1,596 results on '"JAIN, MOHIT"'
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2. Genetic divergence studies of fodder yield and quality attributing characteristics in promising maize (Zea mays L.) composites
- Author
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Singh, Devinder Pal, Jain, Mohit, Goyal, Meenakshi, and Sandhu, Surinder
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- 2023
- Full Text
- View/download PDF
3. Phase-Informed Tool Segmentation for Manual Small-Incision Cataract Surgery
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Sachdeva, Bhuvan, Akash, Naren, Ashraf, Tajamul, Muller, Simon, Schultz, Thomas, Wintergerst, Maximilian W. M., Prasad, Niharika Singri, Murali, Kaushik, and Jain, Mohit
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Cataract surgery is the most common surgical procedure globally, with a disproportionately higher burden in developing countries. While automated surgical video analysis has been explored in general surgery, its application to ophthalmic procedures remains limited. Existing works primarily focus on Phaco cataract surgery, an expensive technique not accessible in regions where cataract treatment is most needed. In contrast, Manual Small-Incision Cataract Surgery (MSICS) is the preferred low-cost, faster alternative in high-volume settings and for challenging cases. However, no dataset exists for MSICS. To address this gap, we introduce Cataract-MSICS, the first comprehensive dataset containing 53 surgical videos annotated for 18 surgical phases and 3,527 frames with 13 surgical tools at the pixel level. We benchmark this dataset on state-of-the-art models and present ToolSeg, a novel framework that enhances tool segmentation by introducing a phase-conditional decoder and a simple yet effective semi-supervised setup leveraging pseudo-labels from foundation models. Our approach significantly improves segmentation performance, achieving a $23.77\%$ to $38.10\%$ increase in mean Dice scores, with a notable boost for tools that are less prevalent and small. Furthermore, we demonstrate that ToolSeg generalizes to other surgical settings, showcasing its effectiveness on the CaDIS dataset.
- Published
- 2024
4. HEALTH-PARIKSHA: Assessing RAG Models for Health Chatbots in Real-World Multilingual Settings
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Gumma, Varun, Raghunath, Anandhita, Jain, Mohit, and Sitaram, Sunayana
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Computer Science - Computation and Language - Abstract
Assessing the capabilities and limitations of large language models (LLMs) has garnered significant interest, yet the evaluation of multiple models in real-world scenarios remains rare. Multilingual evaluation often relies on translated benchmarks, which typically do not capture linguistic and cultural nuances present in the source language. This study provides an extensive assessment of 24 LLMs on real world data collected from Indian patients interacting with a medical chatbot in Indian English and 4 other Indic languages. We employ a uniform Retrieval Augmented Generation framework to generate responses, which are evaluated using both automated techniques and human evaluators on four specific metrics relevant to our application. We find that models vary significantly in their performance and that instruction tuned Indic models do not always perform well on Indic language queries. Further, we empirically show that factual correctness is generally lower for responses to Indic queries compared to English queries. Finally, our qualitative work shows that code-mixed and culturally relevant queries in our dataset pose challenges to evaluated models., Comment: Under Review
- Published
- 2024
5. Global 13C tracing and metabolic flux analysis of intact human liver tissue ex vivo.
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Grankvist, Nina, Jönsson, Cecilia, Hedin, Karin, Sundqvist, Nicolas, Sandström, Per, Björnsson, Bergthor, Begzati, Arjana, Mickols, Evgeniya, Artursson, Per, Jain, Mohit, Cedersund, Gunnar, and Nilsson, Roland
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Humans ,Liver ,Carbon Isotopes ,Metabolic Flux Analysis ,Glucose ,Male ,Metabolic Networks and Pathways ,Mass Spectrometry - Abstract
Liver metabolism is central to human physiology and influences the pathogenesis of common metabolic diseases. Yet, our understanding of human liver metabolism remains incomplete, with much of current knowledge based on animal or cell culture models that do not fully recapitulate human physiology. Here, we perform in-depth measurement of metabolism in intact human liver tissue ex vivo using global 13C tracing, non-targeted mass spectrometry and model-based metabolic flux analysis. Isotope tracing allowed qualitative assessment of a wide range of metabolic pathways within a single experiment, confirming well-known features of liver metabolism but also revealing unexpected metabolic activities such as de novo creatine synthesis and branched-chain amino acid transamination, where human liver appears to differ from rodent models. Glucose production ex vivo correlated with donor plasma glucose, suggesting that cultured liver tissue retains individual metabolic phenotypes, and could be suppressed by postprandial levels of nutrients and insulin, and also by pharmacological inhibition of glycogen utilization. Isotope tracing ex vivo allows measuring human liver metabolism with great depth and resolution in an experimentally tractable system.
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- 2024
6. ASHABot: An LLM-Powered Chatbot to Support the Informational Needs of Community Health Workers
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Ramjee, Pragnya, Chhokar, Mehak, Sachdeva, Bhuvan, Meena, Mahendra, Abdullah, Hamid, Vashistha, Aditya, Nagar, Ruchit, and Jain, Mohit
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Computer Science - Human-Computer Interaction - Abstract
Community health workers (CHWs) provide last-mile healthcare services but face challenges due to limited medical knowledge and training. This paper describes the design, deployment, and evaluation of ASHABot, an LLM-powered, experts-in-the-loop, WhatsApp-based chatbot to address the information needs of CHWs in India. Through interviews with CHWs and their supervisors and log analysis, we examine factors affecting their engagement with ASHABot, and ASHABot's role in addressing CHWs' informational needs. We found that ASHABot provided a private channel for CHWs to ask rudimentary and sensitive questions they hesitated to ask supervisors. CHWs trusted the information they received on ASHABot and treated it as an authoritative resource. CHWs' supervisors expanded their knowledge by contributing answers to questions ASHABot failed to answer, but were concerned about demands on their workload and increased accountability. We emphasize positioning LLMs as supplemental fallible resources within the community healthcare ecosystem, instead of as replacements for supervisor support.
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- 2024
7. Learnings from a Large-Scale Deployment of an LLM-Powered Expert-in-the-Loop Healthcare Chatbot
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Sachdeva, Bhuvan, Ramjee, Pragnya, Fulari, Geeta, Murali, Kaushik, and Jain, Mohit
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Computer Science - Human-Computer Interaction - Abstract
Large Language Models (LLMs) are widely used in healthcare, but limitations like hallucinations, incomplete information, and bias hinder their reliability. To address these, researchers released the Build Your Own expert Bot (BYOeB) platform, enabling developers to create LLM-powered chatbots with integrated expert verification. CataractBot, its first implementation, provides expert-verified responses to cataract surgery questions. A pilot evaluation showed its potential; however the study had a small sample size and was primarily qualitative. In this work, we conducted a large-scale 24-week deployment of CataractBot involving 318 patients and attendants who sent 1,992 messages, with 91.71% of responses verified by seven experts. Analysis of interaction logs revealed that medical questions significantly outnumbered logistical ones, hallucinations were negligible, and experts rated 84.52% of medical answers as accurate. As the knowledge base expanded with expert corrections, system performance improved by 19.02%, reducing expert workload. These insights guide the design of future LLM-powered chatbots., Comment: The first two authors contributed equally to this research
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- 2024
8. A Deadline-Aware Scheduler for Smart Factory using WiFi 6
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Jain, Mohit, Mishra, Anis, Das, Syamantak, Wiese, Andreas, Bhattacharya, Arani, and Maity, Mukulika
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Computer Science - Networking and Internet Architecture - Abstract
A key strategy for making production in factories more efficient is to collect data about the functioning of machines, and dynamically adapt their working. Such smart factories have data packets with a mix of stringent and non-stringent deadlines with varying levels of importance that need to be delivered via a wireless network. However, the scheduling of packets in the wireless network is crucial to satisfy the deadlines. In this work, we propose a technique of utilizing IEEE 802.11ax, popularly known as WiFi 6, for such applications. IEEE 802.11ax has a few unique characteristics, such as specific configurations of dividing the channels into resource units (RU) for packet transmission and synchronized parallel transmissions. We model the problem of scheduling packets by assigning profit to each packet and then maximizing the sum of profits. We first show that this problem is strongly NP-Hard, and then propose an approximation algorithm with a 12-approximate algorithm. Our approximation algorithm uses a variant of local search to associate the right RU configuration to each packet and identify the duration of each parallel transmission. Finally, we extensively simulate different scenarios to show that our algorithm works better than other benchmarks.
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- 2024
9. CataractBot: An LLM-Powered Expert-in-the-Loop Chatbot for Cataract Patients
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Ramjee, Pragnya, Sachdeva, Bhuvan, Golechha, Satvik, Kulkarni, Shreyas, Fulari, Geeta, Murali, Kaushik, and Jain, Mohit
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Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
The healthcare landscape is evolving, with patients seeking reliable information about their health conditions and available treatment options. Despite the abundance of information sources, the digital age overwhelms individuals with excess, often inaccurate information. Patients primarily trust medical professionals, highlighting the need for expert-endorsed health information. However, increased patient loads on experts has led to reduced communication time, impacting information sharing. To address this gap, we developed CataractBot, an experts-in-the-loop chatbot powered by LLMs, in collaboration with an eye hospital in India. CataractBot answers cataract surgery related questions instantly by querying a curated knowledge base and provides expert-verified responses asynchronously. It has multimodal and multilingual capabilities. In an in-the-wild deployment study with 55 participants, CataractBot proved valuable, providing anytime accessibility, saving time, accommodating diverse literacy levels, alleviating power differences, and adding a privacy layer between patients and doctors. Users reported that their trust in the system was established through expert verification. Broadly, our results could inform future work on designing expert-mediated LLM bots.
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- 2024
10. Greengenes2 unifies microbial data in a single reference tree
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McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T, Nicolaou, Giorgia, Parks, Donovan H, Karst, Søren M, Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S, Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash, and Knight, Rob
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,RNA ,Ribosomal ,16S ,Phylogeny ,Metagenomics ,Bacteria ,Databases ,Genetic ,Metagenome - Abstract
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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- 2024
11. Effect of Anthropometrical Measurements on Liver Span Using Ultrasonography
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Singla, Bhavna, Singh, Tajinder, Jain, Mohit, Savani, Sejal, and Oli, Sharad
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- 2017
12. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation.
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Padmanabhan, Arun, de Soysa, T, Pelonero, Angelo, Sapp, Valerie, Shah, Parisha, Wang, Qiaohong, Li, Li, Lee, Clara, Sadagopan, Nandhini, Nishino, Tomohiro, Ye, Lin, Yang, Rachel, Karnay, Ashley, Poleshko, Andrey, Bolar, Nikhita, Linares-Saldana, Ricardo, Ranade, Sanjeev, Alexanian, Michael, Morton, Sarah, Jain, Mohit, Haldar, Saptarsi, Srivastava, Deepak, and Jain, Rajan
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Myocytes ,Cardiac ,Transcription Factors ,Animals ,Cell Differentiation ,Induced Pluripotent Stem Cells ,Humans ,CRISPR-Cas Systems ,Cell Cycle Proteins ,Mice ,Mouse Embryonic Stem Cells ,Nuclear Proteins ,Gene Expression Regulation ,Developmental ,Cell Lineage ,Cells ,Cultured ,Single-Cell Analysis ,Bromodomain Containing Proteins - Abstract
Human induced pluripotent stem cell (hiPSC) to cardiomyocyte (CM) differentiation has reshaped approaches to studying cardiac development and disease. In this study, we employed a genome-wide CRISPR screen in a hiPSC to CM differentiation system and reveal here that BRD4, a member of the bromodomain and extraterminal (BET) family, regulates CM differentiation. Chemical inhibition of BET proteins in mouse embryonic stem cell (mESC)-derived or hiPSC-derived cardiac progenitor cells (CPCs) results in decreased CM differentiation and persistence of cells expressing progenitor markers. In vivo, BRD4 deletion in second heart field (SHF) CPCs results in embryonic or early postnatal lethality, with mutants demonstrating myocardial hypoplasia and an increase in CPCs. Single-cell transcriptomics identified a subpopulation of SHF CPCs that is sensitive to BRD4 loss and associated with attenuated CM lineage-specific gene programs. These results highlight a previously unrecognized role for BRD4 in CM fate determination during development and a heterogenous requirement for BRD4 among SHF CPCs.
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- 2024
13. Functional EPAS1/HIF2A missense variant is associated with hematocrit in Andean highlanders
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Lawrence, Elijah S, Gu, Wanjun, Bohlender, Ryan J, Anza-Ramirez, Cecilia, Cole, Amy M, Yu, James J, Hu, Hao, Heinrich, Erica C, O’Brien, Katie A, Vasquez, Carlos A, Cowan, Quinn T, Bruck, Patrick T, Mercader, Kysha, Alotaibi, Mona, Long, Tao, Hall, James E, Moya, Esteban A, Bauk, Marco A, Reeves, Jennifer J, Kong, Mitchell C, Salem, Rany M, Vizcardo-Galindo, Gustavo, Macarlupu, Jose-Luis, Figueroa-Mujíca, Rómulo, Bermudez, Daniela, Corante, Noemi, Gaio, Eduardo, Fox, Keolu P, Salomaa, Veikko, Havulinna, Aki S, Murray, Andrew J, Malhotra, Atul, Powel, Frank L, Jain, Mohit, Komor, Alexis C, Cavalleri, Gianpiero L, Huff, Chad D, Villafuerte, Francisco C, and Simonson, Tatum S
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Biological Sciences ,Genetics ,Clinical Research ,2.1 Biological and endogenous factors ,Aetiology ,Humans ,Adaptation ,Physiological ,Altitude ,East Asian People ,Hematocrit ,Hypoxia ,Mutation ,Missense ,South American People - Abstract
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.
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- 2024
14. Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort.
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Koponen, Kari, Kambur, Oleg, Joseph, Bijoy, Ruuskanen, Matti, Jousilahti, Pekka, Salido, Rodolfo, Brennan, Caitriona, Jain, Mohit, Meric, Guillaume, Inouye, Michael, Lahti, Leo, Niiranen, Teemu, Havulinna, Aki, Knight, Rob, and Salomaa, Veikko
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diabetes mellitus ,type 2 ,metagenome ,microbiota ,prospective studies ,statins ,Humans ,Hydroxymethylglutaryl-CoA Reductase Inhibitors ,Gastrointestinal Microbiome ,Cross-Sectional Studies ,Diabetes Mellitus ,Type 2 ,Dyslipidemias - Abstract
BACKGROUND: Dyslipidemia is treated effectively with statins, but treatment has the potential to induce new-onset type-2 diabetes. Gut microbiota may contribute to this outcome variability. We assessed the associations of gut microbiota diversity and composition with statins. Bacterial associations with statin-associated new-onset type-2 diabetes (T2D) risk were also prospectively evaluated. METHODS: We examined shallow-shotgun-sequenced fecal samples from 5755 individuals in the FINRISK-2002 population cohort with a 17+-year-long register-based follow-up. Alpha-diversity was quantified using Shannon index and beta-diversity with Aitchison distance. Species-specific differential abundances were analyzed using general multivariate regression. Prospective associations were assessed with Cox regression. Applicable results were validated using gradient boosting. RESULTS: Statin use associated with differing taxonomic composition (R2, 0.02%; q=0.02) and 13 differentially abundant species in fully adjusted models (MaAsLin; q
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- 2024
15. Evolutional development & design of an adjustable single gear tooth testing procedure for polymer gearing
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Jain, Mohit, Salim, Samarth, Patil, Santosh, and Chowdhury, Shambo Roy
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- 2024
- Full Text
- View/download PDF
16. Examining the challenges of blood pressure estimation via photoplethysmogram
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Mehta, Suril, Kwatra, Nipun, Jain, Mohit, and McDuff, Daniel
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- 2024
- Full Text
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17. PwR: Exploring the Role of Representations in Conversational Programming
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YM, Pradyumna, Ganesan, Vinod, Arumugam, Dinesh Kumar, Gupta, Meghna, Shadagopan, Nischith, Dixit, Tanay, Segal, Sameer, Kumar, Pratyush, Jain, Mohit, and Rajamani, Sriram
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Computer Science - Human-Computer Interaction ,Computer Science - Software Engineering ,H.5.2 - Abstract
Large Language Models (LLMs) have revolutionized programming and software engineering. AI programming assistants such as GitHub Copilot X enable conversational programming, narrowing the gap between human intent and code generation. However, prior literature has identified a key challenge--there is a gap between user's mental model of the system's understanding after a sequence of natural language utterances, and the AI system's actual understanding. To address this, we introduce Programming with Representations (PwR), an approach that uses representations to convey the system's understanding back to the user in natural language. We conducted an in-lab task-centered study with 14 users of varying programming proficiency and found that representations significantly improve understandability, and instilled a sense of agency among our participants. Expert programmers use them for verification, while intermediate programmers benefit from confirmation. Natural language-based development with LLMs, coupled with representations, promises to transform software development, making it more accessible and efficient., Comment: 23 pages, 3 figures, 2 tables, under submission for ACM CHI 2024
- Published
- 2023
18. The Art of Embedding Fusion: Optimizing Hate Speech Detection
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Khan, Mohammad Aflah, Yadav, Neemesh, Jain, Mohit, and Goyal, Sanyam
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Computer Science - Computation and Language ,Computer Science - Machine Learning - Abstract
Hate speech detection is a challenging natural language processing task that requires capturing linguistic and contextual nuances. Pre-trained language models (PLMs) offer rich semantic representations of text that can improve this task. However there is still limited knowledge about ways to effectively combine representations across PLMs and leverage their complementary strengths. In this work, we shed light on various combination techniques for several PLMs and comprehensively analyze their effectiveness. Our findings show that combining embeddings leads to slight improvements but at a high computational cost and the choice of combination has marginal effect on the final outcome. We also make our codebase public at https://github.com/aflah02/The-Art-of-Embedding-Fusion-Optimizing-Hate-Speech-Detection ., Comment: Published as a Tiny Paper at ICLR 2023, 12 Pages
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- 2023
19. 'Can't Take the Pressure?': Examining the Challenges of Blood Pressure Estimation via Pulse Wave Analysis
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Mehta, Suril, Kwatra, Nipun, Jain, Mohit, and McDuff, Daniel
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Electrical Engineering and Systems Science - Signal Processing ,Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
The use of observed wearable sensor data (e.g., photoplethysmograms [PPG]) to infer health measures (e.g., glucose level or blood pressure) is a very active area of research. Such technology can have a significant impact on health screening, chronic disease management and remote monitoring. A common approach is to collect sensor data and corresponding labels from a clinical grade device (e.g., blood pressure cuff), and train deep learning models to map one to the other. Although well intentioned, this approach often ignores a principled analysis of whether the input sensor data has enough information to predict the desired metric. We analyze the task of predicting blood pressure from PPG pulse wave analysis. Our review of the prior work reveals that many papers fall prey data leakage, and unrealistic constraints on the task and the preprocessing steps. We propose a set of tools to help determine if the input signal in question (e.g., PPG) is indeed a good predictor of the desired label (e.g., blood pressure). Using our proposed tools, we have found that blood pressure prediction using PPG has a high multi-valued mapping factor of 33.2% and low mutual information of 9.8%. In comparison, heart rate prediction using PPG, a well-established task, has a very low multi-valued mapping factor of 0.75% and high mutual information of 87.7%. We argue that these results provide a more realistic representation of the current progress towards to goal of wearable blood pressure measurement via PPG pulse wave analysis.
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- 2023
20. Metabolic programs of T cell tissue residency empower tumour immunity.
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Reina-Campos, Miguel, Heeg, Maximilian, Kennewick, Kelly, Mathews, Ian, Galletti, Giovanni, Luna, Vida, Nguyen, Quynhanh, Huang, Hongling, Milner, J, Hu, Kenneth, Vichaidit, Amy, Santillano, Natalie, Boland, Brigid, Chang, John, Jain, Mohit, Sharma, Sonia, Krummel, Matthew, Chi, Hongbo, Bensinger, Steven, and Goldrath, Ananda
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Animals ,Humans ,Mice ,CD8-Positive T-Lymphocytes ,Cell Respiration ,Cholesterol ,Immunologic Memory ,Intestine ,Small ,Lymphocytes ,Tumor-Infiltrating ,Metabolomics ,Mevalonic Acid ,Neoplasms ,Ubiquinone ,Virus Diseases ,Viruses ,Mitochondria - Abstract
Tissue resident memory CD8+ T (TRM) cells offer rapid and long-term protection at sites of reinfection1. Tumour-infiltrating lymphocytes with characteristics of TRM cells maintain enhanced effector functions, predict responses to immunotherapy and accompany better prognoses2,3. Thus, an improved understanding of the metabolic strategies that enable tissue residency by T cells could inform new approaches to empower immune responses in tissues and solid tumours. Here, to systematically define the basis for the metabolic reprogramming supporting TRM cell differentiation, survival and function, we leveraged in vivo functional genomics, untargeted metabolomics and transcriptomics of virus-specific memory CD8+ T cell populations. We found that memory CD8+ T cells deployed a range of adaptations to tissue residency, including reliance on non-steroidal products of the mevalonate-cholesterol pathway, such as coenzyme Q, driven by increased activity of the transcription factor SREBP2. This metabolic adaptation was most pronounced in the small intestine, where TRM cells interface with dietary cholesterol and maintain a heightened state of activation4, and was shared by functional tumour-infiltrating lymphocytes in diverse tumour types in mice and humans. Enforcing synthesis of coenzyme Q through deletion of Fdft1 or overexpression of PDSS2 promoted mitochondrial respiration, memory T cell formation following viral infection and enhanced antitumour immunity. In sum, through a systematic exploration of TRM cell metabolism, we reveal how these programs can be leveraged to fuel memory CD8+ T cell formation in the context of acute infections and enhance antitumour immunity.
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- 2023
21. Understanding Journalists' Workflows in News Curation
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Atreja, Shubham, Srinath, Shruthi, Jain, Mohit, and Pal, Joyojeet
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Computer Science - Computers and Society ,Computer Science - Human-Computer Interaction - Abstract
With the increasing dominance of the internet as a source of news consumption, there has been a rise in the production and popularity of email newsletters compiled by individual journalists. However, there is little research on the processes of aggregation, and how these differ between expert journalists and trained machines. In this paper, we interviewed journalists who curate newsletters from around the world. Through an in-depth understanding of journalists' workflows, our findings lay out the role of their prior experience in the value they bring into the curation process, their use of algorithms in finding stories for their newsletter, and their internalization of their readers' interests and the context they are curating for. While identifying the role of human expertise, we highlight the importance of hybrid curation and provide design insights on how technology can support the work of these experts., Comment: accepted at CHI'23
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- 2023
- Full Text
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22. Assessment of Factors Affecting Productivity of Pilot Tube Micro-tunneling Operation Through Case Study
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Jain, Mohit, Reja, Varun Kumar, Varghese, Koshy, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Kashyap, Anil, editor, Raghavan, N., editor, Singh, Indrasen, editor, Renganaidu, Venkatesan, editor, and Chandramohan, Arun, editor
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- 2024
- Full Text
- View/download PDF
23. Visual Reinforcement Learning With Self-Supervised 3D Representations
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Ze, Yanjie, Hansen, Nicklas, Chen, Yinbo, Jain, Mohit, and Wang, Xiaolong
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Basic Behavioral and Social Science ,Behavioral and Social Science ,Three-dimensional displays ,Task analysis ,Visualization ,Cameras ,Representation learning ,Training ,Robot vision systems ,Reinforcement learning ,representation learning ,deep learning for visual perception ,Mechanical Engineering - Published
- 2023
24. Visual Reinforcement Learning with Self-Supervised 3D Representations
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Ze, Yanjie, Hansen, Nicklas, Chen, Yinbo, Jain, Mohit, and Wang, Xiaolong
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Computer Science - Machine Learning ,Computer Science - Robotics - Abstract
A prominent approach to visual Reinforcement Learning (RL) is to learn an internal state representation using self-supervised methods, which has the potential benefit of improved sample-efficiency and generalization through additional learning signal and inductive biases. However, while the real world is inherently 3D, prior efforts have largely been focused on leveraging 2D computer vision techniques as auxiliary self-supervision. In this work, we present a unified framework for self-supervised learning of 3D representations for motor control. Our proposed framework consists of two phases: a pretraining phase where a deep voxel-based 3D autoencoder is pretrained on a large object-centric dataset, and a finetuning phase where the representation is jointly finetuned together with RL on in-domain data. We empirically show that our method enjoys improved sample efficiency in simulated manipulation tasks compared to 2D representation learning methods. Additionally, our learned policies transfer zero-shot to a real robot setup with only approximate geometric correspondence, and successfully solve motor control tasks that involve grasping and lifting from a single, uncalibrated RGB camera. Code and videos are available at https://yanjieze.com/3d4rl/ ., Comment: Accepted in RA-L 2023 and IROS 2023. Project page: https://yanjieze.com/3d4rl/
- Published
- 2022
25. Towards Automating Retinoscopy for Refractive Error Diagnosis
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Aggarwal, Aditya, Gairola, Siddhartha, Upadhyay, Uddeshya, Vasishta, Akshay P, Rao, Diwakar, Goyal, Aditya, Murali, Kaushik, Kwatra, Nipun, and Jain, Mohit
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Computer Science - Human-Computer Interaction ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Refractive error is the most common eye disorder and is the key cause behind correctable visual impairment, responsible for nearly 80% of the visual impairment in the US. Refractive error can be diagnosed using multiple methods, including subjective refraction, retinoscopy, and autorefractors. Although subjective refraction is the gold standard, it requires cooperation from the patient and hence is not suitable for infants, young children, and developmentally delayed adults. Retinoscopy is an objective refraction method that does not require any input from the patient. However, retinoscopy requires a lens kit and a trained examiner, which limits its use for mass screening. In this work, we automate retinoscopy by attaching a smartphone to a retinoscope and recording retinoscopic videos with the patient wearing a custom pair of paper frames. We develop a video processing pipeline that takes retinoscopic videos as input and estimates the net refractive error based on our proposed extension of the retinoscopy mathematical model. Our system alleviates the need for a lens kit and can be performed by an untrained examiner. In a clinical trial with 185 eyes, we achieved a sensitivity of 91.0% and specificity of 74.0% on refractive error diagnosis. Moreover, the mean absolute error of our approach was 0.75$\pm$0.67D on net refractive error estimation compared to subjective refraction measurements. Our results indicate that our approach has the potential to be used as a retinoscopy-based refractive error screening tool in real-world medical settings., Comment: This paper is accepted for publication in IMWUT 2022
- Published
- 2022
26. Regulation of Human Endogenous Metabolites by Drug Transporters and Drug Metabolizing Enzymes: An Analysis of Targeted SNP-Metabolite Associations
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Granados, Jeffry C, Watrous, Jeramie D, Long, Tao, Rosenthal, Sara Brin, Cheng, Susan, Jain, Mohit, and Nigam, Sanjay K
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Medical Biochemistry and Metabolomics ,Pharmacology and Pharmaceutical Sciences ,Patient Safety ,Digestive Diseases ,Generic health relevance ,transporters ,enzymes ,ADME ,metabolomics ,SNPs ,pharmacogenomics ,fatty acids ,eicosanoids ,homeostasis ,OAT ,OATP ,MRP ,Analytical Chemistry ,Biochemistry and Cell Biology ,Clinical Sciences ,Biochemistry and cell biology ,Medical biochemistry and metabolomics ,Analytical chemistry - Abstract
Drug transporters and drug-metabolizing enzymes are primarily known for their role in the absorption, distribution, metabolism, and excretion (ADME) of small molecule drugs, but they also play a key role in handling endogenous metabolites. Recent cross-tissue co-expression network analyses have revealed a "Remote Sensing and Signaling Network" of multispecific, oligo-specific, and monospecific transporters and enzymes involved in endogenous metabolism. This includes many proteins from families involved in ADME (e.g., SLC22, SLCO, ABCC, CYP, UGT). Focusing on the gut-liver-kidney axis, we identified the endogenous metabolites potentially regulated by this network of ~1000 proteins by associating SNPs in these genes with the circulating levels of thousands of small, polar, bioactive metabolites, including free fatty acids, eicosanoids, bile acids, and other signaling metabolites that act in part via G-protein coupled receptors (GPCRs), nuclear receptors, and kinases. We identified 77 genomic loci associated with 7236 unique metabolites. This included metabolites that were associated with multiple, distinct loci, indicating coordinated regulation between multiple genes (including drug transporters and drug-metabolizing enzymes) of specific metabolites. We analyzed existing pharmacogenomic data and noted SNPs implicated in endogenous metabolite handling (e.g., rs4149056 in SLCO1B1) also affecting drug ADME. The overall results support the existence of close relationships, via interactions with signaling metabolites, between drug transporters and drug-metabolizing enzymes that are part of the Remote Sensing and Signaling Network, and with GPCRs and nuclear receptors. These analyses highlight the potential for drug-metabolite interactions at the interfaces of the Remote Sensing and Signaling Network and the ADME protein network.
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- 2023
27. Metabolomic Profiles Differentiate Scleroderma-PAH From Idiopathic PAH and Correspond With Worsened Functional Capacity
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Alotaibi, Mona, Shao, Junzhe, Pauciulo, Michael W, Nichols, William C, Hemnes, Anna R, Malhotra, Atul, Kim, Nick H, Yuan, Jason X-J, Fernandes, Timothy, Kerr, Kim M, Alshawabkeh, Laith, Desai, Ankit A, Bujor, Andreea M, Lafyatis, Robert, Watrous, Jeramie D, Long, Tao, Cheng, Susan, Chan, Stephen Y, and Jain, Mohit
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Medical Biochemistry and Metabolomics ,Biomedical and Clinical Sciences ,Autoimmune Disease ,Scleroderma ,Lung ,Rare Diseases ,Clinical Research ,Orphan Drug ,Inflammatory and immune system ,Humans ,Familial Primary Pulmonary Hypertension ,Hypertension ,Pulmonary ,Scleroderma ,Systemic ,Prognosis ,Lipids ,biomarkers ,metabolomics ,pulmonary hypertension ,scleroderma ,Clinical Sciences ,Respiratory System ,Cardiovascular medicine and haematology ,Clinical sciences - Abstract
BackgroundThe prognosis and therapeutic responses are worse for pulmonary arterial hypertension associated with systemic sclerosis (SSc-PAH) compared with idiopathic pulmonary arterial hypertension (IPAH). This discrepancy could be driven by divergence in underlying metabolic determinants of disease.Research questionAre circulating bioactive metabolites differentially altered in SSc-PAH vs IPAH, and can this alteration explain clinical disparity between these PAH subgroups?Study design and methodsPlasma biosamples from 400 patients with SSc-PAH and 1,082 patients with IPAH were included in the study. Another cohort of 100 patients with scleroderma with no PH and 44 patients with scleroderma with PH was included for external validation. More than 700 bioactive lipid metabolites, representing a range of vasoactive and immune-inflammatory pathways, were assayed in plasma samples from independent discovery and validation cohorts using liquid chromatography/high-resolution mass spectrometry-based approaches. Regression analyses were used to identify metabolites that exhibited differential levels between SSc-PAH and IPAH and associated with disease severity.ResultsFrom hundreds of circulating bioactive lipid molecules, five metabolites were found to distinguish between SSc-PAH and IPAH, as well as associate with markers of disease severity. Relative to IPAH, patients with SSc-PAH carried increased levels of fatty acid metabolites, including lignoceric acid and nervonic acid, as well as eicosanoids/oxylipins and sex hormone metabolites.InterpretationPatients with SSc-PAH are characterized by an unfavorable bioactive metabolic profile that may explain the poor and limited response to therapy. These data provide important metabolic insights into the molecular heterogeneity underlying differences between subgroups of PAH.
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- 2023
28. Keratoconus Classifier for Smartphone-based Corneal Topographer
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Gairola, Siddhartha, Joshi, Pallavi, Balasubramaniam, Anand, Murali, Kaushik, Kwatra, Nipun, and Jain, Mohit
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Computers and Society - Abstract
Keratoconus is a severe eye disease that leads to deformation of the cornea. It impacts people aged 10-25 years and is the leading cause of blindness in that demography. Corneal topography is the gold standard for keratoconus diagnosis. It is a non-invasive process performed using expensive and bulky medical devices called corneal topographers. This makes it inaccessible to large populations, especially in the Global South. Low-cost smartphone-based corneal topographers, such as SmartKC, have been proposed to make keratoconus diagnosis accessible. Similar to medical-grade topographers, SmartKC outputs curvature heatmaps and quantitative metrics that need to be evaluated by doctors for keratoconus diagnosis. An automatic scheme for evaluation of these heatmaps and quantitative values can play a crucial role in screening keratoconus in areas where doctors are not available. In this work, we propose a dual-head convolutional neural network (CNN) for classifying keratoconus on the heatmaps generated by SmartKC. Since SmartKC is a new device and only had a small dataset (114 samples), we developed a 2-stage transfer learning strategy -- using historical data collected from a medical-grade topographer and a subset of SmartKC data -- to satisfactorily train our network. This, combined with our domain-specific data augmentations, achieved a sensitivity of 91.3% and a specificity of 94.2%., Comment: 4 pages
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- 2022
29. Global Readiness of Language Technology for Healthcare: What would it Take to Combat the Next Pandemic?
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Mondal, Ishani, Ahuja, Kabir, Jain, Mohit, Neil, Jacki O, Bali, Kalika, and Choudhury, Monojit
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Computer Science - Computers and Society ,Computer Science - Computation and Language - Abstract
The COVID-19 pandemic has brought out both the best and worst of language technology (LT). On one hand, conversational agents for information dissemination and basic diagnosis have seen widespread use, and arguably, had an important role in combating the pandemic. On the other hand, it has also become clear that such technologies are readily available for a handful of languages, and the vast majority of the global south is completely bereft of these benefits. What is the state of LT, especially conversational agents, for healthcare across the world's languages? And, what would it take to ensure global readiness of LT before the next pandemic? In this paper, we try to answer these questions through survey of existing literature and resources, as well as through a rapid chatbot building exercise for 15 Asian and African languages with varying amount of resource-availability. The study confirms the pitiful state of LT even for languages with large speaker bases, such as Sinhala and Hausa, and identifies the gaps that could help us prioritize research and investment strategies in LT for healthcare., Comment: Under Revision
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- 2022
30. Anterior Rotator Interval Lesion (ARIL), its association with glenoid labrum pathology in patients with anterior shoulder pain and surgical outcome of Arthroscopic Rotator Interval Closure (ARIC)
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Jain, Mohit J., Medina, Giovanna, Jog, Aashish V., Bartolozzi, Arthur R., and Morgan, Craig
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- 2024
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31. Look Closer: Bridging Egocentric and Third-Person Views with Transformers for Robotic Manipulation
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Jangir, Rishabh, Hansen, Nicklas, Ghosal, Sambaran, Jain, Mohit, and Wang, Xiaolong
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Computer Science - Robotics ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Learning to solve precision-based manipulation tasks from visual feedback using Reinforcement Learning (RL) could drastically reduce the engineering efforts required by traditional robot systems. However, performing fine-grained motor control from visual inputs alone is challenging, especially with a static third-person camera as often used in previous work. We propose a setting for robotic manipulation in which the agent receives visual feedback from both a third-person camera and an egocentric camera mounted on the robot's wrist. While the third-person camera is static, the egocentric camera enables the robot to actively control its vision to aid in precise manipulation. To fuse visual information from both cameras effectively, we additionally propose to use Transformers with a cross-view attention mechanism that models spatial attention from one view to another (and vice-versa), and use the learned features as input to an RL policy. Our method improves learning over strong single-view and multi-view baselines, and successfully transfers to a set of challenging manipulation tasks on a real robot with uncalibrated cameras, no access to state information, and a high degree of task variability. In a hammer manipulation task, our method succeeds in 75% of trials versus 38% and 13% for multi-view and single-view baselines, respectively., Comment: Accepted in Robotics and Automation Letters Journal (RA-L 2022). Website at https://jangirrishabh.github.io/lookcloser .8 Pages
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- 2022
32. One-Year Effects of High-Intensity Statin on Bioactive Lipids: Findings From the JUPITER Trial
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Hoshi, Rosangela Akemi, Alotaibi, Mona, Liu, Yanyan, Watrous, Jeramie D., Ridker, Paul M, Glynn, Robert J., Serhan, Charles N., Luttmann-Gibson, Heike, Moorthy, M. Vinayaga, Jain, Mohit, Demler, Olga V., and Mora, Samia
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- 2024
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33. SmartKC: Smartphone-based Corneal Topographer for Keratoconus Detection
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Gairola, Siddhartha, Bohra, Murtuza, Shaheer, Nadeem, Jayaprakash, Navya, Joshi, Pallavi, Balasubramaniam, Anand, Murali, Kaushik, Kwatra, Nipun, and Jain, Mohit
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Computer Science - Human-Computer Interaction - Abstract
Keratoconus is a severe eye disease affecting the cornea (the clear, dome-shaped outer surface of the eye), causing it to become thin and develop a conical bulge. The diagnosis of keratoconus requires sophisticated ophthalmic devices which are non-portable and very expensive. This makes early detection of keratoconus inaccessible to large populations in low- and middle-income countries, making it a leading cause for partial/complete blindness among such populations. We propose SmartKC, a low-cost, smartphone-based keratoconus diagnosis system comprising of a 3D-printed placido's disc attachment, an LED light strip, and an intelligent smartphone app to capture the reflection of the placido rings on the cornea. An image processing pipeline analyzes the corneal image and uses the smartphone's camera parameters, the placido rings' 3D location, the pixel location of the reflected placido rings and the setup's working distance to construct the corneal surface, via the Arc-Step method and Zernike polynomials based surface fitting. In a clinical study with 101 distinct eyes, we found that SmartKC achieves a sensitivity of 94.1% and a specificity of 100.0%. Moreover, the quantitative curvature estimates (sim-K) strongly correlate with a gold-standard medical device (Pearson correlation coefficient =0.78). Our results indicate that SmartKC has the potential to be used as a keratoconus screening tool under real-world medical settings., Comment: Change Log: + Fixed sim-K computation (updated Section 5.5.3); re-ran our pipeline with the updated sim-K values (updated Figure 7); + Conducted the comparative evaluation with doctors again (total 4 doctors), and got improved results (updated Section 7.2 and Table 2); [Note: This is an updated version of the paper that was accepted for publication in IMWUT 2021.]
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- 2021
34. A genome-wide CRISPR screen reveals that antagonism of glutamine metabolism sensitizes head and neck squamous cell carcinoma to ferroptotic cell death
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Allevato, Michael M., Trinh, Sally, Koshizuka, Keiichi, Nachmanson, Daniela, Nguyen, Thien-Tu C., Yokoyama, Yumi, Wu, Xingyu, Andres, Allen, Wang, Zhiyong, Watrous, Jeramie, Molinolo, Alfredo A., Mali, Prashant, Harismendy, Olivier, Jain, Mohit, Wild, Robert, and Gutkind, J. Silvio
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- 2024
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35. Demographic and clinical characteristics associated with variations in antibody response to BNT162b2 COVID-19 vaccination among healthcare workers at an academic medical centre: a longitudinal cohort analysis
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Ebinger, Joseph E, Joung, Sandy, Liu, Yunxian, Wu, Min, Weber, Brittany, Claggett, Brian, Botting, Patrick G, Sun, Nancy, Driver, Matthew, Kao, Yu Hung, Khuu, Briana, Wynter, Timothy, Nguyen, Trevor-Trung, Alotaibi, Mona, Prostko, John C, Frias, Edwin C, Stewart, James L, Goodridge, Helen S, Chen, Peter, Jordan, Stanley C, Jain, Mohit, Sharma, Sonia, Fert-Bober, Justyna, Van Eyk, Jennifer E, Minissian, Margo B, Arditi, Moshe, Melmed, Gil Y, Braun, Jonathan G, McGovern, Dermot PB, Cheng, Susan, and Sobhani, Kimia
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Prevention ,Immunization ,Infectious Diseases ,Vaccine Related ,Clinical Research ,Emerging Infectious Diseases ,Infection ,Good Health and Well Being ,Academic Medical Centers ,Adult ,Antibodies ,Viral ,Antibody Formation ,BNT162 Vaccine ,COVID-19 ,COVID-19 Vaccines ,Cohort Studies ,Demography ,Female ,Health Personnel ,Humans ,Hypertension ,Immunoglobulin G ,Longitudinal Studies ,Male ,Middle Aged ,Prospective Studies ,SARS-CoV-2 ,Vaccination ,hypertension ,infectious diseases ,Clinical Sciences ,Public Health and Health Services ,Other Medical and Health Sciences - Abstract
ObjectivesWe sought to understand the demographic and clinical factors associated with variations in longitudinal antibody response following completion of two-dose regiment of BNT162b2 vaccination.DesignThis study is a 10-month longitudinal cohort study of healthcare workers and serially measured anti-spike protein IgG (IgG-S) antibody levels using mixed linear models to examine their associations with participant characteristics.SettingA large, multisite academic medical centre in Southern California, USA.ParticipantsA total of 843 healthcare workers met inclusion criteria including completion of an initial two-dose course of BNT162b2 vaccination, complete clinical history and at least two blood samples for analysis. Patients had an average age of 45±13 years, were 70% female and 7% with prior SARS-CoV-2 infection.ResultsVaccine-induced IgG-S levels remained in the positive range for 99.6% of individuals up to 10 months after initial two-dose vaccination. Prior SARS-CoV-2 infection was the primary correlate of sustained higher postvaccination IgG-S levels (partial R2=0.133), with a 1.74±0.11 SD higher IgG-S response (p
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- 2022
36. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
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Zhu, Qiyun, Huang, Shi, Gonzalez, Antonio, McGrath, Imran, McDonald, Daniel, Haiminen, Niina, Armstrong, George, Vázquez-Baeza, Yoshiki, Yu, Julian, Kuczynski, Justin, Sepich-Poore, Gregory D, Swafford, Austin D, Das, Promi, Shaffer, Justin P, Lejzerowicz, Franck, Belda-Ferre, Pedro, Havulinna, Aki S, Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Kim, Ho-Cheol, Jain, Mohit, Inouye, Michael, Gilbert, Jack A, and Knight, Rob
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Human Genome ,Genetics ,Biotechnology ,Life Below Water ,Humans ,Phylogeny ,Metagenome ,RNA ,Ribosomal ,16S ,Microbiota ,Ecology ,operational genomic unit ,taxonomy independent ,reference phylogeny ,UniFrac ,supervised learning ,metagenomics - Abstract
We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.
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- 2022
37. Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults
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Ruuskanen, Matti O, Erawijantari, Pande P, Havulinna, Aki S, Liu, Yang, Méric, Guillaume, Tuomilehto, Jaakko, Inouye, Michael, Jousilahti, Pekka, Salomaa, Veikko, Jain, Mohit, Knight, Rob, Lahti, Leo, and Niiranen, Teemu J
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Nutrition ,Diabetes ,Prevention ,Metabolic and endocrine ,Adult ,Cohort Studies ,Cross-Sectional Studies ,Diabetes Mellitus ,Type 2 ,Female ,Finland ,Gastrointestinal Microbiome ,Humans ,Male ,Middle Aged - Abstract
ObjectiveTo examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort.Research design and methodsWe collected fecal samples from 5,572 Finns (mean age 48.7 years; 54.1% women) in 2002 who were followed up for incident type 2 diabetes until 31 December 2017. The samples were sequenced using shotgun metagenomics. We examined associations between gut microbiome composition and incident diabetes using multivariable-adjusted Cox regression models. We first used the eastern Finland subpopulation to obtain initial findings and validated these in the western Finland subpopulation.ResultsAltogether, 432 cases of incident diabetes occurred over the median follow-up of 15.8 years. We detected four species and two clusters consistently associated with incident diabetes in the validation models. These four species were Clostridium citroniae (hazard ratio [HR] 1.21; 95% CI 1.04-1.42), C. bolteae (HR 1.20; 95% CI 1.04-1.39), Tyzzerella nexilis (HR 1.17; 95% CI 1.01-1.36), and Ruminococcus gnavus (HR 1.17; 95% CI 1.01-1.36). The positively associated clusters, cluster 1 (HR 1.18; 95% CI 1.02-1.38) and cluster 5 (HR 1.18; 95% CI 1.02-1.36), mostly consisted of these same species.ConclusionsWe observed robust species-level taxonomic features predictive of incident type 2 diabetes over long-term follow-up. These findings build on and extend previous mainly cross-sectional evidence and further support links between dietary habits, metabolic diseases, and type 2 diabetes that are modulated by the gut microbiome. The gut microbiome can potentially be used to improve disease prediction and uncover novel therapeutic targets for diabetes.
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- 2022
38. Triclosan administration to humanized UDP-glucuronosyltransferase 1 neonatal mice induces UGT1A1 through a dependence on PPARα and ATF4
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Weber, André A., Yang, Xiaojing, Mennillo, Elvira, Wong, Samantha, Le, Sabrina, Ashley Teo, Jia Ying, Chang, Max, Benner, Christopher W., Ding, Jeffrey, Jain, Mohit, Chen, Shujuan, Karin, Michael, and Tukey, Robert H.
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- 2024
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39. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
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Qin, Youwen, Havulinna, Aki S, Liu, Yang, Jousilahti, Pekka, Ritchie, Scott C, Tokolyi, Alex, Sanders, Jon G, Valsta, Liisa, Brożyńska, Marta, Zhu, Qiyun, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Loomba, Rohit, Cheng, Susan, Jain, Mohit, Niiranen, Teemu, Lahti, Leo, Knight, Rob, Salomaa, Veikko, Inouye, Michael, and Méric, Guillaume
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Microbiology ,Biological Sciences ,Genetics ,Prevention ,Digestive Diseases ,Nutrition ,Human Genome ,Clinical Research ,Aetiology ,2.1 Biological and endogenous factors ,Oral and gastrointestinal ,ABO Blood-Group System ,Bifidobacterium ,Clostridiales ,Cohort Studies ,Colorectal Neoplasms ,Depressive Disorder ,Major ,Diet ,Dietary Fiber ,Enterococcus faecalis ,Gastrointestinal Microbiome ,Gastrointestinal Tract ,Genetic Variation ,Genome-Wide Association Study ,Host Microbial Interactions ,Humans ,Lactase ,Mediator Complex ,Mendelian Randomization Analysis ,Metagenome ,Morganella ,Polymorphism ,Single Nucleotide ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.
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- 2022
40. Height Estimation of Children under Five Years using Depth Images
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Trivedi, Anusua, Jain, Mohit, Gupta, Nikhil Kumar, Hinsche, Markus, Singh, Prashant, Matiaschek, Markus, Behrens, Tristan, Militeri, Mirco, Birge, Cameron, Kaushik, Shivangi, Mohapatra, Archisman, Chatterjee, Rita, Dodhia, Rahul, and Ferres, Juan Lavista
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Malnutrition is a global health crisis and is the leading cause of death among children under five. Detecting malnutrition requires anthropometric measurements of weight, height, and middle-upper arm circumference. However, measuring them accurately is a challenge, especially in the global south, due to limited resources. In this work, we propose a CNN-based approach to estimate the height of standing children under five years from depth images collected using a smart-phone. According to the SMART Methodology Manual [5], the acceptable accuracy for height is less than 1.4 cm. On training our deep learning model on 87131 depth images, our model achieved an average mean absolute error of 1.64% on 57064 test images. For 70.3% test images, we estimated height accurately within the acceptable 1.4 cm range. Thus, our proposed solution can accurately detect stunting (low height-for-age) in standing children below five years of age.
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- 2021
41. Benchmarking Scene Text Recognition in Devanagari, Telugu and Malayalam
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Mathew, Minesh, Jain, Mohit, and Jawahar, CV
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Inspired by the success of Deep Learning based approaches to English scene text recognition, we pose and benchmark scene text recognition for three Indic scripts - Devanagari, Telugu and Malayalam. Synthetic word images rendered from Unicode fonts are used for training the recognition system. And the performance is bench-marked on a new IIIT-ILST dataset comprising of hundreds of real scene images containing text in the above mentioned scripts. We use a segmentation free, hybrid but end-to-end trainable CNN-RNN deep neural network for transcribing the word images to the corresponding texts. The cropped word images need not be segmented into the sub-word units and the error is calculated and backpropagated for the the given word image at once. The network is trained using CTC loss, which is proven quite effective for sequence-to-sequence transcription tasks. The CNN layers in the network learn to extract robust feature representations from word images. The sequence of features learnt by the convolutional block is transcribed to a sequence of labels by the RNN+CTC block. The transcription is not bound by word length or a lexicon and is ideal for Indian languages which are highly inflectional. IIIT-ILST dataset, synthetic word images dataset and the script used to render synthetic images are available at http://cvit.iiit.ac.in/research/projects/cvit-projects/iiit-ilst, Comment: This work was accepted at MOCR Workshop, ICDAR 2017 Uploading updated draft which includes links to download datasets and rendering script
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- 2021
42. Author Correction: Greengenes2 unifies microbial data in a single reference tree
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McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash, and Knight, Rob
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- 2024
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43. Extended Applications of Trauma Implants to Prevent or Treat Fractures in Pathological Bone
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Johari, Ashok, Andreacchio, Antonio, Canavese, Federico, Jain, Mohit J., Banerjee, Arindam, editor, Biberthaler, Peter, editor, and Shanmugasundaram, Saseendar, editor
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- 2023
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44. Challenges Faced by the Employed Indian DHH Community
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Sridhar, Advaith, Poddar, Roshni, Jain, Mohit, Kumar, Pratyush, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Abdelnour Nocera, José, editor, Kristín Lárusdóttir, Marta, editor, Petrie, Helen, editor, Piccinno, Antonio, editor, and Winckler, Marco, editor
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- 2023
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45. 'Do we like this, or do we like like this?': Reflections on a Human-Centered Machine Learning Approach to Sentiment Analysis
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Ghosh, Sourojit, Ali, Murtaza, Batra, Anna, Guo, Cheng, Jain, Mohit, Kang, Joseph, Kharchenko, Julia, Suravajhela, Varun, Zhou, Vincent, Aragon, Cecilia, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Degen, Helmut, editor, and Ntoa, Stavroula, editor
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- 2023
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46. Precise Temperature Control Scheme for Nonlinear CSTR Using Equilibrium Optimizer Tuned 2-DOF FOPID Controller
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Shivhare, Riya, Rastogi, Nandini, Bhardwaj, Muskan, Kumari, Ekta, Agrawal, Nitin, Jain, Mohit, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Shukla, Anupam, editor, Murthy, B. K., editor, Hasteer, Nitasha, editor, and Van Belle, Jean-Paul, editor
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- 2023
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47. Phase Segmenting Process in Ultra-High Carbon Steels Using Deep Vision Approach
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Jain, Mohit, Jain, Varnit, Choudhury, Amitava, Ghosh, Manojit, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Tiwari, Shailesh, editor, Trivedi, Munesh C., editor, Kolhe, Mohan L., editor, and Singh, Brajesh Kumar, editor
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- 2023
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48. Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
- Author
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Armstrong, George, Cantrell, Kalen, Huang, Shi, McDonald, Daniel, Haiminen, Niina, Carrieri, Anna Paola, Zhu, Qiyun, Gonzalez, Antonio, McGrath, Imran, Beck, Kristen L, Hakim, Daniel, Havulinna, Aki S, Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Jain, Mohit, Inouye, Michael, Swafford, Austin D, Kim, Ho-Cheol, Parida, Laxmi, Vázquez-Baeza, Yoshiki, and Knight, Rob
- Subjects
Microbiology ,Biological Sciences ,Aging ,Microbiota ,Phylogeny ,Medical and Health Sciences ,Bioinformatics ,Genetics - Abstract
The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.
- Published
- 2021
49. RespireNet: A Deep Neural Network for Accurately Detecting Abnormal Lung Sounds in Limited Data Setting
- Author
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Gairola, Siddhartha, Tom, Francis, Kwatra, Nipun, and Jain, Mohit
- Subjects
Computer Science - Sound ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Auscultation of respiratory sounds is the primary tool for screening and diagnosing lung diseases. Automated analysis, coupled with digital stethoscopes, can play a crucial role in enabling tele-screening of fatal lung diseases. Deep neural networks (DNNs) have shown a lot of promise for such problems, and are an obvious choice. However, DNNs are extremely data hungry, and the largest respiratory dataset ICBHI has only 6898 breathing cycles, which is still small for training a satisfactory DNN model. In this work, RespireNet, we propose a simple CNN-based model, along with a suite of novel techniques -- device specific fine-tuning, concatenation-based augmentation, blank region clipping, and smart padding -- enabling us to efficiently use the small-sized dataset. We perform extensive evaluation on the ICBHI dataset, and improve upon the state-of-the-art results for 4-class classification by 2.2%, Comment: Code visible at https://github.com/microsoft/RespireNet
- Published
- 2020
50. Gaze-based Autism Detection for Adolescents and Young Adults using Prosaic Videos
- Author
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Ahuja, Karan, Bose, Abhishek, Jain, Mohit, Dey, Kuntal, Joshi, Anil, Achary, Krishnaveni, Varkey, Blessin, Harrison, Chris, and Goel, Mayank
- Subjects
Computer Science - Human-Computer Interaction ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Autism often remains undiagnosed in adolescents and adults. Prior research has indicated that an autistic individual often shows atypical fixation and gaze patterns. In this short paper, we demonstrate that by monitoring a user's gaze as they watch commonplace (i.e., not specialized, structured or coded) video, we can identify individuals with autism spectrum disorder. We recruited 35 autistic and 25 non-autistic individuals, and captured their gaze using an off-the-shelf eye tracker connected to a laptop. Within 15 seconds, our approach was 92.5% accurate at identifying individuals with an autism diagnosis. We envision such automatic detection being applied during e.g., the consumption of web media, which could allow for passive screening and adaptation of user interfaces.
- Published
- 2020
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