Miracle-dz/UniFAR-FTUs huggingface dataset:
A Mixed Convolutional Neural Network for Pre-miRNA Classification

The biogenesis of miRNA is divided into two types based upon their different pathways. One of them is known as the canonical pathway and the other one is the mirtron pathway. This pathway depends on splicing rather than any enzyme. As the mirtron pathway is recently discovered, their identification is quite challenging due to less number of annotations. So the identification of mirtrons can be quite productive in understanding their functionality. Several machine learning algorithms have been introduced over the years based mostly upon calculated feature selection which produced good classification performance. We have also seen that neural networks like convolutional neural networks (CNN) applied on modified nucleotide sequences have given better performance. In this paper, we introduced an improved mixed convolutional neural network with multiple different sized filters and max-pooling layers using binary "one-hot" encoding and padding. We also used k-fold cross-validation and grid search to choose the values of hyperparameters. As we know neural networks tend to extract features automatically, our model did the same in the convolution and max-pooling layers. We evaluated our model in an independent test set and the results were quite satisfactory. We think our model can be used to predict mirtrons from nucleotide sequences. Even though we tried our best to fine-tune our model, we believe there’s still room for improvement as CNN involves tuning of a number of hyperparameters. The files and source codes are available at https://github.com/zahidemon/Pre-miRNA-Classification
Self-supervised Document Clustering Based on BERT with Data Augment

Contrastive learning is a good way to pursue discriminative unsupervised learning, which can inherit advantages and experiences of well-studied deep models without complexly novel model designing. In this paper, we propose two learning method for document clustering, the one is a partial contrastive learning with unsupervised data augment, and the other is a self-supervised contrastive learning. Both methods achieve state-of-the-art results in clustering accuracy when compared to recently proposed unsupervised clustering approaches.
Privacy-preserving Data Analysis through Representation Learning and Transformation

The abundance of data from the sensors embedded in mobile and Internet of Things (IoT) devices and the remarkable success of deep neural networks in uncovering hidden patterns in time series data have led to mounting privacy concerns in recent years. In this paper, we aim to navigate the trade-off between data utility and privacy by learning low-dimensional representations that are useful for data anonymization. We propose probabilistic transformations in the latent space of a variational autoencoder to synthesize time series data such that intrusive inferences are prevented while desired inferences can still be made with a satisfactory level of accuracy. We compare our technique with state-of-the-art autoencoder-based anonymization techniques and additionally show that it can anonymize data in real time on resource-constrained edge devices.
2D+3D Facial Expression Recognition via Discriminative Dynamic Range Enhancement and Multi-Scale Learning

In 2D+3D facial expression recognition (FER), existing methods generate multi-view geometry maps to enhance the depth feature representation. However, this may introduce false estimations due to local plane fitting from incomplete point clouds. In this paper, we propose a novel Map Generation technique from the viewpoint of information theory, to boost the slight 3D expression differences from strong personality variations. First, we examine the HDR depth data to extract the discriminative dynamic range $r_{dis}$, and maximize the entropy of $r_{dis}$ to a global optimum. Then, to prevent the large deformation caused by over-enhancement, we introduce a depth distortion constraint and reduce the complexity from $O(KN^2)$ to $O(KN\tau)$. Furthermore, the constrained optimization is modeled as a $K$-edges maximum weight path problem in a directed acyclic graph, and we solve it efficiently via dynamic programming. Finally, we also design an efficient Facial Attention structure to automatically locate subtle discriminative facial parts for multi-scale learning, and train it with a proposed loss function $\mathcal{L}_{FA}$ without any facial landmarks. Experimental results on different datasets show that the proposed method is effective and outperforms the state-of-the-art 2D+3D FER methods in both FER accuracy and the output entropy of the generated maps.
Nonparametric Bayesian volatility estimation for gamma-driven stochastic differential equations

We study a nonparametric Bayesian approach to estimation of the volatility function of a stochastic differential equation driven by a gamma process. The volatility function is modelled a priori as piecewise constant, and we specify a gamma prior on its values. This leads to a straightforward procedure for posterior inference via an MCMC procedure. We give theoretical performance guarantees (contraction rates for the posterior) for the Bayesian estimate in terms of the regularity of the unknown volatility function. We illustrate the method on synthetic and real data examples.
Lensed CMB power spectrum biases from masking extragalactic sources

The cosmic microwave background (CMB) is gravitationally lensed by large-scale structure, which distorts observations of the primordial anisotropies in any given direction. Averaged over the sky, this important effect is routinely modeled with the lensed CMB power spectra. This accounts for the variance of this distortion, where the leading variance effect is quadratic in the lensing deflections. However, we show that if bright extragalactic sources correlated with the large-scale structure are masked in a CMB map, the power spectrum measured over the unmasked area using a standard pseudo-${C}_{\ensuremath{\ell}}$ estimator has an additional linear lensing effect arising from correlations between the masked area and the lensing. This induces a scale-dependent average demagnification of the unlensed distance between unmasked pairs of observed points and a negative contribution to the CMB correlation function peaking at $\ensuremath{\sim}10\text{ }\text{ }\mathrm{arcmin}$. We give simple analytic models for point sources and a threshold mask constructed on a correlated Gaussian foreground field. We demonstrate the consistency of their predictions for masks removing radio sources and peaks of Sunyaev-Zeldovich and cosmic infrared background emissions using realistic numerical simulations. We discuss simple diagnostics that can be used to test for the effect in the absence of a good model for the masked sources and show that by constructing specific masks the effect can be observed on Planck data. For masks employed in the analysis of Planck and other current data sets, the effect is likely to be negligible, but may become an important subpercent correction for future surveys if substantial populations of resolved sources are masked.
Sim-to-Real Task Planning and Execution from Perception via Reactivity and Recovery

Zero-shot execution of unseen robotic tasks is an important problem in robotics. One potential approach is through task planning: combining known skills based on their preconditions and effects to achieve a user-specified goal. In this work, we propose such a task planning approach to build a reactive system for multi-step manipulation tasks that can be trained on simulation data and applied in the real-world. We explore a block-stacking task because it has a clear structure, where multiple skills must be chained together: pick up a block, place it on top of another block, etc. We learn these skills, along with a set of predicate preconditions and termination conditions, entirely in simulation. All components are learned as PointNet++ models, parameterized by the masks of relevant objects. The predicates allow us to create high-level plans combining different skills. They also serve as precondition functions for the skills, which enables the system to recognize failures and accomplish long-horizon tasks from perceptual input, which is critical for real-world execution. We evaluate our proposed approach in both simulation and in the real-world, showing an increase in success rate from 91.6% to 98% in simulation and from 10% to 80% success rate in the real-world as compared with naive baselines.
AXES: Approximation Manager for Emerging Memory Architectures

Memory approximation techniques are commonly limited in scope, targeting individual levels of the memory hierarchy. Existing approximation techniques for a full memory hierarchy determine optimal configurations at design-time provided a goal and application. Such policies are rigid: they cannot adapt to unknown workloads and must be redesigned for different memory configurations and technologies. We propose AXES: the first self-optimizing runtime manager for coordinating configurable approximation knobs across all levels of the memory hierarchy. AXES continuously updates and optimizes its approximation management policy throughout runtime for diverse workloads. AXES optimizes the approximate memory configuration to minimize power consumption without compromising the quality threshold specified by application developers. AXES can (1) learn a policy at runtime to manage variable application quality of service (QoS) constraints, (2) automatically optimize for a target metric within those constraints, and (3) coordinate runtime decisions for interdependent knobs and subsystems. We demonstrate AXES' ability to efficiently provide functions 1-3 on a RISC-V Linux platform with approximate memory segments in the on-chip cache and main memory. We demonstrate AXES' ability to save up to 37% energy in the memory subsystem without any design-time overhead. We show AXES' ability to reduce QoS violations by 75% with $<5\%$ additional energy.
Learning Efficient GANs using Differentiable Masks and co-Attention Distillation

Generative Adversarial Networks (GANs) have been widely-used in image translation, but their high computational and storage costs impede the deployment on mobile devices. Prevalent methods for CNN compression cannot be directly applied to GANs due to the complicated generator architecture and the unstable adversarial training. To solve these, in this paper, we introduce a novel GAN compression method, termed DMAD, by proposing a Differentiable Mask and a co-Attention Distillation. The former searches for a light-weight generator architecture in a training-adaptive manner. To overcome channel inconsistency when pruning the residual connections, an adaptive cross-block group sparsity is further incorporated. The latter simultaneously distills informative attention maps from both the generator and discriminator of a pre-trained model to the searched generator, effectively stabilizing the adversarial training of our light-weight model. Experiments show that DMAD can reduce the Multiply Accumulate Operations (MACs) of CycleGAN by 13x and that of Pix2Pix by 4x while retaining a comparable performance against the full model. Code is available at this https URL.
Efficient and Effective Community Search on Large-scale Bipartite Graphs

Bipartite graphs are widely used to model relation-ships between two types of entities. Community search retrieves densely connected subgraphs containing a query vertex, which has been extensively studied on unipartite graphs. However, com-munity search on bipartite graphs remains largely unexplored. Moreover, all existing cohesive subgraph models on bipartite graphs can only be applied to measure the structure cohesiveness between two sets of vertices while overlooking the edge weight in forming the community. In this paper, we study the significant (α, β)-community search problem on weighted bipartite graphs. Given a query vertex q, we aim to find the significant (α, β)-community ℛ of q which adopts (α, β)-core to characterize the engagement level of vertices, and maximizes the minimum edge weight (significance) within ℛ. To support fast retrieval of ℛ, we first retrieve the maximal connected subgraph of (α, β)-core containing the query vertex (the (α, β)-community), and the search space is limited to this subgraph with a much smaller size than the original graph. A novel index structure is presented which can be built in O(δ•m) time and takes O(δ•m) space where m is the number of edges in G, δ is bounded by $\sqrt m $ and is much smaller in practice. Utilizing the index, the (α, β)-community can be retrieved in optimal time. To further obtain ℛ, we develop peeling and expansion algorithms to conduct searches by shrinking from the (α, β)-community and expanding from the query vertex, respectively. The experimental results on real graphs not only demonstrate the effectiveness of the significant (α, β)-community model but also validate the efficiency of our query processing and indexing techniques.
Optimal Transport-Based Coverage Control for Swarm Robot Systems: Generalization of the Voronoi Tessellation-Based Method

Swarm robot systems, which consist of many cooperating mobile robots, have attracted attention for their environmental adaptability and fault tolerance advantages. One of the most important tasks for such systems is coverage control, in which robots autonomously deploy to approximate a given spatial distribution. In this letter, we formulate a coverage control paradigm using the concept of optimal transport and propose a novel control technique, which we have termed the optimal transport-based coverage control (OTCC) method. The proposed OTCC, derived via the gradient flow of the cost function in the Kantorovich dual problem, is shown to cover a widely used existing control method as a special case. We also perform a Lyapunov stability analysis of the controlled system, and provide numerical calculations to show that the OTCC reproduces target distributions with better performance than the existing control method.
CG-Net: Conditional GIS-Aware Network for Individual Building Segmentation in VHR SAR Images

Object retrieval and reconstruction from very-high-resolution (VHR) synthetic aperture radar (SAR) images are of great importance for urban SAR applications, yet highly challenging due to the complexity of SAR data. This article addresses the issue of individual building segmentation from a single VHR SAR image in large-scale urban areas. To achieve this, we introduce building footprints from geographic information system (GIS) data as a complementary information and propose a novel conditional GIS-aware network (CG-Net). The proposed model learns multilevel visual features and employs building footprints to normalize the features for predicting building masks in the SAR image. We validate our method using a high-resolution spotlight TerraSAR-X image collected over Berlin. Experimental results show that the proposed CG-Net effectively brings improvements with variant backbones. We further compare two representations of building footprints, namely, complete building footprints and sensor-visible footprint segments, for our task, and conclude that the use of the former leads to better segmentation results. Moreover, we investigate the impact of inaccurate GIS data on our CG-Net, and this study shows that CG-Net is robust against positioning errors in the GIS data. In addition, we propose an approach of ground truth generation of buildings from an accurate digital elevation model (DEM), which can be used to generate large-scale SAR image data sets. The segmentation results can be applied to reconstruct 3-D building models at level-of-detail (LoD) 1, which is demonstrated in our experiments.
Variation Free Density Functional Theory: Data-driven Stochastic Optimization

Density functional theory (DFT) is an efficient instrument for describing a wide range of nanoscale phenomena: wetting transition, capillary condensation, adsorption, etc. In this paper, we suggest a method for obtaining the equilibrium fluid density in a nanopore using DFT without calculating the free energy variation -- Variation Free Density Functional Theory (VF-DFT). This technique can be used to explore fluids with a complex type of interactions, systems with additional constraints and to speed up calculations. The fluid density is represented as a decomposition over a limited set of basis functions in VF-DFT. To build basis functions, we applied principal component analysis (PCA). PCA is used to extract the main patterns of the fluid density in the nanopore. The decomposition coefficients of the fluid density by the basis are sought by stochastic optimization algorithms: genetic algorithm (GA), particle swarm optimization (PSO) to minimize the free energy of the system. In this work, two different fluids were studied: nitrogen at a temperature of 77.4 K and argon 87.3 K, at a pore of 3.6 nm, and the performance of optimization algorithms was compared. We also introduce the Hybrid Density Functional Theory (H-DFT) approach based on stochastic optimization methods and the classical Picard iteration method to find the equilibrium fluid density in the pore. The combination of this method helps to significantly speed up the calculations of equilibrium density in the system without losing quality of the solution.
User Clustering in mmWave-NOMA Systems With User Decoding Capability Constraints for B5G Networks

This article proposes a millimeter wave-NOMA (mmWave-NOMA) system that takes into account the end-user signal processing capabilities, an important practical consideration. The implementation of NOMA in the downlink (DL) direction requires successive interference cancellation (SIC) to be performed at the user terminals, which comes at the cost of additional complexity. In NOMA, the weakest user only has to decode its own signal, while the strongest user has to decode the signals of all other users in the SIC procedure. Hence, the additional implementation complexity required of the user to perform SIC for DL NOMA depends on its position in the SIC decoding order. Beyond fifth-generation (B5G) communication systems are expected to support a wide variety of end-user devices, each with their own processing capabilities. We envision a system where users report their SIC decoding capability to the base station (BS), i.e., the number of other users signals a user is capable of decoding in the SIC procedure. We investigate the rate maximization problem in such a system, by breaking it down into a user clustering and ordering problem (UCOP), followed by a power allocation problem. We propose a NOMA-minimum exact cover (NOMA-MEC) heuristic algorithm that converts the UCOP into a cluster minimization problem from a derived set of valid cluster combinations after factoring in the SIC decoding capability. The complexity of NOMA-MEC is analyzed for various algorithm and system parameters. For a homogeneous system of users that all have the same decoding capabilities, we show that this equates to a simple maximum number of users per cluster constraint and propose a lower complexity NOMA-best beam (NOMA-BB) algorithm. Simulation results demonstrate the performance superiority in terms of sum rate compared to orthogonal multiple access (OMA) and traditional NOMA clustering schemes that do not incorporate individual users’ SIC decoding capability constraints.
Quantum algorithms for learning graphs and beyond

We study the problem of learning an unknown graph provided via an oracle using a quantum algorithm. We consider three query models. In the first model ("OR queries"), the oracle returns whether a given subset of the vertices contains any edges. In the second ("parity queries"), the oracle returns the parity of the number of edges in a subset. In the third model, we are given copies of the graph state corresponding to the graph. We give quantum algorithms that achieve speedups over the best possible classical algorithms in the OR and parity query models, for some families of graphs, and give quantum algorithms in the graph state model whose complexity is similar to the parity query model. For some parameter regimes, the speedups can be exponential in the parity query model. On the other hand, without any promise on the graph, no speedup is possible in the OR query model. A main technique we use is the quantum algorithm for solving the combinatorial group testing problem, for which a query-efficient quantum algorithm was given by Belovs. Here we additionally give a time-efficient quantum algorithm for this problem, based on the algorithm of Ambainis et al.\ for a "gapped" version of the group testing problem. We also give simple time-efficient quantum algorithms based on Fourier sampling and amplitude amplification for learning the exact-half and majority functions, which almost match the optimal complexity of Belovs' algorithms.
A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

Abstract Background From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe. Methods We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India. Results We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade. Conclusions The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10–3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.
Dynamic Energy Dispatch Based on Deep Reinforcement Learning in IoT-Driven Smart Isolated Microgrids

Microgrids (MGs) are small, local power grids that can operate independently from the larger utility grid. Combined with the Internet of Things (IoT), a smart MG can leverage the sensory data and machine learning techniques for intelligent energy management. This article focuses on deep reinforcement learning (DRL)-based energy dispatch for IoT-driven smart isolated MGs with diesel generators (DGs), photovoltaic (PV) panels, and a battery. A finite-horizon partial observable Markov decision process (POMDP) model is formulated and solved by learning from historical data to capture the uncertainty in future electricity consumption and renewable power generation. In order to deal with the instability problem of DRL algorithms and unique characteristics of finite-horizon models, two novel DRL algorithms, namely, finite-horizon deep deterministic policy gradient (FH-DDPG) and finite-horizon recurrent deterministic policy gradient (FH-RDPG), are proposed to derive energy dispatch policies with and without fully observable state information. A case study using real isolated MG data is performed, where the performance of the proposed algorithms are compared with the other baseline DRL and non-DRL algorithms. Moreover, the impact of uncertainties on MG performance is decoupled into two levels and evaluated, respectively.