViVA can achieve better visualization quality as well as classification accuracy on multiple challenging datasets compared to several visualization baselines, including t-SNE and UMAP.

Clinical trials play important roles in drug development but often suffer from expensive, inaccurate and insufficient patient recruitment. The availability of massive electronic health records (EHR) data and trial eligibility criteria (EC) bring a new opportunity to data driven patient recruitment. One key task named patient-trial matching is to find qualified patients for clinical trials given structured EHR and unstructured EC text (both inclusion and exclusion criteria). How to match complex EC text with longitudinal patient EHRs? How to embed many-to-many relationships between patients and trials? How to explicitly handle the difference between inclusion and exclusion criteria? In this paper, we proposed CrOss-Modal PseudO-SiamEse network (COMPOSE) to address these challenges for patient-trial matching. One path of the network encodes EC using convolutional highway network. The other path processes EHR with multi-granularity memory network that encodes structured patient records into multiple levels based on medical ontology. Using the EC embedding as query, COMPOSE performs attentional record alignment and thus enables dynamic patient-trial matching. COMPOSE also introduces a composite loss term to maximize the similarity between patient records and inclusion criteria while minimize the similarity to the exclusion criteria. Experiment results show COMPOSE can reach 98.0% AUC on patient-criteria matching and 83.7% accuracy on patient-trial matching, which leads 24.3% improvement over the best baseline on real-world patient-trial matching tasks.

Deep learning models have achieved expert-level performance in healthcare with an exclusive focus on training accurate models. However, in many clinical environments such as intensive care unit (ICU), real-time model serving is equally if not more important than accuracy, because in ICU patient care is simultaneously more urgent and more expensive. Clinical decisions and their timeliness, therefore, directly affect both the patient outcome and the cost of care. To make timely decisions, we argue the underlying serving system must be latency-aware. To compound the challenge, health analytic applications often require a combination of models instead of a single model, to better specialize individual models for different targets, multi-modal data, different prediction windows, and potentially personalized predictions. To address these challenges, we propose HOLMES---an online model ensemble serving framework for healthcare applications. HOLMES dynamically identifies the best performing set of models to ensemble for highest accuracy, while also satisfying sub-second latency constraints on end-to-end prediction. We demonstrate that HOLMES is able to navigate the accuracy/latency tradeoff efficiently, compose the ensemble, and serve the model ensemble pipeline, scaling to simultaneously streaming data from 100 patients, each producing waveform data at 250~Hz. HOLMES outperforms the conventional offline batch-processed inference for the same clinical task in terms of accuracy and latency (by order of magnitude). HOLMES is tested on risk prediction task on pediatric cardio ICU data with above 95% prediction accuracy and sub-second latency on 64-bed simulation.

Binary data with one-class missing values are ubiquitous in real-world applications. They can be represented by irregular tensors with varying sizes in one dimension, where value one means presence of a feature while zero means unknown (i.e., either presence or absence of a feature). Learning accurate low-rank approximations from such binary irregular tensors is a challenging task. However, none of the existing models developed for factorizing irregular tensors take the missing values into account, and they assume Gaussian distributions, resulting in a distribution mismatch when applied to binary data. In this paper, we propose Logistic PARAFAC2 (LogPar) by modeling the binary irregular tensor with Bernoulli distribution parameterized by an underlying real-valued tensor. Then we approximate the underlying tensor with a positive-unlabeled learning loss function to account for the missing values. We also incorporate uniqueness and temporal smoothness regularization to enhance the interpretability. Extensive experiments using large-scale real-world datasets show that LogPar outperforms all baselines in both irregular tensor completion and downstream predictive tasks. For the irregular tensor completion, LogPar achieves up to 26% relative improvement compared to the best baseline. Besides, LogPar obtains relative improvement of 13.2% for heart failure prediction and 14% for mortality prediction on average compared to the state-of-the-art PARAFAC2 models.

Taxonomies are important knowledge ontologies that underpin numerous applications on a daily basis, but many taxonomies used in practice suffer from the low coverage issue. We study the taxonomy expansion problem, which aims to expand existing taxonomies with new concept terms. We propose a self-supervised taxonomy expansion model named STEAM, which leverages natural supervision in the existing taxonomy for expansion. To generate natural self-supervision signals, STEAM samples mini-paths from the existing taxonomy, and formulates a node attachment prediction task between anchor mini-paths and query terms. To solve the node attachment task, it learns feature representations for query-anchor pairs from multiple views and performs multi-view co-training for prediction. Extensive experiments show that STEAM outperforms state-of-the-art methods for taxonomy expansion by 11.6% in accuracy and 7.0% in mean reciprocal rank on three public benchmarks. The code and data for STEAM can be found at https://github.com/yueyu1030/STEAM.

Generating clinical reports from raw recordings such as X-rays and electroencephalogram (EEG) is an essential and routine task for doctors. However, it is often time-consuming to write accurate and detailed reports. Most existing methods try to generate the whole reports from the raw input with limited success because 1) generated reports often contain errors that need manual review and correction, 2) it does not save time when doctors want to write additional information into the report, and 3) the generated reports are not customized based on individual doctors’ preference. We propose CLinicAl Report Auto-completion (, an interactive method that generates reports in a sentence by sentence fashion based on doctors’ anchor words and partially completed sentences. earches for most relevant sentences from existing reports as the template for the current report. The retrieved sentences are sequentially modified by combining with the input feature representations to create the final report. In our experimental evaluation chieved 0.393 CIDEr and 0.248 BLEU-4 on X-ray reports and 0.482 CIDEr and 0.491 BLEU-4 for EEG reports for sentence-level generation, which is up to 35% improvement over the best baseline. Also via our qualitative evaluation, s shown to produce reports which have a significantly higher level of approval by doctors in a user study (3.74 out of 5 for s 2.52 out of 5 for the baseline).

In recent years, significant attention has been devoted towards integrating deep learning technologies in the healthcare domain. However, to safely and practically deploy deep learning models for home health monitoring, two significant challenges must be addressed: the models should be (1) robust against noise; and (2) compact and energy-efficient. We propose Rest , a new method that simultaneously tackles both issues via 1) adversarial training and controlling the Lipschitz constant of the neural network through spectral regularization while 2) enabling neural network compression through sparsity regularization. We demonstrate that Rest produces highly-robust and efficient models that substantially outperform the original full-sized models in the presence of noise. For the sleep staging task over single-channel electroencephalogram (EEG), the Rest model achieves a macro-F1 score of 0.67 vs. 0.39 achieved by a state-of-the-art model in the presence of Gaussian noise while obtaining 19 × parameter reduction and 15 × MFLOPS reduction on two large, real-world EEG datasets. By deploying these models to an Android application on a smartphone, we quantitatively observe that Rest allows models to achieve up to 17 × energy reduction and 9 × faster inference. We open source the code repository with this paper: https://github.com/duggalrahul/REST.

Deep learning has demonstrated success in health risk prediction especially for patients with chronic and progressing conditions. Most existing works focus on learning disease patterns from longitudinal patient data, but pay little attention to the disease progression stage itself. To fill the gap, we propose a Stage-aware neural Network (StageNet) model to extract disease stage information from patient data and integrate it into risk prediction. StageNet is enabled by (1) a stage-aware long short-term memory (LSTM) module that extracts health stage variations unsupervisedly; (2) a stage-adaptive convolutional module that incorporates stage-related progression patterns into risk prediction. We evaluate StageNet on two real-world datasets and show that StageNet outperforms state-of-the-art models in risk prediction task and patient subtyping task. Compared to the best baseline model, StageNet achieves up to 12% higher AUPRC for risk prediction task on two real-world patient datasets. StageNet also achieves over 58% higher Calinski-Harabasz score (a cluster quality metric) for a patient subtyping task.

Clinical trials are essential for drug development but often suffer from expensive, inaccurate and insufficient patient recruitment. The core problem of patient-trial matching is to find qualified patients for a trial, where patient information is stored in electronic health records (EHR) while trial eligibility criteria (EC) are described in text documents available on the web. How to represent longitudinal patient EHR? How to extract complex logical rules from EC? Most existing works rely on manual rule-based extraction, which is time consuming and inflexible for complex inference. To address these challenges, we proposed a cross-modal inference learning model to jointly encode enrollment criteria (text) and patients records (tabular data) into a shared latent space for matching inference. pplies a pre-trained Bidirectional Encoder Representations from Transformers(BERT) model to encode clinical trial information into sentence embedding. And uses a hierarchical embedding model to represent patient longitudinal EHR. In addition, s augmented by a numerical information embedding and entailment module to reason over numerical information in both EC and EHR. These encoders are trained jointly to optimize patient-trial matching score. We evaluated n the trial-patient matching task with demonstrated on real world datasets. utperformed the best baseline by up to 12.4% in average F1.

In silico modeling of medicine refers to the direct use of computational methods in support of drug discovery and development. Machine learning and data mining methods have become an integral part of in silico modeling and demonstrated promising performance at various phases of the drug discovery and development process. In this tutorial we will introduce data analytic methods in drug discovery and development. For the first half, we will provide an overview about related data and analytic tasks, and then present the enabling data analytic methods for these tasks. For the second half, we will describe concrete applications of each of those tasks. The tutorial will be concluded with open problems and a Q&A session.

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.

Although deep learning models trained on electronic health records (EHR) data have shown state-of-the-art performance in many predictive clinical tasks, the discovery of adversarial examples (i.e., input data that are engineered to cause misclassification) has exposed vulnerabilities with lab and imaging data. We specifically consider adversarial examples with longitudinal EHR data, an area that has not been previously examined because of the challenges with temporal high-dimensional and sparse features. We propose Longitudinal AdVersarial Attack (, a saliency score based adversarial example using a method that requires a minimal number of perturbations and that automatically minimizes the likelihood of detection. Features are selected and modified by jointly modeling a saliency map and attention mechanism. Experimental results with longitudinal EHR data show that an substantially reduce model performance for attention-based target models (from AUPR = 0.5 to AUPR = 0.08).

In order to reduce the possibility of neural injury from seizures and sidestep the need for a neurologist to spend hours on manually reviewing the EEG recording, it is critical to automatically detect and classify "interictal-ictal continuum" (IIC) patterns from EEG data. However, the existing IIC classification techniques are shown to be not accurate and robust enough for clinical use because of the lack of high quality labels of EEG segments as training data. Obtaining high-quality labeled data is traditionally a manual process by trained clinicians that can be tedious, time-consuming, and error-prone. In this work, we propose Smile, an industrial scale system that provides an end-to-end solution to the IIC pattern classification problem. The core components of Smile include a visualization-based time series labeling module and a deep-learning based active learning module. The labeling module enables the users to explore and label 350 million EEG segments (30TB) at interactive speed. The multiple coordinated views allow the users to examine the EEG signals from both time domain and frequency domain simultaneously. The active learning module first trains a deep neural network that automatically extracts both the local features with respect to each segment itself and the long term dynamics of the EEG signals to classify IIC patterns. Then leveraging the output of the deep learning model, the EEG segments that can best improve the model are selected and prompted to clinicians to label. This process is iterated until the clinicians and the models show high degree of agreement. Our initial experimental results show that our Smile system allows the clinicians to label the EEG segments at will with a response time below 500 ms. The accuracy of the model is progressively improved as more and more high quality labels are acquired over time.

PARAFAC2 has demonstrated success in modeling irregular tensors, where the tensor dimensions vary across one of the modes. An example scenario is modeling treatments across a set of patients with the varying number of medical encounters over time. Despite recent improvements on unconstrained PARAFAC2, its model factors are usually dense and sensitive to noise which limits their interpretability. As a result, the following open challenges remain: a) various modeling constraints, such as temporal smoothness, sparsity and non-negativity, are needed to be imposed for interpretable temporal modeling and b) a scalable approach is required to support those constraints efficiently for large datasets. To tackle these challenges, we propose a COnstrained PARAFAC2 (COPA) method, which carefully incorporates optimization constraints such as temporal smoothness, sparsity, and non-negativity in the resulting factors. To efficiently support all those constraints, COPA adopts a hybrid optimization framework using alternating optimization and alternating direction method of multiplier (AO-ADMM). As evaluated on large electronic health record (EHR) datasets with hundreds of thousands of patients, COPA achieves significant speedups (up to 36 times faster) over prior PARAFAC2 approaches that only attempt to handle a subset of the constraints that COPA enables. Overall, our method outperforms all the baselines attempting to handle a subset of the constraints in terms of speed, while achieving the same level of accuracy. Through a case study on temporal phenotyping of medically complex children, we demonstrate how the constraints imposed by COPA reveal concise phenotypes and meaningful temporal profiles of patients. The clinical interpretation of both the phenotypes and the temporal profiles was confirmed by a medical expert.

This paper presents a new method, which we call SUSTain, that extends real-valued matrix and tensor factorizations to data where values are integers. Such data are common when the values correspond to event counts or ordinal measures. The conventional approach is to treat integer data as real, and then apply real-valued factorizations. However, doing so fails to preserve important characteristics of the original data, thereby making it hard to interpret the results. Instead, our approach extracts factor values from integer datasets as scores that are constrained to take values from a small integer set. These scores are easy to interpret: a score of zero indicates no feature contribution and higher scores indicate distinct levels of feature importance. At its core, SUSTain relies on: a) a problem partitioning into integer-constrained subproblems, so that they can be optimally solved in an efficient manner; and b) organizing the order of the subproblems' solution, to promote reuse of shared intermediate results. We propose two variants, SUSTain_M and SUSTain_T, to handle both matrix and tensor inputs, respectively. We evaluate SUSTain against several state-of-the-art baselines on both synthetic and real Electronic Health Record (EHR) datasets. Comparing to those baselines, SUSTain shows either significantly better fit or orders of magnitude speedups that achieve a comparable fit (up to 425× faster). We apply SUSTain to EHR datasets to extract patient phenotypes (i.e., clinically meaningful patient clusters). Furthermore, 87% of them were validated as clinically meaningful phenotypes related to heart failure by a cardiologist.

With the improvement of medical data capturing, vast amount of continuous patient monitoring data, e.g., electrocardiogram (ECG), real-time vital signs and medications, become available for clinical decision support at intensive care units (ICUs). However, it becomes increasingly challenging to model such data, due to high density of the monitoring data, heterogeneous data types and the requirement for interpretable models.

accuracy, data needs, interpretability) of GRAM to various methods including the recurrent neural network (RNN) in two sequential diagnoses prediction tasks and one heart failure prediction task. Compared to the basic RNN, GRAM achieved 10% higher accuracy for predicting diseases rarely observed in the training data and 3% improved area under the ROC curve for predicting heart failure using an order of magnitude less training data. Additionally, unlike other methods, the medical concept representations learned by GRAM are well aligned with the medical ontology. Finally, GRAM exhibits intuitive attention behaviors by adaptively generalizing to higher level concepts when facing data insufficiency at the lower level concepts.

Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospitals, in which direct patient-level data sharing is not possible (e.g., due to institutional policies). In this paper, we developed a novel solution to enable federated tensor factorization for computational phenotyping without sharing patient-level data. We developed secure data harmonization and federated computation procedures based on alternating direction method of multipliers (ADMM). Using this method, the multiple hospitals iteratively update tensors and transfer secure summarized information to a central server, and the server aggregates the information to generate phenotypes. We demonstrated with real medical datasets that our method resembles the centralized training model (based on combined datasets) in terms of accuracy and phenotypes discovery while respecting privacy.

In exploratory tensor mining, a common problem is how to analyze a set of variables across a set of subjects whose observations do not align naturally. For example, when modeling medical features across a set of patients, the number and duration of treatments may vary widely in time, meaning there is no meaningful way to align their clinical records across time points for analysis purposes. To handle such data, the state-of-the-art tensor model is the so-called PARAFAC2, which yields interpretable and robust output and can naturally handle sparse data. However, its main limitation up to now has been the lack of efficient algorithms that can handle large-scale datasets.

Managing patients with complex multimorbidity has long been recognized as a difficult problem due to complex disease and medication dependencies and the potential risk of adverse drug interactions. Existing work either uses complicated rule-based protocols which are hard to implement and maintain, or simple statistical models that treat each disease independently, which may lead to sub-optimal or even harmful drug combinations. In this work, we propose the LEAP (LEArn to Prescribe) algorithm to decompose the treatment recommendation into a sequential decision-making process while automatically determining the appropriate number of medications. A recurrent decoder is used to model label dependencies and content-based attention is used to capture label instance mapping. We further leverage reinforcement learning to fine tune the model parameters to ensure accuracy and completeness. We incorporate external clinical knowledge into the design of the reinforcement reward to effectively prevent generating unfavorable drug combinations. Both quantitative experiments and qualitative case studies are conducted on two real world electronic health record datasets to verify the effectiveness of our solution. On both datasets, LEAP significantly outperforms baselines by up to 10-30% in terms of mean Jaccard coefficient and removes 99.8% adverse drug interactions in the recommended treatment sets.

We study the problem of Polyadic Prediction, where the input consists of an ordered tuple of objects, and the goal is to predict a measurement associated with them. Many tasks can be naturally framed as Polyadic Prediction problems. In drug discovery, for instance, it is important to estimate the treatment effect of a drug on various tissue-specific diseases, as it is expressed over the available genes. Thus, we essentially predict the expression value measurements for several (drug, gene, tissue) triads. To tackle Polyadic Prediction problems, we propose a general framework, called Polyadic Regression, predicting measurements associated with multiple objects. Our framework is inductive, in the sense of enabling predictions for new objects, unseen during training. Our model is expressive, exploring high-order, polyadic interactions in an efficient manner. An alternating Proximal Gradient Descent procedure is proposed to fit our model. We perform an extensive evaluation using real-world chemogenomics data, where we illustrate the superior performance of Polyadic Regression over the prior art. Our method achieves an increase of 0.06 and 0.1 in Spearman correlation between the predicted and the actual measurement vectors, for predicting missing polyadic data and predicting polyadic data for new drugs, respectively.

Proper representations of medical concepts such as diagnosis, medication, procedure codes and visits from Electronic Health Records (EHR) has broad applications in healthcare analytics. Patient EHR data consists of a sequence of visits over time, where each visit includes multiple medical concepts, e.g., diagnosis, procedure, and medication codes. This hierarchical structure provides two types of relational information, namely sequential order of visits and co-occurrence of the codes within a visit. In this work, we propose Med2Vec, which not only learns the representations for both medical codes and visits from large EHR datasets with over million visits, but also allows us to interpret the learned representations confirmed positively by clinical experts. In the experiments, Med2Vec shows significant improvement in prediction accuracy in clinical applications compared to baselines such as Skip-gram, GloVe, and stacked autoencoder, while providing clinically meaningful interpretation.

Modern data science relies on data analytic pipelines to organize interdependent computational steps. Such analytic pipelines often involve different algorithms across multiple steps, each with its own hyperparameters. To achieve the best performance, it is often critical to select optimal algorithms and to set appropriate hyperparameters, which requires large computational efforts. Bayesian optimization provides a principled way for searching optimal hyperparameters for a single algorithm. However, many challenges remain in solving pipeline optimization problems with high-dimensional and highly conditional search space. In this work, we propose Fast LineAr SearcH (FLASH), an efficient method for tuning analytic pipelines. FLASH is a two-layer Bayesian optimization framework, which firstly uses a parametric model to select promising algorithms, then computes a nonparametric model to fine-tune hyperparameters of the promising algorithms. FLASH also includes an effective caching algorithm which can further accelerate the search process. Extensive experiments on a number of benchmark datasets have demonstrated that FLASH significantly outperforms previous state-of-the-art methods in both search speed and accuracy. Using 50% of the time budget, FLASH achieves up to 20% improvement on test error rate compared to the baselines. FLASH also yields state-of-the-art performance on a real-world application for healthcare predictive modeling.

Signed social networks have become increasingly important in recent years because of the ability to model trust-based relationships in review sites like Slashdot, Epinions, and Wikipedia. As a result, many traditional network mining problems have been re-visited in the context of networks in which signs are associated with the links. Examples of such problems include community detection, link prediction, and low rank approximation. In this paper, we will examine the problem of ranking nodes in signed networks. In particular, we will design a ranking model, which has a clear physical interpretation in terms of the sign of the edges in the network. Specifically, we propose the Troll-Trust model that models the probability of trustworthiness of individual data sources as an interpretation for the underlying ranking values. We will show the advantages of this approach over a variety of baselines.

Modeling disease relationships and temporal progression are two key problems in health analytics, which have not been studied together due to data and technical challenges. Thanks to the increasing adoption of Electronic Health Records (EHR), rich patient information is being collected over time. Using EHR data as input, we propose a multivariate context-sensitive Hawkes process or cHawkes, which simultaneously infers the disease relationship network and models temporal progression of patients. Besides learning disease network and temporal progression model, cHawkes is able to predict when a specific patient might have other related diseases in future given the patient history, which in turn can have many potential applications in predictive health analytics, public health policy development and customized patient care. Extensive experiments on real EHR data demonstrate that cHawkes not only can uncover meaningful disease relations and model accurate temporal progression of patients, but also has significantly better predictive performance compared to several baseline models.

We propose a new tensor factorization method, called the Sparse Hierarchical-Tucker (Sparse H-Tucker), for sparse and high-order data tensors. Sparse H-Tucker is inspired by its namesake, the classical Hierarchical Tucker method, which aims to compute a tree-structured factorization of an input data set that may be readily interpreted by a domain expert. However, Sparse H-Tucker uses a nested sampling technique to overcome a key scalability problem in Hierarchical Tucker, which is the creation of an unwieldy intermediate dense core tensor, the result of our approach is a faster, more space-efficient, and more accurate method. We test our method on a real healthcare dataset, which is collected from 30K patients and results in an 18th order sparse data tensor. Unlike competing methods, Sparse H-Tucker can analyze the full data set on a single multi-threaded machine. It can also do so more accurately and in less time than the state-of-the-art: on a 12th order subset of the input data, Sparse H-Tucker is 18x more accurate and 7.5x faster than a previously state-of-the-art method. Moreover, we observe that Sparse H-Tucker scales nearly linearly in the number of non-zero tensor elements. The resulting model also provides an interpretable disease hierarchy, which is confirmed by a clinical expert.

Computational phenotyping is the process of converting heterogeneous electronic health records (EHRs) into meaningful clinical concepts. Unsupervised phenotyping methods have the potential to leverage a vast amount of labeled EHR data for phenotype discovery. However, existing unsupervised phenotyping methods do not incorporate current medical knowledge and cannot directly handle missing, or noisy data. We propose Rubik, a constrained non-negative tensor factorization and completion method for phenotyping. Rubik incorporates 1) guidance constraints to align with existing medical knowledge, and 2) pairwise constraints for obtaining distinct, non-overlapping phenotypes. Rubik also has built-in tensor completion that can significantly alleviate the impact of noisy and missing data. We utilize the Alternating Direction Method of Multipliers (ADMM) framework to tensor factorization and completion, which can be easily scaled through parallel computing. We evaluate Rubik on two EHR datasets, one of which contains 647,118 records for 7,744 patients from an outpatient clinic, the other of which is a public dataset containing 1,018,614 CMS claims records for 472,645 patients. Our results show that Rubik can discover more meaningful and distinct phenotypes than the baselines. In particular, by using knowledge guidance constraints, Rubik can also discover sub-phenotypes for several major diseases. Rubik also runs around seven times faster than current state-of-the-art tensor methods. Finally, Rubik is scalable to large datasets containing millions of EHR records.

Recognizing entity instances in documents according to a knowledge base is a fundamental problem in many data mining applications. The problem is extremely challenging for short documents in complex domains such as social media and biomedical domains. Large concept spaces and instance ambiguity are key issues that need to be addressed. Most of the documents are created in a social context by common authors via social interactions, such as reply and citations. Such social contexts are largely ignored in the instance-recognition literature. How can users' interactions help entity instance recognition? How can the social context be modeled so as to resolve the ambiguity of different instances?

The rapidly increasing availability of electronic health records (EHRs) from multiple heterogeneous sources has spearheaded the adoption of data-driven approaches for improved clinical research, decision making, prognosis, and patient management. Unfortunately, EHR data do not always directly and reliably map to phenotypes, or medical concepts, that clinical researchers need or use. Existing phenotyping approaches typically require labor intensive supervision from medical experts. We propose Marble, a novel sparse non-negative tensor factorization method to derive phenotype candidates with virtually no human supervision. Marble decomposes the observed tensor into two terms, a bias tensor and an interaction tensor. The bias tensor represents the baseline characteristics common amongst the overall population and the interaction tensor defines the phenotypes. We demonstrate the capability of our proposed model on both simulated and patient data from a publicly available clinical database. Our results show that Marble derived phenotypes provide at least a 42.8% reduction in the number of non-zero element and also retains predictive power for classification purposes. Furthermore, the resulting phenotypes and baseline characteristics from real EHR data are consistent with known characteristics of the patient population. Thus it can potentially be used to rapidly characterize, predict, and manage a large number of diseases, thereby promising a novel, data-driven solution that can benefit very large segments of the population.

Large amounts of heterogeneous medical data have become available in various healthcare organizations (payers, providers, pharmaceuticals). Those data could be an enabling resource for deriving insights for improving care delivery and reducing waste. The enormity and complexity of these datasets present great challenges in analyses and subsequent applications to a practical clinical environment. In this tutorial, we introduce the characteristics and related mining challenges on dealing with big medical data. Many of those insights come from medical informatics community, which is highly related to data mining but focuses on biomedical specifics. We survey various related papers from data mining venues as well as medical informatics venues to share with the audiences key problems and trends in healthcare analytics research, with different applications ranging from clinical text mining, predictive modeling, survival analysis, patient similarity, genetic data analysis, and public health. The tutorial will include several case studies dealing with some of the important healthcare applications.

Conformity is a type of social influence involving a change in opinion or behavior in order to fit in with a group. Employing several social networks as the source for our experimental data, we study how the effect of conformity plays a role in changing users' online behavior. We formally define several major types of conformity in individual, peer, and group levels. We propose Confluence model to formalize the effects of social conformity into a probabilistic model. Confluence can distinguish and quantify the effects of the different types of conformities. To scale up to large social networks, we propose a distributed learning method that can construct the Confluence model efficiently with near-linear speedup. Our experimental results on four different types of large social networks, i.e., Flickr, Gowalla, Weibo and Co-Author, verify the existence of the conformity phenomena. Leveraging the conformity information, Confluence can accurately predict actions of users. Our experiments show that Confluence significantly improves the prediction accuracy by up to 5-10% compared with several alternative methods.

Traditionally, feature construction and feature selection are two important but separate processes in data mining. However, many real world applications require an integrated approach for creating, refining and selecting features. To address this problem, we propose FeaFiner (short for Feature Refiner), an efficient formulation that simultaneously generalizes low-level features into higher level concepts and then selects relevant concepts based on the target variable. Specifically, we formulate a double sparsity optimization problem that identifies groups in the low-level features, generalizes higher level features using the groups and performs feature selection. Since in many clinical researches non- overlapping groups are preferred for better interpretability, we further improve the formulation to generalize features using mutually exclusive feature groups. The proposed formulation is challenging to solve due to the orthogonality constraints, non-convexity objective and non-smoothness penal- ties. We apply a recently developed augmented Lagrangian method to solve this formulation in which each subproblem is solved by a non-monotone spectral projected gradient method. Our numerical experiments show that this approach is computationally efficient and also capable of producing solutions of high quality. We also present a generalization bound showing the consistency and the asymptotic behavior of the learning process of our proposed formulation.

The patient risk prediction model aims at assessing the risk of a patient in developing a target disease based on his/her health profile. As electronic health records (EHRs) become more prevalent, a large number of features can be constructed in order to characterize patient profiles. This wealth of data provides unprecedented opportunities for data mining researchers to address important biomedical questions. Practical data mining challenges include: How to correctly select and rank those features based on their prediction power? What predictive model performs the best in predicting a target disease using those features? In this paper, we propose top-k stability selection, which generalizes a powerful sparse learning method for feature selection by overcoming its limitation on parameter selection. In particular, our proposed top-k stability selection includes the original stability selection method as a special case given k = 1. Moreover, we show that the top-k stability selection is more robust by utilizing more information from selection probabilities than the original stability selection, and provides stronger theoretical properties. In a large set of real clinical prediction datasets, the top-k stability selection methods outperform many existing feature selection methods including the original stability selection. We also compare three competitive classification methods (SVM, logistic regression and random forest) to demonstrate the effectiveness of selected features by our proposed method in the context of clinical prediction applications. Finally, through several clinical applications on predicting heart failure related symptoms, we show that top-k stability selection can successfully identify important features that are clinically meaningful.

Social influence is the behavioral change of a person because of the perceived relationship with other people, organizations and society in general. Social influence has been a widely accepted phenomenon in social networks for decades. Many applications have been built based around the implicit notation of social influence between people, such as marketing, advertisement and recommendations. With the exponential growth of online social network services such as Facebook and Twitter, social influence can for the first time be measured over a large population. In this tutorial, we survey the research on social influence analysis with a focus on the computational aspects. First, we introduce how to verify the existence of social influence in various social networks. Second, we present computational models for quantifying social influence. Third, we describe how social influence can help real applications. In particular, we will focus on opinion leader finding and influence maximization for viral marketing. Finally, we apply the selected algorithms of social influence analysis on different social network data, such as twitter, arnetminer data, weibo, and slashdot forum.

It is often challenging to incorporate users' interactions into a recommendation framework in an online model. In this paper, we propose a novel interactive learning framework to formulate the problem of recommending patent partners into a factor graph model. The framework involves three phases: 1) candidate generation, where we identify the potential set of collaborators; 2) candidate refinement, where a factor graph model is used to adjust the candidate rankings; 3) interactive learning method to efficiently update the existing recommendation model based on inventors' feedback. We evaluate our proposed model on large enterprise patent networks. Experimental results demonstrate that the recommendation accuracy of the proposed model significantly outperforms several baselines methods using content similarity, collaborative filtering and SVM-Rank. We also demonstrate the effectiveness and efficiency of the interactive learning, which performs almost as well as offline re-training, but with only 1 percent of the running time.

Large collections of electronic clinical records today provide us with a vast source of information on medical practice. However, the utilization of those data for exploratory analysis to support clinical decisions is still limited. Extracting useful patterns from such data is particularly challenging because it is longitudinal, sparse and heterogeneous. In this paper, we propose a Nonnegative Matrix Factorization (NMF) based framework using a convolutional approach for open-ended temporal pattern discovery over large collections of clinical records. We call the method One-Sided Convolutional NMF (OSC-NMF). Our framework can mine common as well as individual shift-invariant temporal patterns from heterogeneous events over different patient groups, and handle sparsity as well as scalability problems well. Furthermore, we use an event matrix based representation that can encode quantitatively all key temporal concepts including order, concurrency and synchronicity. We derive efficient multiplicative update rules for OSC-NMF, and also prove theoretically its convergence. Finally, the experimental results on both synthetic and real world electronic patient data are presented to demonstrate the effectiveness of the proposed method.

This paper presents Latent Association Analysis (LAA), a generative model that analyzes the topics within two document sets simultaneously, as well as the correlations between the two topic structures, by considering the semantic associations among document pairs. LAA defines a correlation factor that represents the connection between two documents, and considers the topic proportion of paired documents based on this factor. Words in the documents are assumed to be randomly generated by particular topic assignments and topic-to-word probability distributions. The paper also presents a new ranking algorithm, based on LAA, that can be used to retrieve target documents that are potentially associated with a given source document. The ranking algorithm uses the latent factor in LAA to rank target documents by the strength of their semantic associations with the source document. We evaluate the LAA algorithm with real datasets, specifically, the IT-Change and the IT-Solution document sets from the IBM IT service environment and the Symptom-Treatment document sets from Google Health. Experimental results demonstrate that the LAA algorithm significantly outperforms existing algorithms.

As an integral part of Electronic Health Records (EHRs), clinical notes pose special challenges for analyzing EHRs due to their unstructured nature. In this paper, we present a general mining framework SympGraph for modeling and analyzing symptom relationships in clinical notes.

Interdisciplinary collaborations have generated huge impact to society. However, it is often hard for researchers to establish such cross-domain collaborations. What are the patterns of cross-domain collaborations? How do those collaborations form? Can we predict this type of collaborations?

Random walk graph kernel has been used as an important tool for various data mining tasks including classification and similarity computation. Despite its usefulness, however, it suffers from the expensive computational cost which is at least O(n3) or O(m2) for graphs with n nodes and m edges. In this paper, we propose ARK, a set of fast algorithms for random walk graph kernel computation. ARK is based on the observation that real graphs have much lower intrinsic ranks, compared with the orders of the graphs. ARK exploits the low rank structure to quickly compute random walk graph kernels in O(n2) or O(m) time. Experimental results show that our method is up to 97,865× faster than the existing algorithms, while providing more than 91.3% of the accuracies.

As more clinical information with increasing diversity become available for analysis, a large number of features can be constructed and leveraged for predictive modeling. Feature selection is a classic analytic component that faces new challenges due to the new applications: How to handle a diverse set of high dimensional features? How to select features with high predictive power, but low redundant information? How to design methods that can select globally optimal features with theoretical guarantee? How to incorporate and extend existing knowledge driven approach? In this paper, we present Scalable Orthogonal Regression (SOR), an optimization-based feature selection method with the following novelties: 1) Scalability: SOR achieves nearly linear scale-up with respect to the number of input features and the number of samples; 2) Optimality: SOR is formulated as an alternative convex optimization problem with theoretical convergence and global optimality guarantee; 3) Low-redundancy: thanks to the orthogonality objective, SOR is designed specifically to select less redundant features without sacrificing quality; 4) Extendability: SOR can enhance an existing set of preselected features by adding additional features that complement the existing feature set but still with strong predictive power. We present evaluation results showing that SOR consistently outperforms state of the art feature selection methods in a range of quality metrics on several real world data sets. We demonstrate a case study of a large-scale clinical application for predicting early onset of Heart Failure (HF) using real Electronic Health Records (EHRs) data of over 10K patients for over 7 years. Leveraging SOR, we are able to construct accurate and robust predictive models and derive potential clinical insights.

Social influence, the phenomenon that the actions of a user can induce her/his friends to behave in a similar way, plays a key role in many (online) social systems. For example, a company wants to market a new product through the effect of "word of mouth'' in the social network. It wishes to find and convince a small number of influential users to adopt the product, and the goal is to trigger a large cascade of further adoptions. Fundamentally, we need to answer the following question: how to quantify the influence between two users in a large social network? To address this question, we propose a pair wise factor graph (PFG) model to model the social influence in social networks. An efficient algorithm is designed to learn the model and make inference. We further propose a dynamic factor graph (DFG) model to incorporate the time information. Experimental results on three different genres of data sets show that the proposed approaches can efficiently infer the dynamic social influence. The results are applied to the influence maximization problem, which aims to find a small subset of nodes (users) in a social network that could maximize the spread of influence. Experiments show that the proposed approach can facilitate the application.

Documents in rich text corpora often contain multiple facets of information. For example, an article from a medical document collection might consist of multifaceted information about symptoms, treatments, causes, diagnoses, prognoses, and preventions. Thus, documents in the collection may have different relations across each of these various facets. Topic analysis and exploration for such multi-relational corpora is a challenging visual analytic task. This paper presents Solar Map, a multifaceted visual analytic technique for visually exploring topics in multi-relational data. Solar Map simultaneously visualizes the topic distribution of the underlying entities from one facet together with keyword distributions that convey the semantic definition of each cluster along a secondary facet. Solar Map combines several visual techniques including 1) topic contour clusters and interactive multifaceted keyword topic rings, 2) a global layout optimization algorithm that aligns each topic cluster with its corresponding keywords, and 3) 2) an optimal temporal network segmentation and layout method that renders temporal evolution of clusters. Finally, the paper concludes with two case studies and quantitative user evaluation which show the power of the Solar Map technique.

Graphs appear in numerous applications including cyber-security, the Internet, social networks, protein networks, recommendation systems, and many more. Graphs with millions or even billions of nodes and edges are common-place. How to store such large graphs efficiently? What are the core operations/queries on those graph? How to answer the graph queries quickly? We propose GBASE, a scalable and general graph management and mining system. The key novelties lie in 1) our storage and compression scheme for a parallel setting and 2) the carefully chosen graph operations and their efficient implementation. We designed and implemented an instance of GBASE using MapReduce/Hadoop. GBASE provides a parallel indexing mechanism for graph mining operations that both saves storage space, as well as accelerates queries. We ran numerous experiments on real graphs, spanning billions of nodes and edges, and we show that our proposed GBASE is indeed fast, scalable and nimble, with significant savings in space and time.

Node centrality measures are important in a large number of graph applications, from search and ranking to social and biological network analysis. In this paper we study node centrality for very large graphs, up to billions of nodes and edges. Various definitions for centrality have been proposed, ranging from very simple (e.g., node degree) to more elaborate. However, measuring centrality in billion-scale graphs poses several challenges. Many of the “traditional” definitions such as closeness and betweenness were not designed with scalability in mind. Therefore, it is very difficult, if not impossible, to compute them both accurately and efficiently. In this paper, we propose centrality measures suitable for very large graphs, as well as scalable methods to effectively compute them. More specifically, we propose effective closeness and LineRank which are designed for billion-scale graphs. We also develop algorithms to compute the proposed centrality measures in MapReduce, a modern paradigm for large-scale, distributed data processing. We present extensive experimental results on both synthetic and real datasets, which demonstrate the scalability of our approach to very large graphs, as well as interesting findings and anomalies.

Patient similarity assessment is an important task in the context of patient cohort identification for comparative effectiveness studies and clinical decision support applications. The goal is to derive clinically meaningful distance metric to measure the similarity between patients represented by their key clinical indicators. It is desirable to learn the distance metric based on experts' knowledge of clinical similarity among subjects. However, often different physicians have different understandings of patient similarity based on the specifics of the cases. The distance metric learned for each individual physician often leads to a limited view of the true underlying distance metric. The key challenge will be how to integrate the individual distance metrics obtained for a group of physicians into a globally consistent unified metric. In this paper, we propose the Composite Distance Integration (Comdi) approach. In this approach we first construct discriminative neighborhoods from each individual metrics, then we combine them into a single optimal distance metric. We formulate Comdi as a quadratic optimization problem and propose an efficient alternating strategy to find the optimal solution. Besides learning a globally consistent metric, Comdi provides an elegant way to share knowledge across multiple experts (physicians) without sharing the underlying data, which enables the privacy preserving collaboration. Our experiments on several benchmark data sets show approximately 10% improvement in classification accuracy over baseline. These results show that Comdi is an effective and general metric learning approach. An application of our approach to real patient data has also been presented in the results.

Patient similarity assessment aims at providing a clinically meaningful distance measure for case retrieval in the context of clinical decision intelligence. Two of the key challenges are how to incorporate physician feedback with regard to the retrieval results and how to interactively update the underlying similarity measure based on the feedback. In this paper, we present the interactive Metric learning (iMet) method that can incrementally adjust the underlying distance metric based on latest supervision information. iMet is designed to scale linearly with the data set size based on matrix perturbation theory which allows the derivation of sound theoretical guarantees. We show empirical results demonstrating that iMet outperforms the baseline by three orders of magnitude in speed while obtaining comparable accuracy on several benchmark datasets. We also describe the application of the algorithm in a real world physician decision support system.

This work aims at discovering community structure in rich media social networks through analysis of time-varying, multirelational data. Community structure represents the latent social context of user actions. It has important applications such as search and recommendation. The problem is particularly useful in the enterprise domain, where extracting emergent community structure on enterprise social media can help in forming new collaborative teams, in expertise discovery, and in the long term reorganization of enterprises based on collaboration patterns. There are several unique challenges: (a) In social media, the context of user actions is constantly changing and coevolving; hence the social context contains time-evolving multidimensional relations. (b) The social context is determined by the available system features and is unique in each social media platform; hence the analysis of such data needs to flexibly incorporate various system features. In this article we propose MetaFac (MetaGraph Factorization), a framework that extracts community structures from dynamic, multidimensional social contexts and interactions. Our work has three key contributions: (1) metagraph, a novel relational hypergraph representation for modeling multirelational and multidimensional social data; (2) an efficient multirelational factorization method for community extraction on a given metagraph; (3) an online method to handle time-varying relations through incremental metagraph factorization. Extensive experiments on real-world social data collected from an enterprise and the public Digg social media Web site suggest that our technique is scalable and is able to extract meaningful communities from social media contexts. We illustrate the usefulness of our framework through two prediction tasks: (1) in the enterprise dataset, the task is to predict users’ future interests on tag usage, and (2) in the Digg dataset, the task is to predict users’ future interests in voting and commenting on Digg stories. Our prediction significantly outperforms baseline methods (including aspect model and tensor analysis), indicating the promising direction of using metagraphs for handling time-varying social relational contexts.

No abstract available.

Many applications generate a large volume of parallel document collections. A parallel document collection consists of two sets of documents where the documents in each set correspond to each other and form semantic pairs (e.g., pairs of problem and solution descriptions in a help-desk setting). Although much work has been done on text mining, little previous work has attempted to mine such a novel kind of text data. In this paper, we propose a new probabilistic topic model, called Probabilistic Topic Mapping (PTM) model, to mine parallel document collections to simultaneously discover latent topics in both sets of documents as well as the mapping of topics in one set to those in the other. We evaluate the PTM model on one real parallel document collection in IT service domain. We show that PTM can effectively discover meaningful topics, as well as their mappings, and it's also useful for improving text matching and retrieval when there's a vocabulary gap.

We present a mining system that can predict the future health status of the patient using the temporal trajectories of health status of a set of similar patients. The main novelties of this system are its use of stream processing technology for handling the incoming physiological time series data and incorporating domain knowledge in learning the similarity metric between patients represented by their temporal data. The proposed approach and system were tested using the MIMIC II database, which consists of physiological waveforms, and accompanying clinical data obtained for ICU patients. The study was carried out on 1500 patients from this database. In the experiments we report the efficiency and throughput of the stream processing unit for feature extraction, the effectiveness of the supervised similarity measure both in the context of classification and retrieval tasks compared to unsupervised approaches, and the accuracy of the temporal projections of the patient data.

Human emotion is one important underlying force affecting and affected by the dynamics of social networks. An interesting question is “can we predict a person's mood based on his historic emotion log and his social network?”. In this paper, we propose a Mood Cast method based on a dynamic continuous factor graph model for modeling and predicting users' emotions in a social network. Mood Cast incorporates users' dynamic status information (e.g., locations, activities, and attributes) and social influence from users' friends into a unified model. Based on the historical information (e.g., network structure and users' status from time 0 to t-1), Mood Cast learns a discriminative model for predicting users' emotion status at time t. To the best of our knowledge, this work takes the first step in designing a principled model for emotion prediction in social networks. Our experimental results on both real social network and virtual web-based network show that we can accurately predict emotion status of more than 62% of users and 8+% improvement than the baseline methods.

It is well known that users' behaviors (actions) in a social network are influenced by various factors such as personal interests, social influence, and global trends. However, few publications systematically study how social actions evolve in a dynamic social network and to what extent different factors affect the user actions.

Accurately capturing user preferences over time is a great practical challenge in recommender systems. Simple correlation over time is typically not meaningful, since users change their preferences due to different external events. User behavior can often be determined by individual's long-term and short-term preferences. How to represent users' long-term and short-term preferences? How to leverage them for temporal recommendation? To address these challenges, we propose Session-based Temporal Graph (STG) which simultaneously models users' long-term and short-term preferences over time. Based on the STG model framework, we propose a novel recommendation algorithm Injected Preference Fusion (IPF) and extend the personalized Random Walk for temporal recommendation. Finally, we evaluate the effectiveness of our method using two real datasets on citations and social bookmarking, in which our proposed method IPF gives 15%-34% improvement over the previous state-of-the-art.

Huge amounts of rich context social network data are generated everyday from various applications such as FaceBook and Twitter. These data involve multiple social relations which are community-driven and dynamic in nature. The complex interplay of these characteristics poses tremendous challenges on the users who try to understand the underlying patterns in the social media. We introduce an exploratory analytical framework, ContexTour, which generates visual representations for exploring multiple dimensions of community activities, including relevant topics, representative users and the community-generated content, as well as their evolutions. ContexTour consists of two novel and complementary components: (1) Dynamic Relational Clustering (DRC) that efficiently tracks the community evolution and smoothly adapts to the community changes, and (2) Dynamic Network Contour-map (DNC) that visualizes the community activities and evolutions in various dimensions. In our experiments, we demonstrate ContexTour through case studies on the DBLP dataset. The visual results capture interesting and reasonable evolution in Computer Science research communities. Quantitatively, we show 85-165X performance gain of our DRC algorithm over the baseline method.

SmallBlue is a social networking application that unlocks the valuable business intelligence of 'who knows what?', 'who knows whom?' and 'who knows what about whom' within an organization, without requiring explicit involvement of individuals. The aim of SmallBlue is to locate knowledgeable colleagues, communities, and knowledge networks in companies. The suite also helps users manage their personal networks, and reach out to their extended network (the friends of their friends) to find and access expertise and information.

Large IT service providers track service requests and their execution through problem/change tickets. It is important to classify the tickets based on the problem/change description in order to understand service quality and to optimize service processes. However, two challenges exist in solving this classification problem: 1) ticket descriptions from different classes are of highly diverse characteristics, which invalidates most standard distance metrics; 2) it is very expensive to obtain high-quality labeled data. To address these challenges, we develop two seemingly independent methods 1) discriminative neighborhood metric learning (DNML) and 2) active learning with median selection (ALMS), both of which are, however, based on the same core technique: iterated representative selection. A case study on real IT service classification application is presented to demonstrate the effectiveness and efficiency of our proposed methods.

This paper aims at discovering community structure in rich media social networks, through analysis of time-varying, multi-relational data. Community structure represents the latent social context of user actions. It has important applications in information tasks such as search and recommendation. Social media has several unique challenges. (a) In social media, the context of user actions is constantly changing and co-evolving; hence the social context contains time-evolving multi-dimensional relations. (b) The social context is determined by the available system features and is unique in each social media website. In this paper we propose MetaFac (MetaGraph Factorization), a framework that extracts community structures from various social contexts and interactions. Our work has three key contributions: (1) metagraph, a novel relational hypergraph representation for modeling multi-relational and multi-dimensional social data; (2) an efficient factorization method for community extraction on a given metagraph; (3) an on-line method to handle time-varying relations through incremental metagraph factorization. Extensive experiments on real-world social data collected from the Digg social media website suggest that our technique is scalable and is able to extract meaningful communities based on the social media contexts. We illustrate the usefulness of our framework through prediction tasks. We outperform baseline methods (including aspect model and tensor analysis) by an order of magnitude.

In large social networks, nodes (users, entities) are influenced by others for various reasons. For example, the colleagues have strong influence on one's work, while the friends have strong influence on one's daily life. How to differentiate the social influences from different angles(topics)? How to quantify the strength of those social influences? How to estimate the model on real large networks?

With the explosion of social media, scalability becomes a key challenge. There are two main aspects of the problems that arise: 1) data volume: how to manage and analyze huge datasets to efficiently extract patterns, 2) data understanding: how to facilitate understanding of the patterns by users? To address both aspects of the scalability challenge, we present a hybrid approach that leverages two complementary disciplines, data mining and information visualization. In particular, we propose 1) an analytic data model for content-based networks using tensors; 2) an efficient high-order clustering framework for analyzing the data; 3) a scalable context-sensitive graph visualization to present the clusters. We evaluate the proposed methods using both synthetic and real datasets. In terms of computational efficiency, the proposed methods are an order of magnitude faster compared to the baseline. In terms of effectiveness, we present several case studies of real corporate social networks.

Social media websites promote diverse user interaction on media objects as well as user actions with respect to other users. The goal of this work is to discover community structure in rich media social networks, and observe how it evolves over time, through analysis of multi-relational data. The problem is important in the enterprise domain where extracting emergent community structure on enterprise social media, can help in forming new collaborative teams, aid in expertise discovery, and guide long term enterprise reorganization. Our approach consists of three main parts: (1) a relational hypergraph model for modeling various social context and interactions; (2) a novel hypergraph factorization method for community extraction on multi-relational social data; (3) an on-line method to handle temporal evolution through incremental hypergraph factorization. Extensive experiments on real-world enterprise data suggest that our technique is scalable and can extract meaningful communities. To evaluate the quality of our mining results, we use our method to predict users' future interests. Our prediction outperforms baseline methods (frequency counts, pLSA) by 36-250% on the average, indicating the utility of leveraging multi-relational social context by using our method.

Motivated by the enormous amounts of data collected in a large IT service provider organization, this paper presents a method for quickly and automatically summarizing and extracting meaningful insights from the data. Termed Clustered Subset Selection (CSS), our method enables program-guided data explorations of high-dimensional data matrices. CSS combines clustering and subset selection into a coherent and intuitive method for data analysis. In addition to a general framework, we introduce a family of CSS algorithms with different clustering components such as k-means and Close-to-Rank-One (CRO) clustering, and Subset Selection components such as best rank-one approximation and Rank-Revealing QR (RRQR) decomposition.

Modern applications such as Internet traffic, telecommunication records, and large-scale social networks generate massive amounts of data with multiple aspects and high dimensionalities. Tensors (i.e., multi-way arrays) provide a natural representation for such data. Consequently, tensor decompositions such as Tucker become important tools for summarization and analysis. One major challenge is how to deal with high-dimensional, sparse data. In other words, how do we compute decompositions of tensors where most of the entries of the tensor are zero. Specialized techniques are needed for computing the Tucker decompositions for sparse tensors because standard algorithms do not account for the sparsity of the data. As a result, a surprising phenomenon is observed by practitioners: Despite the fact that there is enough memory to store both the input tensors and the factorized output tensors, memory overflows occur during the tensor factorization process. To address this intermediate blowup problem, we propose Memory-Efficient Tucker (MET). Based on the available memory, MET adaptively selects the right execution strategy during the decomposition. We provide quantitative and qualitative evaluation of MET on real tensors. It achieves over 1000X space reduction without sacrificing speed; it also allows us to work with much larger tensors that were too big to handle before. Finally, we demonstrate a data mining case-study using MET.

Huge datasets are becoming prevalent; even as researchers, we now routinely have to work with datasets that are up to a few terabytes in size. Interesting real-world applications produce huge volumes of messy data. The mining process involves several steps, starting from pre-processing the raw data to estimating the final models. As data become more abundant, scalable and easy-to-use tools for distributed processing are also emerging. Among those, Map-Reduce has been widely embraced by both academia and industry. In database terms, Map-Reduce is a simple yet powerful execution engine, which can be complemented with other data storage and management components, as necessary. In this paper we describe our experiences and findings in applying Map-Reduce, from raw data to final models, on an important mining task. In particular, we focus on co-clustering, which has been studied in many applications such as text mining, collaborative filtering, bio-informatics, graph mining. We propose the distributed co-clustering (DisCo) framework, which introduces practical approaches for distributed data pre-processing, and co-clustering. We develop DisCo using Hadoop, an open source Map-Reduce implementation. We show that DisCo can scale well and efficiently process and analyze extremely large datasets (up to several hundreds of gigabytes) on commodity hardware.

Low-rank approximations of the adjacency matrix of a graph are essential in finding patterns (such as communities) and detecting anomalies. Additionally, it is desirable to track the low-rank structure as the graph evolves over time, efficiently and within limited storage. Real graphs typically have thousands or millions of nodes, but are usually very sparse. However, standard decompositions such as SVD do not preserve sparsity. This has led to the development of methods such as CUR and CMD, which seek a non-orthogonal basis by sampling the columns and/or rows of the sparse matrix.

How do we find patterns in author-keyword associations, evolving over time? Or in data cubes (tensors), with product-branchcustomer sales information? And more generally, how to summarize high-order data cubes (tensors)? How to incrementally update these patterns over time? Matrix decompositions, like principal component analysis (PCA) and variants, are invaluable tools for mining, dimensionality reduction, feature selection, rule identification in numerous settings like streaming data, text, graphs, social networks, and many more settings. However, they have only two orders (i.e., matrices, like author and keyword in the previous example). We propose to envision such higher-order data as tensors, and tap the vast literature on the topic. However, these methods do not necessarily scale up, let alone operate on semi-infinite streams. Thus, we introduce a general framework, incremental tensor analysis (ITA), which efficiently computes a compact summary for high-order and high-dimensional data, and also reveals the hidden correlations. Three variants of ITA are presented: (1) dynamic tensor analysis (DTA); (2) streaming tensor analysis (STA); and (3) window-based tensor analysis (WTA). In paricular, we explore several fundamental design trade-offs such as space efficiency, computational cost, approximation accuracy, time dependency, and model complexity. We implement all our methods and apply them in several real settings, such as network anomaly detection, multiway latent semantic indexing on citation networks, and correlation study on sensor measurements. Our empirical studies show that the proposed methods are fast and accurate and that they find interesting patterns and outliers on the real datasets.

We address the problem of preserving privacy in streams, which has received surprisingly limited attention. For static data, a well-studied and widely used approach is based on random perturbation of the data values. However, streams pose additional challenges. First, analysis of the data has to be performed incrementally, using limited processing time and buffer space, making batch approaches unsuitable. Second, the characteristics of streams evolve over time. Consequently, approaches based on global analysis of the data are not adequate. We show that it is possible to efficiently and effectively track the correlation and autocorrelation structure of multivariate streams and leverage it to add noise which maximally preserves privacy, in the sense that it is very hard to remove. Our techniques achieve much better results than previous static, global approaches, while requiring limited processing time and memory. We provide both a mathematical analysis and experimental evaluation on real data to validate the correctness, efficiency, and effectiveness of our algorithms.

How can we find communities in dynamic networks of socialinteractions, such as who calls whom, who emails whom, or who sells to whom? How can we spot discontinuity time-points in such streams of graphs, in an on-line, any-time fashion? We propose GraphScope, that addresses both problems, using information theoretic principles. Contrary to the majority of earlier methods, it needs no user-defined parameters. Moreover, it is designed to operate on large graphs, in a streaming fashion. We demonstrate the efficiency and effectiveness of our GraphScope on real datasets from several diverse domains. In all cases it produces meaningful time-evolving patterns that agree with human intuition.

Given a large sparse graph, how can we find patterns and anomalies? Several important applications can be modeled as large sparse graphs, e.g., network traffic monitoring, research citation network analysis, social network analysis, and regulatory networks in genes. Low rank decompositions, such as SVD and CUR, are powerful techniques for revealing latent/hidden variables and associated patterns from high dimensional data. However, those methods often ignore the sparsity property of the graph, and hence usually incur too high memory and computational cost to be practical. We propose a novel method, the Compact Matrix Decomposition (CMD), to compute sparse low rank approximations. CMD dramatically reduces both the computation cost and the space requirements over existing decomposition methods (SVD, CUR). Using CMD as the key building block, we further propose procedures to efficiently construct and analyze dynamic graphs from real-time application data. We provide theoretical guarantee for our methods, and present results on two real, large datasets, one on network flow data (100GB trace of 22K hosts over one month) and one on DBLP (200MB over 25 years). We show that CMD is often an order of magnitude more efficient than the state of the art (SVD and CUR): it is over 10X faster, but requires less than 1/10 of the space, for the same reconstruction accuracy. Finally, we demonstrate how CMD is used for detecting anomalies and monitoring time-evolving graphs, in which it successfully detects worm-like hierarchical scanning patterns in real network data.

Coevolving streams of numerical measurements, as well astime evolving graphs, can well be represented as tensors. Here we review the fundamental matrix and tensors tools forthe analysis and mining of large scale streams and graphs.

We address the problem of capturing and tracking local correlations among time evolving time series. Our approach is based on comparing the local auto-covariance matrices (via their spectral decompositions) of each series and generalizes the notion of linear cross-correlation. In this way, it is possible to concisely capture a wide variety of local patterns or trends. Our method produces a general similarity score, which evolves over time, and accurately reflects the changing relationships. Finally, it can also be estimated incrementally, in a streaming setting. We demonstrate its usefulness, robustness and efficiency on a wide range of real datasets.

Data stream values are often associated with multiple aspects. For example, each value from environmental sensors may have an associated type (e.g., temperature, humidity, etc) as well as location. Aside from timestamp, type and location are the two additional aspects. How to model such streams? How to simultaneously find patterns within and across the multiple aspects? How to do it incrementally in a streaming fashion? In this paper, all these problems are addressed through a general data model, tensor streams, and an effective algorithmic framework, window-based tensor analysis (WTA). Two variations of WTA, independent- window tensor analysis (IW) and moving-window tensor analysis (MW), are presented and evaluated extensively on real datasets. Finally, we illustrate one important application, multi-aspect correlation analysis (MACA), which uses WTA and we demonstrate its effectiveness on an environmental monitoring application.

How do we find patterns in author-keyword associations, evolving over time? Or in Data Cubes, with product-branch-customer sales information? Matrix decompositions, like principal component analysis (PCA) and variants, are invaluable tools for mining, dimensionality reduction, feature selection, rule identification in numerous settings like streaming data, text, graphs, social networks and many more. However, they have only two orders, like author and keyword, in the above example.We propose to envision such higher order data as tensors,and tap the vast literature on the topic. However, these methods do not necessarily scale up, let alone operate on semi-infinite streams. Thus, we introduce the dynamic tensor analysis (DTA) method, and its variants. DTA provides a compact summary for high-order and high-dimensional data, and it also reveals the hidden correlations. Algorithmically, we designed DTA very carefully so that it is (a) scalable, (b) space efficient (it does not need to store the past) and (c) fully automatic with no need for user defined parameters. Moreover, we propose STA, a streaming tensor analysis method, which provides a fast, streaming approximation to DTA.We implemented all our methods, and applied them in two real settings, namely, anomaly detection and multi-way latent semantic indexing. We used two real, large datasets, one on network flow data (100GB over 1 month) and one from DBLP (200MB over 25 years). Our experiments show that our methods are fast, accurate and that they find interesting patterns and outliers on the real datasets.

Sensor networks attract increasing interest, for a broad range of applications. Given a sensor network, one key issue becomes how to utilize it efficiently and effectively. In particular, how can we detect the underlying correlations (latent variables) among many co-evolving sensor measurements? Can we do it incrementally? We present a system that can (1) collect the measurements from the real wireless sensors; (2) process them in real-time; and (3) determine the correlations (latent variables) among the sensor streams on the fly.

Many real applications can be modeled using bipartite graphs, such as users vs. files in a P2P system, traders vs. stocks in a financial trading system, conferences vs. authors in a scientific publication network, and so on. We introduce two operations on bipartite graphs: 1) identifying similar nodes (Neighborhood formation), and 2) finding abnormal nodes (Anomaly detection). And we propose algorithms to compute the neighborhood for each node using random walk with restarts and graph partitioning; we also propose algorithms to identify abnormal nodes, using neighborhood information. We evaluate the quality of neighborhoods based on semantics of the datasets, and we also measure the performance of the anomaly detection algorithm with manually injected anomalies. Both effectiveness and efficiency of the methods are confirmed by experiments on several real datasets.

Moving objects (e.g., vehicles in road networks) continuously generate large amounts of spatio-temporal information in the form of data streams. Efficient management of such streams is a challenging goal due to the highly dynamic nature of the data and the need for fast, online computations. We present a novel approach for approximate query processing about the present, past, or the future in spatio-temporal databases. In particular, we first propose an incrementally updateable, multidimensional histogram for present-time queries. Second, we develop a general architecture for maintaining and querying historical data. Third, we implement a stochastic approach for predicting the results of queries that refer to the future. Finally, we experimentally prove the effectiveness and efficiency of our techniques using a realistic simulation.

We propose a cost model for selectivity estimation of predictive spatio-temporal window queries. Initially, we focus on uniform data proposing formulae that capture both points and rectangles, and any type of object/query mobility combination (i.e., dynamic objects, dynamic queries or both). Then, we apply the model to nonuniform datasets by introducing spatio-temporal histograms, which in addition to the spatial, also consider the velocity distributions during partitioning. The advantages of our techniques are (i) high accuracy (1-2 orders of magnitude lower error than previous techniques), (ii) ability to handle all query types, and (iii) efficient handling of updates.

Given a set of objects S , a spatio-temporal window query q retrieves the objects of S that will intersect the window during the (future) interval q T . A nearest neighbor query q retrieves the objects of S closest to q during q T . Given a threshold d , a spatio-temporal join retrieves the pairs of objects from two datasets that will come within distance d from each other during q T . In this article, we present probabilistic cost models that estimate the selectivity of spatio-temporal window queries and joins, and the expected distance between a query and its nearest neighbor(s). Our models capture any query/object mobility combination (moving queries, moving objects or both) and any data type (points and rectangles) in arbitrary dimensionality. In addition, we develop specialized spatio-temporal histograms, which take into account both location and velocity information, and can be incrementally maintained. Extensive performance evaluation verifies that the proposed techniques produce highly accurate estimation on both uniform and non-uniform data.