There has been a recent surge in the field of Explainable AI (XAI) which tackles the problem of p... more There has been a recent surge in the field of Explainable AI (XAI) which tackles the problem of providing insights into the behavior of black-box machine learning models. Within this field, feature attribution encompasses methods which assign relevance scores to input features and visualize them as a heatmap. Designing flexible accelerators for multiple such algorithms is challenging since the hardware mapping of these algorithms has not been studied yet. In this work, we first analyze the dataflow of gradient backpropagation based feature attribution algorithms to determine the resource overhead required over inference. The gradient computation is optimized to minimize the memory overhead. Second, we develop a High-Level Synthesis (HLS) based configurable FPGA design that is targeted for edge devices and supports three feature attribution algorithms. Tile based computation is employed to maximally use on-chip resources while adhering to the resource constraints. Representative CNNs are trained on CIFAR-10 dataset and implemented on multiple Xilinx FPGAs using 16-bit fixed-point precision demonstrating flexibility of our library. Finally, through efficient reuse of allocated hardware resources, our design methodology demonstrates a pathway to repurpose inference accelerators to support feature attribution with minimal overhead, thereby enabling real-time XAI on the edge.
Proceedings of the Great Lakes Symposium on VLSI 2022
In this work, we present a comprehensive analysis of explainability of Neural Network (NN) models... more In this work, we present a comprehensive analysis of explainability of Neural Network (NN) models in the context of power Side-Channel Analysis (SCA), to gain insight into which features or Points of Interest (PoI) contribute the most to the classification decision. Although many existing works claim state-of-the-art accuracy in recovering secret key from cryptographic implementations, it remains to be seen whether the models actually learn representations from the leakage points. In this work, we evaluated the reasoning behind the success of a NN model, by validating the relevance scores of features derived from the network to the ones identified by traditional statistical PoI selection methods. Thus, utilizing the explainability techniques as a standard validation technique for NN models is justified. CCS CONCEPTS • Security and privacy → Side-channel analysis and countermeasures.
This work involved the study and formulation of the 3D ultrasound frontend system specifications ... more This work involved the study and formulation of the 3D ultrasound frontend system specifications for various blocks in order to identify the key design bottlenecks and possible opportunities for innovation for next-gen Philips Ultrasound probes. The second part of the project focused on the schematic design of a high resolution, high speed, low power SAR ADC in 65nm CMOS technology based upon the previous system level derived specifications
Recognizing sarcasm in text is an important task for Natural Language processing to avoid misinte... more Recognizing sarcasm in text is an important task for Natural Language processing to avoid misinterpretation of sarcastic statements as literal statements. Accuracy and robustness of NLP models are often affected by untruthful sentiments that are often of sarcastic nature. Thus, it is important to filter out noisy data from the training data inputs for various NLP related tasks. For example, a sentence like ”So thrilled to be on call for work the entire weekend!” could be naively classified as a sentence with a high positive sentiment. However, its actually the negative sentiment that is cleverly implied through sarcasm.
Adolescents with depression who participate in behavioral activation therapy may find it hard to ... more Adolescents with depression who participate in behavioral activation therapy may find it hard to be motivated to perform tasks at home that their therapists recommend. We describe the initial design and usability evaluation of a home device (“PlantBot”) that could be used to remind young adults with depression at home of their behavioral activation therapy-related tasks. The prototype features electronics in a two-layer base, with a fake plant on top and supported using the Amazon Echo voice agent. We use an online panel study to evaluate the usability of our system with youth with past depression ( N = 30). Initial findings highlight the device’s usability, potential benefit, and attractiveness of the plant component, as well as multiple improvements to be made.
Repeat-induced point mutation (RIP) in Neurospora results in inactivation of duplicated DNA seque... more Repeat-induced point mutation (RIP) in Neurospora results in inactivation of duplicated DNA sequences. RIP is thought to provide protection against foreign elements such as retrotransposons, only one of which has been found in N. crassa. To examine the role of RIP in nature, we have examined seven N. crassa strains, identified among 446 wild isolates scored for dominant suppression of RIP. The test system involved a small duplication that targets RIP to the easily scorable gene erg-3. We previously showed that RIP in a small duplication is suppressed if another, larger duplication is present in the cross, as expected if the large duplication competes for the RIP machinery. In two of the strains, RIP suppression was associated with a barren phenotype—a characteristic of Neurospora duplications that is thought to result in part from a gene-silencing process called meiotic silencing by unpaired DNA (MSUD). A suppressor of MSUD (Sad-1) was shown not to prevent known large duplications f...
In Neurospora crassa the ability of an ectopic gene-sized duplication to induce repeat-induced po... more In Neurospora crassa the ability of an ectopic gene-sized duplication to induce repeat-induced point mutation (RIP) in its target gene was suppressed in crosses that were heterozygous for another larger chromosome segment duplication. Specifically, the frequency of RIP in the erg-3 gene due to a 1.3-kb duplication was reduced if the chromosome segment duplications Dp(IIIR > [I;II]) AR17, Dp(VIR > IIIR) OY329, or Dp(IVR > VII) S1229 were present in either the same or the other parental nucleus of the premeiotic dikaryon. We suggest that the larger duplications act as sinks to titrate the RIP machinery away from the smaller duplication. In contrast, RIP efficiency was relatively unaffected in comparably unproductive interspecies crosses with N. intermedia and N. tetrasperma. These findings offer a novel explanation for the observed persistence of the transposable element Tad in only a subset of Neurospora strains.
Companion of the 2020 ACM/IEEE International Conference on Human-Robot Interaction, 2020
The PlantBot is a home device that shows iconographic or simple lights to depict actions that it ... more The PlantBot is a home device that shows iconographic or simple lights to depict actions that it requests a young person (its user) to do as part of Behavioral Activation therapy. In this initial prototype, a separate conversational speech agent (i.e., Amazon Alexa) is wizarded to act as a second system the user can interact with.
The clinical role of pharmacists in a correctional facility has not been fully described. We repo... more The clinical role of pharmacists in a correctional facility has not been fully described. We report the proportion of patients assessed by a pharmacist within 48 hours of admission to a large correctional facility. Of those assessed, the frequency and type of pharmacist interventions were described. A retrospective chart review was conducted for patients admitted to the Edmonton Remand Center (ERC) from September to November 2017. From 1,500 patients, 518 (34.5%) were assessed by a pharmacist, and 511 (98.6%) of those received one or more pharmacist interventions. Interventions were most commonly health care provider interactions (89.0%) and drug therapy interventions (76.1%). ERC pharmacists assessed a sizable proportion of admitted patients, with most receiving at least one pharmacist intervention.
The duplication Dp(D305) is shown to cover the erg-3 locus (which encodes the ergosterol biosynth... more The duplication Dp(D305) is shown to cover the erg-3 locus (which encodes the ergosterol biosynthetic enzyme C-14 reductase). Additionally the efficiency of RIP in Dp(D305) is shown to be very low. This low efficiency may be due to the marked instability of the duplication in the premeiotic stage of the sexual cross. Premeiotic instability might also account for the low frequency with which duplication progeny are recovered from Dp(D305) x Normal crosses. In Neurospora crassa the complex translocation, T(IIIR-> X; IIIR; VIL) D305 (also referred to as T(D305)) translocates a LG IIIR segment into another unidentified chromosome (Perkins 1997 Adv. Genet. 36: 239-397). When this translocation is crossed by normal sequence some of the progeny are duplicated for the translocated IIIR segment. The duplication progeny are referred to as Dp(D305) (also as Dp(IIIR)D305). Dp(D305) was reported earlier to cover the LG III markers phe-2, tyr-1, un-17, het-7 and dow but not acr-2, thi-2, trp-1, and ro-2 (Perkins 1997 Adv. Genet. 36: 239-397). We show here that Dp(D305) also covers erg-3 (the structural gene for the ergosterol biosynthetic enzyme C-14 reductase) which is located distal to dow (Perkins et al. 2001 The Neurospora Compendium Chromosomal Loci. Academic Press, San Diego, USA). Additionally, the frequency of mutants generated by RIP in crosses heterozygous for Dp(D305) was found to be unexpectedly low. This apparent low frequency of RIP could be attributed to an instability of Dp(D305) in the premeiotic stage of the sexual cross. Dp(D305) covers erg-3: A cross was performed between T(D305) A (FGSC # 2139) and dow erg-3 a (FGSC # 7244) and the following phenotypic classes were obtained amongst 125 progeny: 72 Dow + Erg-3 + , 44 Dow-Erg-3-, 7 Dow + Erg-3-, and 2 Dow-Erg-3 +. It should be noted that one-fourth of the progeny are expected to be inviable because of partial deletion of LG IIIR. If Dp(IIIR)D305 covers erg-3, the duplication progeny should have the Dow + Erg-3 + phenotype, otherwise they should be Dow + Erg-3-. Furthermore, crossing the duplication segregants with the wild type should yield Dow-Erg-3progeny. Thirty Dow + Erg-3 + segregants were crossed with the wild type strains 74-OR23-1 A or OR8-1 a, progeny were analyzed from 26 crosses and five yielded Dow-Erg-3segregants. These results indicate that Dp(IIIR)D305 covers erg-3. In fact, it is possible that Dp(D305) covers the whole chromosome arm from between ro-2 and phe-3 to TipIIIR. The four crosses that were not analysed produced very few ascospores and we could not be sure that they represented non-Dp(D305) segregants. The proportion of confirmed duplication progeny amongst the Dow + Erg-3 + segregants (5/26) was lower than the expected 1/2. The lowered recovery of duplication progeny has been noted previously (Perkins 1997 Adv. Genet. 36: 239-397).
Crosses homozygous for the duplication Dp(AR17) are barren regardless of RIP. Sad-1, a semi-domin... more Crosses homozygous for the duplication Dp(AR17) are barren regardless of RIP. Sad-1, a semi-dominant suppressor of meiotic silencing, suppresses the barrenness of duplication-heterozygous but not of duplicationhomozygous crosses. Could it be that in the context of the homozygous cross the sad-1+ allele is not detected as being unpaired, and consequently, Sad-1 fails to suppress meiotic silencing?
(2001) "Wild-isolated Neurospora crassa strains that increase fertility of crosses with segmental... more (2001) "Wild-isolated Neurospora crassa strains that increase fertility of crosses with segmental aneuploids used to establish that a large duplication suppresses RIP in a smaller duplication," Fungal Genetics
Windows TM Dam Analysis Modules (WinDAM) is a set of modular software components that can be used... more Windows TM Dam Analysis Modules (WinDAM) is a set of modular software components that can be used to analyze overtopped earthen embankments and internal erosion of embankment dams. Sandia National Laboratories' DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides algorithms to perform iterative analysis with the help of built-in algorithms for uncertainty quantification with sampling and parameter study methods. This software integrates Sandia National Laboratories' DAKOTA software suite with WinDAM. It provides a user-interface for input and manipulation of parameters and performs various (centered and multi-dimensional) parameter studies on a wide range of parameters. This software takes advantage of the various algorithms present in DAKOTA to perform parameter studies on the various properties of WinDAM and provides users with detailed output on the changes caused by these variations. I also take this opportunity to express a deep sense of gratitude to Dr. Daniel Anderson, Dr. Torben Amtoft for their cordial support, valuable information and guidance. Lastly, I thank almighty, my parents, brother and friends for their constant encouragement without which this assignment would not be possible.
The pseudohomothallic fungus Neurospora tetrasperma is naturally resistant to the antibiotic hygr... more The pseudohomothallic fungus Neurospora tetrasperma is naturally resistant to the antibiotic hygromycin. We discovered that mutation of its erg-3 (sterol C-14 reductase) gene confers a hygromycin-sensitive phenotype that can be used to select transformants on hygromycin medium by complementation with the N. crassa erg-3+ and bacterial hph genes. Cotransformation of hph with PCR-amplified DNA of other genes enabled us to construct strains duplicated for the amplified DNA. Using transformation we constructed self-fertile strains that were homoallelic for an ectopic erg-3+ transgene and a mutant erg-3 allele at the endogenous locus. Self-crosses of these strains yielded erg-3 mutant ascospores that produced colonies with the characteristic morphology on Vogel's sorbose agar described previously for erg-3 mutants of N. crassa. The mutants were generated by repeat-induced point mutation (RIP), a genome defense process that causes numerous G:C to A:T mutations in duplicated DNA sequen...
There has been a recent surge in the field of Explainable AI (XAI) which tackles the problem of p... more There has been a recent surge in the field of Explainable AI (XAI) which tackles the problem of providing insights into the behavior of black-box machine learning models. Within this field, feature attribution encompasses methods which assign relevance scores to input features and visualize them as a heatmap. Designing flexible accelerators for multiple such algorithms is challenging since the hardware mapping of these algorithms has not been studied yet. In this work, we first analyze the dataflow of gradient backpropagation based feature attribution algorithms to determine the resource overhead required over inference. The gradient computation is optimized to minimize the memory overhead. Second, we develop a High-Level Synthesis (HLS) based configurable FPGA design that is targeted for edge devices and supports three feature attribution algorithms. Tile based computation is employed to maximally use on-chip resources while adhering to the resource constraints. Representative CNNs are trained on CIFAR-10 dataset and implemented on multiple Xilinx FPGAs using 16-bit fixed-point precision demonstrating flexibility of our library. Finally, through efficient reuse of allocated hardware resources, our design methodology demonstrates a pathway to repurpose inference accelerators to support feature attribution with minimal overhead, thereby enabling real-time XAI on the edge.
Proceedings of the Great Lakes Symposium on VLSI 2022
In this work, we present a comprehensive analysis of explainability of Neural Network (NN) models... more In this work, we present a comprehensive analysis of explainability of Neural Network (NN) models in the context of power Side-Channel Analysis (SCA), to gain insight into which features or Points of Interest (PoI) contribute the most to the classification decision. Although many existing works claim state-of-the-art accuracy in recovering secret key from cryptographic implementations, it remains to be seen whether the models actually learn representations from the leakage points. In this work, we evaluated the reasoning behind the success of a NN model, by validating the relevance scores of features derived from the network to the ones identified by traditional statistical PoI selection methods. Thus, utilizing the explainability techniques as a standard validation technique for NN models is justified. CCS CONCEPTS • Security and privacy → Side-channel analysis and countermeasures.
This work involved the study and formulation of the 3D ultrasound frontend system specifications ... more This work involved the study and formulation of the 3D ultrasound frontend system specifications for various blocks in order to identify the key design bottlenecks and possible opportunities for innovation for next-gen Philips Ultrasound probes. The second part of the project focused on the schematic design of a high resolution, high speed, low power SAR ADC in 65nm CMOS technology based upon the previous system level derived specifications
Recognizing sarcasm in text is an important task for Natural Language processing to avoid misinte... more Recognizing sarcasm in text is an important task for Natural Language processing to avoid misinterpretation of sarcastic statements as literal statements. Accuracy and robustness of NLP models are often affected by untruthful sentiments that are often of sarcastic nature. Thus, it is important to filter out noisy data from the training data inputs for various NLP related tasks. For example, a sentence like ”So thrilled to be on call for work the entire weekend!” could be naively classified as a sentence with a high positive sentiment. However, its actually the negative sentiment that is cleverly implied through sarcasm.
Adolescents with depression who participate in behavioral activation therapy may find it hard to ... more Adolescents with depression who participate in behavioral activation therapy may find it hard to be motivated to perform tasks at home that their therapists recommend. We describe the initial design and usability evaluation of a home device (“PlantBot”) that could be used to remind young adults with depression at home of their behavioral activation therapy-related tasks. The prototype features electronics in a two-layer base, with a fake plant on top and supported using the Amazon Echo voice agent. We use an online panel study to evaluate the usability of our system with youth with past depression ( N = 30). Initial findings highlight the device’s usability, potential benefit, and attractiveness of the plant component, as well as multiple improvements to be made.
Repeat-induced point mutation (RIP) in Neurospora results in inactivation of duplicated DNA seque... more Repeat-induced point mutation (RIP) in Neurospora results in inactivation of duplicated DNA sequences. RIP is thought to provide protection against foreign elements such as retrotransposons, only one of which has been found in N. crassa. To examine the role of RIP in nature, we have examined seven N. crassa strains, identified among 446 wild isolates scored for dominant suppression of RIP. The test system involved a small duplication that targets RIP to the easily scorable gene erg-3. We previously showed that RIP in a small duplication is suppressed if another, larger duplication is present in the cross, as expected if the large duplication competes for the RIP machinery. In two of the strains, RIP suppression was associated with a barren phenotype—a characteristic of Neurospora duplications that is thought to result in part from a gene-silencing process called meiotic silencing by unpaired DNA (MSUD). A suppressor of MSUD (Sad-1) was shown not to prevent known large duplications f...
In Neurospora crassa the ability of an ectopic gene-sized duplication to induce repeat-induced po... more In Neurospora crassa the ability of an ectopic gene-sized duplication to induce repeat-induced point mutation (RIP) in its target gene was suppressed in crosses that were heterozygous for another larger chromosome segment duplication. Specifically, the frequency of RIP in the erg-3 gene due to a 1.3-kb duplication was reduced if the chromosome segment duplications Dp(IIIR > [I;II]) AR17, Dp(VIR > IIIR) OY329, or Dp(IVR > VII) S1229 were present in either the same or the other parental nucleus of the premeiotic dikaryon. We suggest that the larger duplications act as sinks to titrate the RIP machinery away from the smaller duplication. In contrast, RIP efficiency was relatively unaffected in comparably unproductive interspecies crosses with N. intermedia and N. tetrasperma. These findings offer a novel explanation for the observed persistence of the transposable element Tad in only a subset of Neurospora strains.
Companion of the 2020 ACM/IEEE International Conference on Human-Robot Interaction, 2020
The PlantBot is a home device that shows iconographic or simple lights to depict actions that it ... more The PlantBot is a home device that shows iconographic or simple lights to depict actions that it requests a young person (its user) to do as part of Behavioral Activation therapy. In this initial prototype, a separate conversational speech agent (i.e., Amazon Alexa) is wizarded to act as a second system the user can interact with.
The clinical role of pharmacists in a correctional facility has not been fully described. We repo... more The clinical role of pharmacists in a correctional facility has not been fully described. We report the proportion of patients assessed by a pharmacist within 48 hours of admission to a large correctional facility. Of those assessed, the frequency and type of pharmacist interventions were described. A retrospective chart review was conducted for patients admitted to the Edmonton Remand Center (ERC) from September to November 2017. From 1,500 patients, 518 (34.5%) were assessed by a pharmacist, and 511 (98.6%) of those received one or more pharmacist interventions. Interventions were most commonly health care provider interactions (89.0%) and drug therapy interventions (76.1%). ERC pharmacists assessed a sizable proportion of admitted patients, with most receiving at least one pharmacist intervention.
The duplication Dp(D305) is shown to cover the erg-3 locus (which encodes the ergosterol biosynth... more The duplication Dp(D305) is shown to cover the erg-3 locus (which encodes the ergosterol biosynthetic enzyme C-14 reductase). Additionally the efficiency of RIP in Dp(D305) is shown to be very low. This low efficiency may be due to the marked instability of the duplication in the premeiotic stage of the sexual cross. Premeiotic instability might also account for the low frequency with which duplication progeny are recovered from Dp(D305) x Normal crosses. In Neurospora crassa the complex translocation, T(IIIR-> X; IIIR; VIL) D305 (also referred to as T(D305)) translocates a LG IIIR segment into another unidentified chromosome (Perkins 1997 Adv. Genet. 36: 239-397). When this translocation is crossed by normal sequence some of the progeny are duplicated for the translocated IIIR segment. The duplication progeny are referred to as Dp(D305) (also as Dp(IIIR)D305). Dp(D305) was reported earlier to cover the LG III markers phe-2, tyr-1, un-17, het-7 and dow but not acr-2, thi-2, trp-1, and ro-2 (Perkins 1997 Adv. Genet. 36: 239-397). We show here that Dp(D305) also covers erg-3 (the structural gene for the ergosterol biosynthetic enzyme C-14 reductase) which is located distal to dow (Perkins et al. 2001 The Neurospora Compendium Chromosomal Loci. Academic Press, San Diego, USA). Additionally, the frequency of mutants generated by RIP in crosses heterozygous for Dp(D305) was found to be unexpectedly low. This apparent low frequency of RIP could be attributed to an instability of Dp(D305) in the premeiotic stage of the sexual cross. Dp(D305) covers erg-3: A cross was performed between T(D305) A (FGSC # 2139) and dow erg-3 a (FGSC # 7244) and the following phenotypic classes were obtained amongst 125 progeny: 72 Dow + Erg-3 + , 44 Dow-Erg-3-, 7 Dow + Erg-3-, and 2 Dow-Erg-3 +. It should be noted that one-fourth of the progeny are expected to be inviable because of partial deletion of LG IIIR. If Dp(IIIR)D305 covers erg-3, the duplication progeny should have the Dow + Erg-3 + phenotype, otherwise they should be Dow + Erg-3-. Furthermore, crossing the duplication segregants with the wild type should yield Dow-Erg-3progeny. Thirty Dow + Erg-3 + segregants were crossed with the wild type strains 74-OR23-1 A or OR8-1 a, progeny were analyzed from 26 crosses and five yielded Dow-Erg-3segregants. These results indicate that Dp(IIIR)D305 covers erg-3. In fact, it is possible that Dp(D305) covers the whole chromosome arm from between ro-2 and phe-3 to TipIIIR. The four crosses that were not analysed produced very few ascospores and we could not be sure that they represented non-Dp(D305) segregants. The proportion of confirmed duplication progeny amongst the Dow + Erg-3 + segregants (5/26) was lower than the expected 1/2. The lowered recovery of duplication progeny has been noted previously (Perkins 1997 Adv. Genet. 36: 239-397).
Crosses homozygous for the duplication Dp(AR17) are barren regardless of RIP. Sad-1, a semi-domin... more Crosses homozygous for the duplication Dp(AR17) are barren regardless of RIP. Sad-1, a semi-dominant suppressor of meiotic silencing, suppresses the barrenness of duplication-heterozygous but not of duplicationhomozygous crosses. Could it be that in the context of the homozygous cross the sad-1+ allele is not detected as being unpaired, and consequently, Sad-1 fails to suppress meiotic silencing?
(2001) "Wild-isolated Neurospora crassa strains that increase fertility of crosses with segmental... more (2001) "Wild-isolated Neurospora crassa strains that increase fertility of crosses with segmental aneuploids used to establish that a large duplication suppresses RIP in a smaller duplication," Fungal Genetics
Windows TM Dam Analysis Modules (WinDAM) is a set of modular software components that can be used... more Windows TM Dam Analysis Modules (WinDAM) is a set of modular software components that can be used to analyze overtopped earthen embankments and internal erosion of embankment dams. Sandia National Laboratories' DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides algorithms to perform iterative analysis with the help of built-in algorithms for uncertainty quantification with sampling and parameter study methods. This software integrates Sandia National Laboratories' DAKOTA software suite with WinDAM. It provides a user-interface for input and manipulation of parameters and performs various (centered and multi-dimensional) parameter studies on a wide range of parameters. This software takes advantage of the various algorithms present in DAKOTA to perform parameter studies on the various properties of WinDAM and provides users with detailed output on the changes caused by these variations. I also take this opportunity to express a deep sense of gratitude to Dr. Daniel Anderson, Dr. Torben Amtoft for their cordial support, valuable information and guidance. Lastly, I thank almighty, my parents, brother and friends for their constant encouragement without which this assignment would not be possible.
The pseudohomothallic fungus Neurospora tetrasperma is naturally resistant to the antibiotic hygr... more The pseudohomothallic fungus Neurospora tetrasperma is naturally resistant to the antibiotic hygromycin. We discovered that mutation of its erg-3 (sterol C-14 reductase) gene confers a hygromycin-sensitive phenotype that can be used to select transformants on hygromycin medium by complementation with the N. crassa erg-3+ and bacterial hph genes. Cotransformation of hph with PCR-amplified DNA of other genes enabled us to construct strains duplicated for the amplified DNA. Using transformation we constructed self-fertile strains that were homoallelic for an ectopic erg-3+ transgene and a mutant erg-3 allele at the endogenous locus. Self-crosses of these strains yielded erg-3 mutant ascospores that produced colonies with the characteristic morphology on Vogel's sorbose agar described previously for erg-3 mutants of N. crassa. The mutants were generated by repeat-induced point mutation (RIP), a genome defense process that causes numerous G:C to A:T mutations in duplicated DNA sequen...
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