Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppression of termite feeding and symbiotic protozoans by the dye, Sudan Red 7 B

Laboratory groups of the Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae), were fed for 14 days on wood shavings soaked in acetone solutions of 0%, 0.5% or 1% concentrations of the dye, Sudan Red 7B or on shavings not soaked in acetone (0% non‐acetone, NA). Termites feeding on dyed wood became visibly stained red. Groups of dyed or non‐dyed termites were then placed in containers and allowed to feed on non‐dyed wood for 21 days. Dyed termites had lower numbers of symbiotic protozoans, lower feeding rates, and lower survivorship than did non‐dyed termites. Survivorship was significantly lower in the 1% concentration than in the 0.5% concentration. Covariate analyses suggested that Sudan Red acts both directly and indirectly (via suppression of gut fauna) to reduce vigor in termites. Because there is variable survival response to this dye by different populations of C. formosanus, we recommend preliminary tests of dye toxicity before using it extensively in experiments.
Evaluation of Mulch Types on Growth and Development of Native Wild Roses (Rosa spp.) for Rose Hip Production in Prince Edward Island, Canada

This study was carried out to assess the impact of five different mulch types (straw, bark, woodchips, sawdust, and black plastic) on growth and yield of domestically cultivated native wild roses (Rosa spp.) in Prince Edward Island, Canada. The experiment was carried out at the Agriculture and Agri-Food Canada, Crops and Livestock Research Centre, Harrington Research Farm in Harrington, Prince Edward Island from 2005–2009. A replicated trial was set up with each plot divided equally into hand-weeded and non-weeded treatments. Straw mulch proved to be a practical choice for commercial producers as it was conducive to plant growth—with greater height, spread, and rose hip yield—as well as being inexpensive and easily obtainable. Black plastic mulch also supported good plant growth and production as well as being easy to maintain. Generally, hand-weeding in combination with mulching was most effective in establishing healthy, productive wild rose plantations.
Read what you need: Controllable Aspect-based Opinion Summarization of Tourist Reviews

Manually extracting relevant aspects and opinions from large volumes of user-generated text is a time-consuming process. Summaries, on the other hand, help readers with limited time budgets to quickly consume the key ideas from the data. State-of-the-art approaches for multi-document summarization, however, do not consider user preferences while generating summaries. In this work, we argue the need and propose a solution for generating personalized aspect-based opinion summaries from large collections of online tourist reviews. We let our readers decide and control several attributes of the summary such as the length and specific aspects of interest among others. Specifically, we take an unsupervised approach to extract coherent aspects from tourist reviews posted onTripAdvisor. We then propose an Integer Linear Programming (ILP) based extractive technique to select an informative subset of opinions around the identified aspects while respecting the user-specified values for various control parameters. Finally, we evaluate and compare our summaries using crowdsourcing and ROUGE-based metrics and obtain competitive results.
FastSpeech 2: Fast and High-Quality End-to-End Text to Speech

Advanced text to speech (TTS) models such as FastSpeech can synthesize speech significantly faster than previous autoregressive models with comparable quality. The training of FastSpeech model relies on an autoregressive teacher model for duration prediction (to provide more information as input) and knowledge distillation (to simplify the data distribution in output), which can ease the one-to-many mapping problem (i.e., multiple speech variations correspond to the same text) in TTS. However, FastSpeech has several disadvantages: 1) the teacher-student distillation pipeline is complicated, 2) the duration extracted from the teacher model is not accurate enough, and the target mel-spectrograms distilled from teacher model suffer from information loss due to data simplification, both of which limit the voice quality. In this paper, we propose FastSpeech 2, which addresses the issues in FastSpeech and better solves the one-to-many mapping problem in TTS by 1) directly training the model with ground-truth target instead of the simplified output from teacher, and 2) introducing more variation information of speech (e.g., pitch, energy and more accurate duration) as conditional inputs. Specifically, we extract duration, pitch and energy from speech waveform and directly take them as conditional inputs during training and use predicted values during inference. We further design FastSpeech 2s, which is the first attempt to directly generate speech waveform from text in parallel, enjoying the benefit of full end-to-end training and even faster inference than FastSpeech. Experimental results show that 1) FastSpeech 2 and 2s outperform FastSpeech in voice quality with much simplified training pipeline and reduced training time; 2) FastSpeech 2 and 2s can match the voice quality of autoregressive models while enjoying much faster inference speed.
Deep hierarchical pooling design for cross-granularity action recognition

In this paper, we introduce a novel hierarchical aggregation design that captures different levels of temporal granularity in action recognition. Our design principle is coarse-to-fine and achieved using a tree-structured network; as we traverse this network top-down, pooling operations are getting less invariant but timely more resolute and well localized. Learning the combination of operations in this network -- which best fits a given ground-truth -- is obtained by solving a constrained minimization problem whose solution corresponds to the distribution of weights that capture the contribution of each level (and thereby temporal granularity) in the global hierarchical pooling process. Besides being principled and well grounded, the proposed hierarchical pooling is also video-length agnostic and resilient to misalignments in actions. Extensive experiments conducted on the challenging UCF-101 database corroborate these statements.
Autonomous Power Allocation Based on Distributed Deep Learning for Device-to-Device Communication Underlaying Cellular Network

For Device-to-device (D2D) communication of Internet-of-Things (IoT) enabled 5G system, there is a limit to allocating resources considering a complicated interference between different links in a centralized manner. If D2D link is controlled by an enhanced node base station (eNB), and thus, remains a burden on the eNB and it causes delayed latency. This paper proposes a fully autonomous power allocation method for IoT-D2D communication underlaying cellular networks using deep learning. In the proposed scheme, an IoT-D2D transmitter decides the transmit power independently from an eNB and other IoT-D2D devices. In addition, the power set can be nearly optimized by deep learning with distributed manner to achieve higher cell throughput. We present a distributed deep learning architecture in which the devices are trained as a group but operate independently. The deep learning can attain near optimal cell throughput while suppressing interference to eNB.
Dosimetry for FLASH Radiotherapy: A Review of Tools and the Role of Radioluminescence and Cherenkov Emission

While spatial dose conformity delivered to a target volume has been pushed to its practical limits with advanced treatment planning and delivery, investigations in novel temporal dose delivery are unfolding new mechanisms. Recent advances in ultra-high dose radiotherapy, abbreviated as FLASH, indicate the potential for reduction in healthy tissue damage while preserving tumor control. FLASH therapy relies on very high dose rate of > 40Gy/s with sub-second temporal beam modulation, taking a seemingly opposite direction from the conventional paradigm of fractionated therapy. FLASH brings unique challenges to dosimetry, beam control, and verification, as well as complexity of radiobiological effective dose through altered tissue response. In this review, we compare the dosimetric methods capable of operating under high dose rate environments. Due to excellent dose-rate independence, superior spatial (~ <1 mm) and temporal (~ns) resolution achievable with Cherenkov and scintillation-based detectors, we show that luminescent detectors have a key role to play in the development of FLASH, as the field rapidly progresses toward clinical adaptation. Additionally, we show that the unique ability of certain luminescence-based methods to provide tumor oxygenation maps in real-time with submillimeter resolution can elucidate the radiobiological mechanisms behind the FLASH effect. In particular, such techniques will be crucial for understanding the role of oxygen in mediating the FLASH effect.
Primal Wasserstein Imitation Learning

Imitation Learning (IL) methods seek to match the behavior of an agent with that of an expert. In the present work, we propose a new IL method based on a conceptually simple algorithm: Primal Wasserstein Imitation Learning (PWIL), which ties to the primal form of the Wasserstein distance between the expert and the agent state-action distributions. We present a reward function which is derived offline, as opposed to recent adversarial IL algorithms that learn a reward function through interactions with the environment, and which requires little fine-tuning. We show that we can recover expert behavior on a variety of continuous control tasks of the MuJoCo domain in a sample efficient manner in terms of agent interactions and of expert interactions with the environment. Finally, we show that the behavior of the agent we train matches the behavior of the expert with the Wasserstein distance, rather than the commonly used proxy of performance.
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays

Abstract Summary Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. Availability and implementation The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics. org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. Supplementary information Supplementary data are available at Bioinformatics online.
Semi-Supervised Learning for Vision-and-Language Tasks using MixMatch

Semi-supervised learning algorithms attempt to train a model with limited labeled data by leveraging a large amount of unlabelled samples . However, there is limited literature on using such a strategy for visual-language tasks, mainly due to the complexity and the discreteness of the input space. We attempt to reformulate MixMatch , a recently proposed semi-supervised learning strategy, on a state-of-the-art multi-modal framework LXMERT , and report the performance on the NLVR2 dataset. We compare these results with suitable baseline experiments. To assess the applicability of textual interpolation, we conduct an interesting experiment on GPT-2. Towards the end, we pro-pose two more modiﬁcations that were planned but couldn’t be executed due to the constraint of time.
Adversarial Optimal Transport Through The Convolution Of Kernels With Evolving Measures

A novel algorithm is proposed to solve the sample-based optimal transport problem. An adversarial formulation of the push-forward condition uses a test function built as a convolution between an adaptive kernel and an evolving probability distribution $\nu$ over a latent variable $b$. Approximating this convolution by its simulation over evolving samples $b^i(t)$ of $\nu$, the parameterization of the test function reduces to determining the flow of these samples. This flow, discretized over discrete time steps $t_n$, is built from the composition of elementary maps. The optimal transport also follows a flow that, by duality, must follow the gradient of the test function. The representation of the test function as the Monte Carlo simulation of a distribution makes the algorithm robust to dimensionality, and its evolution under a memory-less flow produces rich, complex maps from simple parametric transformations. The algorithm is illustrated with numerical examples.
Generative Design of Hardware-aware DNNs

To efficiently run DNNs on the edge/cloud, many new DNN inference accelerators are being designed and deployed frequently. To enhance the resource efficiency of DNNs, model quantization is a widely-used approach. However, different accelerator/HW has different resources leading to the need for specialized quantization strategy of each HW. Moreover, using the same quantization for every layer may be sub-optimal, increasing the designspace of possible quantization choices. This makes manual-tuning infeasible. Recent work in automatically determining quantization for each layer is driven by optimization methods such as reinforcement learning. However, these approaches need re-training the RL for every new HW platform. We propose a new way for autonomous quantization and HW-aware tuning. We propose a generative model, AQGAN, which takes a target accuracy as the condition and generates a suite of quantization configurations. With the conditional generative model, the user can autonomously generate different configurations with different targets in inference time. Moreover, we propose a simplified HW-tuning flow, which uses the generative model to generate proposals and execute simple selection based on the HW resource budget, whose process is fast and interactive. We evaluate our model on five of the widely-used efficient models on the ImageNet dataset. We compare with existing uniform quantization and state-of-the-art autonomous quantization methods. Our generative model shows competitive achieved accuracy, however, with around two degrees less search cost for each design point. Our generative model shows the generated quantization configuration can lead to less than 3.5% error across all experiments.
Cross-Domain Segmentation with Adversarial Loss and Covariate Shift for Biomedical Imaging

Despite the widespread use of deep learning methods for semantic segmentation of images that are acquired from a single source, clinicians often use multi-domain data for a detailed analysis. For instance, CT and MRI have advantages over each other in terms of imaging quality, artifacts, and output characteristics that lead to differential diagnosis. The capacity of current segmentation techniques is only allow to work for an individual domain due to their differences. However, the models that are capable of working on all modalities are essentially needed for a complete solution. Furthermore, robustness is drastically affected by the number of samples in the training step, especially for deep learning models. Hence, there is a necessity that all available data regardless of data domain should be used for reliable methods. For this purpose, this manuscript aims to implement a novel model that can learn robust representations from cross-domain data by encapsulating distinct and shared patterns from different modalities. Precisely, covariate shift property is retained with structural modification and adversarial loss where sparse and rich representations are obtained. Hence, a single parameter set is used to perform cross-domain segmentation task. The superiority of the proposed method is that no information related to modalities are provided in either training or inference phase. The tests on CT and MRI liver data acquired in routine clinical workflows show that the proposed model outperforms all other baseline with a large margin. Experiments are also conducted on Covid-19 dataset that it consists of CT data where significant intra-class visual differences are observed. Similarly, the proposed method achieves the best performance.
Efficient MCMC Sampling for Bayesian Matrix Factorization by Breaking Posterior Symmetries

Bayesian low-rank matrix factorization techniques have become an essential tool for relational data analysis and matrix completion. A standard approach is to assign zero-mean Gaussian priors on the columns or rows of factor matrices to create a conjugate system. This choice of prior leads to symmetries in the posterior distribution and can severely reduce the efficiency of Markov-chain Monte-Carlo (MCMC) sampling approaches. In this paper, we propose a simple modification to the prior choice that provably breaks these symmetries and maintains/improves accuracy. Specifically, we provide conditions that the Gaussian prior mean and covariance must satisfy so the posterior does not exhibit invariances that yield sampling difficulties. For example, we show that using non-zero linearly independent prior means significantly lowers the autocorrelation of MCMC samples, and can also lead to lower reconstruction errors.
Extracting Cellular Location of Human Proteins Using Deep Learning

Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and accurate enough to process a large amount of data and it often leads to bias. To resolve this problem, we attempted to create an automatic image classifier using Machine Learning to locate human proteins with higher speed and accuracy than human beings. We implemented a Convolution Neural Network with Residue and Squeeze-Excitation layers classifier to locate given proteins of any type in a subcellular structure. After training the model using a series of techniques, it can locate thousands of proteins in 27 different human cell types into 28 subcellular locations, way significant than historical approaches. The model can classify 4,500 images per minute with an accuracy of 63.07%, surpassing human performance in accuracy (by 35%) and speed. Because our system can be implemented on different cell types, it opens a new vision of understanding in the biomedical field. From the locational information of the human proteins, doctors can easily detect cell's abnormal behaviors including viral infection, pathogen invasion, and malignant tumor development. Given the amount of data generalized by experiments are greater than that human can analyze, the model cut down the human resources and time needed to analyze data. Moreover, this locational information can be used in different scenarios like subcellular engineering, medical care, and etiology inspection.
EDCompress: Energy-Aware Model Compression with Dataflow

Edge devices demand low energy consumption, cost and small form factor. To efficiently deploy convolutional neural network (CNN) models on edge device, energy-aware model compression becomes extremely important. However, existing work did not study this problem well because the lack of considering the diversity of dataflow types in hardware architectures. In this paper, we propose EDCompress, an Energy-aware model compression method for various Dataflows. It can effectively reduce the energy consumption of various edge devices, with different dataflow types. Considering the very nature of model compression procedures, we recast the optimization process to a multi-step problem, and solve it by reinforcement learning algorithms. Experiments show that EDCompress could improve 20X, 17X, 37X energy efficiency in VGG-16, MobileNet, LeNet-5 networks, respectively, with negligible loss of accuracy. EDCompress could also find the optimal dataflow type for specific neural networks in terms of energy consumption, which can guide the deployment of CNN models on hardware systems.
Photoacoustic Microscopy with Sparse Data Enabled by Convolutional Neural Networks for Fast Imaging

Photoacoustic microscopy (PAM) has been a promising biomedical imaging technology in recent years. However, the point-by-point scanning mechanism results in low-speed imaging, which limits the application of PAM. Reducing sampling density can naturally shorten image acquisition time, which is at the cost of image quality. In this work, we propose a method using convolutional neural networks (CNNs) to improve the quality of sparse PAM images, thereby speeding up image acquisition while keeping good image quality. The CNN model utilizes both squeeze-and-excitation blocks and residual blocks to achieve the enhancement, which is a mapping from a 1/4 or 1/16 low-sampling sparse PAM image to a latent fully-sampled image. The perceptual loss function is applied to keep the fidelity of images. The model is mainly trained and validated on PAM images of leaf veins. The experiments show the effectiveness of our proposed method, which significantly outperforms existing methods quantitatively and qualitatively. Our model is also tested using in vivo PAM images of blood vessels of mouse ears and eyes. The results show that the model can enhance the image quality of the sparse PAM image of blood vessels from several aspects, which may help fast PAM and facilitate its clinical applications.
A Novel Algorithm for Optimized Real Time Anomaly Detection in Timeseries

Observations in data which are significantly different from its neighbouring points but cannot be classified as noise are known as anomalies or outliers. These anomalies are a cause of concern and a timely warning about their presence could be valuable. In this paper, we have evaluated and compared the performance of popular algorithms from domains of Machine Learning and Statistics in detecting anomalies on both offline data as well as real time data. Our aim is to come up with an algorithm which can handle all types of seasonal and non-seasonal data effectively and is fast enough to be of practical utility in real time. It is not only important to detect anomalies at the global but also the ones which are anomalies owing to their local surroundings. Such outliers can be termed as contextual anomalies as they derive their context from the neighbouring observations. Also, we require a methodology to automatically determine the presence of seasonality in the given data. For detecting the seasonality, the proposed algorithm takes up a curve fitting approach rather than model based anomaly detection. The proposed model also introduces a unique filter which assess the relative significance of local outliers and removes the ones deemed as insignificant. Since, the proposed model fits polynomial in buckets of timeseries data, it does not suffer from problems such as heteroskedasticity and breakout as compared to its statistical alternatives such as ARIMA, SARIMA and Winter Holt. Experimental results the proposed algorithm performs better on both real time as well as artificial generated datasets.