6,024 research outputs found
Evaluation Methodologies in Software Protection Research
Man-at-the-end (MATE) attackers have full control over the system on which
the attacked software runs, and try to break the confidentiality or integrity
of assets embedded in the software. Both companies and malware authors want to
prevent such attacks. This has driven an arms race between attackers and
defenders, resulting in a plethora of different protection and analysis
methods. However, it remains difficult to measure the strength of protections
because MATE attackers can reach their goals in many different ways and a
universally accepted evaluation methodology does not exist. This survey
systematically reviews the evaluation methodologies of papers on obfuscation, a
major class of protections against MATE attacks. For 572 papers, we collected
113 aspects of their evaluation methodologies, ranging from sample set types
and sizes, over sample treatment, to performed measurements. We provide
detailed insights into how the academic state of the art evaluates both the
protections and analyses thereon. In summary, there is a clear need for better
evaluation methodologies. We identify nine challenges for software protection
evaluations, which represent threats to the validity, reproducibility, and
interpretation of research results in the context of MATE attacks
Artificial Intelligence, Robots, and Philosophy
This book is a collection of all the papers published in the special issue “Artificial Intelligence, Robots, and Philosophy,” Journal of Philosophy of Life, Vol.13, No.1, 2023, pp.1-146. The authors discuss a variety of topics such as science fiction and space ethics, the philosophy of artificial intelligence, the ethics of autonomous agents, and virtuous robots. Through their discussions, readers are able to think deeply about the essence of modern technology and the future of humanity. All papers were invited and completed in spring 2020, though because of the Covid-19 pandemic and other problems, the publication was delayed until this year. I apologize to the authors and potential readers for the delay. I hope that readers will enjoy these arguments on digital technology and its relationship with philosophy. ***
Contents***
Introduction
: Descartes and Artificial Intelligence;
Masahiro Morioka***
Isaac Asimov and the Current State of Space Science Fiction
: In the Light of Space Ethics;
Shin-ichiro Inaba***
Artificial Intelligence and Contemporary Philosophy
: Heidegger, Jonas, and Slime Mold;
Masahiro Morioka***
Implications of Automating Science
: The Possibility of Artificial Creativity and the Future of Science;
Makoto Kureha***
Why Autonomous Agents Should Not Be Built for War;
István Zoltán Zárdai***
Wheat and Pepper
: Interactions Between Technology and Humans;
Minao Kukita***
Clockwork Courage
: A Defense of Virtuous Robots;
Shimpei Okamoto***
Reconstructing Agency from Choice;
Yuko Murakami***
Gushing Prose
: Will Machines Ever be Able to Translate as Badly as
Humans?;
Rossa Ó Muireartaigh**
More Than Machines?
We know that robots are just machines. Why then do we often talk about them as if they were alive? Laura Voss explores this fascinating phenomenon, providing a rich insight into practices of animacy (and inanimacy) attribution to robot technology: from science-fiction to robotics R&D, from science communication to media discourse, and from the theoretical perspectives of STS to the cognitive sciences. Taking an interdisciplinary perspective, and backed by a wealth of empirical material, Voss shows how scientists, engineers, journalists - and everyone else - can face the challenge of robot technology appearing »a little bit alive« with a reflexive and yet pragmatic stance
Understanding the Code of Life: Holistic Conceptual Modeling of the Genome
[ES] En las últimas décadas, los avances en la tecnología de secuenciación han producido cantidades significativas de datos genómicos, hecho que ha revolucionado nuestra comprensión de la biología. Sin embargo, la cantidad de datos generados ha superado con creces nuestra capacidad para interpretarlos.
Descifrar el código de la vida es un gran reto. A pesar de los numerosos avances realizados, nuestra comprensión del mismo sigue siendo mínima, y apenas estamos empezando a descubrir todo su potencial, por ejemplo, en áreas como la medicina de precisión o la farmacogenómica.
El objetivo principal de esta tesis es avanzar en nuestra comprensión de la vida proponiendo una aproximación holística mediante un enfoque basado en modelos que consta de tres artefactos: i) un esquema conceptual del genoma, ii) un método para su aplicación en el mundo real, y iii) el uso de ontologías fundacionales para representar el conocimiento del dominio de una forma más precisa y explícita. Las dos primeras contribuciones se han validado mediante la implementación de sistemas de información genómicos basados en modelos conceptuales. La tercera contribución se ha validado mediante experimentos empíricos que han evaluado si el uso de ontologías fundacionales conduce a una mejor comprensión del dominio genómico.
Los artefactos generados ofrecen importantes beneficios. En primer lugar, se han generado procesos de gestión de datos más eficientes, lo que ha permitido mejorar los procesos de extracción de conocimientos. En segundo lugar, se ha logrado una mejor comprensión y comunicación del dominio.[CA] En les últimes dècades, els avanços en la tecnologia de seqüenciació han produït quantitats significatives de dades genòmiques, fet que ha revolucionat la nostra comprensió de la biologia. No obstant això, la quantitat de dades generades ha superat amb escreix la nostra capacitat per a interpretar-los.
Desxifrar el codi de la vida és un gran repte. Malgrat els nombrosos avanços realitzats, la nostra comprensió del mateix continua sent mínima, i a penes estem començant a descobrir tot el seu potencial, per exemple, en àrees com la medicina de precisió o la farmacogenómica.
L'objectiu principal d'aquesta tesi és avançar en la nostra comprensió de la vida proposant una aproximació holística mitjançant un enfocament basat en models que consta de tres artefactes: i) un esquema conceptual del genoma, ii) un mètode per a la seua aplicació en el món real, i iii) l'ús d'ontologies fundacionals per a representar el coneixement del domini d'una forma més precisa i explícita. Les dues primeres contribucions s'han validat mitjançant la implementació de sistemes d'informació genòmics basats en models conceptuals. La tercera contribució s'ha validat mitjançant experiments empírics que han avaluat si l'ús d'ontologies fundacionals condueix a una millor comprensió del domini genòmic.
Els artefactes generats ofereixen importants beneficis. En primer lloc, s'han generat processos de gestió de dades més eficients, la qual cosa ha permés millorar els processos d'extracció de coneixements. En segon lloc, s'ha aconseguit una millor comprensió i comunicació del domini.[EN] Over the last few decades, advances in sequencing technology have produced significant amounts of genomic data, which has revolutionised our understanding of biology. However, the amount of data generated has far exceeded our ability to interpret it.
Deciphering the code of life is a grand challenge. Despite our progress, our understanding of it remains minimal, and we are just beginning to uncover its full potential, for instance, in areas such as precision medicine or pharmacogenomics.
The main objective of this thesis is to advance our understanding of life by proposing a holistic approach, using a model-based approach, consisting of three artifacts: i) a conceptual schema of the genome, ii) a method for its application in the real-world, and iii) the use of foundational ontologies to represent domain knowledge in a more unambiguous and explicit way. The first two contributions have been validated by implementing genome information systems based on conceptual models. The third contribution has been validated by empirical experiments assessing whether using foundational ontologies leads to a better understanding of the genomic domain.
The artifacts generated offer significant benefits. First, more efficient data management processes were produced, leading to better knowledge extraction processes. Second, a better understanding and communication of the domain was achieved.Las fructíferas discusiones y los resultados derivados de los proyectos INNEST2021
/57, MICIN/AEI/10.13039/501100011033, PID2021-123824OB-I00, CIPROM/2021/023 y PDC2021-
121243-I00 han contribuido en gran medida a la calidad final de este tesis.García Simón, A. (2022). Understanding the Code of Life: Holistic Conceptual Modeling of the Genome [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/19143
On the Security Blind Spots of Software Composition Analysis
Modern software heavily relies on the use of components. Those components are
usually published in central repositories, and managed by build systems via
dependencies. Due to issues around vulnerabilities, licenses and the
propagation of bugs, the study of those dependencies is of utmost importance,
and numerous software composition analysis tools have emerged to address those
issues. A particular challenge are hidden dependencies that are the result of
cloning or shading where code from a component is "inlined", and, in the case
of shading, moved to different namespaces. We present an approach to detect
cloned and shaded artifacts in the Maven repository. Our approach is
lightweight in that it does not require the creation and maintenance of an
index, and uses a custom AST-based clone detection. Our analysis focuses on the
detection of vulnerabilities in artifacts which use cloning or shading.
Starting with eight vulnerabilities with assigned CVEs (four of those
classified as critical) and proof-of-vulnerability projects demonstrating the
presence of a vulnerability in an artifact, we query the Maven repository and
retrieve over 16k potential clones of the vulnerable artifacts. After running
our analysis on this set, we detect 554 artifacts with the respective
vulnerabilities (49 if versions are ignored). We synthesize a testable
proof-of-vulnerability project for each of those. We demonstrate that existing
SCA tools often miss these exposures.Comment: 16 pages, 1 figur
Program and Proceedings: The Nebraska Academy of Sciences 1880-2023. 142th Anniversary Year. One Hundred-Thirty-Third Annual Meeting April 21, 2023. Hybrid Meeting: Nebraska Wesleyan University & Online, Lincoln, Nebraska
AERONAUTICS & SPACE SCIENCE Chairperson(s): Dr. Scott Tarry & Michaela Lucas
HUMANS PAST AND PRESENT Chairperson(s): Phil R. Geib & Allegra Ward
APPLIED SCIENCE & TECHNOLOGY SECTION Chairperson(s): Mary Ettel
BIOLOGY Chairpersons: Lauren Gillespie, Steve Heinisch, and Paul Davis
BIOMEDICAL SCIENCES Chairperson(s): Annemarie Shibata, Kimberly Carlson, Joseph Dolence, Alexis Hobbs, James Fletcher, Paul Denton
CHEM Section Chairperson(s): Nathanael Fackler
EARTH SCIENCES Chairpersons: Irina Filina, Jon Schueth, Ross Dixon, Michael Leite
ENVIRONMENTAL SCIENCE Chairperson: Mark Hammer
PHYSICS Chairperson(s): Dr. Adam Davis
SCIENCE EDUCATION Chairperson: Christine Gustafson
2023 Maiben Lecturer: Jason Bartz
2023 FRIEND OF SCIENCE AWARD TO: Ray Ward and Jim Lewi
Autophagy beyond convention : plant-specific mechanisms for cellular recycling
Autophagy is an evolutionarily conserved catabolic pathway in eukaryotes, mediated by AuTophaGy related proteins (ATGs). It serves as a housekeeping mechanism by degrading diverse cellular components ranging from protein aggregates to entire organelles. Autophagy can either execute bulk degradation or exhibit high selectivity in targeting its cargo in response to the prevailing environmental conditions. In this thesis, we began by investigating adaptations of autophagy in the autotrophic and heterotrophic organs of plants. Our study revealed organ-specific dynamics of autophagic response in Arabidopsis thaliana under different stress conditions, with roots consistently exhibiting an earlier and more robust activity than shoots. We further identified the spatiotemporal autophagic selectivity towards different organelles under bulk autophagy-inducing conditions. In an effort to uncover distinctions in the autophagy machinery responsible for these plant-specific autophagic responses, we discovered that the ATG4-mediated delipidation of ATG8, previously considered a fundamental step in all eukaryotes, is dispensable in Arabidopsis thaliana. Further investigation into the plant ATG proteins led to the discovery of their potential roles beyond autophagy, as exemplified by the interactome of ATG5 which includes, among others, proteins involved in the endomembrane trafficking system and components of the ubiquitin-proteasome system. We developed two specialized tools to enable the above studies: SPIRO, an automated time-lapse imaging system designed for conducting phenotypical assays, and RoPod, dedicated microscopy chambers that aid in low-stress imaging of Arabidopsis roots
Chemically crosslinked protein hydrogels for tissue engineering
Tissue engineering aims at replacing or repair organ that have lost function
due to injury or disease via the development of appropriate biomaterials. In order
to restore function, biomaterials for tissue regeneration must mimic the biophysical
properties of the native physiological environment. In the literature several synthetic
and natural based biomaterials have been implemented to mimic the physiological
environment and restore functionality to injured tissues. However, most biomaterials
are based on difficult to modify natural or synthetic components that are
limited in their ability to adapt to the native physiological environment due to their
intrinsic properties. Recombinant proteins have recently emerged as an interesting
alternative to traditional biomaterials because their building blocks can be modified
at the DNA level to suit the specific needs of the chosen environment, overcoming
the issues linked to the suboptimal ability to chemically modify polymer and natural
proteins alike. In particular an engineered approach using functionalised protein
hydrogels allows to specify the biophysical properties independently and customise
them to suit a particular physiological environment. I have successfully designed
and programmed engineered proteins to form covalent molecular networks with
defined physical characteristics able to sustain mammalian cell culture without loss
of viability. The hydrogel design incorporates the SpyTag (ST) peptide and Spy-
Catcher (SC) protein to spontaneously form covalent-crosslinks upon mixing. The
genetically encoded chemistry allows to easily incorporate different recombinant
proteins in the hydrogels and induce a wide array of controlled biophysical charxvi
acteristics. By changing the crosslinker protein and ratios of the protein building
blocks (ST:SC), I demonstrated that I could alter both the viscoelastic properties
and gelation speeds of the resulting hydrogels. Fine tuning the rate of gelation
of the biocompatible hydrogels allowed me to adapt the design to biofabrication
techniques, such as 3D printing. Finally, I showed that the ST-SC protein hydrogels
can be used as a substrate for cell culture, can encapsulate mammalian cells
in 3D, and can drive increased mammalian cell attachment. My work demonstrates
how protein engineering could be applied to precise medical applications, bridging
synthetic biology and tissue engineering
Regulatory Mechanisms of Gene Transcription in Escherichia Coli
Bacteria have always been exposed to a wide variety of environments, many of which are fluctuating. In order to survive in these environments, they have had to develop the ability to adapt to changing conditions, particularly hostile ones. The adaptiveness of these microorganisms primarily depends upon their gene regulatory mechanisms. Some of these are ‘local’, affecting only a few genes. For example, when a specific nutrient appears in the media, it activates a few genes. Other regulatory mechanisms are more complex, involving a large number of genes that need to be activated and/or repressed at specific time moments.
The survival of bacterial species, in some cases, depends on the existence of diversity in their genes’ expression across the cell population, particularly since it is not always possible to predict the best action to take next. Understanding the mechanisms of bacteria that regulate the diversity in gene expression would help the bioindustries to benefit from them. Moreover, it would help finding ways to mitigate the harm caused by some species.
Bacterial genes are primarily regulated by their promoter strength in recruiting RNAP and specificity to a σ factor and, in some cases, by one or more global regulators. In addition, many genes are also regulated by specific transcription factors that can act as activators or as repressors, when present. Aside from these, other influential factors are the supercoiling in the DNA region occupied by the gene, whether there are other promoters closely spaced to the promoter of interest and, if so, their orientation, etc (Dash, et al., 2021).
This thesis focused on the study of some of the mechanisms that can affect genes’ transcription kinetics. We focused on three mechanisms: i) Building up of positive supercoils, ii) Transcription interference between closely spaced promoters in tandem formation, and iii) Global regulation by input transcription factors.
First, we studied how the intrinsic and extrinsic sources of noise in gene expression could be regulated by tuning the relative duration of transcription initiation. The study was done using stochastic models. It was found that the diversity in transcription kinetics across a cell population increases with the increase in the relative duration of the closed complex formation.
Second, a method was proposed to dissect the kinetics of transcription locking due to the effects of positive supercoiling buildup. Using RNA fluorescent protein tagging and microscopy, RNA transcripts were quantified in individual cells. It was found that increasing intracellular gyrase concentration decreases how often a promoter goes into the locked state, which in turn increases the gene’s transcription rate. Using that information, it is possible to infer how long the promoter is locked.
Third, a method was proposed to quantify the RNA numbers in individual cells using information from flow cytometry. This method allows the quantification of RNA numbers in thousands of cells, and thus the mean and variability in those cells, with much less manual labour and in much lesser time than when using microscopy and image analysis.
Fourth, a method was proposed to dissect the rate-liming steps of gene transcription regulated by promoters in tandem orientation. Using protein fusion library and flow cytometry, the protein abundance was quantified. It was found that the gene’s expression could be regulated by tuning the transcriptional interference by varying the promoters’ strength and the distance between the transcription start site of the promoters.
Overall, the four studies above allow for, first, better extracting raw data from microscopy and flow cytometry, and from there, to either dissect the kinetics of rate- limiting steps during transcription initiation or, inversely, how they can be tuned to regulate the single-cell RNA and protein numbers.
Having studied two core mechanisms regulating transcription, the fifth and final study focus on a third mechanism, which is transcription factor (TF) regulation. For this, we used RNA-seq to study how RNAP and TFs affect the kinetics of gene cohorts from measurements after RNAP shifts. We found that the magnitude of genes’ response is proportional to the asymmetry in the number of activators and repressors regulating them.
Overall, the works conducted in this thesis show that the gene expression and its
products diversity in cell populations can be regulated by varying the rate-limiting steps in transcription. These rate-limiting steps can be tuned by various mechanisms, such as the tuning of the accumulation of positive coils, tuning transcriptional interference of closely spaced promoters in tandem orientation and, tuning which and how many transcription factors act on each gene
Learning disentangled speech representations
A variety of informational factors are contained within the speech signal and a single short recording of speech reveals much more than the spoken words. The best method to extract and represent informational factors from the speech signal ultimately depends on which informational factors are desired and how they will be used. In addition, sometimes methods will capture more than one informational factor at the same time such as speaker identity, spoken content, and speaker prosody.
The goal of this dissertation is to explore different ways to deconstruct the speech signal into abstract representations that can be learned and later reused in various speech technology tasks. This task of deconstructing, also known as disentanglement, is a form of distributed representation learning. As a general approach to disentanglement, there are some guiding principles that elaborate what a learned representation should contain as well as how it should function. In particular, learned representations should contain all of the requisite information in a more compact manner, be interpretable, remove nuisance factors of irrelevant information, be useful in downstream tasks, and independent of the task at hand. The learned representations should also be able to answer counter-factual questions.
In some cases, learned speech representations can be re-assembled in different ways according to the requirements of downstream applications. For example, in a voice conversion task, the speech content is retained while the speaker identity is changed. And in a content-privacy task, some targeted content may be concealed without affecting how surrounding words sound. While there is no single-best method to disentangle all types of factors, some end-to-end approaches demonstrate a promising degree of generalization to diverse speech tasks.
This thesis explores a variety of use-cases for disentangled representations including phone recognition, speaker diarization, linguistic code-switching, voice conversion, and content-based privacy masking. Speech representations can also be utilised for automatically assessing the quality and authenticity of speech, such as automatic MOS ratings or detecting deep fakes. The meaning of the term "disentanglement" is not well defined in previous work, and it has acquired several meanings depending on the domain (e.g. image vs. speech). Sometimes the term "disentanglement" is used interchangeably with the term "factorization". This thesis proposes that disentanglement of speech is distinct, and offers a viewpoint of disentanglement that can be considered both theoretically and practically
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