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2. AI Model Utilization Measurements For Finding Class Encoding Patterns

Author

Bajcsy, Peter, Cardone, Antonio, Ling, Chenyi, Dessauw, Philippe, Majurski, Michael, Blattner, Tim, Juba, Derek, and Keyrouz, Walid

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Cryptography and Security, Computer Science - Computer Vision and Pattern Recognition
Abstract

This work addresses the problems of (a) designing utilization measurements of trained artificial intelligence (AI) models and (b) explaining how training data are encoded in AI models based on those measurements. The problems are motivated by the lack of explainability of AI models in security and safety critical applications, such as the use of AI models for classification of traffic signs in self-driving cars. We approach the problems by introducing theoretical underpinnings of AI model utilization measurement and understanding patterns in utilization-based class encodings of traffic signs at the level of computation graphs (AI models), subgraphs, and graph nodes. Conceptually, utilization is defined at each graph node (computation unit) of an AI model based on the number and distribution of unique outputs in the space of all possible outputs (tensor-states). In this work, utilization measurements are extracted from AI models, which include poisoned and clean AI models. In contrast to clean AI models, the poisoned AI models were trained with traffic sign images containing systematic, physically realizable, traffic sign modifications (i.e., triggers) to change a correct class label to another label in a presence of such a trigger. We analyze class encodings of such clean and poisoned AI models, and conclude with implications for trojan injection and detection., Comment: 45 pages, 29 figures, 7 tables

Published
2022

3. A New Assessment of Convolutional Neural Networks for Texture Directionality Detection

Author

Kociołek, Marcin, Cardone, Antonio, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Burduk, Robert, editor, Choraś, Michał, editor, Kozik, Rafał, editor, Ksieniewicz, Paweł, editor, Marciniak, Tomasz, editor, and Trajdos, Paweł, editor

Published
2023
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5. Rapid, Quantitative Therapeutic Screening for Alzheimer's Enzymes Enabled by Optimal Signal Transduction with Transistors

Author

Le, Son T., Morris, Michelle A., Cardone, Antonio, Guros, Nicholas B., Klauda, Jeffery B., Sperling, Brent A., Richter, Curt A., Pant, Harish C., and Balijepalli, Arvind

Subjects
Physics - Applied Physics, Condensed Matter - Mesoscale and Nanoscale Physics, Quantitative Biology - Quantitative Methods
Abstract

We show that simple, commercially sourced n-channel silicon field-effect transistors (nFETs) operating under closed loop control exhibit an ~3-fold improvement in pH readout resolution to (7.2+/-0.3)x10^-3 at a bandwidth of 10 Hz when compared with the open loop operation commonly employed by integrated ion-sensitive field-effect transistors (ISFETs). We leveraged the improved nFET performance to measure the change in solution pH arising from the activity of a pathological form of the kinase Cdk5, an enzyme implicated in Alzheimer's disease, and showed quantitative agreement with previous measurements. The improved pH resolution was realized while the devices were operated in a remote sensing configuration with the pH sensing element off-chip and connected electrically to the FET gate terminal. We compared these results with those measured by using a custom-built dual-gate 2D field-effect transistor (dg2DFET) fabricated with 2D semi-conducting MoS2 channels and a moderate device gain, alpha=8. Under identical solution conditions the pH resolution of the nFETs was only 2-fold worse than the dg2DFETs pH resolution of (3.9+/-0.7)x10^-3. Finally, using the nFETs, we demonstrated the effectiveness of a custom polypeptide, p5, as a therapeutic agent in restoring the function of Cdk5. We expect that the straight-forward modifications to commercially sourced nFETs demonstrated here will lower the barrier to widespread adoption of these remote-gate devices and enable sensitive bioanalytical measurements for high throughput screening in drug discovery and precision medicine applications.

Published
2019
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6. Quantum Capacitance-Limited MoS2 Biosensors Enable Remote Label-Free Enzyme Measurements

Author

Le, Son T., Guros, Nicholas B., Bruce, Robert C., Cardone, Antonio, Amin, Niranjana D., Zhang, Siyuan, Klauda, Jeffery B., Pant, Harish C., Richter, Curt A., and Balijepalli, Arvind

Subjects
Quantitative Biology - Quantitative Methods, Physics - Applied Physics
Abstract

We have demonstrated atomically thin, quantum capacitance-limited, field-effect transistors (FETs) that enable the detection of pH changes with ~75-fold higher sensitivity (4.4 V/pH) over the Nernst value of 59 mV/pH at room temperature when used as a biosensor. The transistors, which are fabricated from a monolayer of MoS2 with a room temperature ionic liquid (RTIL) in place of a conventional oxide gate dielectric, exhibit very low intrinsic noise resulting in a pH limit of detection (LOD) of 92x10^-6 at 10 Hz. This high device performance, which is a function of the structure of our device, is achieved by remotely connecting the gate to a pH sensing element allowing the FETs to be reused. Because pH measurements are fundamentally important in biotechnology, the low limit of detection demonstrated here will benefit numerous applications ranging from pharmaceutical manufacturing to clinical diagnostics. As an example, we experimentally quantified the function of the kinase Cdk5, an enzyme implicated in Alzheimer's disease, at concentrations that are 5-fold lower than physiological values, and with sufficient time-resolution to allow the estimation of both steady-state and kinetic parameters in a single experiment. The high sensitivity, low LOD and fast turnaround time of the measurements will allow the development of early diagnostic tools and novel therapeutics to detect and treat neurological conditions years before currently possible.

Published
2018
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16. Synthesis and Investigation of Electro-Optical Properties of H-Shape Dibenzofulvene Derivatives

Author

Giangregorio, Maria Michela, primary, Gambino, Salvatore, additional, Fabiano, Eduardo, additional, Leoncini, Mauro, additional, Cardone, Antonio, additional, Corrente, Giuseppina Anna, additional, Beneduci, Amerigo, additional, Accorsi, Gianluca, additional, Gigli, Giuseppe, additional, Losurdo, Maria, additional, Termine, Roberto, additional, and Capodilupo, Agostina-Lina, additional

Published
2022
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21. Overlap-based cell tracker

Author

Chalfoun, Joe, Cardone, Antonio, Dima, Alden A., Allen, Daniel P., and Halter, Michael W.

Subjects
Image processing -- Computer programs -- Methods, Electronic data processing -- Methods, Cells -- Physiological aspects, Image processing software, Chemistry, Physics, Science and technology
Abstract

In order to facilitate the extraction of quantitative data from live cell image sets, automated image analysis methods are needed. This paper presents an introduction to the general principle of [...]

Published
2010

31. Effects of donor position on dibenzofulvene-based organic dyes for photovoltaics

Author

Corrente, Giuseppina Anna, Fabiano, Eduardo, De Marco, Luisa, Accorsi, Gianluca, Giannuzzi, Roberto, Cardone, Antonio, Gigli, Giuseppe, Ciccarella, Giuseppe, Capodilupo, Agostina-Lina, Corrente, Giuseppina Anna, Fabiano, Eduardo, De Marco, Luisa, Accorsi, Gianluca, Giannuzzi, Roberto, Cardone, Antonio, Gigli, Giuseppe, Ciccarella, Giuseppe, and Capodilupo, Agostina-Lina

Subjects
Atomic and Molecular Physics, and Optic, Electronic, Optical and Magnetic Material, Condensed Matter Physic, Electrical and Electronic Engineering
Abstract

A series of push–pull organic dyes based on the cyanoacrylic acid as the acceptor/anchoring group, a dibenzofulvene (DBF) connected with thienyl rings as the π-bridge, and donor units linked to different positions of the DBF molecule were synthetized and studied. The effects of the donor position on optical and photovoltaic properties were investigated through photophysics, electrochemical and photovoltaic measurements. The results uphold photovoltaic performances largely depend on the electronic structure of the dyes with a synergistic interaction between donor and acceptor groups. In detail, a fine tuning of the photophysical properties can be reached simply selecting the position of the donor unit on the DBF molecule. In particular, the dyes bearing the donor unit on the 3,6-positions of the DBF show better performances in term of light absorption and cell efficiency with respect to the dyes with the donor unit on the 2,7-positions.

Published
2017

33. Deep-Learning-Assisted Volume Visualization

Author

Cheng, Hsueh-Chien, primary, Cardone, Antonio, additional, Jain, Somay, additional, Krokos, Eric, additional, Narayan, Kedar, additional, Subramaniam, Sriram, additional, and Varshney, Amitabh, additional

Published
2019
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35. Overlap-based cell tracker

Author

Chalfoun, Joe, primary, Cardone, Antonio, additional, Dima, Alden A, additional, Allen, Daniel P, additional, and Halter, Michael W, additional

Published
2009
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48. A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches

Author

Florczyk, Stephen J., Simon, Mylene, Juba, Derek, Pine, P. Scott, Sarkar, Sumona, Chen, Desu, Baker, Paula J., Bodhak, Subhadip, Cardone, Antonio, Brady, Mary C., Bajcsy, Peter, and Simon, Carl G.

Abstract

Many biomaterial scaffolds have been advanced to provide synthetic cell niches for tissue engineering and drug screening applications; however, current methods for comparing scaffold niches focus on cell functional outcomes or attempt to normalize materials properties between different scaffold formats. We demonstrate a three-dimensional (3D) cellular morphotyping strategy for comparing biomaterial scaffold cell niches between different biomaterial scaffold formats. Primary human bone marrow stromal cells (hBMSCs) were cultured on 8 different biomaterial scaffolds, including fibrous scaffolds, hydrogels, and porous sponges, in 10 treatment groups to compare a variety of biomaterial scaffolds and cell morphologies. A bioinformatics approach was used to determine the 3D cellular morphotype for each treatment group by using 82 shape metrics to analyze approximately 1000 cells. We found that hBMSCs cultured on planar substrates yielded planar cell morphotypes, while those cultured in 3D scaffolds had elongated or equiaxial cellular morphotypes with greater height. Multivariate analysis was effective at distinguishing mean shapes of cells in flat substrates from cells in scaffolds, as was the metric L1-depth (the cell height along its shortest axis after aligning cells with a characteristic ellipsoid). The 3D cellular morphotyping technique enables direct comparison of cellular microenvironments between widely different types of scaffolds and design of scaffolds based on cell structure–function relationships.

Published
2024
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49. Using Iterative Strategies for Aligning Attributed Points in Space

Author

Cardone, Antonio, ISR, Cardone, Antonio, Gupta, Satyandra K., Mount, Dave, Cardone, Antonio, ISR, Cardone, Antonio, Gupta, Satyandra K., and Mount, Dave

Abstract

Signatures based on shape features are expected to be useful for several similarity assessment applications. Such signatures can extract the relevant shape information needed for similarity assessment and ignore the shape information not needed for a particular application. Since different feature-based models are created in different coordinate systems, in order to compute distance between two sets of features, one needs to include geometric transformations for aligning features. Optimal alignment is the alignment that results in the minimum distance between two sets of features. In general, features can be viewed as attributed points in space. Hence, we need to develop techniques for aligning attributed points in space. This report introduces iterative strategies for optimally aligning attributed points in space. Iterative strategies presented in this report involve successively applying algorithms that perform alignment under restricted rigid body transformations (e.g., rotations only or translations only) to solve point alignment problems that require higher dimension transformations (e.g., combinations rotations and translations). Our preliminary experimental results show that the idea of using of iterative strategies to solve higher dimension attributed point alignment problems is promising and can be used to perform feature-based shape similarity assessment.

Published
2005

50. Capitale e Ricchezza

Author

Cardone, Antonio

Subjects
Measurement, Public Capital, Capital, Wealth, Measurement, Public Capital, Capital, Wealth
Published
2014

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