Deficient sleep, altered hypothalamic functional connectivity, depression and anxiety in cigarette smokers.

Background: Deficient sleep is implicated in nicotine dependence as well as depressive and anxiety disorders. The hypothalamus regulates the sleep-wake cycle and supports motivated behavior, and hypothalamic dysfunction may underpin comorbid nicotine dependence, depression and anxiety. We aimed to investigate whether and how the resting state functional connectivities (rsFCs) of the hypothalamus relate to cigarette smoking, deficient sleep, depression and anxiety. Methods: We used the data of 64 smokers and 198 age- and sex-matched adults who never smoked, curated from the Human Connectome Project. Deficient sleep and psychiatric problems were each assessed with Pittsburgh Sleep Quality Index (PSQI) and Achenbach Adult Self-Report. We processed the imaging data with published routines and evaluated the results at a corrected threshold, all with age, sex, and the severity of alcohol use as covariates. Results: Smokers vs. never smokers showed poorer sleep quality and greater severity of depression and anxiety. In smokers only, the total PSQI score, indicating more sleep deficits, was positively associated with hypothalamic rsFCs with the right inferior frontal/insula/superior temporal and postcentral (rPoCG) gyri. Stronger hypothalamus-rPoCG rsFCs were also associated with greater severity of depression and anxiety in smokers but not never smokers. Additionally, in smokers, the PSQI score completely mediated the relationships of hypothalamus-rPoCG rsFCs with depression and anxiety severity. Conclusions: These findings associate hypothalamic circuit dysfunction to sleep deficiency and severity of depression and anxiety symptoms in adults who smoke. Future studies may investigate the roles of the hypothalamic circuit in motivated behaviors to better characterize the inter-related neural markers of smoking, deficient sleep, depression and anxiety.

Machine Learning of Functional Connectivity to Biotype Alcohol and Nicotine Use Disorders.

BACKGROUND: Magnetic resonance imaging provides noninvasive tools to investigate alcohol use disorder (AUD) and nicotine use disorder (NUD) and neural phenotypes for genetic studies. A data-driven transdiagnostic approach could provide a new perspective on the neurobiology of AUD and NUD. METHODS: Using samples of individuals with AUD (n = 140), individuals with NUD (n = 249), and healthy control participants (n = 461) from the UK Biobank, we integrated clinical, neuroimaging, and genetic markers to identify biotypes of AUD and NUD. We partitioned participants with AUD and NUD based on resting-state functional connectivity (FC) features associated with clinical metrics. A multitask artificial neural network was trained to evaluate the cluster-defined biotypes and jointly infer AUD and NUD diagnoses. RESULTS: Three biotypes-primary NUD, mixed NUD/AUD with depression and anxiety, and mixed AUD/NUD-were identified. Multitask classifiers incorporating biotype knowledge achieved higher area under the curve (AUD: 0.76, NUD: 0.74) than single-task classifiers without biotype differentiation (AUD: 0.61, NUD: 0.64). Cerebellar FC features were important in distinguishing the 3 biotypes. The biotype of mixed NUD/AUD with depression and anxiety demonstrated the largest number of FC features (n = 5), all related to the visual cortex, that significantly differed from healthy control participants and were validated in a replication sample (p < .05). A polymorphism in TNRC6A was associated with the mixed AUD/NUD biotype in both the discovery (p = 7.3 × 10-5) and replication (p = 4.2 × 10-2) sets. CONCLUSIONS: Biotyping and multitask learning using FC features can characterize the clinical and genetic profiles of AUD and NUD and help identify cerebellar and visual circuit markers to differentiate the AUD/NUD group from the healthy control group. These markers support a new growing body of literature.

Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures.

MOTIVATION: Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B DNA play an important role in basic cellular processes and are associated with genomic instability, gene regulation, and oncogenesis. Experimental methods are low-throughput and can detect only a limited set of non-B DNA structures, while computational methods rely on non-B DNA base motifs, which are necessary but not sufficient indicators of non-B structures. Oxford Nanopore sequencing is an efficient and low-cost platform, but it is currently unknown whether nanopore reads can be used for identifying non-B structures. RESULTS: We build the first computational pipeline to predict non-B DNA structures from nanopore sequencing. We formalize non-B detection as a novelty detection problem and develop the GoFAE-DND, an autoencoder that uses goodness-of-fit (GoF) tests as a regularizer. A discriminative loss encourages non-B DNA to be poorly reconstructed and optimizing Gaussian GoF tests allows for the computation of P-values that indicate non-B structures. Based on whole genome nanopore sequencing of NA12878, we show that there exist significant differences between the timing of DNA translocation for non-B DNA bases compared with B-DNA. We demonstrate the efficacy of our approach through comparisons with novelty detection methods using experimental data and data synthesized from a new translocation time simulator. Experimental validations suggest that reliable detection of non-B DNA from nanopore sequencing is achievable. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/bayesomicslab/ONT-nonb-GoFAE-DND.

Fragment-based deep molecular generation using hierarchical chemical graph representation and multi-resolution graph variational autoencoder.

Graph generative models have recently emerged as an interesting approach to construct molecular structures atom-by-atom or fragment-by-fragment. In this study, we adopt the fragment-based strategy and decompose each input molecule into a set of small chemical fragments. In drug discovery, a few drug molecules are designed by replacing certain chemical substituents with their bioisosteres or alternative chemical moieties. This inspires us to group decomposed fragments into different fragment clusters according to their local structural environment around bond-breaking positions. In this way, an input structure can be transformed into an equivalent three-layer graph, in which individual atoms, decomposed fragments, or obtained fragment clusters act as graph nodes at each corresponding layer. We further implement a prototype model, named multi-resolution graph variational autoencoder (MRGVAE), to learn embeddings of constituted nodes at each layer in a fine-to-coarse order. Our decoder adopts a similar but conversely hierarchical structure. It first predicts the next possible fragment cluster, then samples an exact fragment structure out of the determined fragment cluster, and sequentially attaches it to the preceding chemical moiety. Our proposed approach demonstrates comparatively good performance in molecular evaluation metrics compared with several other graph-based molecular generative models. The introduction of the additional fragment cluster graph layer will hopefully increase the odds of assembling new chemical moieties absent in the original training set and enhance their structural diversity. We hope that our prototyping work will inspire more creative research to explore the possibility of incorporating different kinds of chemical domain knowledge into a similar multi-resolution neural network architecture.

Cognitive Challenges Are Better in Distinguishing Binge From Nonbinge Drinkers: An Exploratory Deep-Learning Study of fMRI Data of Multiple Behavioral Tasks and Resting State.

BACKGROUND: Studies have identified imaging markers of binge drinking. Functional connectivity during both task challenges and resting state was shown to distinguish binge and nonbinge drinkers. However, no studies have compared the efficacy of task and resting data in the classification. HYPOTHESIS: Task outperforms resting-state functional magnetic resonance imaging (fMRI) data in the differentiation of binge and nonbinge drinkers. We tested the hypothesis via multiple deep learning algorithms. STUDY TYPE: Cross-sectional; retrospective. POPULATION: A total of 149 binge (107 men) and 151 demographically matched, nonbinge (92 men) drinkers curated from the Human Connectome Project, with 80% randomly selected for model development and 20% for validation/test. FIELD STRENGTH/SEQUENCE: A 3 T; fMRI with a blood oxygen level-dependent (BOLD) gradient-echo echo-planar sequence. ASSESSMENT: FMRI data of resting state and seven behavioral tasks were acquired. Graph convolutional network (GCN), long short-term memory, convolutional, and recurrent neural network models were built to distinguish bingers and nonbingers using connectivity matrices of 8, 116, and 268 regions of interest (ROI). Nodal metrics including betweenness centrality, degree centrality, clustering coefficient, efficiency, local efficiency, and shortest path length were calculated from the GCN model. STATISTICAL TESTS: Model performance was quantified by the area under the curve (AUC) in receiver operating characteristic analysis. A P value < 0.05 was considered statistically significant. RESULTS: Task outperformed resting data in classification by approximately 8% by AUC in the test set. Across models and ROI sets, the gambling, motor, language and working memory tasks, each with AUC of 0.614, 0.612, 0.605, and 0.603, performed better than resting data (AUC = 0.548). Models with 116 ROIs (AUC = 0.602) consistently outperformed those with 8 ROIs (AUC = 0.569). Task data performed best with GCN (AUC = 0.619). Nodal metrics of left supplementary motor area and right cuneus showed significant group main effect across tasks. CONCLUSION: Neural responses to cognitive challenges relative to resting state better characterize binge drinking. The performance of different network models may depend on behavioral tasks and the number of ROIs. EVIDENCE LEVEL: 3 TECHNICAL EFFICACY: Stage 2.

Identifying alcohol misuse biotypes from neural connectivity markers and concurrent genetic associations.

Alcohol use behaviors are highly heterogeneous, posing significant challenges to etiologic research of alcohol use disorder (AUD). Magnetic resonance imaging (MRI) provides intermediate endophenotypes in characterizing problem alcohol use and assessing the genetic architecture of addictive behavior. We used connectivity features derived from resting state functional MRI to subtype alcohol misuse (AM) behavior. With a machine learning pipeline of feature selection, dimension reduction, clustering, and classification we identified three AM biotypes-mild, comorbid, and moderate AM biotypes (MIA, COA, and MOA)-from a Human Connectome Project (HCP) discovery sample (194 drinkers). The three groups and controls (397 non-drinkers) demonstrated significant differences in alcohol use frequency during the heaviest 12-month drinking period (MOA > MIA; COA > non-drinkers) and were distinguished by connectivity features involving the frontal, parietal, subcortical and default mode networks. Further, COA relative to MIA, MOA and controls endorsed significantly higher scores in antisocial personality. A genetic association study identified that an alcohol use and antisocial behavior related variant rs16930842 from LINC01414 was significantly associated with COA. Using a replication HCP sample (28 drinkers and 46 non-drinkers), we found that subtyping helped in classifying AM from controls (area under the curve or AUC = 0.70, P < 0.005) in comparison to classifiers without subtyping (AUC = 0.60, not significant) and successfully reproduced the genetic association. Together, the results suggest functional connectivities as important features in classifying AM subgroups and the utility of reducing the heterogeneity in connectivity features among AM subgroups in advancing the research of etiological neural markers of AUD.

Calibrating the Adaptive Learning Rate to Improve Convergence of ADAM.

Adaptive gradient methods (AGMs) have become popular in optimizing the nonconvex problems in deep learning area. We revisit AGMs and identify that the adaptive learning rate (A-LR) used by AGMs varies significantly across the dimensions of the problem over epochs (i.e., anisotropic scale), which may lead to issues in convergence and generalization. All existing modified AGMs actually represent efforts in revising the A-LR. Theoretically, we provide a new way to analyze the convergence of AGMs and prove that the convergence rate of Adam also depends on its hyper-parameter є, which has been overlooked previously. Based on these two facts, we propose a new AGM by calibrating the A-LR with an activation (softplus) function, resulting in the Sadam and SAMSGrad methods. We further prove that these algorithms enjoy better convergence speed under nonconvex, non-strongly convex, and Polyak-Lojasiewicz conditions compared with Adam. Empirical studies support our observation of the anisotropic A-LR and show that the proposed methods outperform existing AGMs and generalize even better than S-Momentum in multiple deep learning tasks.

An Efficient Algorithm for Deep Stochastic Contextual Bandits.

In stochastic contextual bandit (SCB) problems, an agent selects an action based on certain observed context to maximize the cumulative reward over iterations. Recently there have been a few studies using a deep neural network (DNN) to predict the expected reward for an action, and the DNN is trained by a stochastic gradient based method. However, convergence analysis has been greatly ignored to examine whether and where these methods converge. In this work, we formulate the SCB that uses a DNN reward function as a non-convex stochastic optimization problem, and design a stage-wise stochastic gradient descent algorithm to optimize the problem and determine the action policy. We prove that with high probability, the action sequence chosen by this algorithm converges to a greedy action policy respecting a local optimal reward function. Extensive experiments have been performed to demonstrate the effectiveness and efficiency of the proposed algorithm on multiple real-world datasets.

Perceived stress, self-efficacy, and the cerebral morphometric markers in binge-drinking young adults.

Studies have identified cerebral morphometric markers of binge drinking and implicated cortical regions in support of self-efficacy and stress regulation. However, it remains unclear how cortical structures of self-control play a role in ameliorating stress and alcohol consumption or how chronic alcohol exposure alters self-control and leads to emotional distress. We examined the data of 180 binge (131 men) and 256 non-binge (83 men) drinkers from the Human Connectome Project. We obtained data on regional cortical thickness from the HCP and derived gray matter volumes (GMVs) with voxel-based morphometry. At a corrected threshold, binge relative to non-binge drinking men showed diminished posterior cingulate cortex (PCC) thickness and dorsomedial prefrontal cortex (dmPFC) GMV. PCC thickness and dmPFC GMVs were positively and negatively correlated with self-efficacy and perceived stress, respectively, as assessed with the NIH Emotion Toolbox. Mediation and path analyses to query the inter-relationships between the neural markers and clinical variables showed a best fit of the model with daily drinks â†’ lower PCC thickness and dmPFC GMV â†’ lower self-efficacy â†’ higher perceived stress in men. In contrast, binge and non-binge drinking women did not show significant differences in regional cortical thickness or GMVs. These findings suggest a pathway whereby chronic alcohol consumption alters cortical structures and self-efficacy mediates the effects of cortical structural deficits on perceived stress in men. The findings also suggest the need to investigate multimodal neural markers underlying the interplay between stress, self-control and alcohol use behavior in women.

OctSurf: Efficient hierarchical voxel-based molecular surface representation for protein-ligand affinity prediction.

Voxel-based 3D convolutional neural networks (CNNs) have been applied to predict protein-ligand binding affinity. However, the memory usage and computation cost of these voxel-based approaches increase cubically with respect to spatial resolution and sometimes make volumetric CNNs intractable at higher resolutions. Therefore, it is necessary to develop memory-efficient alternatives that can accelerate the convolutional operation on 3D volumetric representations of the protein-ligand interaction. In this study, we implement a novel volumetric representation, OctSurf, to characterize the 3D molecular surface of protein binding pockets and bound ligands. The OctSurf surface representation is built based on the octree data structure, which has been widely used in computer graphics to efficiently represent and store 3D object data. Vanilla 3D-CNN approaches often divide the 3D space of objects into equal-sized voxels. In contrast, OctSurf recursively partitions the 3D space containing the protein-ligand pocket into eight subspaces called octants. Only those octants containing van der Waals surface points of protein or ligand atoms undergo the recursive subdivision process until they reach the predefined octree depth, whereas unoccupied octants are kept intact to reduce the memory cost. Resulting non-empty leaf octants approximate molecular surfaces of the protein pocket and bound ligands. These surface octants, along with their chemical and geometric features, are used as the input to 3D-CNNs. Two kinds of CNN architectures, VGG and ResNet, are applied to the OctSurf representation to predict binding affinity. The OctSurf representation consumes much less memory than the conventional voxel representation at the same resolution. By restricting the convolution operation to only octants of the smallest size, our method also alleviates the overall computational overhead of CNN. A series of experiments are performed to demonstrate the disk storage and computational efficiency of the proposed learning method. Our code is available at the following GitHub repository: https://github.uconn.edu/mldrugdiscovery/OctSurf.

Fusing Location Data for Depression Prediction.

Recent studies have demonstrated that geographic location features collected using smartphones can be a powerful predictor for depression. While location information can be conveniently gathered by GPS, typical datasets suffer from significant periods of missing data due to various factors (e.g., phone power dynamics, limitations of GPS). A common approach is to remove the time periods with significant missing data before data analysis. In this paper, we develop an approach that fuses location data collected from two sources: GPS and WiFi association records, on smartphones, and evaluate its performance using a dataset collected from 79 college students. Our evaluation demonstrates that our data fusion approach leads to significantly more complete data. In addition, the features extracted from the more complete data present stronger correlation with self-report depression scores, and lead to depression prediction with much higher F 1 scores (up to 0.76 compared to 0.5 before data fusion). We further investigate the scenerio when including an additional data source, i.e., the data collected from a WiFi network infrastructure. Our results show that, while the additional data source leads to even more complete data, the resultant F 1 scores are similar to those when only using the location data (i.e., GPS and WiFi association records) from the phones.

Asynchronous Parallel Stochastic Quasi-Newton Methods.

Although first-order stochastic algorithms, such as stochastic gradient descent, have been the main force to scale up machine learning models, such as deep neural nets, the second-order quasi-Newton methods start to draw attention due to their effectiveness in dealing with ill-conditioned optimization problems. The L-BFGS method is one of the most widely used quasi-Newton methods. We propose an asynchronous parallel algorithm for stochastic quasi-Newton (AsySQN) method. Unlike prior attempts, which parallelize only the calculation for gradient or the two-loop recursion of L-BFGS, our algorithm is the first one that truly parallelizes L-BFGS with a convergence guarantee. Adopting the variance reduction technique, a prior stochastic L-BFGS, which has not been designed for parallel computing, reaches a linear convergence rate. We prove that our asynchronous parallel scheme maintains the same linear convergence rate but achieves significant speedup. Empirical evaluations in both simulations and benchmark datasets demonstrate the speedup in comparison with the non-parallel stochastic L-BFGS, as well as the better performance than first-order methods in solving ill-conditioned problems.

A Survey on Multi-View Clustering.

Clustering is a machine learning paradigm of dividing sample subjects into a number of groups such that subjects in the same groups are more similar to those in other groups. With advances in information acquisition technologies, samples can frequently be viewed from different angles or in different modalities, generating multi-view data. Multi-view clustering, that clusters subjects into subgroups using multi-view data, has attracted more and more attentions. Although MVC methods have been developed rapidly, there has not been enough survey to summarize and analyze the current progress. Therefore, we propose a novel taxonomy of the MVC approaches. Similar to other machine learning methods, we categorize them into generative and discriminative classes. In discriminative class, based on the way of view integration, we split it further into five groups: Common Eigenvector Matrix, Common Coefficient Matrix, Common Indicator Matrix, Direct Combination and Combination After Projection. Furthermore, we relate MVC to other topics: multi-view representation, ensemble clustering, multi-task clustering, multi-view supervised and semi-supervised learning. Several representative real-world applications are elaborated for practitioners. Some benchmark multi-view datasets are introduced and representative MVC algorithms from each group are empirically evaluated to analyze how they perform on benchmark datasets. To promote future development of MVC approaches, we point out several open problems that may require further investigation and thorough examination.

Effect of three-dimensional porosity gradients of biomimetic coatings on their bonding strength and cell behavior.

Surface modification techniques are often used to enhance the properties of Ti-based materials as hard-tissue replacements. While the microstructure of the coating and the quality of the interface between the substrate and coating are essential to evaluate the reliability and applicability of the surface modification. In this study, both a hydroxyapatite (HA) coating and a collagen-hydroxyapatite (Col-HA) composite coating were deposited onto a Ti-6Al-4V substrate using a biomimetic coating process. Importantly, a gradient cross-sectional structure with a porous coating toward the surface, while a dense layer adjacent to the interface between the coating and substrate was observed in three-dimensional (3D) from both the HA and Col-HA coatings via a dual-beam focused ion beam-scanning electron microscope (FIB-SEM). Moreover, the pore distributions within the entire coatings were reconstructed in 3D using Avizo, and the pores size distributions along the coating depth were calculated using RStudio. By evaluating the mechanical property and biocompatibility of these materials and closely observing the cross-sectional cell-coating-substrate interfaces using FIB-SEM, it was revealed that the porous surface created by both coatings well supports osteoblast cell adhesion while the dense inner layer facilitates a good bonding between the coating and the substrate. Although the mechanical property of the coating decreased with the addition of collagen, it is still strong enough for implant handling and the biocompatibility was promoted.

Convolutional neural network for automated mass segmentation in mammography.

BACKGROUND: Automatic segmentation and localization of lesions in mammogram (MG) images are challenging even with employing advanced methods such as deep learning (DL) methods. We developed a new model based on the architecture of the semantic segmentation U-Net model to precisely segment mass lesions in MG images. The proposed end-to-end convolutional neural network (CNN) based model extracts contextual information by combining low-level and high-level features. We trained the proposed model using huge publicly available databases, (CBIS-DDSM, BCDR-01, and INbreast), and a private database from the University of Connecticut Health Center (UCHC). RESULTS: We compared the performance of the proposed model with those of the state-of-the-art DL models including the fully convolutional network (FCN), SegNet, Dilated-Net, original U-Net, and Faster R-CNN models and the conventional region growing (RG) method. The proposed Vanilla U-Net model outperforms the Faster R-CNN model significantly in terms of the runtime and the Intersection over Union metric (IOU). Training with digitized film-based and fully digitized MG images, the proposed Vanilla U-Net model achieves a mean test accuracy of 92.6%. The proposed model achieves a mean Dice coefficient index (DI) of 0.951 and a mean IOU of 0.909 that show how close the output segments are to the corresponding lesions in the ground truth maps. Data augmentation has been very effective in our experiments resulting in an increase in the mean DI and the mean IOU from 0.922 to 0.951 and 0.856 to 0.909, respectively. CONCLUSIONS: The proposed Vanilla U-Net based model can be used for precise segmentation of masses in MG images. This is because the segmentation process incorporates more multi-scale spatial context, and captures more local and global context to predict a precise pixel-wise segmentation map of an input full MG image. These detected maps can help radiologists in differentiating benign and malignant lesions depend on the lesion shapes. We show that using transfer learning, introducing augmentation, and modifying the architecture of the original model results in better performance in terms of the mean accuracy, the mean DI, and the mean IOU in detecting mass lesion compared to the other DL and the conventional models.

Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search.

Structurally similar analogues of given query compounds can be rapidly retrieved from chemical databases by the molecular similarity search approaches. However, the computational cost associated with the exhaustive similarity search of a large compound database will be quite high. Although the latest indexing algorithms can greatly speed up the search process, they cannot be readily applicable to molecular similarity search problems due to the lack of Tanimoto similarity metric implementation. In this paper, we first implement Python or C++ codes to enable the Tanimoto similarity search via several recent indexing algorithms, such as Hnsw and Onng. Moreover, there are increasing interests in computational communities to develop robust benchmarking systems to access the performance of various computational algorithms. Here, we provide a benchmark to evaluate the molecular similarity searching performance of these recent indexing algorithms. To avoid the potential package dependency issues, two separate benchmarks are built based on currently popular container technologies, Docker and Singularity. The Singularity container is a rather new container framework specifically designed for the high-performance computing (HPC) platform and does not need the privileged permissions or the separated daemon process. Both benchmarking methods are extensible to incorporate other new indexing algorithms, benchmarking data sets, and different customized parameter settings. Our results demonstrate that the graph-based methods, such as Hnsw and Onng, consistently achieve the best trade-off between searching effectiveness and searching efficiencies. The source code of the entire benchmark systems can be downloaded from https://github.uconn.edu/mldrugdiscovery/MssBenchmark.

Automatic Depression Prediction Using Internet Traffic Characteristics on Smartphones.

Depression is a serious mental health problem. Recently, researchers have proposed novel approaches that use sensing data collected passively on smartphones for automatic depression screening. While these studies have explored several types of sensing data (e.g., location, activity, conversation), none of them has leveraged Internet traffic of smartphones, which can be collected with little energy consumption and the data is insensitive to phone hardware. In this paper, we explore using coarse-grained meta-data of Internet traffic on smartphones for depression screening. We develop techniques to identify Internet usage sessions (i.e., time periods when a user is online) and extract a novel set of features based on usage sessions from the Internet traffic meta-data. Our results demonstrate that Internet usage features can reflect the different behavioral characteristics between depressed and non-depressed participants, confirming findings in psychological sciences, which have relied on surveys or questionnaires instead of real Internet traffic as in our study. Furthermore, we develop machine learning based prediction models that use these features to predict depression. Our evaluation shows that Internet usage features can be used for effective depression prediction, leading to F 1 score as high as 0.80.

Hybrid-DCA: A double asynchronous approach for stochastic dual coordinate ascent.

In prior works, stochastic dual coordinate ascent (SDCA) has been parallelized in a multi-core environment where the cores communicate through shared memory, or in a multi-processor distributed memory environment where the processors communicate through message passing. In this paper, we propose a hybrid SDCA framework for multi-core clusters, the most common high performance computing environment that consists of multiple nodes each having multiple cores and its own shared memory. We distribute data across nodes where each node solves a local problem in an asynchronous parallel fashion on its cores, and then the local updates are aggregated via an asynchronous across-node update scheme. The proposed double asynchronous method converges to a global solution for L-Lipschitz continuous loss functions, and at a linear convergence rate if a smooth convex loss function is used. Extensive empirical comparison has shown that our algorithm scales better than the best known shared-memory methods and runs faster than previous distributed-memory methods. Big datasets, such as one of 280 GB from the LIBSVM repository, cannot be accommodated on a single node and hence cannot be solved by a parallel algorithm. For such a dataset, our hybrid algorithm takes less than 30 seconds to achieve a duality gap of 10-5 on 16 nodes each using 12 cores, which is significantly faster than the best known distributed algorithms, such as CoCoA+, that take more than 160 seconds on 16 nodes.

Grant Report on SCH: Personalized Depression Treatment Supported by Mobile Sensor Analytics.

We report on the newly started project "SCH: Personalized Depression Treatment Supported by Mobile Sensor Analytics". The current best practice guidelines for treating depression call for close monitoring of patients, and periodically adjusting treatment as needed. This project will advance personalized depression treatment by developing a system, DepWatch, that leverages mobile health technologies and machine learning tools. The objective of DepWatch is to assist clinicians with their decision making process in the management of depression. The project comprises two studies. Phase I collects sensory data and other data, e.g., clinical data, ecological momentary assessments (EMA), tolerability and safety data from 250 adult participants with unstable depression symptomatology initiating depression treatment. The data thus collected will be used to develop and validate assessment and prediction models, which will be incorporated into DepWatch system. In Phase II, three clinicians will use DepWatch to support their clinical decision making process. A total of 128 participants under treatment by the three participating clinicians will be recruited for the study. A number of new machine learning techniques will be developed.

Machine-Learning-Assisted De Novo Design of Organic Molecules and Polymers: Opportunities and Challenges.

Organic molecules and polymers have a broad range of applications in biomedical, chemical, and materials science fields. Traditional design approaches for organic molecules and polymers are mainly experimentally-driven, guided by experience, intuition, and conceptual insights. Though they have been successfully applied to discover many important materials, these methods are facing significant challenges due to the tremendous demand of new materials and vast design space of organic molecules and polymers. Accelerated and inverse materials design is an ideal solution to these challenges. With advancements in high-throughput computation, artificial intelligence (especially machining learning, ML), and the growth of materials databases, ML-assisted materials design is emerging as a promising tool to flourish breakthroughs in many areas of materials science and engineering. To date, using ML-assisted approaches, the quantitative structure property/activity relation for material property prediction can be established more accurately and efficiently. In addition, materials design can be revolutionized and accelerated much faster than ever, through ML-enabled molecular generation and inverse molecular design. In this perspective, we review the recent progresses in ML-guided design of organic molecules and polymers, highlight several successful examples, and examine future opportunities in biomedical, chemical, and materials science fields. We further discuss the relevant challenges to solve in order to fully realize the potential of ML-assisted materials design for organic molecules and polymers. In particular, this study summarizes publicly available materials databases, feature representations for organic molecules, open-source tools for feature generation, methods for molecular generation, and ML models for prediction of material properties, which serve as a tutorial for researchers who have little experience with ML before and want to apply ML for various applications. Last but not least, it draws insights into the current limitations of ML-guided design of organic molecules and polymers. We anticipate that ML-assisted materials design for organic molecules and polymers will be the driving force in the near future, to meet the tremendous demand of new materials with tailored properties in different fields.