Bias and Fairness of Evasion Attacks in Image Perturbation

When talking about protecting privacy of personal images, adversarial attack methods play key roles. These methods are created to protect against the unauthorized usage of personal images. Such methods protect personal privacy by adding some amount of perturbations, otherwise known as noise , to input images to enhance privacy protection. Fawkes in Clean Attack method is one adversarial machine learning approach aimed at protecting personal privacy against abuse of personal images by unauthorized AI systems. In leveraging the Fawkes in Evasion Attack method and through running additional experiments against the Fawkes system, we were able to prove that the effectiveness of perturbations added in privacy protection of images depends on how we stratify the input population based on demographic features such as race and gender, showing that we need to be able to quantify and take into account various potential areas of bias when leveraging adversarial attack methods to ensure optimal protection of all input images. As it currently stands, the Fawkes system has a fixed set of hyper parameters for amount of perturbations added per image, which essentially means that they consider all users be treated identically in terms of amount of perturbations added. However, from testing our hypothesis through running various experiments, we found that the protection performance is statistically significantly different when the input images are from different groups of people based on demographic features like race and gender when applying the original parameter settings. For example, we found that for light skin toned females, the original Fawkes settings work well in ensuring privacy protection. However, the original Fawkes settings do not perform well with dark skin toned males in ensuring privacy protection of these images. In order to ensure fairness from the system, we propose guidelines for taking into account these demographic differences in order to get optimized solution sets for hyper parameter tuning, making future users of the model aware of existing biases and how to mitigate and take them into account. Our proposed solution for hyper parameter tuning takes into account demographic features with internal system settings, aimed at improving the protection performance for all skin tones and gender. We categorized inputs based on demographic features (namely, race and gender) and then used the current Fawkes model to process the categorized input images with different parameters. In our experiments, the main metric we use to evaluate and determine the optimal hyper parameters is the output of custom classifier models (e.g., confidence values) built from Microsoft Cognitive Services Face API. From a high-level, we first test the effectiveness of the Fawkes model applied in Evasion Attack Scenario. Then we ran experiments with curated datasets to prove the existence of demographic bias in the current Fawkes model with its default parameters. Next, we performed experiments on changing the default parameters of Fawkes to analyze the influence of different parameters on different input images. Based on the previous experiment results, we propose guidelines and solution sets that optimize the internal settings to ensure Fawkes model takes into account potential demographic biases and ensure fair protection for all input images. Our proposed solution and devised set of guidelines takes into account various demographic features (e.g., race and gender) and internal settings together by using grid-search like methods, namely pair-to-pair. By applying our proposed set of guidelines, we ensure optimal protection performance by all skin tones and gender, improving bias and enhancing fairness of the Fawkes model

Macro-ecological patterns in seed removal by animals

This thesis aims to improve our understanding of several long-held ideas concerning seed removal by animals across large-scale gradients. By assembling a database of 13,135 animal-seed interactions across all vertebrate taxa, I provided the first broad test of the idea that large animals ingest large seeds. Surprisingly, I found that the size of ingested seeds was significantly negatively correlated with animal body weight. This negative relationship was driven by large animals, particularly ungulates, ingesting small seeds. The results show that the loss of large animals could have negative effects on the dispersal of small-seeded plants, in addition to the more widely acknowledged impacts on large-seeded plants. Next, I used data for 4008 Australian species to provide the first quantitative analysis of the idea that fleshy fruits are more prevalent towards the tropics. Plants were more likely to bear fleshy fruits at low latitudes, and in regions with warm, wet and stable climates. Fruit type was more strongly affected by conditions during the parts of the year in which they grow than by conditions during the harshest parts of the year, suggesting that some current theories on plant traits may focus on the wrong aspects of climate. Finally, I performed a field study across 25 sites spanning 28 degree of latitude along the east coast of Australia, to provide the first empirical test of the idea that seed predation and seed defense are greater towards the tropics. Contrary to traditional expectations, neither seed predation nor seed physical defence was more intense at low latitudes. In fact, pre-dispersal predation and defence were greater at higher latitudes. My results are consistent with recent findings on latitudinal gradients in herbivory and defences in leaves. My findings cast further doubt on the generality of latitudinal gradients in biotic interactions, and suggest that increased seed/seedling mortality as predicted by the Janzen-Connell hypothesis does not provide a plausible explanation for the greater diversity of tropical ecosystems. My thesis has tested several well-accepted ideas on seed removal by animals, and shown that our understanding of the factors that shape global patterns in biodiversity needs to be reshaped

Genome-Wide Association Study and Subsequent Exclusion of ATCAY as a Candidate Gene Involved in Equine Neuroaxonal Dystrophy Using Two Animal Models.

Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (eNAD/EDM) is an inherited neurodegenerative disorder of unknown etiology. Clinical signs of neurological deficits develop within the first year of life in vitamin E (vitE) deficient horses. A genome-wide association study (GWAS) was carried out using 670,000 SNP markers in 27 case and 42 control Quarter Horses. Two markers, encompassing a 2.5 Mb region on ECA7, were associated with the phenotype (p = 2.05 × 10-7 and 4.72 × 10-6). Within this region, caytaxin (ATCAY) was identified as a candidate gene due to its known role in Cayman Ataxia and ataxic/dystonic phenotypes in mouse models. Whole-genome sequence data in four eNAD/EDM and five unaffected horses identified 199 associated variants within the ECA7 region. MassARRAY® genotyping was performed on these variants within the GWAS population. The three variants within ATCAY were not concordant with the disease phenotype. No difference in expression or alternative splicing was identified using qRT-PCR in brainstem across the ATCAY transcript. Atcayji-hes mice were then used to conduct functional analysis in a second animal model. Histologic lesions were not identified in the central nervous system of Atcayji-hes mice. Additionally, supplementation of homozygous Atcayji-hes mice with 600 IU/day of dl-α-tocopheryl acetate (vitE) during gestation, lactation, and adulthood did not improve the phenotype. ATCAY has therefore been excluded as a candidate gene for eNAD/EDM

Energy Optimization in Multi-UAV-Assisted Edge Data Collection System

In the IoT (Internet of Things) system, the introduction of UAV (Unmanned Aerial Vehicle) as a new data collection platform can solve the problem that IoT devices are unable to transmit data over long distances due to the limitation of their battery energy. However, the unreasonable distribution of UAVs will still lead to the problem of the high total energy consumption of the system. In this work, to deal with the problem, a deployment model of a mobile edge computing (MEC) system based on multi-UAV is proposed. The goal of the model is to minimize the energy consumption of the system in the process of data transmission by optimizing the deployment of UAVs. The DEVIPSK (differential evolution algorithm with variable population size based on a mutation strategy pool initialized by K-Means) is proposed to solve the model. In DEVIPSK, the population is initialized by K-Means to obtain better initial positions of UAVs. Besides, considering the limitation of the fixed mutation strategy in the traditional evolutionary algorithm, a mutation strategy pool is used to update the positions of UAVs. The experimental results show the superiority of the DEVIPSK and provide guidance for the deployment of UAVs in the field of edge data collection in the IoT system

Successful ATAC-Seq From Snap-Frozen Equine Tissues

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000– 33,000 accessible chromatin regions in lamina and 22–61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments

Optimization for Variable Height Wind Farm Layout Model

The optimization of wind farm layouts is very important for the effective utilization of wind resources. A fixed wind turbine hub height in the layout of wind farms leads to a low wind energy utilization and a higher LCOE (levelized cost of electricity). WOMH (Wind Farm Layout Optimization Model Considering Multiple Hub Heights) is proposed in this paper to tackle the above problem. This model is different from the traditional fixed hub height model, as it uses a variable height wind turbine. In WOMH, the Jensen wake and Weibull distribution are used to describe the wake effect on the wind turbines and wind speed distribution, respectively. An algorithm called DEGM (differential evolution and greedy method with multiple strategies) is proposed to solve WOMH, which is NP hard. In the DEGM, seven strategies are designed to adjust the distribution coordinates of wind turbines so that the height of the wind turbines will be arranged from low to high in the wind direction. This layout reduces the Jensen wake effect, thus reducing the value of the LCOE. The experimental results show that in the DEGM, when the number of wind turbines is 5, 10, 20, 30 and 50, the WOMH reduces the LCOE by 13.96%, 12.54%, 8.22%, 6.14% and 7.77% compared with the fixed hub height model, respectively. In addition, the quality of the solution of the DEGM is more satisfactory than that of the three-dimensional greedy algorithm and the DEEM (differential evolution with a new encoding mechanism) algorithm. In the case of five different numbers of wind turbines, the LCOE of DEGM is at least 3.67% lower than that of DEEM, and an average of 6.83% lower than that of three-dimensional greedy. The model and algorithm in this paper provide an effective solution for the field of wind farm layout optimization

The unconventional cytoplasmic sensing mechanism for ethanol chemotaxis in Bacillus subtilis

Motile bacteria sense chemical gradients using chemoreceptors, which consist of distinct sensing and signaling domains. The general model is that the sensing domain binds the chemical and the signaling domain induces the tactic response. Here, we investigated the unconventional sensing mechanism for ethanol taxis in Bacillus subtilis. Ethanol and other short-chain alcohols are attractants for B. subtilis. Two chemoreceptors, McpB and HemAT, sense these alcohols. In the case of McpB, the signaling domain directly binds ethanol. We were further able to identify a single amino-acid residue Ala431 on the cytoplasmic signaling domain of McpB, that when mutated to a serine, reduces taxis to ethanol. Molecular dynamics simulations suggest ethanol binds McpB near residue Ala431 and mutation of this residue to serine increases coiled-coil packing within the signaling domain, thereby reducing the ability of ethanol to bind between the helices of the signaling domain. In the case of HemAT, the myoglobin-like sensing domain binds ethanol, likely between the helices encapsulating the heme group. Aside from being sensed by an unconventional mechanism, ethanol also differs from many other chemoattractants because it is not metabolized by B. subtilis and is toxic. We propose that B. subtilis uses ethanol and other short-chain alcohols to locate prey, namely alcohol-producing microorganisms

Decoding the Equine Genome: Lessons from ENCODE

The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era

Mandibulofacial Dysostosis Attributed to a Recessive Mutation of CYP26C1 in Hereford Cattle

In spring 2020, six Hereford calves presented with congenital facial deformities attributed to a condition we termed mandibulofacial dysostosis (MD). Affected calves shared hallmark features of a variably shortened and/or asymmetric lower mandible and bilateral skin tags present 2–10 cm caudal to the commissure of the lips. Pedigree analysis revealed a single common ancestor shared by the sire and dam of each affected calf. Whole-genome sequencing (WGS) of 20 animals led to the discovery of a variant (Chr26 g. 14404993T\u3eC) in Exon 3 of CYP26C1 associated with MD. This missense mutation (p.L188P), is located in an α helix of the protein, which the identified amino acid substitution is predicted to break. The implication of this mutation was further validated through genotyping 2 additional affected calves, 760 other Herefords, and by evaluation of available WGS data from over 2500 other individuals. Only the a_ected individuals were homozygous for the variant and all heterozygotes had at least one pedigree tie to the suspect founder. CYP26C1 plays a vital role in tissue-specific regulation of retinoic acid (RA) during embryonic development. Dysregulation of RA can result in teratogenesis by altering the endothelin-1 signaling pathway affecting the expression of Dlx genes, critical to mandibulofacial development. We postulate that this recessive missense mutation in CYP26C1 impacts the catalytic activity of the encoded enzyme, leading to excess RA resulting in the observed MD phenotype