Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of irrigation rates on cotton yield as affected by soil physical properties and topography in the southern high plains

Lack of precipitation and groundwater for irrigation limits crop production in semi-arid regions, such as the Southern High Plains (SHP). Advanced technologies, such as variable rate irrigation (VRI), can conserve water and improve water use efficiency for sustainable agriculture. However, the adoption of VRI is hindered by the lack of on-farm research focusing on the feasibility of VRI. The objective of this study was to assess the effect of irrigation rates on cotton yield as affected by soil physical properties and topography in the Southern High Plains. This study was conducted in two fields within a 194-ha commercially managed farm in Hale County, Texas, in 2017. An irrigation treatment with three rates was implemented in a randomized complete block design with two replications as separate blocks in each field. A total of 230 composite soil samples were collected from the farm in spring 2017 and analyzed for texture. Information on apparent soil electrical conductivity (ECa), elevation, and final yield were collected from the fields. A statistical model showed that the effect of irrigation rates on cotton yield depended on its interaction with soil physical properties and topography. For example, areas with slope >2% and sand content >50% had no significant response to higher irrigation rates. This model suggests that applying irrigation amounts based on the yield response can be a basis for VRI. This study provides valuable information for site-specific irrigation to optimize crop production in fields with significant variability in soil physical properties and topography.
Arabidopsis assemble distinct root-associated microbiomes through the synthesis of an array of defense metabolites

Plant associated microbiomes are known to confer fitness advantages to the host. Understanding how plant factors including biochemical traits influence host associated microbiome assembly could facilitate the development of microbiome-mediated solutions for sustainable plant production. Here, we examined microbial community structures of a set of well-characterized Arabidopsis thaliana mutants disrupted in metabolic pathways for the production of glucosinolates, flavonoids, or a number of defense signalling molecules. A. thaliana lines were grown in a natural soil and maintained under greenhouse conditions for 4 weeks before collection of roots for bacterial and fungal community profiling. We found distinct relative abundances and diversities of bacterial and fungal communities assembled in the individual A. thaliana mutants compared to their parental lines. Bacterial and fungal genera were mostly enriched than depleted in secondary metabolite and defense signaling mutants, except for flavonoid mutations on fungi communities. Bacterial genera Azospirillum and Flavobacterium were significantly enriched in most of the glucosinolate, flavonoid and signalling mutants while the fungal taxa Sporobolomyces and Emericellopsis were enriched in several glucosinolates and signalling mutants. Whilst the present study revealed marked differences in microbiomes of Arabidopsis mutants and their parental lines, it is suggestive that unknown enzymatic and pleiotropic activities of the mutated genes could contribute to the identified host-associated microbiomes. Notwithstanding, this study revealed interesting gene-microbiota links, and thus represents valuable resource data for selecting candidate A. thaliana mutants for analyzing the links between host genetics and the associated microbiome.
Estimating preharvest density, adult sex ratio, and fecundity of white‐tailed deer using noninvasive sampling techniques

Abstract Adult sex ratio and fecundity (juveniles per female) are key population parameters in sustainable wildlife management, but inferring these requires abundance estimates of at least three age/sex classes of the population (male and female adults and juveniles). Prior to harvest, we used an array of 36 wildlife camera traps during 2 and 3 weeks in the early autumn of 2016 and 2017, respectively. We recorded white‐tailed deer adult males, adult females, and fawns from the pictures. Simultaneously, we collected fecal DNA (fDNA) from 92 20 m × 20 m plots placed in 23 clusters of four plots between the camera traps. We identified individuals from fDNA samples with microsatellite markers and estimated the total sex ratio and population density using spatial capture–recapture (SCR). The fDNA‐SCR analysis concluded equal sex ratio in the first year and female bias in the second year, and no difference in space use between sexes (fawns and adults combined). Camera information was analyzed in a spatial capture (SC) framework assuming an informative prior for animals’ space use, either (a) as estimated by fDNA‐SCR (same for all age/sex classes), (b) as assumed from the literature (space use of adult males larger than adult females and fawns), or (c) by inferring adult male space use from individually identified males from the camera pictures. These various SC approaches produced plausible inferences on fecundity, but also inferred total density to be lower than the estimate provided by fDNA‐SCR in one of the study years. SC approaches where adult male and female were allowed to differ in their space use suggested the population had a female‐biased adult sex ratio. In conclusion, SC approaches allowed estimating the preharvest population parameters of interest and provided conservative density estimates.
A Novel S100 Family-Based Signature Associated with Prognosis and Immune Microenvironment in Glioma

Background Glioma is the most common central nervous system (CNS) cancer with a short survival period and a poor prognosis. The S100 family gene, comprising 25 members, relates to diverse biological processes of human malignancies. Nonetheless, the significance of S100 genes in predicting the prognosis of glioma remains largely unclear. We aimed to build an S100 family-based signature for glioma prognosis. Methods We downloaded 665 and 313 glioma patients, respectively, from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) database with RNAseq data and clinical information. This study established a prognostic signature based on the S100 family genes through multivariate COX and LASSO regression. The Kaplan–Meier curve was plotted to compare overall survival (OS) among groups, whereas Receiver Operating Characteristic (ROC) analysis was performed to evaluate model accuracy. A representative gene S100B was further verified by in vitro experiments. Results An S100 family-based signature comprising 5 genes was constructed to predict the glioma that stratified TCGA-derived cases as a low- or high-risk group, whereas the significance of prognosis was verified based on CGGA-derived cases. Kaplan–Meier analysis revealed that the high-risk group was associated with the dismal prognosis. Furthermore, the S100 family-based signature was proved to be closely related to immune microenvironment. In vitro analysis showed S100B gene in the signature promoted glioblastoma (GBM) cell proliferation and migration. Conclusions We constructed and verified a novel S100 family-based signature associated with tumor immune microenvironment (TIME), which may shed novel light on the glioma diagnosis and treatment.
A bioinformatics pipeline for Mycobacterium tuberculosis sequencing that cleans contaminant reads from sputum samples

Next-Generation Sequencing (NGS) is widely used to investigate genomic variation. In several studies, the genetic variation of Mycobacterium tuberculosis has been analyzed in sputum samples without previous culture, using target enrichment methodologies for NGS. Alignments obtained by different programs generally map the sequences under default parameters, and from these results, it is assumed that only Mycobacterium reads will be obtained. However, variants of interest microorganism in clinical samples can be confused with a vast collection of reads from other bacteria, viruses, and human DNA. Currently, there are no standardized pipelines, and the cleaning success is never verified since there is a lack of rigorous controls to identify and remove reads from other sputum-microorganisms genetically similar to M. tuberculosis. Therefore, we designed a bioinformatic pipeline to process NGS data from sputum samples, including several filters and quality control points to identify and eliminate non-M. tuberculosis reads to obtain a reliable genetic variant report. Our proposal uses the SURPI software as a taxonomic classifier to filter input sequences and perform a mapping that provides the highest percentage of Mycobacterium reads, minimizing the reads from other microorganisms. We then use the filtered sequences to perform variant calling with the GATK software, ensuring the mapping quality, realignment, recalibration, hard-filtering, and post-filter to increase the reliability of the reported variants. Using default mapping parameters, we identified reads of contaminant bacteria, such as Streptococcus, Rhotia, Actinomyces, and Veillonella. Our final mapping strategy allowed a sequence identity of 97.8% between the input reads and the whole M. tuberculosis reference genome H37Rv using a genomic edit distance of three, thus removing 98.8% of the off-target sequences with a Mycobacterium reads loss of 1.7%. Finally, more than 200 unreliable genetic variants were removed during the variant calling, increasing the report’s reliability.
Latent Equilibrium: A unified learning theory for arbitrarily fast computation with arbitrarily slow neurons

The response time of physical computational elements is finite, and neurons are no exception. In hierarchical models of cortical networks each layer thus introduces a response lag. This inherent property of physical dynamical systems results in delayed processing of stimuli and causes a timing mismatch between network output and instructive signals, thus afflicting not only inference, but also learning. We introduce Latent Equilibrium, a new framework for inference and learning in networks of slow components which avoids these issues by harnessing the ability of biological neurons to phase-advance their output with respect to their membrane potential. This principle enables quasi-instantaneous inference independent of network depth and avoids the need for phased plasticity or computationally expensive network relaxation phases. We jointly derive disentangled neuron and synapse dynamics from a prospective energy function that depends on a network's generalized position and momentum. The resulting model can be interpreted as a biologically plausible approximation of error backpropagation in deep cortical networks with continuous-time, leaky neuronal dynamics and continuously active, local plasticity. We demonstrate successful learning of standard benchmark datasets, achieving competitive performance using both fully-connected and convolutional architectures, and show how our principle can be applied to detailed models of cortical microcircuitry. Furthermore, we study the robustness of our model to spatio-temporal substrate imperfections to demonstrate its feasibility for physical realization, be it in vivo or in silico.
Adversarial Neuron Pruning Purifies Backdoored Deep Models

As deep neural networks (DNNs) are growing larger, their requirements for computational resources become huge, which makes outsourcing training more popular. Training in a third-party platform, however, may introduce potential risks that a malicious trainer will return backdoored DNNs, which behave normally on clean samples but output targeted misclassifications whenever a trigger appears at the test time. Without any knowledge of the trigger, it is difficult to distinguish or recover benign DNNs from backdoored ones. In this paper, we first identify an unexpected sensitivity of backdoored DNNs, that is, they are much easier to collapse and tend to predict the target label on clean samples when their neurons are adversarially perturbed. Based on these observations, we propose a novel model repairing method, termed Adversarial Neuron Pruning (ANP), which prunes some sensitive neurons to purify the injected backdoor. Experiments show, even with only an extremely small amount of clean data (e.g., 1%), ANP effectively removes the injected backdoor without causing obvious performance degradation.
Vector-valued Gaussian Processes on Riemannian Manifolds via Gauge Equivariant Projected Kernels

Gaussian processes are machine learning models capable of learning unknown functions in a way that represents uncertainty, thereby facilitating construction of optimal decision-making systems. Motivated by a desire to deploy Gaussian processes in novel areas of science, a rapidly-growing line of research has focused on constructively extending these models to handle non-Euclidean domains, including Riemannian manifolds, such as spheres and tori. We propose techniques that generalize this class to model vector ﬁelds on Riemannian manifolds, which are important in a number of application areas in the physical sciences. To do so, we present a general recipe for constructing gauge equivariant kernels, which induce Gaussian vector ﬁelds, i.e. vector-valued Gaussian processes coherent with geometry, from scalar-valued Riemannian kernels. We extend standard Gaussian process training methods, such as variational inference, to this setting. This enables vector-valued Gaussian processes on Riemannian manifolds to be trained using standard methods and makes them accessible to machine learning practitioners.
CBIR using Pre-Trained Neural Networks

Much of the recent research work in image retrieval, has been focused around using Neural Networks as the core component. Many of the papers in other domain have shown that training multiple models, and then combining their outcomes, provide good results. This is since, a single Neural Network model, may not extract sufficient information from the input. In this paper, we aim to follow a different approach. Instead of the using a single model, we use a pretrained Inception V3 model, and extract activation of its last fully connected layer, which forms a low dimensional representation of the image. This feature matrix, is then divided into branches and separate feature extraction is done for each branch, to obtain multiple features flattened into a vector. Such individual vectors are then combined, to get a single combined feature. We make use of CUB200-2011 Dataset, which comprises of 200 birds classes to train the model on. We achieved a training accuracy of 99.46% and validation accuracy of 84.56% for the same. On further use of 3 branched global descriptors, we improve the validation accuracy to 88.89%. For this, we made use of MS-RMAC feature extraction method.
Polynomial-Spline Neural Networks with Exact Integrals

Using neural networks to solve variational problems, and other scientific machine learning tasks, has been limited by a lack of consistency and an inability to exactly integrate expressions involving neural network architectures. We address these limitations by formulating a novel neural network architecture incorporating free knot B1-spline basis functions into a polynomial mixture-of-experts model. Effectively, our architecture performs piecewise polynomial approximation on each cell of a trainable partition of unity while ensuring the neural network and its derivatives can be integrated exactly, obviating a reliance on sampling or quadrature and enabling error-free computation of variational forms. We demonstrate hp-convergence for regression problems at convergence rates expected from approximation theory and solve elliptic problems in one and two dimensions to show an effective dimension reduction compared to adaptive finite elements.
High performance distributed feedback quantum dot lasers with laterally coupled dielectric grating

The combination of grating-based frequency-selective optical feedback mechanisms, such as distributed feedback (DFB) or distributed Bragg reflector (DBR) structures, with quantum dot (QD) gain materials is a main approach towards ultra-high-performance semiconductor lasers for many key novel applications, either as stand-alone sources or as on-chip sources in photonic integrated circuits. However, the fabrication of conventional buried Bragg grating structures on GaAs, GaAs/Si, GaSb and other material platforms have been met with major material regrowth difficulties. We report a novel and universal approach of introducing laterally coupled dielectric Bragg gratings to semiconductor lasers that allows highly controllable, reliable and strong coupling between the grating and the optical mode. We implement such a grating structure in a low-loss amorphous silicon material alongside GaAs lasers with InAs/GaAs QD gain layers. The resulting DFB laser arrays emit at pre-designed 0.8 THz LWDM frequency intervals in the 1300 nm band with record performance parameters, including side mode suppression ratios as high as 52.7 dB, continuous-wave output power of 27.7 mW (room-temperature) and 10 mW (at 70°C), and ultra-low relative intensity noise (RIN) of < -165 dB/Hz (2.5-25 GHz). The devices are also capable of operating isolator-free under very high external reflection levels of up to -12.3 dB whilst maintaining the high spectral and ultra-low RIN qualities. These results validate the novel laterally coupled dielectric grating as a technologically superior and potentially cost-effective approach for fabricating DFB and DBR lasers free of their semiconductor material constraints, thus universally applicable across different material platforms and wavelength bands.
Over-the-Air Aggregation for Federated Learning: Waveform Superposition and Prototype Validation

In this paper, we develop an orthogonal-frequency-division-multiplexing (OFDM)-based over-the-air (OTA) aggregation solution for wireless federated learning (FL). In particular, the local gradients in massive IoT devices are modulated by an analog waveform and are then transmitted using the same wireless resources. To this end, achieving perfect waveform superposition is the key challenge, which is difficult due to the existence of frame timing offset (TO) and carrier frequency offset (CFO). In order to address these issues, we propose a two-stage waveform pre-equalization technique with a customized multiple access protocol that can estimate and then mitigate the TO and CFO for the OTA aggregation. Based on the proposed solution, we develop a hardware transceiver and application software to train a real-world FL task, which learns a deep neural network to predict the received signal strength with global positioning system information. Experiments verify that the proposed OTA aggregation solution can achieve comparable performance to offline learning procedures with high prediction accuracy.
HSVI fo zs-POSGs using Concavity, Convexity and Lipschitz Properties

Dynamic programming and heuristic search are at the core of state-of-the-art solvers for sequential decision-making problems. In partially observable or collaborative settings (\eg, POMDPs and Dec-POMDPs), this requires introducing an appropriate statistic that induces a fully observable problem as well as bounding (convex) approximators of the optimal value function. This approach has succeeded in some subclasses of 2-player zero-sum partially observable stochastic games (zs-POSGs) as well, but failed in the general case despite known concavity and convexity properties, which only led to heuristic algorithms with poor convergence guarantees. We overcome this issue, leveraging on these properties to derive bounding approximators and efficient update and selection operators, before deriving a prototypical solver inspired by HSVI that provably converges to an $\epsilon$-optimal solution in finite time, and which we empirically evaluate. This opens the door to a novel family of promising approaches complementing those relying on linear programming or iterative methods.
Don't read, just look: Main content extraction from web pages using visually apparent features

The extraction of main content provides only primary informative blocks by removing a web page’s minor areas like navigation menu, ads, and site templates. It has various applications: information retrieval, search engine optimization, and browser reader mode. We tested the existing four main content extraction methods (Firefox Readability.js, Chrome DOM Distiller, Web2Text, and Boilernet) in web pages datasets of two English datasets from the global websites and seven non-English datasets from seven local regions each. It shows that the performance decreases by up to 40% in non-English datasets over English datasets. This paper proposes a multilingual main content extraction method that uses visually apparent features such as the elements’ positions, size, and distances from the centers of the browser window and the web document. These are based on the authors’ intention: the elements’ placement and appearance in web pages have constraints because of humans’ narrow central vision. Hence, our method, Grid-Center-Expand (GCE), finds the closest leaf node to the centroid of the web page from which minor areas have been removed. For the main content, the leaf node repeatedly ascends to the parent node of the DOM tree until this node fits one of the following conditions: <article> tag, containing specific attributes, or sudden width change. In the non-English datasets, our method performs better than up to 13% over Boilernet, especially 56% in the Japan dataset and 7% in the English dataset. Therefore, our method performs well regardless of the regional and linguistic characteristics of the web page. In addition, we create DNN models using Google’s TabNet with GCE’s features. The best of our models has similar performance to Boilernet and Web2text in all datasets. Accordingly, we show that these features can be useful to machine learning models for extracting main content.
SOAT: A Scene- and Object-Aware Transformer for Vision-and-Language Navigation

Natural language instructions for visual navigation often use scene descriptions (e.g.,"bedroom") and object references (e.g.,"green chairs") to provide a breadcrumb trail to a goal location. This work presents a transformer-based vision-and-language navigation (VLN) agent that uses two different visual encoders -- a scene classification network and an object detector -- which produce features that match these two distinct types of visual cues. In our method, scene features contribute high-level contextual information that supports object-level processing. With this design, our model is able to use vision-and-language pretraining (i.e., learning the alignment between images and text from large-scale web data) to substantially improve performance on the Room-to-Room (R2R) and Room-Across-Room (RxR) benchmarks. Specifically, our approach leads to improvements of 1.8% absolute in SPL on R2R and 3.7% absolute in SR on RxR. Our analysis reveals even larger gains for navigation instructions that contain six or more object references, which further suggests that our approach is better able to use object features and align them to references in the instructions.