Abstract

Space, time, and number are fundamental to human cognition. The mental representations on these entities are crucial for planning and decision-making. In our everyday lives, we are always thinking in terms of quantities — how long would we take to reach the workplace, what would be a shorter route to get to a specific store from where we are, how many cupcakes should we prepare for the people we have invited, how do we throw a stone that will dislodge a shuttlecock stuck in the tree, and so on. Even for simple tasks like grasping, reaching, or catching a ball, subtle calculations involving distance, speed, and time are essential. To successfully execute our actions, we need to synchronize these entities efficiently. For example, to grab an object kept on the table, one needs to integrate information from time, space, and number dimensions to evaluate the obstacles present in that environment and the distance between the object and our body. Further, spatiotemporal integration of information is needed for successful reaching and grasping. Over the last two decades, numerous studies have advanced our knowledge of how humans utilize perceptual information to estimate magnitudes such as space, time, and number. One of the most popular theories of magnitude processing, A Theory of Magnitude (ATOM), suggests that a generalized magnitude system in the brain processes information related to space, time, and numbers. Since these magnitudes are processed by a common magnitude system, they interact with one another. Earlier studies investigating the number-time interaction have provided support to ATOM’s predictions. On the contrary, more recent studies have argued against ATOM and suggested that the cross-dimensional magnitude interactions may emerge from cognitive factors like attention and memory. Such contradicting findings raise a fundamental question as to whether a common magnitude system indeed exists, or such crossdimensional magnitude interactions result from cognitive factors. This is still an unsettled question. In the present thesis, we examine the influence of numerical magnitude on temporal processing in a different experimental setup. More specifically, we investigated whether numerical magnitude affects our temporal experience or simply biases judgment of time. Further, we examined whether large numerical magnitude is always perceived to be longer in time (as predicted by ATOM) or attentional modulation can cause such crossdimensional magnitude interactions. We also tested the generality of the ATOM framework in a cross-modal setting wherein numerical magnitude and temporal information were presented in two different modalities and evaluated ATOM’s prediction in a cross-domain setting. The overall results from the five empirical investigations suggest that the processing of numbers and time may not require to invoke a common magnitude processing system. The cross-dimensional magnitude interactions (in this case, number and time) may emerge from the modulation of attentional mechanisms.

Abstract

Retail stores have become a part of our daily lives and play a vital economic role in society. It has been reported that shelf-space allocation decisions in a retail store significantly impact the retailer’s revenue. So, developing approaches for efficient product placement in available shelf space in retail stores is one of the key research issues. Several research efforts have been made to propose approaches for improving product placement in retail stores based on the knowledge of customer purchase history. Traditionally, several dynamic programming model based approaches were proposed to solve this problem. More recently, data mining approaches, like frequent pattern mining and utility pattern mining, have been employed to improve product placement based on the patterns extracted from customer purchase transactions. In this thesis, we address the issue of product placement in a retail store by considering the diversity of products. Providing diverse options to customers can be useful in increasing the long term sustainability of retail stores. Other recommendation systems have also used increasing diversity to improve user interest. In the context of retail stores, a store that can cater to the needs of a diverse customer base (by providing diverse recommendations) has a higher chance to stay relevant for customers in the long term, thus, facilitating long term sustainability of retail businesses. We have proposed an approach for facilitating the placement of items in a diversified manner in a given retail store based on the concept hierarchy that exists among the items without compromising the revenue. In the proposed approach, a concept hierarchy based approach is employed to determine the diversity value of the itemset quantitatively. The diversity of the given itemset captures the extent of its items belonging to multiple categories. By combining the notion of utility and diversity, we propose a framework to compute diverse net revenue of the itemset. Given a set of transactions, price values of items, and concept hierarchy, we propose a methodology to build the Concept Hierarchy Utility Itemset Index (CHUI), which contains potential itemsets with high revenue and diversity. Next, we propose the approach to perform product placement based on the knowledge of itemsets in the CHUI. We conduct experiments on a real dataset, namely, Instacart retail dataset (containing 49,688 items and 1,31,208 transactions), to demonstrate the proposed approach’s overall effectiveness

Abstract

Rice is a fascinating and complex plant. Consumed by more than half of the world’s population, it is important to have a comprehensive understanding of the organism to advance crop engineering and breeding strategies. Abiotic stresses like drought, high temperature, salinity and flood have affected its growth and productivity. Furthermore, global climate change has added to the severity of these stresses, suggesting the need for varieties with improved stress tolerance for sustainable crop production. Improving stress tolerance requires an in-depth understanding of the biological processes, transcriptional pathways and hormone signaling involved in stress response. With the surge in omics data, it has paved the way for deciphering the biological information underlying complex traits. However, dealing with such large datasets calls for the development of powerful bioinformatics methods for a thorough transcriptome analysis. A popular approach is the construction and analysis of co-expression networks representing transcriptionally coordinated genes that are often part of the same biological process. Using prior knowledge and data integration further enhances the elucidation of gene regulatory relationships in this network. With this objective we have developed NetREx, a Network based Rice Expression Analysis Server, that hosts ranked co-expression networks of Oryza sativa using publicly available mRNAseq data across uniform experimental conditions. It provides a range of interactable data viewers and modules for analysing user queried genes across different stress conditions (drought, flood, cold and osmosis) and hormonal treatments (abscisic and jasmonic acid) and tissues (root and shoot). Subnetworks of user-defined genes can be queried in preconstructed tissue-specific networks, allowing users to view the fold-change, module memberships, gene annotations and analysis of their neighborhood genes and associated pathways. The webserver also allows querying of orthologous from Arabidopsis, wheat, maize, barley, and sorghum. Here we demonstrate that NetREx can be used to identify novel candidate genes and tissue-specific interactions under stress conditions and can aid in the analysis and understanding of complex phenotypes linked to stress response in rice. Available at: https://bioinf.iiit.ac.in/netrex/. In the second part of the thesis, we present a meta-analytic study using co-expressed modules to understand the biological functions associated with different abiotic stresses in the root tissue. The osmotic stress condition is an extremely severe stress condition involving the effects of multiple stresses like drought, salinity and ionic stress and is discussed in detail. The early responsive modules are analyzed and a causal flow of mechanisms and signaling pathways is established.

Abstract

Typically, anatomy is taught through dissection, 2D images, presentations, and cross-sections. While these methods are convenient, they are non-interactive and fail to capture the spatial relationships and functional aspects of anatomy. New visualization technologies such as virtual reality and 3D can compensate for the impediments and provide better understanding while captivating the students. With recent advances in the industry, the methods to provide a 3D experience are economical. In this thesis, we introduce a low-cost 3D-interactive anatomy system designed for an audience of typical medical college students in an anatomy class. The setup used to achieve 3D visualization is Dual projector polarization. While there are other ways to achieve 3D visualization, like alternate frame sequencing and virtual reality, this technique can target a large audience and requires minimum accessories for the setup enabling this to be a low-cost solution for an immersive 3D experience. The 3D interactive Neuroanatomy solution is an end-to-end framework capable of designing anatomy lessons and visualizing the 3D stereoscopic projection of those anatomy lessons. To ensure superior comprehension of students, we incorporate each teacher’s unique teaching approach while developing anatomy lessons by providing the ability to create their own lessons. We have created anatomy lessons based on the human brain which is a vital organ and has a complex anatomy. Our aim is to help medical students to understand the complexity of organ systems from not just an anatomical perspective but also a radiological perspective. We use annotations on clinical case data such as MRI, MRA, etc., to create 3D models for anatomy visualization incorporating clinical information and illustrating real cases. Annotations for structures of interest are done using manual, automatic, and semi-automatic segmentation methods. Manual delineation of the structure boundaries is very tedious and time-consuming. Automatic segmentation is quick and convenient. However, manual annotations were done for the 3D anatomy viewer for small and complex structures due to substandard automatic segmentation. There is a need to improve automatic segmentation performance for those structures. While segmentation is an essential step in 3D modeling, it plays a critical role in many neurological disease diagnoses as well, which are associated with degradation in the sub-cortical region. Therefore accurate algorithms are needed for sub-cortical structure segmentation. Variance in the size of structures is significant, which introduces a performance bias towards larger structures in many deep learning approaches. In this part of the thesis, we aim to remove size bias in sub-cortical structure segmentation. The proposed method addresses this problem with a pre-training step used to learn tissue characteristics, an ROI extraction step that aids in focusing on the local context, and using structure ROIs elevates the influence of smaller structures in the network.

Abstract

FPGAs are increasingly significant for deploying convolutional neural network (CNN) inference models because of performance demands and power constraints in embedded and data centre applications. The compute intensity of these models makes prototyping highly complex and time-consuming with traditional RTL approaches. The release of new generation high-level synthesis tools (HLS), such as Intel FPGA SDK for OpenCL, and Xilinx’s VITIS Unified Software Development platform, have significantly reduced the time and complexity of prototyping complex designs on FPGA. This work involves building custom FPGA accelerators for image recognition systems using OpenCL-HLS. Object detection and classification are vital steps in building image recognition systems. The first part of the work concerns building an FPGA accelerator for the Traffic Sign Classification problem, a vital step in building traffic sign recognition (TSR) systems that employ vehicle-mounted cameras that identify traffic signs while driving on the road. However, the CNNs for the classification still need the ability to be spatially invariant to the input data. Spatial Transformers are learnable modules that, upon integration with CNN, would allow the spatial manipulation of data within the network, making it invariant to affine transformations. Generic Matrix multiply (GEMM) methods that express convolution as matrix multiplication are widely used in deep-learning frameworks like Caffe, Theano, and Torch with GPU support. im2row is one of the commonly used GEMM methods. In this work, we built a GEMM-based accelerator for a CNN with a Spatial transformer module. We proposed the channel adaptive im2row method, with a lesser on-chip memory footprint than im2row. The system attains a latency of 202 ms (5˜ fps), running at 202 MHz on Intel Arria10 GX FPGA, and attains a speedup of (> 5 X) compared to the CPU. The performance is not state-of-the-art and calls for more FPGA-specific optimizations. Further, from the learnings, we designed a Systolic Array accelerator with a novel load pattern for accelerating the widely-used object detector YOLOv3-tiny optimized explicitly for embedded applications. We build the accelerator for multiple precisions ( FIXED8, FIXED16, FLOAT32 ) of YOLOv3-tiny. The architecture uses a homogenous systolic array architecture with a synchronized pipeline adder tree for convolution, allowing it to be scalable for multiple variants of YOLO with a change in the host driver. It is a deeply pipelined architecture that also exploits three-dimensional spatial parallelism. We evaluated the design on Terasic DE5a-Net-DDR4. The Fixed point (FP-8, FP-16) implementations attain a throughput of 57 GOPs/s (> 23 %) and 46.16 GOPs/s (> 340 %) running at 234 MHz and 227 MHz. We synthesized the first FLOAT32 implementation attaining 11.22 GFLOPs/s, running at 172 MHz

Abstract

Deep Neural Networks (DNNs) have shown remarkable performance in a broad range of computer vision tasks, including in the medical domain. With the advent of DNNs, the medical community has witnessed significant developments in segmentation, classification, and detection. But this success comes with a cost of heavy reliance on the abundance of data. Medical data, however, is often highly limited in volume and quality due to sparsity of patient contact, variability in medical care, and privacy concerns. Hence, to train large networks we seek data from different sources. In such a scenario, it is of interest to design a model that learns continuously and adapts to datasets or tasks as and when they are available. However, one of the important steps to achieve such a never-ending learning process is to overcome Catastrophic Forgetting (CF) of previously seen data or tasks. CF refers to the significant degradation in performance on the old task/dataset. To avoid confusion, we call a training regime Continual Learning (CL) when CAD systems have to handle a sequence of datasets collected over time from different sites with different imaging parameters/populations. Similarly, Incremental Learning (IL) is when CAD systems have to learn new classes as and when new annotations are made available. The work described in this thesis address core aspects of both CL & IL and has been compared against the state-of-the-art methods. In this thesis, we assume that access to the data belonging to previously trained datasets or tasks is not available which makes both CL and IL processes even more challenging. We start with developing a CL system that learns sequentially on different datasets and handles CF using the Uncertainty mechanism. The system consists of an ensemble of models which are trained or finetuned on each dataset and considers the prediction from the model which has the least uncertainty. We then investigate a new way to tackle CF in CL by manifold learning, inspired by the defense mechanisms against adversarial attacks. Our method uses a ‘Reformer’ which is essentially a denoising autoencoder that ‘reforms’ or brings the data from all the datasets together towards a common manifold. These reformed samples are then passed to the network to learn the desired task. Towards IL, we propose a novel approach that ensures that a model remembers the causal factor behind the decisions on the old classes, while incrementally learning new classes. We introduce a common auxiliary task during the course of incremental training, whose hidden representations are shared across all the classification heads. All the experiments for both CL and IL are conducted on multiple datasets and have shown significant performance over the state-of-the-art methods

Abstract

The conformational dynamics of proteins is essential for biological functions. The characterization of binding-induced changes in protein conformational dynamics is of paramount importance to understand the fundamental processes of life. Molecular modelling and molecular dynamics simulations have emerged as useful computational tools to probe atomistic details of molecular recognition and binding-induced dynamical responses of proteins. The interactions of proteins with DNA and small drug molecules play crucial roles in regulating various cellular processes. The present thesis reports results of investigation of the functional roles of protein conformational dynamics in the following two important biological systems: (a) a DNA repair protein complexed with a mistmatched DNA and (b) an inhibitor drug-bound human c-Src kinase. In the former system, our primary objective is to understand the molecular mechanism of how a specific DNA repair protein (RAD4/XPC) binds to a damaged DNA, recognizes lesions and repair them efficiently using molecular dynamics and enhanced sampling simulations. In the latter system, we have investigated drug-induced conformational transitions in human c-Src kinase to understand its activation mechanism using molecular dynamics simulations and nudged elastic band method. DNA damage caused by ultraviolet (UV) radiation can lead to a range of genetic skin conditions and cancers. The protein Rad4/XPC recognizes and repairs these types of DNA damage with high accuracy to safeguard the integrity of the genome. However, the precise mechanism of how Rad4/XPC recognizes DNA damage in the crowded cellular milieu is not yet fully understood. The first part of this thesis investigates the mechanism, energetics, dynamics, and molecular basis of Rad4/XPC’s recognition with base pair mismatched DNA lesions. In particular, the mechanism of association of RAD4 with the mismatched DNA is investigated using molecular dynamics and umbrella sampling simulations. The Rad4-DNA association free energy surfaces are determined for three Rad4-DNA complexes (CCC/CCC, TTT/TTT, and TAT/TAT) and the sequence-dependent specificity of Rad4 for mismatched DNA is explored. The results reveal that Rad4 exhibits higher specificity for CCC/CCC mismatched DNA compared to the other two mismatches. The key molecular interactions contributing to Rad4- DNA association and specificity are characterized. Protein kinases act as biological switches that toggle between ON (active) and OFF (inactive) states in response to specific cellular signals to regulate various cellular processes including growth, cell proliferation and differentiation. Since protein kinases are implicated in tumorigenesis and malignant cell proliferation, they have become favourable targets for cancer therapy. The second part of the thesis focuses on drug-induced conformational transition of c-Src kinase between active (drug-bound) and inactive (drug-free) states using the minimum energy path analysis and molecular dynamics simulation. The crucial role of hydration of the binding pocket in the association/dissociation of drug from the kinase is explored. The coupling between the entry and exit of the drug, influx of water molecules into the binding pocket and critical interactions of key kinase residues near the binding pocket appears to influence the conformational transition between the active and inactive states of the kinase. We believe that the molecular mechanisms elucidated will be useful for rational design of novel therapeutics against cancer and other kinase-related diseases.

Abstract

Drought is a natural hazard with a significant impact on the economy, agriculture, and environment. It is defined as a significant decrease in water availability in all its forms. Droughts are estimated using drought indices. Drought indices are numerical measurements that describe the severity of drought by combining data from one or more variables (indicators), such as precipitation and evapotranspiration (ET), into a single number. Standardized Precipitation Evapotranspiration Index (SPEI) and Standardized precipitation Actual Evapotranspiration Index (SPAEI) are the drought indices used to estimate drought index, which take both precipitation, potential and actual evapotranspiration into account. Since ET is a critical factor in estimating drought, well-grounded ET estimations are required. The major forms of ET are Potential evapotranspiration (PET) and Actual evapotranspiration (AET). PET is described as the loss of water from a significant area that is equally covered with short, green crops that are actively growing. PET is regarded as the maximum amount of evapotranspiration. AET is defined as the total amount of water used in evaporation and transpiration by a crop during the entire growing season. Various methods have been developed to estimate PET and AET depending upon the availability of hydro meteorological variables. Various empirical based methods and hydrological model based simulations of PET and AET have been developed. Advancement of data-driven algorithms also have been extensively developed to estimate ET. In this context, many studies used empirical based estimates of ET for the calculation of drought indices. None of these studies analyzed the sensitivity of various ET methods to assess the drought characteristics. Thus, the present study aimed to include various PET and AET methods in the drought characterization. Various empirical methods, such as Penman-Monteith, Hargreaves, Turc, and Priestley-Taylor and data-driven method of Artificial Neural Network (ANN) has been used to estimate PET. The input variables used to estimate these methods are temperature, wind speed, solar radiation, and relative humidity which are obtained over the period of 1965 to 2015 for Hyderabad station. ANN model was trained and tested with climate variables as input variables and various empirical models as reference models to predict the best PET method. Penman-Monteith, Hargreaves, and Turc method performed better with ANN model estimates. Later, to study the impact of various empirical based PET estimates on drought estimation, SPEI is calculated using various PET estimates at different time scales. All other methods are compared with the Penman-Monteith method, which is considered the standard method because it considers the main meteorological factors. Hargreaves and Turc methods performed better with the standard method and these methods can be useful in estimating drought when minimum data is available. To assess the drought events accurately by various drought indices it is necessary to predict the hydro-meteorological variables (PET and AET) precisely. There are several challenges in estimating AET and PET at the fine spatial resolution. There are various empirical models (Budyko, Penman- Monteith, Hargreaves, and Turc) for estimating AET and PET. Still, these empirical methods does not account for the catchment characteristics, which may underestimates the actual amount of hydrological variables. Further, satellite-based remote sensing data are accessible for extracting evapotranspiration (ET) values. It provides global coverage and continuous observations of land surface variables affecting ET. Another conceptual based approach to estimate PET and AET at catchment scale is hydrological model such as Soil and Water Assessment Tool (SWAT). The present study aimed to include various approaches of empirical (Budyko, Penman-Monteith, Hargreaves, and Turc), modeled (SWAT), and remote sensing in the drought characterization using SPEI and SPAEI. Remote sensing PET and AET are considered as standard methods to compare both empirical and modeled PET and AET estimates. The present methodology was tested on a dry-sub-humid river catchment of India, the Tungabhadra River catchment. It is recommended to use PET instead of AET when estimating drought indices as SPEI values performed relatively better than SPAEI. In the present study it is observed that although PET and AET estimates vary with different models, drought indices SPEI and SPAEI are not differing much at annual scales. Hargreaves and Penman-Monteith performed better results compared to remote sensing method in SPEI calculations. And for SPAEI, Budyko and Turc performed better results. Thus, the present study concludes that empirical models correlated better with the remote sensing data. The study will be prominent for ungauged river basins, where detailed hydrological data is limited and difficult

Abstract

To perform network forensic analysis on an incident in software defined networking (SDN), logs are of the utmost importance. Without any logs, an investigator will not be able to complete and justify the forensic analysis. With the advancement of network and communication technologies, the volume of logs that needs to be collected and retained is growing exponentially big. The network administrators face the problems in maintaining such huge logs for longer period of time for forensic analysis. Network Providers rely on purging data based on a certain stipulated duration expected by the local rules for forensics evidence. SDN providers have limitations in managing such big data since the expense involved is commensurate with the duration of data retention. Here, in this work we propose a novel idea to reduce and summarize large forensic data sets for faster querying as well as reducing its space complexity by using bloom filters. Through this work we aim to propose a system which can deliver more optimized forensic data availability in SDN platform compared to existing systems.

Abstract

In recent years, sentiment analysis has gained popularity as it is essential to moderate and analyse the information across the Internet. It has various applications like opinion mining, social media monitoring, and market research. Aspect Based Sentiment Analysis (ABSA) is an area of sentiment analysis which deals with sentiment at a finer level. ABSA classifies sentiment with respect to each aspect to gain greater insights into the sentiment expressed. Significant contributions have been made in ABSA, but this progress is limited only to a few languages with adequate resources. Telugu lags behind in this area of research despite being one of the most spoken languages in India and an enormous amount of data being created each day. In this thesis, we create a reliable resource for aspect based sentiment analysis in Telugu. The data is annotated for three tasks namely Aspect Term Extraction, Aspect Polarity Classification and Aspect Categorisation. Further, we develop baselines for the tasks using deep learning methods demonstrating the reliability and usefulness of the resource. In addition to this, experimentation has been done with transformer models, as they have led to pivotal changes in the field of NLP. Specifically, the setting of monolingual and multilingual models has been chosen to compare the effective contribution of the dataset created for ABSA in Telugu.