Tri Q. Nguyen

Tien-Phat Nguyen, Trong-Thang Pham, Tri Nguyen et al.

The timing of cell divisions in early embryos during the In-Vitro Fertilization (IVF) process is a key predictor of embryo viability. However, observing cell divisions in Time-Lapse Monitoring (TLM) is a time-consuming process and highly depends on experts. In this paper, we propose EmbryosFormer, a computational model to automatically detect and classify cell divisions from original time-lapse images. Our proposed network is designed as an encoder-decoder deformable transformer with collaborative heads. The transformer contracting path predicts per-image labels and is optimized by a classification head. The transformer expanding path models the temporal coherency between embryo images to ensure monotonic non-decreasing constraint and is optimized by a segmentation head. Both contracting and expanding paths are synergetically learned by a collaboration head. We have benchmarked our proposed EmbryosFormer on two datasets: a public dataset with mouse embryos with 8-cell stage and an in-house dataset with human embryos with 4-cell stage. Source code: https://github.com/UARK-AICV/Embryos.

Henna Kokkonen, Lauri Lovén, Naser Hossein Motlagh et al.

Future AI applications require performance, reliability and privacy that the existing, cloud-dependant system architectures cannot provide. In this article, we study orchestration in the device-edge-cloud continuum, and focus on edge AI for resource orchestration. We claim that to support the constantly growing requirements of intelligent applications in the device-edge-cloud computing continuum, resource orchestration needs to embrace edge AI and emphasize local autonomy and intelligence. To justify the claim, we provide a general definition for continuum orchestration, and look at how current and emerging orchestration paradigms are suitable for the computing continuum. We describe certain major emerging research themes that may affect future orchestration, and provide an early vision of an orchestration paradigm that embraces those research themes. Finally, we survey current key edge AI methods and look at how they may contribute into fulfilling the vision of future continuum orchestration.

Tri Nguyen, Mukul Narwani, Mark Larson et al.

The wiring and connectivity of neurons form a structural basis for the function of the nervous system. Advances in volume electron microscopy (EM) and image segmentation have enabled mapping of circuit diagrams (connectomics) within local regions of the mouse brain. However, applying volume EM over the whole brain is not currently feasible due to technological challenges. As a result, comprehensive maps of long-range connections between brain regions are lacking. Recently, we demonstrated that X-ray holographic nanotomography (XNH) can provide high-resolution images of brain tissue at a much larger scale than EM. In particular, XNH is wellsuited to resolve large, myelinated axon tracts (white matter) that make up the bulk of long-range connections (projections) and are critical for inter-region communication. Thus, XNH provides an imaging solution for brain-wide projectomics. However, because XNH data is typically collected at lower resolutions and larger fields-of-view than EM, accurate segmentation of XNH images remains an important challenge that we present here. In this task, we provide volumetric XNH images of cortical white matter axons from the mouse brain along with ground truth annotations for axon trajectories. Manual voxel-wise annotation of ground truth is a time-consuming bottleneck for training segmentation networks. On the other hand, skeleton-based ground truth is much faster to annotate, and sufficient to determine connectivity. Therefore, we encourage participants to develop methods to leverage skeleton-based training. To this end, we provide two types of ground-truth annotations: a small volume of voxel-wise annotations and a larger volume with skeleton-based annotations. Entries will be evaluated on how accurately the submitted segmentations agree with the ground-truth skeleton annotations.

Shahana Ibrahim, Tri Nguyen, Xiao Fu

Using noisy crowdsourced labels from multiple annotators, a deep learning-based end-to-end (E2E) system aims to learn the label correction mechanism and the neural classifier simultaneously. To this end, many E2E systems concatenate the neural classifier with multiple annotator-specific ``label confusion'' layers and co-train the two parts in a parameter-coupled manner. The formulated coupled cross-entropy minimization (CCEM)-type criteria are intuitive and work well in practice. Nonetheless, theoretical understanding of the CCEM criterion has been limited. The contribution of this work is twofold: First, performance guarantees of the CCEM criterion are presented. Our analysis reveals for the first time that the CCEM can indeed correctly identify the annotators' confusion characteristics and the desired ``ground-truth'' neural classifier under realistic conditions, e.g., when only incomplete annotator labeling and finite samples are available. Second, based on the insights learned from our analysis, two regularized variants of the CCEM are proposed. The regularization terms provably enhance the identifiability of the target model parameters in various more challenging cases. A series of synthetic and real data experiments are presented to showcase the effectiveness of our approach.

Zhan Xiong, Junling He, Pieter Valkema et al.

Renal biopsies are the gold standard for the diagnosis of kidney diseases. Lesion scores made by renal pathologists are semi-quantitative and exhibit high inter-observer variability. Automating lesion classification within segmented anatomical structures can provide decision support in quantification analysis, thereby reducing inter-observer variability. Nevertheless, classifying lesions in regions-of-interest (ROIs) is clinically challenging due to (a) a large amount of densely packed anatomical objects, (b) class imbalance across different compartments (at least 3), (c) significant variation in size and shape of anatomical objects and (d) the presence of multi-label lesions per anatomical structure. Existing models cannot address these complexities in an efficient and generic manner. This paper presents an analysis for a \textbf{generalized solution} to datasets from various sources (pathology departments) with different types of lesions. Our approach utilizes two sub-networks: dense instance segmentation and lesion classification. We introduce \textbf{DiffRegFormer}, an end-to-end dense instance segmentation sub-network designed for multi-class, multi-scale objects within ROIs. Combining diffusion models, transformers, and RCNNs, DiffRegFormer {is a computational-friendly framework that can efficiently recognize over 500 objects across three anatomical classes, i.e., glomeruli, tubuli, and arteries, within ROIs.} In a dataset of 303 ROIs from 148 Jones' silver-stained renal Whole Slide Images (WSIs), our approach outperforms previous methods, achieving an Average Precision of 52.1\% (detection) and 46.8\% (segmentation). Moreover, our lesion classification sub-network achieves 89.2\% precision and 64.6\% recall on 21889 object patches out of the 303 ROIs. Lastly, our model demonstrates direct domain transfer to PAS-stained renal WSIs without fine-tuning.

Tri Nguyen, Siddharth Mishra-Sharma, Reuel Williams et al.

Dwarf galaxies are small, dark matter-dominated galaxies, some of which are embedded within the Milky Way. Their lack of baryonic matter (e.g., stars and gas) makes them perfect test beds for probing the properties of dark matter -- understanding the spatial dark matter distribution in these systems can be used to constrain microphysical dark matter interactions that influence the formation and evolution of structures in our Universe. We introduce a new method that leverages simulation-based inference and graph-based machine learning in order to infer the dark matter density profiles of dwarf galaxies from observable kinematics of stars gravitationally bound to these systems. Our approach aims to address some of the limitations of established methods based on dynamical Jeans modeling. We show that this novel method can place stronger constraints on dark matter profiles and, consequently, has the potential to weigh in on some of the ongoing puzzles associated with the small-scale structure of dark matter halos, such as the core-cusp discrepancy.

Minh Tran, Khoa Vo, Tri Nguyen et al.

Amodal Instance Segmentation (AIS) presents an intriguing challenge, including the segmentation prediction of both visible and occluded parts of objects within images. Previous methods have often relied on shape prior information gleaned from training data to enhance amodal segmentation. However, these approaches are susceptible to overfitting and disregard object category details. Recent advancements highlight the potential of conditioned diffusion models, pretrained on extensive datasets, to generate images from latent space. Drawing inspiration from this, we propose AISDiff with a Diffusion Shape Prior Estimation (DiffSP) module. AISDiff begins with the prediction of the visible segmentation mask and object category, alongside occlusion-aware processing through the prediction of occluding masks. Subsequently, these elements are inputted into our DiffSP module to infer the shape prior of the object. DiffSP utilizes conditioned diffusion models pretrained on extensive datasets to extract rich visual features for shape prior estimation. Additionally, we introduce the Shape Prior Amodal Predictor, which utilizes attention-based feature maps from the shape prior to refine amodal segmentation. Experiments across various AIS benchmarks demonstrate the effectiveness of our AISDiff.

Duy Hoang, Huy Ngo, Khoi Pham et al.

Contrastive learning has become pivotal in unsupervised representation learning, with frameworks like Momentum Contrast (MoCo) effectively utilizing large negative sample sets to extract discriminative features. However, traditional approaches often overlook the full potential of key embeddings and are susceptible to performance degradation from noisy negative samples in the memory bank. This study addresses these challenges by proposing an enhanced contrastive learning framework that incorporates two key innovations. First, we introduce a dual-view loss function, which ensures balanced optimization of both query and key embeddings, improving representation quality. Second, we develop a selective negative sampling strategy that emphasizes the most challenging negatives based on cosine similarity, mitigating the impact of noise and enhancing feature discrimination. Extensive experiments demonstrate that our framework achieves superior performance on downstream tasks, delivering robust and well-structured representations. These results highlight the potential of optimized contrastive mechanisms to advance unsupervised learning and extend its applicability across domains such as computer vision and natural language processing

Gesa Mittmann, Sara Laiouar-Pedari, Hendrik A. Mehrtens et al.

The aggressiveness of prostate cancer, the most common cancer in men worldwide, is primarily assessed based on histopathological data using the Gleason scoring system. While artificial intelligence (AI) has shown promise in accurately predicting Gleason scores, these predictions often lack inherent explainability, potentially leading to distrust in human-machine interactions. To address this issue, we introduce a novel dataset of 1,015 tissue microarray core images, annotated by an international group of 54 pathologists. The annotations provide detailed localized pattern descriptions for Gleason grading in line with international guidelines. Utilizing this dataset, we develop an inherently explainable AI system based on a U-Net architecture that provides predictions leveraging pathologists' terminology. This approach circumvents post-hoc explainability methods while maintaining or exceeding the performance of methods trained directly for Gleason pattern segmentation (Dice score: 0.713 $\pm$ 0.003 trained on explanations vs. 0.691 $\pm$ 0.010 trained on Gleason patterns). By employing soft labels during training, we capture the intrinsic uncertainty in the data, yielding strong results in Gleason pattern segmentation even in the context of high interobserver variability. With the release of this dataset, we aim to encourage further research into segmentation in medical tasks with high levels of subjectivity and to advance the understanding of pathologists' reasoning processes.

Tri Nguyen, Shahana Ibrahim, Xiao Fu

The recent integration of deep learning and pairwise similarity annotation-based constrained clustering -- i.e., $\textit{deep constrained clustering}$ (DCC) -- has proven effective for incorporating weak supervision into massive data clustering: Less than 1% of pair similarity annotations can often substantially enhance the clustering accuracy. However, beyond empirical successes, there is a lack of understanding of DCC. In addition, many DCC paradigms are sensitive to annotation noise, but performance-guaranteed noisy DCC methods have been largely elusive. This work first takes a deep look into a recently emerged logistic loss function of DCC, and characterizes its theoretical properties. Our result shows that the logistic DCC loss ensures the identifiability of data membership under reasonable conditions, which may shed light on its effectiveness in practice. Building upon this understanding, a new loss function based on geometric factor analysis is proposed to fend against noisy annotations. It is shown that even under $\textit{unknown}$ annotation confusions, the data membership can still be $\textit{provably}$ identified under our proposed learning criterion. The proposed approach is tested over multiple datasets to validate our claims.

Arun Balajiee Lekshmi Narayanan, Ligia E. Gomez, Martha Michelle Soto Fernandez et al.

When caregivers ask open--ended questions to motivate dialogue with children, it facilitates the child's reading comprehension skills.Although there is scope for use of technological tools, referred here as "intelligent tutoring systems", to scaffold this process, it is currently unclear whether existing intelligent systems that generate human--language like questions is beneficial. Additionally, training data used in the development of these automated question generation systems is typically sourced without attention to demographics, but people with different cultural backgrounds may ask different questions. As a part of a broader project to design an intelligent reading support app for Latinx children, we crowdsourced questions from Latinx caregivers and noncaregivers as well as caregivers and noncaregivers from other demographics. We examine variations in question--asking within this dataset mediated by individual, cultural, and contextual factors. We then design a system that automatically extracts templates from this data to generate open--ended questions that are representative of those asked by Latinx caregivers.

Allison McCarn Deiana, Nhan Tran, Joshua Agar et al.

In this community review report, we discuss applications and techniques for fast machine learning (ML) in science -- the concept of integrating power ML methods into the real-time experimental data processing loop to accelerate scientific discovery. The material for the report builds on two workshops held by the Fast ML for Science community and covers three main areas: applications for fast ML across a number of scientific domains; techniques for training and implementing performant and resource-efficient ML algorithms; and computing architectures, platforms, and technologies for deploying these algorithms. We also present overlapping challenges across the multiple scientific domains where common solutions can be found. This community report is intended to give plenty of examples and inspiration for scientific discovery through integrated and accelerated ML solutions. This is followed by a high-level overview and organization of technical advances, including an abundance of pointers to source material, which can enable these breakthroughs.