ProtoKD: Learning from Extremely Scarce Data for Parasite Ova Recognition

Developing reliable computational frameworks for early parasite detection, particularly at the ova (or egg) stage is crucial for advancing healthcare and effectively managing potential public health crises. While deep learning has significantly assisted human workers in various tasks, its application and diagnostics has been constrained by the need for extensive datasets. The ability to learn from an extremely scarce training dataset, i.e., when fewer than 5 examples per class are present, is essential for scaling deep learning models in biomedical applications where large-scale data collection and annotation can be expensive or not possible (in case of novel or unknown infectious agents). In this study, we introduce ProtoKD, one of the first approaches to tackle the problem of multi-class parasitic ova recognition using extremely scarce data. Combining the principles of prototypical networks and self-distillation, we can learn robust representations from only one sample per class. Furthermore, we establish a new benchmark to drive research in this critical direction and validate that the proposed ProtoKD framework achieves state-of-the-art performance. Additionally, we evaluate the framework's generalizability to other downstream tasks by assessing its performance on a large-scale taxonomic profiling task based on metagenomes sequenced from real-world clinical data.

Shape-Graph Matching Network (SGM-net): Registration for Statistical Shape Analysis

This paper focuses on the statistical analysis of shapes of data objects called shape graphs, a set of nodes connected by articulated curves with arbitrary shapes. A critical need here is a constrained registration of points (nodes to nodes, edges to edges) across objects. This, in turn, requires optimization over the permutation group, made challenging by differences in nodes (in terms of numbers, locations) and edges (in terms of shapes, placements, and sizes) across objects. This paper tackles this registration problem using a novel neural-network architecture and involves an unsupervised loss function developed using the elastic shape metric for curves. This architecture results in (1) state-of-the-art matching performance and (2) an order of magnitude reduction in the computational cost relative to baseline approaches. We demonstrate the effectiveness of the proposed approach using both simulated data and real-world 2D and 3D shape graphs. Code and data will be made publicly available after review to foster research.

Discovering Novel Actions in an Open World with Object-Grounded Visual Commonsense Reasoning

Learning to infer labels in an open world, i.e., in an environment where the target ``labels'' are unknown, is an important characteristic for achieving autonomy. Foundation models pre-trained on enormous amounts of data have shown remarkable generalization skills through prompting, particularly in zero-shot inference. However, their performance is restricted to the correctness of the target label's search space. In an open world where these labels are unknown, the search space can be exceptionally large. It can require reasoning over several combinations of elementary concepts to arrive at an inference, which severely restricts the performance of such models. To tackle this challenging problem, we propose a neuro-symbolic framework called ALGO - novel Action Learning with Grounded Object recognition that can use symbolic knowledge stored in large-scale knowledge bases to infer activities (verb-noun combinations) in egocentric videos with limited supervision using two steps. First, we propose a novel neuro-symbolic prompting approach that uses object-centric vision-language foundation models as a noisy oracle to ground objects in the video through evidence-based reasoning. Second, driven by prior commonsense knowledge, we discover plausible activities through an energy-based symbolic pattern theory framework and learn to ground knowledge-based action (verb) concepts in the video. Extensive experiments on two publicly available datasets (GTEA Gaze and GTEA Gaze Plus) demonstrate its performance on open-world activity inference and its generalization to unseen actions in an unknown search space. We show that ALGO can be extended to zero-shot settings and demonstrate its competitive performance to multimodal foundation models.

Scalable Pathogen Detection from Next Generation DNA Sequencing with Deep Learning

Next-generation sequencing technologies have enhanced the scope of Internet-of-Things (IoT) to include genomics for personalized medicine through the increased availability of an abundance of genome data collected from heterogeneous sources at a reduced cost. Given the sheer magnitude of the collected data and the significant challenges offered by the presence of highly similar genomic structure across species, there is a need for robust, scalable analysis platforms to extract actionable knowledge such as the presence of potentially zoonotic pathogens. The emergence of zoonotic diseases from novel pathogens, such as the influenza virus in 1918 and SARS-CoV-2 in 2019 that can jump species barriers and lead to pandemic underscores the need for scalable metagenome analysis. In this work, we propose MG2Vec, a deep learning-based solution that uses the transformer network as its backbone, to learn robust features from raw metagenome sequences for downstream biomedical tasks such as targeted and generalized pathogen detection. Extensive experiments on four increasingly challenging, yet realistic diagnostic settings, show that the proposed approach can help detect pathogens from uncurated, real-world clinical samples with minimal human supervision in the form of labels. Further, we demonstrate that the learned representations can generalize to completely unrelated pathogens across diseases and species for large-scale metagenome analysis. We provide a comprehensive evaluation of a novel representation learning framework for metagenome-based disease diagnostics with deep learning and provide a way forward for extracting and using robust vector representations from low-cost next generation sequencing to develop generalizable diagnostic tools.

Iterative Scene Graph Generation with Generative Transformers

Scene graphs provide a rich, structured representation of a scene by encoding the entities (objects) and their spatial relationships in a graphical format. This representation has proven useful in several tasks, such as question answering, captioning, and even object detection, to name a few. Current approaches take a generation-by-classification approach where the scene graph is generated through labeling of all possible edges between objects in a scene, which adds computational overhead to the approach. This work introduces a generative transformer-based approach to generating scene graphs beyond link prediction. Using two transformer-based components, we first sample a possible scene graph structure from detected objects and their visual features. We then perform predicate classification on the sampled edges to generate the final scene graph. This approach allows us to efficiently generate scene graphs from images with minimal inference overhead. Extensive experiments on the Visual Genome dataset demonstrate the efficiency of the proposed approach. Without bells and whistles, we obtain, on average, 20.7% mean recall (mR@100) across different settings for scene graph generation (SGG), outperforming state-of-the-art SGG approaches while offering competitive performance to unbiased SGG approaches.

A Rich Recipe Representation as Plan to Support Expressive Multi Modal Queries on Recipe Content and Preparation Process

Food is not only a basic human necessity but also a key factor driving a society's health and economic well-being. As a result, the cooking domain is a popular use-case to demonstrate decision-support (AI) capabilities in service of benefits like precision health with tools ranging from information retrieval interfaces to task-oriented chatbots. An AI here should understand concepts in the food domain (e.g., recipes, ingredients), be tolerant to failures encountered while cooking (e.g., browning of butter), handle allergy-based substitutions, and work with multiple data modalities (e.g. text and images). However, the recipes today are handled as textual documents which makes it difficult for machines to read, reason and handle ambiguity. This demands a need for better representation of the recipes, overcoming the ambiguity and sparseness that exists in the current textual documents. In this paper, we discuss the construction of a machine-understandable rich recipe representation (R3), in the form of plans, from the recipes available in natural language. R3 is infused with additional knowledge such as information about allergens and images of ingredients, possible failures and tips for each atomic cooking step. To show the benefits of R3, we also present TREAT, a tool for recipe retrieval which uses R3 to perform multi-modal reasoning on the recipe's content (plan objects - ingredients and cooking tools), food preparation process (plan actions and time), and media type (image, text). R3 leads to improved retrieval efficiency and new capabilities that were hither-to not possible in textual representation.

Metagenome2Vec: Building Contextualized Representations for Scalable Metagenome Analysis

Advances in next-generation metagenome sequencing have the potential to revolutionize the point-of-care diagnosis of novel pathogen infections, which could help prevent potential widespread transmission of diseases. Given the high volume of metagenome sequences, there is a need for scalable frameworks to analyze and segment metagenome sequences from clinical samples, which can be highly imbalanced. There is an increased need for learning robust representations from metagenome reads since pathogens within a family can have highly similar genome structures (some more than 90%) and hence enable the segmentation and identification of novel pathogen sequences with limited labeled data. In this work, we propose Metagenome2Vec - a contextualized representation that captures the global structural properties inherent in metagenome data and local contextualized properties through self-supervised representation learning. We show that the learned representations can help detect six (6) related pathogens from clinical samples with less than 100 labeled sequences. Extensive experiments on simulated and clinical metagenome data show that the proposed representation encodes compositional properties that can generalize beyond annotations to segment novel pathogens in an unsupervised setting.

Towards Active Vision for Action Localization with Reactive Control and Predictive Learning

Visual event perception tasks such as action localization have primarily focused on supervised learning settings under a static observer, i.e., the camera is static and cannot be controlled by an algorithm. They are often restricted by the quality, quantity, and diversity of \textit{annotated} training data and do not often generalize to out-of-domain samples. In this work, we tackle the problem of active action localization where the goal is to localize an action while controlling the geometric and physical parameters of an active camera to keep the action in the field of view without training data. We formulate an energy-based mechanism that combines predictive learning and reactive control to perform active action localization without rewards, which can be sparse or non-existent in real-world environments. We perform extensive experiments in both simulated and real-world environments on two tasks - active object tracking and active action localization. We demonstrate that the proposed approach can generalize to different tasks and environments in a streaming fashion, without explicit rewards or training. We show that the proposed approach outperforms unsupervised baselines and obtains competitive performance compared to those trained with reinforcement learning.

MG-NET: Leveraging Pseudo-Imaging for Multi-Modal Metagenome Analysis

The emergence of novel pathogens and zoonotic diseases like the SARS-CoV-2 have underlined the need for developing novel diagnosis and intervention pipelines that can learn rapidly from small amounts of labeled data. Combined with technological advances in next-generation sequencing, metagenome-based diagnostic tools hold much promise to revolutionize rapid point-of-care diagnosis. However, there are significant challenges in developing such an approach, the chief among which is to learn self-supervised representations that can help detect novel pathogen signatures with very low amounts of labeled data. This is particularly a difficult task given that closely related pathogens can share more than 90% of their genome structure. In this work, we address these challenges by proposing MG-Net, a self-supervised representation learning framework that leverages multi-modal context using pseudo-imaging data derived from clinical metagenome sequences. We show that the proposed framework can learn robust representations from unlabeled data that can be used for downstream tasks such as metagenome sequence classification with limited access to labeled data. Extensive experiments show that the learned features outperform current baseline metagenome representations, given only 1000 samples per class.

Learning Actor-centered Representations for Action Localization in Streaming Videos using Predictive Learning

Event perception tasks such as recognizing and localizing actions in streaming videos are essential for tackling visual understanding tasks. Progress has primarily been driven by the use of large-scale, annotated training data in a supervised manner. In this work, we tackle the problem of learning \textit{actor-centered} representations through the notion of continual hierarchical predictive learning to localize actions in streaming videos without any training annotations. Inspired by cognitive theories of event perception, we propose a novel, self-supervised framework driven by the notion of hierarchical predictive learning to construct actor-centered features by attention-based contextualization. Extensive experiments on three benchmark datasets show that the approach can learn robust representations for localizing actions using only one epoch of training, i.e., we train the model continually in streaming fashion - one frame at a time, with a single pass through training videos. We show that the proposed approach outperforms unsupervised and weakly supervised baselines while offering competitive performance to fully supervised approaches. Finally, we show that the proposed model can generalize to out-of-domain data without significant loss in performance without any finetuning for both the recognition and localization tasks.