Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Multimodal Algorithms for the Segmentation of Multiparametric MRI Prostate Images

Prostate segmentation in multiparametric magnetic resonance imaging (mpMRI) can help to support prostate cancer diagnosis and therapy treatment. However, manual segmentation of the prostate is subjective and time-consuming. Many deep learning monomodal networks have been developed for automatic whole prostate segmentation from T2-weighted MR images. We aimed to investigate the added value of multimodal networks in segmenting the prostate into the peripheral zone (PZ) and central gland (CG). We optimized and evaluated monomodal DenseVNet, multimodal ScaleNet, and monomodal and multimodal HighRes3DNet, which yielded dice score coefficients (DSC) of 0.875, 0.848, 0.858, and 0.890 in WG, respectively. Multimodal HighRes3DNet and ScaleNet yielded higher DSC with statistical differences in PZ and CG only compared to monomodal DenseVNet, indicating that multimodal networks added value by generating better segmentation between PZ and CG regions but did not improve the WG segmentation. No significant difference was observed in the apex and base of WG segmentation between monomodal and multimodal networks, indicating that the segmentations at the apex and base were more affected by the general network architecture. The number of training data was also varied for DenseVNet and HighRes3DNet, from 20 to 120 in steps of 20. DenseVNet was able to yield DSC of higher than 0.65 even for special cases, such as TURP or abnormal prostate, whereas HighRes3DNet's performance fluctuated with no trend despite being the best network overall. Multimodal networks did not add value in segmenting special cases but generally reduced variations in segmentation compared to the same matched monomodal network.
FusiformNet: Extracting Discriminative Facial Features on Different Levels

Over the last several years, research on facial recognition based on Deep Neural Network has evolved with approaches like task-specific loss functions, image normalization and augmentation, network architectures, etc. However, there have been few approaches with attention to how human faces differ from person to person. Premising that inter-personal differences are found both generally and locally on the human face, I propose FusiformNet, a novel framework for feature extraction that leverages the nature of discriminative facial features. Tested on Image-Unrestricted setting of Labeled Face in the Wild benchmark, this method achieved a state-of-the-art accuracy of 96.67% without labeled outside data, image augmentation, normalization, or special loss functions. Likewise, the method also performed on par with previous state-of-the-arts when pre-trained on CASIA-WebFace dataset. Considering its ability to extract both general and local facial features, the utility of FusiformNet may not be limited to facial recognition but also extend to other DNN-based tasks.
Two-Level K-FAC Preconditioning for Deep Learning

In the context of deep learning, many optimization methods use gradient covariance information in order to accelerate the convergence of Stochastic Gradient Descent. In particular, starting with Adagrad, a seemingly endless line of research advocates the use of diagonal approximations of the so-called empirical Fisher matrix in stochastic gradient-based algorithms, with the most prominent one arguably being Adam. However, in recent years, several works cast doubt on the theoretical basis of preconditioning with the empirical Fisher matrix, and it has been shown that more sophisticated approximations of the actual Fisher matrix more closely resemble the theoretically well-motivated Natural Gradient Descent. One particularly successful variant of such methods is the so-called K-FAC optimizer, which uses a Kronecker-factored block-diagonal Fisher approximation as preconditioner. In this work, drawing inspiration from two-level domain decomposition methods used as preconditioners in the field of scientific computing, we extend K-FAC by enriching it with off-diagonal (i.e. global) curvature information in a computationally efficient way. We achieve this by adding a coarse-space correction term to the preconditioner, which captures the global Fisher information matrix at a coarser scale. We present a small set of experimental results suggesting improved convergence behaviour of our proposed method.
Learning from Non-Binary Constituency Trees via Tensor Decomposition

Processing sentence constituency trees in binarised form is a common and popular approach in literature. However, constituency trees are non-binary by nature. The binarisation procedure changes deeply the structure, furthering constituents that instead are close. In this work, we introduce a new approach to deal with non-binary constituency trees which leverages tensor-based models. In particular, we show how a powerful composition function based on the canonical tensor decomposition can exploit such a rich structure. A key point of our approach is the weight sharing constraint imposed on the factor matrices, which allows limiting the number of model parameters. Finally, we introduce a Tree-LSTM model which takes advantage of this composition function and we experimentally assess its performance on different NLP tasks.
Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis

Background Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affect mucosal homeostasis and triggers inappropriate immune response. The purpose of the study was to identify significant biomarkers with potential therapeutic targets and the underlying mechanisms. Methods The gene expression profiles of GSE48958, GSE73661, and GSE59071 are from the GEO database. Differentially expressed genes (DEGs) were screened by the GEO2R tool. Next, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was applied to analyze gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Then, protein-protein interaction (PPI) was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). Results There were a total of 128 common DEGs genes, including 86 upregulated genes enriched in extracellular space, regulation of inflammatory response, chemokine-mediated signaling pathway, response to lipopolysaccharide, and cell proliferation, while 42 downregulated genes enriched in the integral component of the membrane, the integral component of the plasma membrane, apical plasma membrane, symporter activity, and chloride channel activity. The KEGG pathway analysis results demonstrated that DEGs were particularly enriched in cytokine-cytokine receptor interaction, TNF signaling pathway, chemokine signaling pathway, pertussis, and rheumatoid arthritis. 18 central modules of the PPI networks were selected with Cytotype MCODE. Furthermore, 18 genes were found to significantly enrich in the extracellular space, inflammatory response, chemokine-mediated signaling pathway, TNF signaling pathway, regulation of cell proliferation, and immune response via reanalysis of DAVID. Conclusion The study identified DEGs, key target genes, functional pathways, and pathway analysis of UC, which may provide potential molecular targets and diagnostic biomarkers for UC.
Towards Personalized Explanation of Robotic Planning via User Feedback

Prior studies have found that providing explanations about robots' decisions and actions help to improve system transparency, increase human users' trust of robots, and enable effective human-robot collaboration. Different users have various preferences about what should be included in explanations. However, little research has been conducted for the generation of personalized explanations. In this paper, we present a system for generating personalized explanations of robotic planning via user feedback. We consider robotic planning using Markov decision processes (MDPs) and develop an algorithm to automatically generate a personalized explanation of an optimal robotic plan (i.e., an optimal MDP policy) based on the user preference regarding four elements (i.e., objective, locality, specificity, and abstraction). In addition, we design the system to interact with users via answering users' further questions about the generated explanations. Users have the option to update their preferences to view different explanations. The system is capable of detecting and resolving any preference conflict via user interaction. Our user study results show that the generated personalized explanations improve user satisfaction, while the majority of users liked the system's capabilities of question-answering, and conflict detection and resolution.
Time Series Forecasting with Stacked Long Short-Term Memory Networks

Long Short-Term Memory (LSTM) networks are often used to capture temporal dependency patterns. By stacking multi-layer LSTM networks, it can capture even more complex patterns. This paper explores the effectiveness of applying stacked LSTM networks in the time series prediction domain, specifically, the traffic volume forecasting. Being able to predict traffic volume more accurately can result in better planning, thus greatly reduce the operation cost and improve overall efficiency.
Sensor-based localization of epidemic sources on human mobility networks

We investigate the source detection problem in epidemiology, which is one of the most important issues for control of epidemics. Mathematically, we reformulate the problem as one of identifying the relevant component in a multivariate Gaussian mixture model. Focusing on the study of cholera and diseases with similar modes of transmission, we calibrate the parameters of our mixture model using human mobility networks within a stochastic, spatially explicit epidemiological model for waterborne disease. Furthermore, we adopt a Bayesian perspective, so that prior information on source location can be incorporated (e.g., reflecting the impact of local conditions). Posterior-based inference is performed, which permits estimates in the form of either individual locations or regions. Importantly, our estimator only requires first-arrival times of the epidemic by putative observers, typically located only at a small proportion of nodes. The proposed method is demonstrated within the context of the 2000-2002 cholera outbreak in the KwaZulu-Natal province of South Africa.
Optimizing Mixed Autonomy Traffic Flow With Decentralized Autonomous Vehicles and Multi-Agent RL

We study the ability of autonomous vehicles to improve the throughput of a bottleneck using a fully decentralized control scheme in a mixed autonomy setting. We consider the problem of improving the throughput of a scaled model of the San Francisco-Oakland Bay Bridge: a two-stage bottleneck where four lanes reduce to two and then reduce to one. Although there is extensive work examining variants of bottleneck control in a centralized setting, there is less study of the challenging multi-agent setting where the large number of interacting AVs leads to significant optimization difficulties for reinforcement learning methods. We apply multi-agent reinforcement algorithms to this problem and demonstrate that significant improvements in bottleneck throughput, from 20\% at a 5\% penetration rate to 33\% at a 40\% penetration rate, can be achieved. We compare our results to a hand-designed feedback controller and demonstrate that our results sharply outperform the feedback controller despite extensive tuning. Additionally, we demonstrate that the RL-based controllers adopt a robust strategy that works across penetration rates whereas the feedback controllers degrade immediately upon penetration rate variation. We investigate the feasibility of both action and observation decentralization and demonstrate that effective strategies are possible using purely local sensing. Finally, we open-source our code at this https URL.
Energetics of critical oscillators in active bacterial baths

We investigate the nonequilibrium energetics near a critical point of a non-linear oscillator immersed in an active bacterial bath. At the critical point, we reveal a scaling exponent of the average power exerted by a constant non-conservative torque ⟨Ẇ⟩∼(Da/τ)1/4 , where D a is the effective diffusivity and τ the correlation time of the bacterial bath described by a Gaussian colored noise. Other features that we investigate are the average stationary power and the variance of the work both below and above the saddle-node bifurcation. Above the bifurcation, the average power attains an optimal, minimum value for finite τ that is below its zero-temperature limit. Furthermore, we reveal a finite-time uncertainty relation for active matter which leads to values of the Fano factor of the work that can be below 2k B T eff, with T eff the effective temperature of the oscillator in the bacterial bath. We analyze different Markovian approximations to describe the nonequilibrium stationary state of the system. Finally, we illustrate our results in the experimental context by considering the example of driven colloidal particles in periodic optical potentials within an E. Coli bacterial bath.
A General Framework for Bandit Problems Beyond Cumulative Objectives

The stochastic multiarmed bandit (MAB) problem is a common model for sequential decision problems. In the standard setup, a decision maker has to choose at every instant between several competing arms; each of them provides a scalar random variable, referred to as a “reward. ” Nearly all research on this topic considers the total cumulative reward as the criterion of interest. This work focuses on other natural objectives that cannot be cast as a sum over rewards but rather, more involved functions of the reward stream. Unlike the case of cumulative criteria, in the problems we study here, the oracle policy, which knows the problem parameters a priori and is used to “center” the regret, is not trivial. We provide a systematic approach to such problems and derive general conditions under which the oracle policy is sufficiently tractable to facilitate the design of optimism-based (upper confidence bound) learning policies. These conditions elucidate an interesting interplay between the arm reward distributions and the performance metric. Our main findings are illustrated for several commonly used objectives, such as conditional value-at-risk, mean-variance trade-offs, Sharpe ratio, and more. Funding: This work was partially funded by the Israel Science Foundation [Contract 2199/20] and by the European Community’s Seventh Framework Programme FP7/2007–2013 [Grant 306638 (Scaling Up Reinforcement Learning: Structure Learning, Skill Acquisition, and Reward Shaping)].
Alternating Direction Method of Multipliers for Constrained Iterative LQR in Autonomous Driving

In the context of autonomous driving, the iterative linear quadratic regulator (iLQR) is known to be an efficient approach to deal with the nonlinear vehicle model in motion planning problems. Particularly, the constrained iLQR algorithm has shown noteworthy advantageous outcomes of computation efficiency in achieving motion planning tasks under general constraints of different types. However, the constrained iLQR methodology requires a feasible trajectory at the first iteration as a prerequisite when the logarithmic barrier function is used. Also, the methodology leaves open the possibility for incorporation of fast, efficient, and effective optimization methods (i.e., fast-solvers) to further speed up the optimization process such that the requirements of real-time implementation can be successfully fulfilled. In this paper, a well-defined and commonly-encountered motion planning problem is formulated under nonlinear vehicle dynamics and various constraints, and the alternating direction method of multipliers (ADMM) is utilized to determine the optimal control actions leveraging the iLQR. With this development, the approach is able to circumvent the feasibility requirement of the trajectory at the first iteration. An illustrative example of motion planning for autonomous vehicles is then investigated with different driving scenarios taken into consideration, and a noteworthy achievement of high computation efficiency is attained with the proposed development. Comparing with the constrained iLQR algorithm based on the logarithmic barrier function, our proposed method reduces the average computation time by 31.93%, 38.52%, and 44.57% in the three scenarios; compared with the optimization solver IPOPT, our proposed method reduces the average computation time by 46.02%, 53.26%, and 88.43% in the three scenarios. As a result, real-time computation and implementation can be realized through our proposed framework, and thus it provides additional safety to the on-road driving tasks.
Impacts of Game-Theoretic Activation on Epidemic Spread over Dynamical Networks

We investigate the evolution of epidemics over dynamical networks when nodes choose to interact with others in a selfish and decentralized manner. Specifically, we analyze the susceptible-asymptomatic-infected-recovered (SAIR) epidemic in the framework of activity-driven networks with heterogeneous node degrees and time-varying activation rates, and derive both individual and degree-based mean-field approximations of the exact state evolution. We then present a game-theoretic model where nodes choose their activation probabilities in a strategic manner using current state information as feedback, and characterize the quantal response equilibrium (QRE) of the proposed setting. We then consider the activity-driven susceptible-infected-susceptible (SIS) epidemic model, characterize equilibrium activation probabilities and analyze epidemic evolution in closed-loop. Our numerical results provide compelling insights into epidemic evolution under game-theoretic activation. Specifically, for the SAIR epidemic, we show that under suitable conditions, the epidemic can persist, as any decrease in infected proportion is counteracted by an increase in activity rates by the nodes. For the SIS epidemic, we show that in regimes where there is an endemic state, the infected proportion could be significantly smaller under game-theoretic activation if the loss upon infection is sufficiently high.
Understanding the morphotropic phase boundary of perovskite solid solutions as a frustrated state

Perovskite solid solutions that have a chemical composition A(C_xD_(1−x))O₃ with transition metals C and D substitutionally occupying the B site of a perovskite lattice are attractive in various applications for their dielectric, piezoelectric and other properties. A remarkable feature of these solid solutions is the morphotropic phase boundary (MPB), the composition across which the crystal symmetry changes. Critically, it has long been observed that the dielectric and piezoelectric as well as the ability to pole a ceramic increases dramatically at the MPB. While this has motivated much study of perovskite MPBs, a number of important questions about the role of disorder remain unanswered. We address these questions using a new approach based on the random-field Ising model with long-range interactions that incorporates the basic elements of the physics at the meso-scale. We show that the MPB emerges naturally in this approach as a frustrated state where stability is exchanged between two well-defined phases. Specifically, long-range interactions suppress the disorder at compositions away from MPB but are unable to do so when there is an exchange of stability. Further, the approach also predicts a number of experimentally observed features like the fragmented domain patterns and superior ability to pole at the MPB. The insights from this model also suggest the possibility of entirely new materials with strong ferroelectric-ferromagnetic coupling using an MPB.
Deconstruct to Reconstruct a Configurable Evaluation Metric for Open-Domain Dialogue Systems

Many automatic evaluation metrics have been proposed to score the overall quality of a response in open-domain dialogue. Generally, the overall quality is comprised of various aspects, such as relevancy, specificity, and empathy, and the importance of each aspect differs according to the task. For instance, specificity is mandatory in a food-ordering dialogue task, whereas fluency is preferred in a language-teaching dialogue system. However, existing metrics are not designed to cope with such flexibility. For example, BLEU score fundamentally relies only on word overlapping, whereas BERTScore relies on semantic similarity between reference and candidate response. Thus, they are not guaranteed to capture the required aspects, i.e., specificity. To design a metric that is flexible to a task, we first propose making these qualities manageable by grouping them into three groups: understandability, sensibleness, and likability, where likability is a combination of qualities that are essential for a task. We also propose a simple method to composite metrics of each aspect to obtain a single metric called USL-H, which stands for Understandability, Sensibleness, and Likability in Hierarchy. We demonstrated that USL-H score achieves good correlations with human judgment and maintains its configurability towards different aspects and metrics.
Reconciling biodiversity conservation, food production and farmers’ demand

Agricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee the provision of ecosystem services that reaches stakeholders’ demands, especially considering the observed biodiversity decline and the current global change predictions that may affect food security. Here, we use a model to examine how landscape composition – fraction of semi-natural habitat (SNH) – affects biodiversity and crop production services in intensively-managed agricultural systems. We analyse three groups of stakeholders assumed to value different ecosystem services most – individual farmers (crop yield per area), agricultural unions (landscape production) and conservationists (biodiversity). We find that trade-offs among stakeholders’ demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder, i.e. function thresholds. Intermediate amounts of SNH can allow for the delivery of relatively high levels of the three ecosystem services. Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, these results suggest ways of managing landscapes to reconcile the demands of several actors and ensure for biodiversity conservation and food production.
A 0.11–0.38 pJ/cycle Differential Ring Oscillator in 65 nm CMOS for Robust Neurocomputing

This paper presents a low-area and low-power consumption CMOS differential current controlled oscillator (CCO) for neuromorphic applications. The oscillation frequency is improved over the conventional one by reducing the number of MOS transistors thus lowering the load capacitor in each stage. The analysis shows that for the same power consumption, the oscillation frequency can be increased about 11% compared with the conventional one without degrading the phase noise. Alternatively, the power consumption can be reduced 15% at the same frequency. The prototype structures are fabricated in a standard 65 nm CMOS technology and measurements demonstrate that the proposed CCO operates from 0.7 – 1.2 V supply with maximum frequencies of 80 MHz and energy/cycle ranging from 0.11 – 0.38 pJ over the tuning range. Further, system level simulations show that the nonlinearity in current-frequency conversion by the CCO does not affect its use as a neuron in a Deep Neural Network if accounted for during training.