-
Deep-Learning Investigation of Vibrational Raman Spectra for Plant-Stress Analysis
Authors:
Anoop C. Patil,
Benny Jian Rong Sng,
Yu-Wei Chang,
Joana B. Pereira,
Chua Nam-Hai,
Rajani Sarojam,
Gajendra Pratap Singh,
In-Cheol Jang,
Giovanni Volpe
Abstract:
Detecting stress in plants is crucial for both open-farm and controlled-environment agriculture. Biomolecules within plants serve as key stress indicators, offering vital markers for continuous health monitoring and early disease detection. Raman spectroscopy provides a powerful, non-invasive means to quantify these biomolecules through their molecular vibrational signatures. However, traditional…
▽ More
Detecting stress in plants is crucial for both open-farm and controlled-environment agriculture. Biomolecules within plants serve as key stress indicators, offering vital markers for continuous health monitoring and early disease detection. Raman spectroscopy provides a powerful, non-invasive means to quantify these biomolecules through their molecular vibrational signatures. However, traditional Raman analysis relies on customized data-processing workflows that require fluorescence background removal and prior identification of Raman peaks of interest-introducing potential biases and inconsistencies. Here, we introduce DIVA (Deep-learning-based Investigation of Vibrational Raman spectra for plant-stress Analysis), a fully automated workflow based on a variational autoencoder. Unlike conventional approaches, DIVA processes native Raman spectra-including fluorescence backgrounds-without manual preprocessing, identifying and quantifying significant spectral features in an unbiased manner. We applied DIVA to detect a range of plant stresses, including abiotic (shading, high light intensity, high temperature) and biotic stressors (bacterial infections). By integrating deep learning with vibrational spectroscopy, DIVA paves the way for AI-driven plant health assessment, fostering more resilient and sustainable agricultural practices.
△ Less
Submitted 21 July, 2025;
originally announced July 2025.
-
A Cytology Dataset for Early Detection of Oral Squamous Cell Carcinoma
Authors:
Garima Jain,
Sanghamitra Pati,
Mona Duggal,
Amit Sethi,
Abhijeet Patil,
Gururaj Malekar,
Nilesh Kowe,
Jitender Kumar,
Jatin Kashyap,
Divyajeet Rout,
Deepali,
Hitesh,
Nishi Halduniya,
Sharat Kumar,
Heena Tabassum,
Rupinder Singh Dhaliwal,
Sucheta Devi Khuraijam,
Sushma Khuraijam,
Sharmila Laishram,
Simmi Kharb,
Sunita Singh,
K. Swaminadtan,
Ranjana Solanki,
Deepika Hemranjani,
Shashank Nath Singh
, et al. (12 additional authors not shown)
Abstract:
Oral squamous cell carcinoma OSCC is a major global health burden, particularly in several regions across Asia, Africa, and South America, where it accounts for a significant proportion of cancer cases. Early detection dramatically improves outcomes, with stage I cancers achieving up to 90 percent survival. However, traditional diagnosis based on histopathology has limited accessibility in low-res…
▽ More
Oral squamous cell carcinoma OSCC is a major global health burden, particularly in several regions across Asia, Africa, and South America, where it accounts for a significant proportion of cancer cases. Early detection dramatically improves outcomes, with stage I cancers achieving up to 90 percent survival. However, traditional diagnosis based on histopathology has limited accessibility in low-resource settings because it is invasive, resource-intensive, and reliant on expert pathologists. On the other hand, oral cytology of brush biopsy offers a minimally invasive and lower cost alternative, provided that the remaining challenges, inter observer variability and unavailability of expert pathologists can be addressed using artificial intelligence. Development and validation of robust AI solutions requires access to large, labeled, and multi-source datasets to train high capacity models that generalize across domain shifts. We introduce the first large and multicenter oral cytology dataset, comprising annotated slides stained with Papanicolaou(PAP) and May-Grunwald-Giemsa(MGG) protocols, collected from ten tertiary medical centers in India. The dataset is labeled and annotated by expert pathologists for cellular anomaly classification and detection, is designed to advance AI driven diagnostic methods. By filling the gap in publicly available oral cytology datasets, this resource aims to enhance automated detection, reduce diagnostic errors, and improve early OSCC diagnosis in resource-constrained settings, ultimately contributing to reduced mortality and better patient outcomes worldwide.
△ Less
Submitted 11 June, 2025;
originally announced June 2025.
-
Evaluation Metric for Quality Control and Generative Models in Histopathology Images
Authors:
Pranav Jeevan,
Neeraj Nixon,
Abhijeet Patil,
Amit Sethi
Abstract:
Our study introduces ResNet-L2 (RL2), a novel metric for evaluating generative models and image quality in histopathology, addressing limitations of traditional metrics, such as Frechet inception distance (FID), when the data is scarce. RL2 leverages ResNet features with a normalizing flow to calculate RMSE distance in the latent space, providing reliable assessments across diverse histopathology…
▽ More
Our study introduces ResNet-L2 (RL2), a novel metric for evaluating generative models and image quality in histopathology, addressing limitations of traditional metrics, such as Frechet inception distance (FID), when the data is scarce. RL2 leverages ResNet features with a normalizing flow to calculate RMSE distance in the latent space, providing reliable assessments across diverse histopathology datasets. We evaluated the performance of RL2 on degradation types, such as blur, Gaussian noise, salt-and-pepper noise, and rectangular patches, as well as diffusion processes. RL2's monotonic response to increasing degradation makes it well-suited for models that assess image quality, proving a valuable advancement for evaluating image generation techniques in histopathology. It can also be used to discard low-quality patches while sampling from a whole slide image. It is also significantly lighter and faster compared to traditional metrics and requires fewer images to give stable metric value.
△ Less
Submitted 2 January, 2025; v1 submitted 1 November, 2024;
originally announced November 2024.
-
PathoGen-X: A Cross-Modal Genomic Feature Trans-Align Network for Enhanced Survival Prediction from Histopathology Images
Authors:
Akhila Krishna,
Nikhil Cherian Kurian,
Abhijeet Patil,
Amruta Parulekar,
Amit Sethi
Abstract:
Accurate survival prediction is essential for personalized cancer treatment. However, genomic data - often a more powerful predictor than pathology data - is costly and inaccessible. We present the cross-modal genomic feature translation and alignment network for enhanced survival prediction from histopathology images (PathoGen-X). It is a deep learning framework that leverages both genomic and im…
▽ More
Accurate survival prediction is essential for personalized cancer treatment. However, genomic data - often a more powerful predictor than pathology data - is costly and inaccessible. We present the cross-modal genomic feature translation and alignment network for enhanced survival prediction from histopathology images (PathoGen-X). It is a deep learning framework that leverages both genomic and imaging data during training, relying solely on imaging data at testing. PathoGen-X employs transformer-based networks to align and translate image features into the genomic feature space, enhancing weaker imaging signals with stronger genomic signals. Unlike other methods, PathoGen-X translates and aligns features without projecting them to a shared latent space and requires fewer paired samples. Evaluated on TCGA-BRCA, TCGA-LUAD, and TCGA-GBM datasets, PathoGen-X demonstrates strong survival prediction performance, emphasizing the potential of enriched imaging models for accessible cancer prognosis.
△ Less
Submitted 1 November, 2024;
originally announced November 2024.
-
A comparative data study on dinosaur, bird and human bone attributes -- A supporting study for convergent evolution
Authors:
Akshita Patil,
Nishchal Dwivedi
Abstract:
For over 165 million years, dinosaurs reigned on this planet. Their entire existence saw variations in their body size and mass . Understanding the relationship between various attributes such as femur length, breadth; humerus length, breadth; tibia length, breadth and body mass of dinosaurs contributes to our understanding of the Jurassic era and further provides reasoning for bone and body size…
▽ More
For over 165 million years, dinosaurs reigned on this planet. Their entire existence saw variations in their body size and mass . Understanding the relationship between various attributes such as femur length, breadth; humerus length, breadth; tibia length, breadth and body mass of dinosaurs contributes to our understanding of the Jurassic era and further provides reasoning for bone and body size evolution of modern day descendants of those from the Dinosauria clade. The following work consists of statistical evidence derived from an encyclopedic data set consisting of a wide variety of measurements pertaining to discovered fossils of a particular taxa of dinosaur. Our study establishes linearly regressive correspondence between femur and humerus length and radii. Furthermore, there is also a comparison with terrestrial bird bone lengths, to verify the claim of birds being closest alive species to dinosaurs. An analysis into bone ratios of early humans shows that terrestrial birds are closer to humans than that of dinosaurs. Not only on one hand it challenges the closeness of birds with dinosaurs, but on the other hand it makes a case of convergent evolution between birds and humans, due to their closeness in regressive fits.
A correlation between bone ratios of dinosaurs and early humans also advances understanding in the structural and physical distinctions between the two species. Overall, the work contains evaluation of dinosaur skeletons and promotes further exploration and research in the paleontological field to strengthen the conclusions drawn thus far.
△ Less
Submitted 21 September, 2023;
originally announced September 2023.
-
Hardware-Friendly Synaptic Orders and Timescales in Liquid State Machines for Speech Classification
Authors:
Vivek Saraswat,
Ajinkya Gorad,
Anand Naik,
Aakash Patil,
Udayan Ganguly
Abstract:
Liquid State Machines are brain inspired spiking neural networks (SNNs) with random reservoir connectivity and bio-mimetic neuronal and synaptic models. Reservoir computing networks are proposed as an alternative to deep neural networks to solve temporal classification problems. Previous studies suggest 2nd order (double exponential) synaptic waveform to be crucial for achieving high accuracy for…
▽ More
Liquid State Machines are brain inspired spiking neural networks (SNNs) with random reservoir connectivity and bio-mimetic neuronal and synaptic models. Reservoir computing networks are proposed as an alternative to deep neural networks to solve temporal classification problems. Previous studies suggest 2nd order (double exponential) synaptic waveform to be crucial for achieving high accuracy for TI-46 spoken digits recognition. The proposal of long-time range (ms) bio-mimetic synaptic waveforms is a challenge to compact and power efficient neuromorphic hardware. In this work, we analyze the role of synaptic orders namely: δ (high output for single time step), 0th (rectangular with a finite pulse width), 1st (exponential fall) and 2nd order (exponential rise and fall) and synaptic timescales on the reservoir output response and on the TI-46 spoken digits classification accuracy under a more comprehensive parameter sweep. We find the optimal operating point to be correlated to an optimal range of spiking activity in the reservoir. Further, the proposed 0th order synapses perform at par with the biologically plausible 2nd order synapses. This is substantial relaxation for circuit designers as synapses are the most abundant components in an in-memory implementation for SNNs. The circuit benefits for both analog and mixed-signal realizations of 0th order synapse are highlighted demonstrating 2-3 orders of savings in area and power consumptions by eliminating Op-Amps and Digital to Analog Converter circuits. This has major implications on a complete neural network implementation with focus on peripheral limitations and algorithmic simplifications to overcome them.
△ Less
Submitted 29 April, 2021;
originally announced April 2021.
-
Visualization for Histopathology Images using Graph Convolutional Neural Networks
Authors:
Mookund Sureka,
Abhijeet Patil,
Deepak Anand,
Amit Sethi
Abstract:
With the increase in the use of deep learning for computer-aided diagnosis in medical images, the criticism of the black-box nature of the deep learning models is also on the rise. The medical community needs interpretable models for both due diligence and advancing the understanding of disease and treatment mechanisms. In histology, in particular, while there is rich detail available at the cellu…
▽ More
With the increase in the use of deep learning for computer-aided diagnosis in medical images, the criticism of the black-box nature of the deep learning models is also on the rise. The medical community needs interpretable models for both due diligence and advancing the understanding of disease and treatment mechanisms. In histology, in particular, while there is rich detail available at the cellular level and that of spatial relationships between cells, it is difficult to modify convolutional neural networks to point out the relevant visual features. We adopt an approach to model histology tissue as a graph of nuclei and develop a graph convolutional network framework based on attention mechanism and node occlusion for disease diagnosis. The proposed method highlights the relative contribution of each cell nucleus in the whole-slide image. Our visualization of such networks trained to distinguish between invasive and in-situ breast cancers, and Gleason 3 and 4 prostate cancers generate interpretable visual maps that correspond well with our understanding of the structures that are important to experts for their diagnosis.
△ Less
Submitted 16 June, 2020;
originally announced June 2020.
-
Image-based phenotyping of diverse Rice (Oryza Sativa L.) Genotypes
Authors:
Mukesh Kumar Vishal,
Dipesh Tamboli,
Abhijeet Patil,
Rohit Saluja,
Biplab Banerjee,
Amit Sethi,
Dhandapani Raju,
Sudhir Kumar,
R N Sahoo,
Viswanathan Chinnusamy,
J Adinarayana
Abstract:
Development of either drought-resistant or drought-tolerant varieties in rice (Oryza sativa L.), especially for high yield in the context of climate change, is a crucial task across the world. The need for high yielding rice varieties is a prime concern for developing nations like India, China, and other Asian-African countries where rice is a primary staple food. The present investigation is carr…
▽ More
Development of either drought-resistant or drought-tolerant varieties in rice (Oryza sativa L.), especially for high yield in the context of climate change, is a crucial task across the world. The need for high yielding rice varieties is a prime concern for developing nations like India, China, and other Asian-African countries where rice is a primary staple food. The present investigation is carried out for discriminating drought tolerant, and susceptible genotypes. A total of 150 genotypes were grown under controlled conditions to evaluate at High Throughput Plant Phenomics facility, Nanaji Deshmukh Plant Phenomics Centre, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi. A subset of 10 genotypes is taken out of 150 for the current investigation. To discriminate against the genotypes, we considered features such as the number of leaves per plant, the convex hull and convex hull area of a plant-convex hull formed by joining the tips of the leaves, the number of leaves per unit convex hull of a plant, canopy spread - vertical spread, and horizontal spread of a plant. We trained You Only Look Once (YOLO) deep learning algorithm for leaves tips detection and to estimate the number of leaves in a rice plant. With this proposed framework, we screened the genotypes based on selected traits. These genotypes were further grouped among different groupings of drought-tolerant and drought susceptible genotypes using the Ward method of clustering.
△ Less
Submitted 6 April, 2020;
originally announced April 2020.
-
Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes
Authors:
Sriganesh Srihari,
Chern Han Yong,
Ashwini Patil,
Limsoon Wong
Abstract:
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organization of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 an…
▽ More
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organization of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight challenges faced by these methods, in particular detection of sparse and small or sub- complexes and discerning of overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area.
△ Less
Submitted 20 May, 2015;
originally announced May 2015.