36,397 results on '"Krishnan A"'
Search Results
2. The roles of patient‐derived xenograft models and artificial intelligence toward precision medicine
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Venkatachalababu Janitri, Kandasamy Nagarajan ArulJothi, Vijay Murali Ravi Mythili, Sachin Kumar Singh, Parteek Prasher, Gaurav Gupta, Kamal Dua, Rakshith Hanumanthappa, Karthikeyan Kaliappan, and Krishnan Anand
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artificial intelligence ,cancer biology ,nanodrug delivery ,patient‐derived xenografts ,PDX model ,personalized medicine ,Medicine - Abstract
Abstract Patient‐derived xenografts (PDX) involve transplanting patient cells or tissues into immunodeficient mice, offering superior disease models compared with cell line xenografts and genetically engineered mice. In contrast to traditional cell‐line xenografts and genetically engineered mice, PDX models harbor the molecular and biologic features from the original patient tumor and are generationally stable. This high fidelity makes PDX models particularly suitable for preclinical and coclinical drug testing, therefore better predicting therapeutic efficacy. Although PDX models are becoming more useful, the several factors influencing their reliability and predictive power are not well understood. Several existing studies have looked into the possibility that PDX models could be important in enhancing our knowledge with regard to tumor genetics, biomarker discovery, and personalized medicine; however, a number of problems still need to be addressed, such as the high cost and time‐consuming processes involved, together with the variability in tumor take rates. This review addresses these gaps by detailing the methodologies to generate PDX models, their application in cancer research, and their advantages over other models. Further, it elaborates on how artificial intelligence and machine learning were incorporated into PDX studies to fast‐track therapeutic evaluation. This review is an overview of the progress that has been done so far in using PDX models for cancer research and shows their potential to be further improved in improving our understanding of oncogenesis.
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- 2024
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3. Exploring the interaction between derivatives of urea with resorcinol-based acridinedione dyes by employing fluorescence methods and molecular docking approach
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Ravichandran Keerthiga, Krishnan Anju, Namasivayam Dhenadhayalan, Murugan Sreedevi Sangeetha, Seba Merin Vinod, Somasundaram Gayathri, Salwa B. AlReshaidan, Ahmed S. Al-Fatesh, Naif Alarifi, Omer Bellahwel, Nadavala Siva Kumar, Perumal Tamizhdurai, and Rajendran Kumaran
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Acridinedione dye ,Derivatives of urea ,Fluorescence techniques ,Fluorescence enhancement ,Fluorescence quenching ,HB and hydrophobic interactions ,Chemistry ,QD1-999 - Abstract
Akyl urea derivatives, either symmetrical or unsymmetrical in nature possessing a free N-H or N-alkyl moieties in the molecular framework of urea governs the excited state properties of acridinedione dye (ADR1) which is a resorcinol-based derivative. Fluorescence enhancement (FE) of ADR1 dye is observed on the addition of unsymmetrical urea derivatives, whereas a decrease in the fluorescence intensity resulted upon the addition of symmetrical urea derivatives. The nature of the urea derivatives controls the suppression of photoinduced electron transfer (PET) via space, which is the cause of the FE. FQ results from the donor and acceptor moieties of ADR1 dye promoting the PET process. Urea (U), symmetrical and unsymmetrical urea derivatives (except Tetramethyl urea (TMU)) results no significant shift of the localized excited (LE) state emission of ADR1 dye. Studies of the ADR1 dye’s fluorescence lifetime in the presence of urea compounds show a significant increase in lifetime. This phenomenon is explained by a significant difference in the hydrogen-bonding (HB) pattern, which causes variation in the microenvironment created by the solute molecules in the aqueous phase. Both the hydrophobic effects of the alkyl group substituents in the urea molecular framework and the HB interactions between the solute and solvent influence the excited state features of ADR1 dye. Further, the role of urea derivatives and ADR1 dye (both are considered as competitive guest molecules) energetics and molecular interactions were studied in the presence of host molecule, Human Serum Albumin (HSA). The binding energy (BE) and several bimolecular interactions driven by urea derivatives in the presence of ADR1-HSA complex in comparison with that of urea derivatives-HSA complex were investigated by molecular docking (Mol.Doc) methodology. Incorporating theoretical research along with steady state and time-resolved fluorescence investigations proved to be an effective method to evaluate the interactions of competing solutes comprising both hydrophobic and HB functional groups.
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- 2024
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4. Role of vertical circulating exosomes biomarkers in preeclampsia
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Ketki Kalele, Sidhanti Nyahatkar, Swarup Sonar, Niren Ray Maharaj, and Krishnan Anand
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Exosomes ,Placental exosomes ,Preeclampsia ,Biomarkers ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Preeclampsia, a hypertensive disorder of pregnancy, poses significant risks to maternal and fetal health. Recent research highlights the potential of vertical circulating exosomes (VCEs) as biomarkers for early detection and monitoring of preeclampsia. Exosomes, small extracellular vesicles involved in intercellular communication, carry bioactive molecules that are messengers of the parental cell status (healthy or undergoing any pathological condition). In preeclampsia, alterations in the cargo of VCEssuch as proteins, lipids, and nucleic acids play the role of biomarkers in pathophysiology complications. These exosomal contents can provide insights into the underlying mechanisms, including endothelial dysfunction, immune response dysregulation, and placental abnormalities. Early identification of specific exosomal biomarkers may facilitate timely therapeutic interventions, improving outcomes for both mother and child. This article explores the emerging role of VCEs in preeclampsia, emphasizing their diagnostic and prognostic potential, and underscores the need for further research to validate these biomarkers and integrate them into clinical practice.
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- 2024
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5. Plant‐derived exosomes: A Green Nanomedicine for Cancer
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Swarup Sonar and Krishnan Anand
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cancer therapeutic ,clinical trials ,drug delivery ,plant exosomes ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Exosomes are signalling molecules related to cell‐to‐cell communication. Based on sources (plants, stem cells, and immune cells derived exosomes) it offers promising therapeutic activity against cancer. Plant‐derived exosomes (PDEs) are natural extracellular vesicles (EVs) that are potent to provide organic precision nanomedicine to cancer therapeutics including targeted drug delivery. PDEs are gaining attention due to their safety and efficacy. There are plenty of different sources of PDEs in nature. This article explores various plants such as carrots, ginger, lemons, cabbages, blueberries, oranges, tomatoes, grapefruits, and tea leaves, which provide exosomes with distinct therapeutic properties, including anti‐inflammatory, antioxidant, and anticancer activities. PDEs exhibit significant potential in drug delivery. Ongoing research and clinical trials predict that PDEs will become effective, and affordable solutions for cancer treatment.
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- 2024
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6. Community-forming traits play role in effective colonization of plant-growth-promoting bacteria and improved plant growth
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Devashish Pathak, Archna Suman, Pushpendra Sharma, Krishnan Aswini, Venkadasamy Govindasamy, Shrikant Gond, and Rana Anshika
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biofilm ,colonization ,microbial community ,microcosm ,plant growth promoting traits ,plant microbe interaction ,Plant culture ,SB1-1110 - Abstract
Community-forming traits (CFts) play an important role in the effective colonization of plant-growth-promoting bacterial communities that influence host plants positively by modulating their adaptive functions. In this study, by considering plant-growth-promoting traits (PGPts) and community-forming traits (CFts), three communities were constructed, viz., SM1 (PGPts), SM2 (CFts), and SM3 (PGPts+CFts). Each category isolates were picked up on the basis of their catabolic diversity of different carbon sources. Results revealed a distinctive pattern in the colonization of the communities possessed with CF traits. It was observed that the community with CFts colonized inside the plant in groups or in large aggregations, whereas the community with only PGPts colonized as separate individual and small colonies inside the plant root and leaf. The effect of SM3 in the microcosm experiment was more significant than the uninoculated control by 22.12%, 27.19%, and 9.11% improvement in germination percentage, chlorophyll content, and plant biomass, respectively. The significant difference shown by the microbial community SM3 clearly demonstrates the integrated effect of CFts and PGPts on effective colonization vis-à-vis positive influence on the host plant. Further detailed characterization of the interaction will take this technology ahead in sustainable agriculture.
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- 2024
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7. Unlocking Exosome-Based Theragnostic Signatures: Deciphering Secrets of Ovarian Cancer Metastasis
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Sayantanee Mukherjee, Sagnik Nag, Nobendu Mukerjee, Swastika Maitra, Raman Muthusamy, Neeraj Kumar Fuloria, Shivkanya Fuloria, Manab Deb Adhikari, Krishnan Anand, Nanasaheb Thorat, Vetriselvan Subramaniyan, and Sukhamoy Gorai
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Chemistry ,QD1-999 - Published
- 2023
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8. Clinical impact of epithelial–mesenchymal transition for cancer therapy
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Nobendu Mukerjee, Sagnik Nag, Bikramjit Bhattacharya, Athanasios Alexiou, Divya Mirgh, Dattatreya Mukherjee, Manab Deb Adhikari, Krishnan Anand, Raman Muthusamy, Sukhamoy Gorai, and Nanasaheb Thorat
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cancer ,EMT ,exosomes ,metastasis ,therapeutic ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract The epithelial–mesenchymal transition (EMT) represents a pivotal frontier in oncology, playing a central role in the metastatic cascade of cancer—a leading global health challenge. This comprehensive review delves into the complexities of EMT, a process where cancer cells gain exceptional mobility, facilitating their invasion into distant organs and the establishment of secondary malignancies. We thoroughly examine the myriad of factors influencing EMT, encompassing transcription factors, signalling pathways, metabolic alterations, microRNAs, long non‐coding RNAs, epigenetic changes, exosomal interactions and the intricate dynamics of the tumour microenvironment. Particularly, the review emphasises the advanced stages of EMT, crucial for the development of highly aggressive cancer phenotypes. During this phase, cancer cells penetrate the vascular barrier and exploit the bloodstream to propagate life‐threatening metastases through the mesenchymal–epithelial transition. We also explore EMT's significant role in fostering tumour dormancy, senescence, the emergence of cancer stem cells and the formidable challenge of therapeutic resistance. Our review transcends a mere inventory of EMT‐inducing elements; it critically assesses the current state of EMT‐focused clinical trials, revealing both the hurdles and significant breakthroughs. Highlighting the potential of EMT research, we project its transformative impact on the future of cancer therapy. This exploration is aimed at paving the way towards an era of effectively managing this relentless disease, positioning EMT at the forefront of innovative cancer research strategies.
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- 2024
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9. Tear exosomes: A messenger of clinical health complication
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Divya Mirgh, Sukhamoy Gorai, Nanasaheb Thorat, and Krishnan Anand
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Therapeutics. Pharmacology ,RM1-950 - Published
- 2023
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10. Endophytic bacterial taxonomic and functional diversity in the seeds of wheat genotypes from different agroecologies
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Pushpendra Sharma, Archna Suman, Krishnan Aswini, Jogdande SaiPrasad, and Shrikant Gond
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Agroecological zones ,bacterial endophytes ,wheat ,diversity ,functional traits ,Plant culture ,SB1-1110 ,Plant ecology ,QK900-989 - Abstract
ABSTRACTPlant genotype and agroecology influence the composition and functionality of seed endophytic bacterial communities. Taxonomic analysis of 123 wheat seeds endophytic bacteria classified these into 23 genera predominantly under Firmicutes followed by Actinobacteria and Proteobacteria. Genus Bacillus was most abundant (30.7%) followed by Streptomyces (18.4%) with other representative genera such as Stenotrophomonas, Paenibacillus, Mixta, Enterobacter, Micrococcus, Pantoea, Alkalihalobacillus, Cortiobacterium, and more. Across agroecologies, the core microbiota of seeds consists of Bacillus, Streptomyces, Paenibacillus, and Stenotrophomonas, with maximum diversity and abundance observed in seeds of the North Western Plain Zone of India. Seed endophytic bacteria had PGP traits; nitrogen fixation (n = 101), production of IAA (n = 65), siderophores (n = 43), ammonia (n = 82) and solubilization of phosphate (n = 47), potassium (n = 37), and zinc (n = 8). The isolates produced HCN and hydrolytic enzymes and displayed antagonism against fungal pathogens. Overall, the information generated on wheat seeds’ endophytic bacterial taxonomy and beneficial traits may pave the path for the development of novel bioinoculants.Key message Wheat seeds from various agro-ecologies of India harbor diverse endophytic bacteria.Firmicutes were dominant followed by Actinobacteria and Proteobacteria.Genus Bacillus, Stenotrophomonas, Streptomyces, and Paenibacillus were core endophytic bacteria in different agro-ecologies.The endophytic bacterial strains were displaying diverse functional traits.
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- 2023
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11. Valorization of surplus onion for the development and characterization of antioxidant-rich gummies
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Krishnan Abinaya, Kumar Sharmila, Santhanvelayudham Priya, Marimuthu Ponmozhi, and Radhakrishnan Linekha
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Quercetin ,Antioxidant ,Food pharmacy ,Confectionery ,Nutrition. Foods and food supply ,TX341-641 ,Nutritional diseases. Deficiency diseases ,RC620-627 - Abstract
Allium cepa is an herbaceous biennial plant cultivated for its edible bulb and the elementary ingredient in Indian cooking. The surplus onion presents a huge loss due to drying rotting, sprouting, fungal damage, etc. Formulating an onion gummy is a rich source of antioxidants that can promote healthy living and prevent diseases. Our study developed an antioxidant-rich gummy using red onion transforming its pungent taste using tamarind. The gummy samples were subjected to physicochemical analysis where the pH of the samples was in the range of 5.64 to 5.51, the moisture and sugar content ranged from 59.6 to 57.9 and 60.97 to 59.10 respectively, the texture properties of the gummy jelly showed hardness in the range from 571.81±0.2 to 378.26±0.9 g, chewiness from 1,819.1 ± 64.22 to 1,390.9 ± 56.7 g, adhesiveness from 57.4 ± 1.33 to 58.6 ± 1.55, and springiness from 48.78±0.2 to 40.73±0.4 and finally the chromaticity values (L*, a*, and b*) of gummy jelly were, lightness in the range from 7.78±0.08 to 5.83±0.08, redness from 3.39±0.10 to 0.54±0.08 and yellowness from 1.65±0.05 to 1.27±0.05. The antioxidant activity was analyzed using DPPH and ABTS radical scavenging activity and was in the range of 29.75 to 78.85% and 18 to 62% respectively. The sensory evaluation showed that buying intention was highly ranked followed by appearance, taste, flavor, overall preference, and texture. In this study, we conclude that the antioxidant-rich red onion gummy jelly (ROGJ) developed with potential antioxidant activity can be commercialized and could be a healthy substitute for commercial unhealthy gummy jellies.
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- 2023
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12. 67 million natural product-like compound database generated via molecular language processing
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Dillon W. P. Tay, Naythan Z. X. Yeo, Krishnan Adaikkappan, Yee Hwee Lim, and Shi Jun Ang
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Science - Abstract
Abstract Natural products are a rich resource of bioactive compounds for valuable applications across multiple fields such as food, agriculture, and medicine. For natural product discovery, high throughput in silico screening offers a cost-effective alternative to traditional resource-heavy assay-guided exploration of structurally novel chemical space. In this data descriptor, we report a characterized database of 67,064,204 natural product-like molecules generated using a recurrent neural network trained on known natural products, demonstrating a significant 165-fold expansion in library size over the approximately 400,000 known natural products. This study highlights the potential of using deep generative models to explore novel natural product chemical space for high throughput in silico discovery.
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- 2023
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13. Optimizing NACA2414 airfoil aerodynamics with PARSEC parametrization and Genetic Algorithm
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Krishnan Anupam, Al-Obaidi Abdulkareem Sh. Mahdi, and Ching Hao Lee
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Environmental sciences ,GE1-350 - Abstract
This research endeavours to contribute to the broader field of wind turbine aerodynamics by investigating a method to enhance the performance of airfoils, with specific attention to the NACA2414 airfoil at a 15-degree angle of attack. The study explores the airfoil’s performance across a range of -10 to 15 degrees angle of attack. It employs both PARSEC parametrization and Genetic Algorithm optimization, achieving significant advancements. At a 15-degree angle of attack, post-optimization, the lift coefficient for the NACA2414 airfoil exhibits a remarkable increase to 1.5275 at a Reynolds number of 105, surpassing the original airfoil’s performance of 1.2407. This progress highlights the effectiveness of utilizing PARSEC parametrization and Genetic Algorithm optimization, particularly in low-speed wind turbine applications. While emphasizing potential applications in low-wind-speed scenarios, the findings underscore the significance of these techniques in renewable energy production.
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- 2024
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14. Cardiovascular diseases prediction by machine learning incorporation with deep learning
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Sivakannan Subramani, Neeraj Varshney, M. Vijay Anand, Manzoore Elahi M. Soudagar, Lamya Ahmed Al-keridis, Tarun Kumar Upadhyay, Nawaf Alshammari, Mohd Saeed, Kumaran Subramanian, Krishnan Anbarasu, and Karunakaran Rohini
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cardiovascular disease ,AI-based technologies ,internet of things ,machine learning ,computational method ,Medicine (General) ,R5-920 - Abstract
It is yet unknown what causes cardiovascular disease (CVD), but we do know that it is associated with a high risk of death, as well as severe morbidity and disability. There is an urgent need for AI-based technologies that are able to promptly and reliably predict the future outcomes of individuals who have cardiovascular disease. The Internet of Things (IoT) is serving as a driving force behind the development of CVD prediction. In order to analyse and make predictions based on the data that IoT devices receive, machine learning (ML) is used. Traditional machine learning algorithms are unable to take differences in the data into account and have a low level of accuracy in their model predictions. This research presents a collection of machine learning models that can be used to address this problem. These models take into account the data observation mechanisms and training procedures of a number of different algorithms. In order to verify the efficacy of our strategy, we combined the Heart Dataset with other classification models. The proposed method provides nearly 96 percent of accuracy result than other existing methods and the complete analysis over several metrics has been analysed and provided. Research in the field of deep learning will benefit from additional data from a large number of medical institutions, which may be used for the development of artificial neural network structures.
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- 2023
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15. Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity
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Krishnan Aswini, Archna Suman, Pushpendra Sharma, Pradeep Kumar Singh, Shrikant Gond, and Devashish Pathak
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heat sensitivity ,seed microbiome ,culturable ,tolerance ,metagenomics ,bacterial diversity ,Plant culture ,SB1-1110 - Abstract
Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.
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- 2023
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16. Optimization Studies on Imatinib Mesylate Loaded Nanoliposomes Using Box-Behnken Design
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Mandeep Dahiya, Rajendra Awasthi, Gaurav Gupta, Sachin Kumar Singh, Monica Gulati, Niraj Kumar Jha, Saurabh Kumar Jha, Ankur Sharma, Parteek Prasher, Krishnan Anand, Dinesh Kumar Chellappan, Kamal Dua, and Harish Dureja
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imatinib mesylate ,nanoliposome ,emulsification ,box-behnken design ,ultrasonication ,cytotoxicity ,Biology (General) ,QH301-705.5 ,Medicine - Abstract
Nanoliposomes are bilayer phospholipid vesicles used to encapsulate and deliver therapeutic agents. The study was aimed to investigate the effects of critical variables on nanoliposomes characteristics. Imatinib mesylate-loaded nanoliposomes were formulated by the two-step emulsification process using a high-speed homogenizer system and probe-type ultrasonicator. The Box-Behnken design was utilized to optimize the process parameters. The mean particle size of nanoliposomes was found to be 211 nm to 623.3 nm with a low value of polydispersity index (0.005 to 0.7). Zeta potential values varied from ‒27.6 mV to ‒9.2 mV in uncoated nanoliposomes to +27.5 mV in chitosan-coated nanoliposomes. The encapsulation efficiency in formulation NLP-H8 containing 200 mg of phosphatidylcholine, homogenization speed of 12000 rpm, and 7 min of sonication time was found to be 76.49% without the coating and 85.4% in 0.2% w/v chitosan-coated nanoliposomes. TEM image confirmed the spherical shape of nanoliposomes. In-vitro drug release study demonstrated that the optimized nanoliposomal formulations released 84.67% of the loaded drug after 24 h in 0.1 N HCl. The IC50 value of formulation NLP-H8 was found to be 7.98 μM. Nanoliposomal formulations were prepared successfully with suitable size, morphology, encapsulation efficiency, and drug release. The models developed in this study may be utilized further as a response surface for the various parameters of nanoliposomes.
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- 2022
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17. Surface polarization strongly influences electrostatics in a nonlocal medium
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Behjatian, Ali, Blossey, Ralf, and Krishnan, Madhavi
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Condensed Matter - Soft Condensed Matter - Abstract
Electrostatics in the solution phase is governed by free electrical charges such as ions, as well as by bound charges that arise when a polarizable medium responds to an applied field. In a local medium, described by a constant dielectric permittivity, the sign of the far-field electrostatic potential distribution around an object is governed by its electrical charge. We demonstrate significant departures from this expectation in a nonlocal medium characterized by a wave vector-dependent dielectric function. Here, surface polarization due to the solvent, or indeed non-solvent dipoles, may wield significant influence at large distances. The polarization correlation length may not only significantly augment the effective screening length, but we show that the electrical contribution from polarization can compete with and even invert the sign of the electrical potential and the field arising from charge alone. These results hold ramifications for a range of apparently anomalous electrically governed observations such as underscreening, electrophoretic mobilities of charge-neutral objects, and long-ranged attraction between like-charged entities in water and other solvents.
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- 2024
18. Get a Grip: Multi-Finger Grasp Evaluation at Scale Enables Robust Sim-to-Real Transfer
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Lum, Tyler Ga Wei, Li, Albert H., Culbertson, Preston, Srinivasan, Krishnan, Ames, Aaron D., Schwager, Mac, and Bohg, Jeannette
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Computer Science - Robotics - Abstract
This work explores conditions under which multi-finger grasping algorithms can attain robust sim-to-real transfer. While numerous large datasets facilitate learning generative models for multi-finger grasping at scale, reliable real-world dexterous grasping remains challenging, with most methods degrading when deployed on hardware. An alternate strategy is to use discriminative grasp evaluation models for grasp selection and refinement, conditioned on real-world sensor measurements. This paradigm has produced state-of-the-art results for vision-based parallel-jaw grasping, but remains unproven in the multi-finger setting. In this work, we find that existing datasets and methods have been insufficient for training discriminitive models for multi-finger grasping. To train grasp evaluators at scale, datasets must provide on the order of millions of grasps, including both positive and negative examples, with corresponding visual data resembling measurements at inference time. To that end, we release a new, open-source dataset of 3.5M grasps on 4.3K objects annotated with RGB images, point clouds, and trained NeRFs. Leveraging this dataset, we train vision-based grasp evaluators that outperform both analytic and generative modeling-based baselines on extensive simulated and real-world trials across a diverse range of objects. We show via numerous ablations that the key factor for performance is indeed the evaluator, and that its quality degrades as the dataset shrinks, demonstrating the importance of our new dataset. Project website at: https://sites.google.com/view/get-a-grip-dataset.
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- 2024
19. Unifying recent experiments on spin-valley locking in TMDC quantum dots
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Shandilya, Aakash, Kapila, Sundeep, Krishnan, Radha, Weber, Bent, and Muralidharan, Bhaskaran
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Condensed Matter - Mesoscale and Nanoscale Physics ,Quantum Physics - Abstract
The spin-valley or Kramers qubit promises significantly enhanced spin-valley lifetimes due to strong coupling of the electrons' spin to their momentum (valley) degrees of freedom. In transition metal dichalcogenides (TMDCs) such spin-valley locking is expected to be particularly strong owing to the significant intrinsic spin-orbit coupling strength. Very recently, a small number of experiments on TMDC quantum dots have put forth evidence for spin-valley locking for the first time at the few-electron limit. Employing quantum transport theory, here we numerically simulate their ground- and excited-state transport spectroscopy signatures in a unified theoretical framework. In doing so, we reveal the operating conditions under which spin-valley locking occurs in TMDC quantum dots, thereby weaving the connection between intrinsic material properties and the experimental data under diverse conditions. Our simulations thus provide a predictive modeling tool for TMDC quantum dots at the few-electron limit allowing us to deduce from experiments the degree of spin-valley locking based on the SOC strength, inter-valley mixing, and the spin and valley $g$-factors. Our theoretical analysis provides an important milestone towards the next challenge of experimentally confirming valley-relaxation times using single-shot projective measurements, Comment: 13 pages, 6 figures with Appendix included, comments welcome
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- 2024
20. Brain age identification from diffusion MRI synergistically predicts neurodegenerative disease
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Gao, Chenyu, Kim, Michael E., Ramadass, Karthik, Kanakaraj, Praitayini, Krishnan, Aravind R., Saunders, Adam M., Newlin, Nancy R., Lee, Ho Hin, Yang, Qi, Taylor, Warren D., Boyd, Brian D., Beason-Held, Lori L., Resnick, Susan M., Barnes, Lisa L., Bennett, David A., Van Schaik, Katherine D., Archer, Derek B., Hohman, Timothy J., Jefferson, Angela L., Išgum, Ivana, Moyer, Daniel, Huo, Yuankai, Schilling, Kurt G., Zuo, Lianrui, Bao, Shunxing, Khairi, Nazirah Mohd, Li, Zhiyuan, Davatzikos, Christos, and Landman, Bennett A.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Estimated brain age from magnetic resonance image (MRI) and its deviation from chronological age can provide early insights into potential neurodegenerative diseases, supporting early detection and implementation of prevention strategies. Diffusion MRI (dMRI), a widely used modality for brain age estimation, presents an opportunity to build an earlier biomarker for neurodegenerative disease prediction because it captures subtle microstructural changes that precede more perceptible macrostructural changes. However, the coexistence of macro- and micro-structural information in dMRI raises the question of whether current dMRI-based brain age estimation models are leveraging the intended microstructural information or if they inadvertently rely on the macrostructural information. To develop a microstructure-specific brain age, we propose a method for brain age identification from dMRI that minimizes the model's use of macrostructural information by non-rigidly registering all images to a standard template. Imaging data from 13,398 participants across 12 datasets were used for the training and evaluation. We compare our brain age models, trained with and without macrostructural information minimized, with an architecturally similar T1-weighted (T1w) MRI-based brain age model and two state-of-the-art T1w MRI-based brain age models that primarily use macrostructural information. We observe difference between our dMRI-based brain age and T1w MRI-based brain age across stages of neurodegeneration, with dMRI-based brain age being older than T1w MRI-based brain age in participants transitioning from cognitively normal (CN) to mild cognitive impairment (MCI), but younger in participants already diagnosed with Alzheimer's disease (AD). Approximately 4 years before MCI diagnosis, dMRI-based brain age yields better performance than T1w MRI-based brain ages in predicting transition from CN to MCI.
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- 2024
21. From Cool Demos to Production-Ready FMware: Core Challenges and a Technology Roadmap
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Rajbahadur, Gopi Krishnan, Oliva, Gustavo A., Lin, Dayi, and Hassan, Ahmed E.
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Computer Science - Software Engineering ,Computer Science - Artificial Intelligence - Abstract
The rapid expansion of foundation models (FMs), such as large language models (LLMs), has given rise to FMware--software systems that integrate FMs as core components. While building demonstration-level FMware is relatively straightforward, transitioning to production-ready systems presents numerous challenges, including reliability, high implementation costs, scalability, and compliance with privacy regulations. This paper provides a thematic analysis of the key obstacles in productionizing FMware, synthesized from industry experience and diverse data sources, including hands-on involvement in the Open Platform for Enterprise AI (OPEA) and FMware lifecycle engineering. We identify critical issues in FM selection, data and model alignment, prompt engineering, agent orchestration, system testing, and deployment, alongside cross-cutting concerns such as memory management, observability, and feedback integration. We discuss needed technologies and strategies to address these challenges and offer guidance on how to enable the transition from demonstration systems to scalable, production-ready FMware solutions. Our findings underscore the importance of continued research and multi-industry collaboration to advance the development of production-ready FMware.
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- 2024
22. Bow Shock and Local Bubble Plasma Unveiled by the Scintillating Millisecond Pulsar J0437$-$4715
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Reardon, Daniel J., Main, Robert, Ocker, Stella Koch, Shannon, Ryan M., Bailes, Matthew, Camilo, Fernando, Geyer, Marisa, Jameson, Andrew, Kramer, Michael, Parthasarathy, Aditya, Spiewak, Renée, van Straten, Willem, and Krishnan, Vivek Venkatraman
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Astrophysics of Galaxies ,Astrophysics - Solar and Stellar Astrophysics - Abstract
The interstellar medium of the Milky Way contains turbulent plasma with structures driven by energetic processes that fuel star formation and shape the evolution of our Galaxy. Radio waves from pulsars are scattered off the small (au-scale and below) structures, resulting in frequency-dependent interference patterns that are modulated in time because of the relative motions of the pulsar, Earth, and plasma. Power spectral analyses of these patterns show parabolic arcs with curvatures that encode the locations and kinematics of individual structures. Here we report the discovery of at least 25 distinct plasma structures in the direction of the brilliant millisecond pulsar, PSR J0437$-$4715, in observations obtained with the MeerKAT radio telescope. Four arcs reveal structures within 5000 au of the pulsar, from a series of shocks induced as the pulsar and its wind interact with the ambient insterstellar medium. The measured radial distance and velocity of the main shock allows us to solve the shock geometry and space velocity of the pulsar in three dimensions, while the velocity of another structure unexpectedly indicates a back flow from the direction of the shock or pulsar-wind tail. The remaining 21 arcs represent a surprising abundance of structures sustained by turbulence within the Local Bubble -- a region of the interstellar medium thought to be depleted of gas by a series of supernova explosions about 14 Myr ago., Comment: 46 pages, 10 figures, 1 table, submitted to Nature Astronomy
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- 2024
23. On the Connectivity of Friends-and-strangers Graphs
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Krishnan, Neil and Li, Rupert
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Mathematics - Combinatorics ,Mathematics - Probability ,05C40, 05C35, 05C80 - Abstract
Friends-and-strangers graphs, coined by Defant and Kravitz, are denoted by $\mathsf{FS}(X,Y)$ where $X$ and $Y$ are both graphs on $n$ vertices. The graph $X$ represents positions and edges mark adjacent positions while the graph $Y$ represents people and edges mark friendships. The vertex set of $\mathsf{FS}(X,Y)$ consists of all one-to-one placements of people on positions, and there is an edge between any two placements if it is possible to swap two people who are friends and on adjacent positions to get from one placement to the other. Previous papers have studied when $\mathsf{FS}(X,Y)$ is connected. In this paper, we consider when $\mathsf{FS}(X,Y)$ is $k$-connected where a graph is $k$-connected if it remains connected after removing any $k-1$ or less vertices. We first consider $\mathsf{FS}(X,Y)$ when $Y$ is a complete graph or star graph. We find tight bounds on their connectivity, proving their connectivity equals their minimum degree. We further consider the size of the connected components of $\mathsf{FS}(X,\mathsf{Star}_n)$ where $X$ is connected. We show that asymptotically similar conditions as the conditions mentioned by Bangachev are sufficient for $\mathsf{FS}(X,Y)$ to be $k$-connected. Finally, we consider when $X$ and $Y$ are independent Erd\H{o}s--R\'enyi random graphs on $n$ vertices and edge probability $p_1$ and $p_2,$ respectively. We show that for $p_0 = n^{-1/2+o(1)},$ if $p_1p_2\geq p_0^2$ and $p_1,$ $p_2 \geq w(n) p_0$ where $w(n) \rightarrow 0$ as $n \rightarrow \infty,$ then $\mathsf{FS}(X,Y)$ is $k$-connected with high probability. This is asymptotically tight as we show that below an asymptotically similar threshold $p_0'=n^{-1/2+o(1)}$, the graph $\mathsf{FS}(X,Y)$ is disconnected with high probability if $p_1p_2 \leq (p_0')^2$., Comment: 35 pages, 9 figures
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- 2024
24. KatzBot: Revolutionizing Academic Chatbot for Enhanced Communication
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Kumar, Sahil, Paikar, Deepa, Vutukuri, Kiran Sai, Ali, Haider, Ainala, Shashidhar Reddy, Krishnan, Aditya Murli, and Zhang, Youshan
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Computer Science - Computation and Language - Abstract
Effective communication within universities is crucial for addressing the diverse information needs of students, alumni, and external stakeholders. However, existing chatbot systems often fail to deliver accurate, context-specific responses, resulting in poor user experiences. In this paper, we present KatzBot, an innovative chatbot powered by KatzGPT, a custom Large Language Model (LLM) fine-tuned on domain-specific academic data. KatzGPT is trained on two university-specific datasets: 6,280 sentence-completion pairs and 7,330 question-answer pairs. KatzBot outperforms established existing open source LLMs, achieving higher accuracy and domain relevance. KatzBot offers a user-friendly interface, significantly enhancing user satisfaction in real-world applications. The source code is publicly available at \url{https://github.com/AiAI-99/katzbot}.
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- 2024
25. Unsupervised Replay Strategies for Continual Learning with Limited Data
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Bazhenov, Anthony, Dewasurendra, Pahan, Krishnan, Giri P., and Delanois, Jean Erik
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Computer Science - Machine Learning - Abstract
Artificial neural networks (ANNs) show limited performance with scarce or imbalanced training data and face challenges with continuous learning, such as forgetting previously learned data after new tasks training. In contrast, the human brain can learn continuously and from just a few examples. This research explores the impact of 'sleep', an unsupervised phase incorporating stochastic activation with local Hebbian learning rules, on ANNs trained incrementally with limited and imbalanced datasets, specifically MNIST and Fashion MNIST. We discovered that introducing a sleep phase significantly enhanced accuracy in models trained with limited data. When a few tasks were trained sequentially, sleep replay not only rescued previously learned information that had been catastrophically forgetting following new task training but often enhanced performance in prior tasks, especially those trained with limited data. This study highlights the multifaceted role of sleep replay in augmenting learning efficiency and facilitating continual learning in ANNs.
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- 2024
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- View/download PDF
26. Simultaneous cooling of qubits via a quantum absorption refrigerator and beyond
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Krishnan, Jithin G., Pushpan, Chandrima B., and Pal, Amit Kumar
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Quantum Physics - Abstract
We design a quantum thermal device that can simultaneously and dynamically cool multiple target qubits. Using a setup with three bosonic heat baths, we propose an engineering of interaction Hamiltonian using operators on different subspaces of the full Hilbert space of the system labelled by different magnetizations. We demonstrate, using the local as well as global quantum master equations, that a set of target qubits can be cooled simultaneously using these interaction Hamiltonians, while equal cooling of all target qubits is possible only when the local quantum master equation is used. However, the amount of cooling obtained from different magnetization subspaces, as quantified by a distance-based measure of qubit-local steady-state temperatures, may vary. We also investigate cooling of a set of target qubits when the interaction Hamiltonian has different magnetization components, and when the design of the quantum thermal device involves two heat baths instead of three. Further, we demonstrate, using local quantum master equation, that during providing cooling to the target qubits, the designed device operates only as a quantum absorption refrigerator. In contrast, use of the global quantum master equation indicates cooling of the target qubits even when the device works outside the operation regime of a quantum absorption refrigerator. We also extend the design to a star network of qubits interacting via Heisenberg interaction among each other, kept in contact with either three, or two heat baths, and discuss cooling of a set of target qubits using this device., Comment: 19 pages, 9 figures
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- 2024
27. Personalized Adaptation via In-Context Preference Learning
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Lau, Allison, Choi, Younwoo, Balazadeh, Vahid, Chidambaram, Keertana, Syrgkanis, Vasilis, and Krishnan, Rahul G.
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Computer Science - Machine Learning ,Computer Science - Computation and Language - Abstract
Reinforcement Learning from Human Feedback (RLHF) is widely used to align Language Models (LMs) with human preferences. However, existing approaches often neglect individual user preferences, leading to suboptimal personalization. We present the Preference Pretrained Transformer (PPT), a novel approach for adaptive personalization using online user feedback. PPT leverages the in-context learning capabilities of transformers to dynamically adapt to individual preferences. Our approach consists of two phases: (1) an offline phase where we train a single policy model using a history-dependent loss function, and (2) an online phase where the model adapts to user preferences through in-context learning. We demonstrate PPT's effectiveness in a contextual bandit setting, showing that it achieves personalized adaptation superior to existing methods while significantly reducing the computational costs. Our results suggest the potential of in-context learning for scalable and efficient personalization in large language models.
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- 2024
28. PromptExp: Multi-granularity Prompt Explanation of Large Language Models
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Dong, Ximing, Wang, Shaowei, Lin, Dayi, Rajbahadur, Gopi Krishnan, Zhou, Boquan, Liu, Shichao, and Hassan, Ahmed E.
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Computer Science - Computation and Language - Abstract
Large Language Models excel in tasks like natural language understanding and text generation. Prompt engineering plays a critical role in leveraging LLM effectively. However, LLMs black-box nature hinders its interpretability and effective prompting engineering. A wide range of model explanation approaches have been developed for deep learning models, However, these local explanations are designed for single-output tasks like classification and regression,and cannot be directly applied to LLMs, which generate sequences of tokens. Recent efforts in LLM explanation focus on natural language explanations, but they are prone to hallucinations and inaccuracies. To address this, we introduce PromptExp , a framework for multi-granularity prompt explanations by aggregating token-level insights. PromptExp introduces two token-level explanation approaches: 1. an aggregation-based approach combining local explanation techniques, and 2. a perturbation-based approach with novel techniques to evaluate token masking impact. PromptExp supports both white-box and black-box explanations and extends explanations to higher granularity levels, enabling flexible analysis. We evaluate PromptExp in case studies such as sentiment analysis, showing the perturbation-based approach performs best using semantic similarity to assess perturbation impact. Furthermore, we conducted a user study to confirm PromptExp's accuracy and practical value, and demonstrate its potential to enhance LLM interpretability., Comment: 11 pages
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- 2024
29. Configurable Embodied Data Generation for Class-Agnostic RGB-D Video Segmentation
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Opipari, Anthony, Krishnan, Aravindhan K, Gayaka, Shreekant, Sun, Min, Kuo, Cheng-Hao, Sen, Arnie, and Jenkins, Odest Chadwicke
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Computer Science - Robotics ,Computer Science - Computer Vision and Pattern Recognition - Abstract
This paper presents a method for generating large-scale datasets to improve class-agnostic video segmentation across robots with different form factors. Specifically, we consider the question of whether video segmentation models trained on generic segmentation data could be more effective for particular robot platforms if robot embodiment is factored into the data generation process. To answer this question, a pipeline is formulated for using 3D reconstructions (e.g. from HM3DSem) to generate segmented videos that are configurable based on a robot's embodiment (e.g. sensor type, sensor placement, and illumination source). A resulting massive RGB-D video panoptic segmentation dataset (MVPd) is introduced for extensive benchmarking with foundation and video segmentation models, as well as to support embodiment-focused research in video segmentation. Our experimental findings demonstrate that using MVPd for finetuning can lead to performance improvements when transferring foundation models to certain robot embodiments, such as specific camera placements. These experiments also show that using 3D modalities (depth images and camera pose) can lead to improvements in video segmentation accuracy and consistency. The project webpage is available at https://topipari.com/projects/MVPd, Comment: Accepted in IEEE Robotics and Automation Letters October 2024
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- 2024
30. Hamiltonian bridge: A physics-driven generative framework for targeted pattern control
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Krishnan, Vishaal, Sinha, Sumit, and Mahadevan, L.
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics ,Computer Science - Artificial Intelligence ,Mathematics - Dynamical Systems ,Mathematics - Optimization and Control - Abstract
Patterns arise spontaneously in a range of systems spanning the sciences, and their study typically focuses on mechanisms to understand their evolution in space-time. Increasingly, there has been a transition towards controlling these patterns in various functional settings, with implications for engineering. Here, we combine our knowledge of a general class of dynamical laws for pattern formation in non-equilibrium systems, and the power of stochastic optimal control approaches to present a framework that allows us to control patterns at multiple scales, which we dub the "Hamiltonian bridge". We use a mapping between stochastic many-body Lagrangian physics and deterministic Eulerian pattern forming PDEs to leverage our recent approach utilizing the Feynman-Kac-based adjoint path integral formulation for the control of interacting particles and generalize this to the active control of patterning fields. We demonstrate the applicability of our computational framework via numerical experiments on the control of phase separation with and without a conserved order parameter, self-assembly of fluid droplets, coupled reaction-diffusion equations and finally a phenomenological model for spatio-temporal tissue differentiation. We interpret our numerical experiments in terms of a theoretical understanding of how the underlying physics shapes the geometry of the pattern manifold, altering the transport paths of patterns and the nature of pattern interpolation. We finally conclude by showing how optimal control can be utilized to generate complex patterns via an iterative control protocol over pattern forming pdes which can be casted as gradient flows. All together, our study shows how we can systematically build in physical priors into a generative framework for pattern control in non-equilibrium systems across multiple length and time scales., Comment: 29 pages, 8 figures
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- 2024
31. MeerKAT observations of pair-plasma induced birefringence in the double pulsar eclipses
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Lower, M. E., Kramer, M., Johnston, S., Breton, R. P., Wex, N., Bailes, M., Buchner, S., Camilo, F., Oswald, L. S., Reardon, D. J., Shannon, R. M., Serylak, M., and Krishnan, V. Venkatraman
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Astrophysics - High Energy Astrophysical Phenomena ,Physics - Plasma Physics - Abstract
PSR J0737$-$3039A/B is unique among double neutron star systems. Its near-perfect edge-on orbit causes the fast spinning pulsar A to be eclipsed by the magnetic field of the slow spinning pulsar B. Using high-sensitivity MeerKAT radio observations combined with updated constraints on the system geometry, we studied the impact of these eclipses on the incident polarization properties of pulsar A. Averaging light curves together after correcting for the rotation of pulsar B revealed enormous amounts of circular polarization and rapid changes in the linear polarization position angle, which occur at phases where emission from pulsar A is partially transmitted through the magnetosphere of pulsar B. These behaviours confirm that the eclipse mechanism is the result of synchrotron absorption in a relativistic pair-plasma confined to the closed-field region of pulsar B's truncated dipolar magnetic field. We demonstrate that changes in circular polarization handedness throughout the eclipses are directly tied to the average line of sight magnetic field direction of pulsar B, from which we unambiguously determine the complete magnetic and viewing geometry of the pulsar., Comment: 8 pages, 6 figures. Accepted for publication in MNRAS
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- 2024
32. A Bilevel Optimization Framework for Imbalanced Data Classification
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Medlin, Karen, Leyffer, Sven, and Raghavan, Krishnan
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Computer Science - Machine Learning ,Mathematics - Optimization and Control ,Statistics - Machine Learning - Abstract
Data rebalancing techniques, including oversampling and undersampling, are a common approach to addressing the challenges of imbalanced data. To tackle unresolved problems related to both oversampling and undersampling, we propose a new undersampling approach that: (i) avoids the pitfalls of noise and overlap caused by synthetic data and (ii) avoids the pitfall of under-fitting caused by random undersampling. Instead of undersampling majority data randomly, our method undersamples datapoints based on their ability to improve model loss. Using improved model loss as a proxy measurement for classification performance, our technique assesses a datapoint's impact on loss and rejects those unable to improve it. In so doing, our approach rejects majority datapoints redundant to datapoints already accepted and, thereby, finds an optimal subset of majority training data for classification. The accept/reject component of our algorithm is motivated by a bilevel optimization problem uniquely formulated to identify the optimal training set we seek. Experimental results show our proposed technique with F1 scores up to 10% higher than state-of-the-art methods.
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- 2024
33. DGRO: Diameter-Guided Ring Optimization for Integrated Research Infrastructure Membership
- Author
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Wu, Shixun, Raghavan, Krishnan, Di, Sheng, Chen, Zizhong, and Cappello, Franck
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Logical ring is a core component in membership protocol. However, the logic ring fails to consider the underlying physical latency, resulting in a high diameter. To address this issue, we introduce Diameter-Guided Ring Optimization (DGRO), which focuses on constructing rings with the smallest possible diameter, selecting the most effective ring configurations, and implementing these configurations in parallel. We first explore an integration of deep Q-learning and graph embedding to optimize the ring topology. We next propose a ring selection strategy that assesses the current topology's average latency against a global benchmark, facilitating integration into modern peer-to-peer protocols and substantially reducing network diameter. To further enhance scalability, we propose a parallel strategy that distributes the topology construction process into separate partitions simultaneously. Our experiment shows that: 1) DGRO efficiently constructs a network topology that achieves up to a 60% reduction in diameter compared to the best results from an extensive search over $10^5$ topologies, all within a significantly shorter computation time, 2) the ring selection of DGRO reduces the diameter of state-of-the-art methods Chord, RAPID, and Perigee by 10%-40%, 44%, and 60%. 3) the parallel construction can scale up to $32$ partitions while maintaining the same diameter compared to the centralized version.
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- 2024
34. Identity-Focused Inference and Extraction Attacks on Diffusion Models
- Author
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Vora, Jayneel, Krishnan, Aditya, Bouacida, Nader, Shankar, Prabhu RV, and Mohapatra, Prasant
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Cryptography and Security ,Computer Science - Machine Learning - Abstract
The increasing reliance on diffusion models for generating synthetic images has amplified concerns about the unauthorized use of personal data, particularly facial images, in model training. In this paper, we introduce a novel identity inference framework to hold model owners accountable for including individuals' identities in their training data. Our approach moves beyond traditional membership inference attacks by focusing on identity-level inference, providing a new perspective on data privacy violations. Through comprehensive evaluations on two facial image datasets, Labeled Faces in the Wild (LFW) and CelebA, our experiments demonstrate that the proposed membership inference attack surpasses baseline methods, achieving an attack success rate of up to 89% and an AUC-ROC of 0.91, while the identity inference attack attains 92% on LDM models trained on LFW, and the data extraction attack achieves 91.6% accuracy on DDPMs, validating the effectiveness of our approach across diffusion models., Comment: 5 figures, 3 tables,12 pages main body content
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- 2024
35. Levels of Binary Equivalence for the Comparison of Binaries from Alternative Builds
- Author
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Dietrich, Jens, White, Tim, Hassanshahi, Behnaz, and Krishnan, Paddy
- Subjects
Computer Science - Cryptography and Security ,Computer Science - Software Engineering ,D.2.13 ,D.3.4 ,F.3.2 - Abstract
In response to challenges in software supply chain security, several organisations have created infrastructures to independently build commodity open source projects and release the resulting binaries. Build platform variability can strengthen security as it facilitates the detection of compromised build environments. Furthermore, by improving the security posture of the build platform and collecting provenance information during the build, the resulting artifacts can be used with greater trust. Such offerings are now available from Google, Oracle and RedHat. The availability of multiple binaries built from the same sources creates new challenges and opportunities, and raises questions such as: 'Does build A confirm the integrity of build B?' or 'Can build A reveal a compromised build B?'. To answer such questions requires a notion of equivalence between binaries. We demonstrate that the obvious approach based on bitwise equality has significant shortcomings in practice, and that there is value in opting for alternative notions. We conceptualise this by introducing levels of equivalence, inspired by clone detection types. We demonstrate the value of these new levels through several experiments. We construct a dataset consisting of Java binaries built from the same sources independently by different providers, resulting in 14,156 pairs of binaries in total. We then compare the compiled class files in those jar files and find that for 3,750 pairs of jars (26.49%) there is at least one such file that is different, also forcing the jar files and their cryptographic hashes to be different. However, based on the new equivalence levels, we can still establish that many of them are practically equivalent. We evaluate several candidate equivalence relations on a semi-synthetic dataset that provides oracles consisting of pairs of binaries that either should be, or must not be equivalent., Comment: 20 pages, 1 figure, 10 tables
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- 2024
36. Z-upscaling: Optical Flow Guided Frame Interpolation for Isotropic Reconstruction of 3D EM Volumes
- Author
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Ferede, Fisseha A., Khalighifar, Ali, John, Jaison, Venkataraman, Krishnan, and Khairy, Khaled
- Subjects
Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
We propose a novel optical flow based approach to enhance the axial resolution of anisotropic 3D EM volumes to achieve isotropic 3D reconstruction. Assuming spatial continuity of 3D biological structures in well aligned EM volumes, we reasoned that optical flow estimation techniques, often applied for temporal resolution enhancement in videos, can be utilized. Pixel level motion is estimated between neighboring 2D slices along z, using spatial gradient flow estimates to interpolate and generate new 2D slices resulting in isotropic voxels. We leverage recent state-of-the-art learning methods for video frame interpolation and transfer learning techniques, and demonstrate the success of our approach on publicly available ultrastructure EM volumes.
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- 2024
37. On the local convergence of integer-valued Lipschitz functions on regular trees
- Author
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Butler, Nathaniel, Krishnan, Kesav, Ray, Gourab, and Spinka, Yinon
- Subjects
Mathematics - Probability ,Mathematical Physics ,Mathematics - Combinatorics ,60CXX (Primary) and 05CXX (Secondary) - Abstract
We study random integer-valued Lipschitz functions on regular trees. It was shown by Peled, Samotij and Yehudayoff that such functions are localized, however, finer questions about the structure of Gibbs measures remain unanswered. Our main result is that the weak limit of a uniformly chosen 1-Lipschitz function with 0 boundary condition on a $d$-ary tree of height $n$ exists as $n \to \infty$ if $2 \le d \le 7$, but not if $d \ge 8$, thereby partially answering a question posed by Peled, Samotij and Yehudayoff. For large $d$, the value at the root alternates between being almost entirely concentrated on 0 for even $n$ and being roughly uniform on $\{-1,0,1\}$ for odd $n$, leading to different limits as $n$ approaches infinity along evens or odds. For $d \ge 8$, the essence of this phenomenon is preserved, which obstructs the convergence. For $d \le 7$, this phenomenon ceases to exist, and the law of the value at the root loses its connection with the parity of $n$. Along the way, we also obtain an alternative proof of localization. The key idea is a fixed point convergence result for a related operator on $\ell^\infty$, and a procedure to show that the iterations get into a `basin of attraction' of the fixed point. We also prove some accompanying analogous `even-odd phenomenon' type results about $M$-lipschitz functions on general non-amenable graphs with high enough expansion (this includes for example the large $d$ case for regular trees). We also prove a convergence result for 1-Lipschitz functions with $\{0,1\}$ boundary condition. This last result relies on an absolute value FKG for uniform 1-Lipschitz functions when shifted by $1/2$., Comment: 36 pages
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- 2024
38. TRAPUM pulsar and transient search in the Sextans A and B galaxies and discovery of background FRB 20210924D
- Author
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Carli, E., Levin, L., Stappers, B. W., Barr, E. D., Breton, R. P., Buchner, S., Burgay, M., Kramer, M., Padmanabh, P. V., Possenti, A., Krishnan, V. Venkatraman, Sridhar, S. S., and Turner, J. D.
- Subjects
Astrophysics - High Energy Astrophysical Phenomena - Abstract
The Small and Large Magellanic Clouds are the only galaxies outside our own in which radio pulsars have been discovered to date. The sensitivity of the MeerKAT radio interferometer offers an opportunity to search for a population of more distant extragalactic pulsars. The TRAPUM (TRansients And PUlsars with MeerKAT) collaboration has performed a radio-domain search for pulsars and transients in the dwarf star-forming galaxies Sextans A and B, situated at the edge of the local group 1.4 Mpc away. We conducted three 2-hour multi-beam observations at L-band (856-1712 MHz) with the full array of MeerKAT. No pulsars were found down to a radio pseudo-luminosity upper limit of 7.9$\pm$0.4 Jy kpc$^{2}$ at 1400 MHz, which is 28 times more sensitive than the previous limit from the Murriyang telescope. This luminosity is 30 per cent greater than that of the brightest known radio pulsar and sets a cut-off on the luminosity distributions of the entire Sextans A and B galaxies for unobscured radio pulsars beamed in our direction. A Fast Radio Burst was detected in one of the Sextans A observations at a Dispersion Measure (DM) of 737 pc cm$^{-3}$. We believe this is a background event not associated with the dwarf galaxy due to its large DM and its S/N being strongest in the wide-field incoherent beam of MeerKAT., Comment: 11 pages, 9 figures, 5 tables. Accepted for publication in Monthly Notices of the Royal Astronomical Society
- Published
- 2024
- Full Text
- View/download PDF
39. Multi-Motor Cargo Navigation in Complex Cytoskeletal Networks
- Author
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Grieb, Mason, Krishnan, Nimisha, and Ross, Jennifer L.
- Subjects
Quantitative Biology - Biomolecules ,Condensed Matter - Soft Condensed Matter - Abstract
The kinesin superfamily of motor proteins is a major driver of anterograde transport of vesicles and organelles within eukaryotic cells via microtubules. Numerous studies have elucidated the step-size, velocities, forces, and navigation ability of kinesins both in reconstituted systems and in live cells. Outside of cells, the kinesin-based transport is physically regulated and can be controlled by obstacles or defects in the path, or the interaction between several motors on the same cargo. To explore the physical control parameters on kinesin-driven transport, we created complex microtubule networks in vitro to test how kinesin cargoes made from quantum dots with one to 10 kinesin motors attached are able to navigate the network. We find that many motors on the quantum dot significantly alter distance walked, time spent bound, the average speed, and the tortuosity of the cargo. We also find that the average mesh size of the microtubule network affects the end-to-end distance of the motion, the run time, average speed and tortuosity of cargoes. Thus, both motor number and network density are physical aspects that regulate where cargoes traverse in space and time., Comment: 7 figures in main text, 1 figure in appendix, 13 tables in appendix
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- 2024
40. Holomorphic Factorization at the Quantum Horizon
- Author
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Krishnan, Chethan and Pathak, Pradipta S.
- Subjects
High Energy Physics - Theory - Abstract
We identify a horizon-skimming limit under which wave equations around large classes of black holes allow a determination of their low-lying (quasi-)degenerate normal modes. Building on our recent work, we use these ``quantum horizon" normal modes to study the thermodynamics of the parent black holes. A key observation is that the UV inputs (the location of the UV regulator, the number of species, and the cut-off in the angular Casimir quantum number) can all be combined into the freedom in a single real parameter. Remarkably, this parameter has an interpretation as the central charge of a holomorphically factorized 2D CFT, and choosing it to be the Kerr-CFT value reproduces the black hole's detailed thermodynamics from the statistical mechanics of normal modes. This perspective provides a heuristic understanding for why the Kerr-CFT central charge is related to the angular momentum of the black hole. The black holes we consider include Kerr-Newman in 3+1 dimensions and Cvetic-Youm in 4+1 dimensions (with all six charges), and they need not be BPS or extremal. Our results show that a refined version of the 't Hooftian quantum gas can be made fully consistent with the thermodynamics of very general black holes. This ``mechanical" approach to the central charge is not directly reliant on asymptotic symmetries in the extremal limit, where the black hole is often unstable., Comment: 38 pages
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- 2024
41. ViDAS: Vision-based Danger Assessment and Scoring
- Author
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Gupta, Pranav, Krishnan, Advith, Nanda, Naman, Eswar, Ananth, Agarwal, Deeksha, Gohil, Pratham, and Goel, Pratyush
- Subjects
Computer Science - Computer Vision and Pattern Recognition - Abstract
We present a novel dataset aimed at advancing danger analysis and assessment by addressing the challenge of quantifying danger in video content and identifying how human-like a Large Language Model (LLM) evaluator is for the same. This is achieved by compiling a collection of 100 YouTube videos featuring various events. Each video is annotated by human participants who provided danger ratings on a scale from 0 (no danger to humans) to 10 (life-threatening), with precise timestamps indicating moments of heightened danger. Additionally, we leverage LLMs to independently assess the danger levels in these videos using video summaries. We introduce Mean Squared Error (MSE) scores for multimodal meta-evaluation of the alignment between human and LLM danger assessments. Our dataset not only contributes a new resource for danger assessment in video content but also demonstrates the potential of LLMs in achieving human-like evaluations., Comment: Preprint
- Published
- 2024
42. AI generated annotations for Breast, Brain, Liver, Lungs and Prostate cancer collections in National Cancer Institute Imaging Data Commons
- Author
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Murugesan, Gowtham Krishnan, McCrumb, Diana, Soni, Rahul, Kumar, Jithendra, Nuernberg, Leonard, Pei, Linmin, Wagner, Ulrike, Granger, Sutton, Fedorov, Andrey Y., Moore, Stephen, and Van Oss, Jeff
- Subjects
Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
AI in Medical Imaging project aims to enhance the National Cancer Institute's (NCI) Image Data Commons (IDC) by developing nnU-Net models and providing AI-assisted segmentations for cancer radiology images. We created high-quality, AI-annotated imaging datasets for 11 IDC collections. These datasets include images from various modalities, such as computed tomography (CT) and magnetic resonance imaging (MRI), covering the lungs, breast, brain, kidneys, prostate, and liver. The nnU-Net models were trained using open-source datasets. A portion of the AI-generated annotations was reviewed and corrected by radiologists. Both the AI and radiologist annotations were encoded in compliance with the the Digital Imaging and Communications in Medicine (DICOM) standard, ensuring seamless integration into the IDC collections. All models, images, and annotations are publicly accessible, facilitating further research and development in cancer imaging. This work supports the advancement of imaging tools and algorithms by providing comprehensive and accurate annotated datasets.
- Published
- 2024
43. Delving Deep into Engagement Prediction of Short Videos
- Author
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Li, Dasong, Li, Wenjie, Lu, Baili, Li, Hongsheng, Ma, Sizhuo, Krishnan, Gurunandan, and Wang, Jian
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Multimedia ,Computer Science - Social and Information Networks - Abstract
Understanding and modeling the popularity of User Generated Content (UGC) short videos on social media platforms presents a critical challenge with broad implications for content creators and recommendation systems. This study delves deep into the intricacies of predicting engagement for newly published videos with limited user interactions. Surprisingly, our findings reveal that Mean Opinion Scores from previous video quality assessment datasets do not strongly correlate with video engagement levels. To address this, we introduce a substantial dataset comprising 90,000 real-world UGC short videos from Snapchat. Rather than relying on view count, average watch time, or rate of likes, we propose two metrics: normalized average watch percentage (NAWP) and engagement continuation rate (ECR) to describe the engagement levels of short videos. Comprehensive multi-modal features, including visual content, background music, and text data, are investigated to enhance engagement prediction. With the proposed dataset and two key metrics, our method demonstrates its ability to predict engagements of short videos purely from video content., Comment: Accepted to ECCV 2024. Project page: https://github.com/dasongli1/SnapUGC_Engagement
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- 2024
44. Collisional Dynamics of Solitons and Pattern Formation in an Integrable Cross Coupled Nonlinear Schrodinger equation with constant background
- Author
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Vinayagam, P. S., Krishnan, D. Aravindha, Kamaleshwaran, R. V., and Radha, R.
- Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems ,Nonlinear Sciences - Pattern Formation and Solitons ,37K40, 35Q51, 35Q55 - Abstract
We investigate the dynamics arising out of the propagation of light pulses with different polarizations through a condensate (referred to as a constant background field) with cross coupling described by a coupled nonlinear Schrodinger equation(NLSE) type equation. We then employ Gauge and Darboux transformation approach to bring out the rich dynamics arising out of the background field and cross coupling. The collisional dynamics of bright solitons is found to be inelastic. The constant background field is found to facilitate the periodic localization of light pulses during propagation. We have also unearthed breathers, bright-bright, bright-dark and dark-bright solitons of the coupled NLSE. While the amplitude of breathers oscillate with time as predicted, their maximum(or minimum) amplitude is found to remain a constant and the addition of cross coupling only contributes to the rapid fluctuations in its amplitude over a period of time. In addition, the reinforcement of cross coupling in the presence of constant wave field facilitates the interference of light pulses leading to interesting pattern formation among bright-bright, bright-dark and dark-bright solitons. The highlight of the results is that one obtains various localized excitations like breathers, bright and dark solitons by simply manipulating the amplitude of the constant wave field., Comment: 14 pages, 6 figures, Accepted for Publication in Romanian Reports in Physics (2024)
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- 2024
45. On the Inductive Bias of Stacking Towards Improving Reasoning
- Author
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Saunshi, Nikunj, Karp, Stefani, Krishnan, Shankar, Miryoosefi, Sobhan, Reddi, Sashank J., and Kumar, Sanjiv
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Given the increasing scale of model sizes, novel training strategies like gradual stacking [Gong et al., 2019, Reddi et al., 2023] have garnered interest. Stacking enables efficient training by gradually growing the depth of a model in stages and using layers from a smaller model in an earlier stage to initialize the next stage. Although efficient for training, the model biases induced by such growing approaches are largely unexplored. In this work, we examine this fundamental aspect of gradual stacking, going beyond its efficiency benefits. We propose a variant of gradual stacking called MIDAS that can speed up language model training by up to 40%. Furthermore we discover an intriguing phenomenon: MIDAS is not only training-efficient but surprisingly also has an inductive bias towards improving downstream tasks, especially tasks that require reasoning abilities like reading comprehension and math problems, despite having similar or slightly worse perplexity compared to baseline training. To further analyze this inductive bias, we construct reasoning primitives -- simple synthetic tasks that are building blocks for reasoning -- and find that a model pretrained with stacking is significantly better than standard pretraining on these primitives, with and without fine-tuning. This provides stronger and more robust evidence for this inductive bias towards reasoning. These findings of training efficiency and inductive bias towards reasoning are verified at 1B, 2B and 8B parameter language models. Finally, we conjecture the underlying reason for this inductive bias by exploring the connection of stacking to looped models and provide strong supporting empirical analysis., Comment: Accepted at NeurIPS 2024
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- 2024
46. Sensitivity of quantitative diffusion MRI tractography and microstructure to anisotropic spatial sampling
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McMaster, Elyssa M., Newlin, Nancy R., Cho, Chloe, Rudravaram, Gaurav, Saunders, Adam M., Krishnan, Aravind R., Remedios, Lucas W., Kim, Michael E., Xu, Hanliang, Schilling, Kurt G., Rheault, François, Cutting, Laurie E., and Landman, Bennett A.
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Electrical Engineering and Systems Science - Signal Processing - Abstract
Purpose: Diffusion weighted MRI (dMRI) and its models of neural structure provide insight into human brain organization and variations in white matter. A recent study by McMaster, et al. showed that complex graph measures of the connectome, the graphical representation of a tractogram, vary with spatial sampling changes, but biases introduced by anisotropic voxels in the process have not been well characterized. This study uses microstructural measures (fractional anisotropy and mean diffusivity) and white matter bundle properties (bundle volume, length, and surface area) to further understand the effect of anisotropic voxels on microstructure and tractography. Methods: The statistical significance of the selected measures derived from dMRI data were assessed by comparing three white matter bundles at different spatial resolutions with 44 subjects from the Human Connectome Project Young Adult dataset scan/rescan data using the Wilcoxon Signed Rank test. The original isotropic resolution (1.25 mm isotropic) was explored with six anisotropic resolutions with 0.25 mm incremental steps in the z dimension. Then, all generated resolutions were upsampled to 1.25 mm isotropic and 1 mm isotropic. Results: There were statistically significant differences between at least one microstructural and one bundle measure at every resolution (p less than or equal to 0.05, corrected for multiple comparisons). Cohen's d coefficient evaluated the effect size of anisotropic voxels on microstructure and tractography. Conclusion: Fractional anisotropy and mean diffusivity cannot be recovered with basic up sampling from low quality data with gold standard data. However, the bundle measures from tractogram become more repeatable when voxels are resampled to 1 mm isotropic.
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- 2024
47. Spin-Dependent Signatures of Majorana Vortex Fusion within Planar Josephson Junctions
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Ganesh, Krishnan, Lee, Derek K. K., and Pachos, Jiannis K.
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Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Superconductivity - Abstract
We investigate the magnetic characteristics and tunnelling signatures of a planar Josephson junction with Rashba spin-orbit coupling during the fusion of two Majorana vortices. By employing the topological phase diagram and conducting tight-binding simulations of the proposed device, we demonstrate that this fusion process induces a parity-dependent magnetic moment aligned with the junction axis. We further propose a method to probe the spin properties of the fusing Majorana zero modes through spin-resolved Andreev conductance measurements at the junction endpoints. To support our findings, we derive a low-energy effective Hamiltonian that provides a detailed microscopic description of the numerically observed phenomena. Our analysis enables the detection of Majorana fusion outcome from accessible spin current measurements, thus paving the way for future experimental verification and potential applications in topological quantum computation.
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- 2024
48. DiaSynth: Synthetic Dialogue Generation Framework for Low Resource Dialogue Applications
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Suresh, Sathya Krishnan, Mengjun, Wu, Pranav, Tushar, and Chng, Eng Siong
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Computer Science - Computation and Language ,Computer Science - Machine Learning - Abstract
The scarcity of domain-specific dialogue datasets limits the development of dialogue systems across applications. Existing research is constrained by general or niche datasets that lack sufficient scale for training dialogue systems. To address this gap, we introduce DiaSynth - a synthetic dialogue generation framework capable of generating high-quality, contextually rich dialogues across a wide range of domains. Unlike existing frameworks, DiaSynth uses Large Language Models (LLMs) and Chain of Thought (CoT) reasoning to generate dynamic, domain-specific dialogues with simulated personas and diverse conversational features. We perform our experiments by generating synthetic data using different LLMs and few-shot examples from DialogSum and SAMSum. The pretrained language models fine-tuned on the synthetic data outperform the base models by 16.47% on dialogue summarization, while the comparison between models fine-tuned on in-domain data and synthetic data shows that the synthetic data is able to capture 90.48% of the performance distribution of the in-domain data on dialogue summarization. The quality of the data generated also increases as we increase the size of LLM from 3B to 8B. These results validate DiaSynth's potential as a robust alternative to traditional data collection methods. We open source the code and data generated for future research., Comment: 13 pages, 1 figure
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- 2024
49. Predictive Covert Communication Against Multi-UAV Surveillance Using Graph Koopman Autoencoder
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Krishnan, Sivaram, Park, Jihong, Sherman, Gregory, Campbell, Benjamin, and Choi, Jinho
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Computer Science - Machine Learning ,Computer Science - Networking and Internet Architecture ,Electrical Engineering and Systems Science - Signal Processing - Abstract
Low Probability of Detection (LPD) communication aims to obscure the presence of radio frequency (RF) signals to evade surveillance. In the context of mobile surveillance utilizing unmanned aerial vehicles (UAVs), achieving LPD communication presents significant challenges due to the UAVs' rapid and continuous movements, which are characterized by unknown nonlinear dynamics. Therefore, accurately predicting future locations of UAVs is essential for enabling real-time LPD communication. In this paper, we introduce a novel framework termed predictive covert communication, aimed at minimizing detectability in terrestrial ad-hoc networks under multi-UAV surveillance. Our data-driven method synergistically integrates graph neural networks (GNN) with Koopman theory to model the complex interactions within a multi-UAV network and facilitating long-term predictions by linearizing the dynamics, even with limited historical data. Extensive simulation results substantiate that the predicted trajectories using our method result in at least 63%-75% lower probability of detection when compared to well-known state-of-the-art baseline approaches, showing promise in enabling low-latency covert operations in practical scenarios.
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- 2024
50. A novel open-source ultrasound dataset with deep learning benchmarks for spinal cord injury localization and anatomical segmentation
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Kumar, Avisha, Kotkar, Kunal, Jiang, Kelly, Bhimreddy, Meghana, Davidar, Daniel, Weber-Levine, Carly, Krishnan, Siddharth, Kerensky, Max J., Liang, Ruixing, Leadingham, Kelley Kempski, Routkevitch, Denis, Hersh, Andrew M., Ashayeri, Kimberly, Tyler, Betty, Suk, Ian, Son, Jennifer, Theodore, Nicholas, Thakor, Nitish, and Manbachi, Amir
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
While deep learning has catalyzed breakthroughs across numerous domains, its broader adoption in clinical settings is inhibited by the costly and time-intensive nature of data acquisition and annotation. To further facilitate medical machine learning, we present an ultrasound dataset of 10,223 Brightness-mode (B-mode) images consisting of sagittal slices of porcine spinal cords (N=25) before and after a contusion injury. We additionally benchmark the performance metrics of several state-of-the-art object detection algorithms to localize the site of injury and semantic segmentation models to label the anatomy for comparison and creation of task-specific architectures. Finally, we evaluate the zero-shot generalization capabilities of the segmentation models on human ultrasound spinal cord images to determine whether training on our porcine dataset is sufficient for accurately interpreting human data. Our results show that the YOLOv8 detection model outperforms all evaluated models for injury localization, achieving a mean Average Precision (mAP50-95) score of 0.606. Segmentation metrics indicate that the DeepLabv3 segmentation model achieves the highest accuracy on unseen porcine anatomy, with a Mean Dice score of 0.587, while SAMed achieves the highest Mean Dice score generalizing to human anatomy (0.445). To the best of our knowledge, this is the largest annotated dataset of spinal cord ultrasound images made publicly available to researchers and medical professionals, as well as the first public report of object detection and segmentation architectures to assess anatomical markers in the spinal cord for methodology development and clinical applications.
- Published
- 2024
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