new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Jul 15

GasTwinFormer: A Hybrid Vision Transformer for Livestock Methane Emission Segmentation and Dietary Classification in Optical Gas Imaging

Livestock methane emissions represent 32% of human-caused methane production, making automated monitoring critical for climate mitigation strategies. We introduce GasTwinFormer, a hybrid vision transformer for real-time methane emission segmentation and dietary classification in optical gas imaging through a novel Mix Twin encoder alternating between spatially-reduced global attention and locally-grouped attention mechanisms. Our architecture incorporates a lightweight LR-ASPP decoder for multi-scale feature aggregation and enables simultaneous methane segmentation and dietary classification in a unified framework. We contribute the first comprehensive beef cattle methane emission dataset using OGI, containing 11,694 annotated frames across three dietary treatments. GasTwinFormer achieves 74.47% mIoU and 83.63% mF1 for segmentation while maintaining exceptional efficiency with only 3.348M parameters, 3.428G FLOPs, and 114.9 FPS inference speed. Additionally, our method achieves perfect dietary classification accuracy (100%), demonstrating the effectiveness of leveraging diet-emission correlations. Extensive ablation studies validate each architectural component, establishing GasTwinFormer as a practical solution for real-time livestock emission monitoring. Please see our project page at gastwinformer.github.io.

baselab BASE Lab @ SIUC
·
Aug 20, 2025

DeepFood: Deep Learning-Based Food Image Recognition for Computer-Aided Dietary Assessment

Worldwide, in 2014, more than 1.9 billion adults, 18 years and older, were overweight. Of these, over 600 million were obese. Accurately documenting dietary caloric intake is crucial to manage weight loss, but also presents challenges because most of the current methods for dietary assessment must rely on memory to recall foods eaten. The ultimate goal of our research is to develop computer-aided technical solutions to enhance and improve the accuracy of current measurements of dietary intake. Our proposed system in this paper aims to improve the accuracy of dietary assessment by analyzing the food images captured by mobile devices (e.g., smartphone). The key technique innovation in this paper is the deep learning-based food image recognition algorithms. Substantial research has demonstrated that digital imaging accurately estimates dietary intake in many environments and it has many advantages over other methods. However, how to derive the food information (e.g., food type and portion size) from food image effectively and efficiently remains a challenging and open research problem. We propose a new Convolutional Neural Network (CNN)-based food image recognition algorithm to address this problem. We applied our proposed approach to two real-world food image data sets (UEC-256 and Food-101) and achieved impressive results. To the best of our knowledge, these results outperformed all other reported work using these two data sets. Our experiments have demonstrated that the proposed approach is a promising solution for addressing the food image recognition problem. Our future work includes further improving the performance of the algorithms and integrating our system into a real-world mobile and cloud computing-based system to enhance the accuracy of current measurements of dietary intake.

  • 6 authors
·
Jun 17, 2016

Res-VMamba: Fine-Grained Food Category Visual Classification Using Selective State Space Models with Deep Residual Learning

Food classification is the foundation for developing food vision tasks and plays a key role in the burgeoning field of computational nutrition. Due to the complexity of food requiring fine-grained classification, recent academic research mainly modifies Convolutional Neural Networks (CNNs) and/or Vision Transformers (ViTs) to perform food category classification. However, to learn fine-grained features, the CNN backbone needs additional structural design, whereas ViT, containing the self-attention module, has increased computational complexity. In recent months, a new Sequence State Space (S4) model, through a Selection mechanism and computation with a Scan (S6), colloquially termed Mamba, has demonstrated superior performance and computation efficiency compared to the Transformer architecture. The VMamba model, which incorporates the Mamba mechanism into image tasks (such as classification), currently establishes the state-of-the-art (SOTA) on the ImageNet dataset. In this research, we introduce an academically underestimated food dataset CNFOOD-241, and pioneer the integration of a residual learning framework within the VMamba model to concurrently harness both global and local state features inherent in the original VMamba architectural design. The research results show that VMamba surpasses current SOTA models in fine-grained and food classification. The proposed Res-VMamba further improves the classification accuracy to 79.54\% without pretrained weight. Our findings elucidate that our proposed methodology establishes a new benchmark for SOTA performance in food recognition on the CNFOOD-241 dataset. The code can be obtained on GitHub: https://github.com/ChiShengChen/ResVMamba.

  • 5 authors
·
Feb 24, 2024

Scraping Social Media Photos Posted in Kenya and Elsewhere to Detect and Analyze Food Types

Monitoring population-level changes in diet could be useful for education and for implementing interventions to improve health. Research has shown that data from social media sources can be used for monitoring dietary behavior. We propose a scrape-by-location methodology to create food image datasets from Instagram posts. We used it to collect 3.56 million images over a period of 20 days in March 2019. We also propose a scrape-by-keywords methodology and used it to scrape ~30,000 images and their captions of 38 Kenyan food types. We publish two datasets of 104,000 and 8,174 image/caption pairs, respectively. With the first dataset, Kenya104K, we train a Kenyan Food Classifier, called KenyanFC, to distinguish Kenyan food from non-food images posted in Kenya. We used the second dataset, KenyanFood13, to train a classifier KenyanFTR, short for Kenyan Food Type Recognizer, to recognize 13 popular food types in Kenya. The KenyanFTR is a multimodal deep neural network that can identify 13 types of Kenyan foods using both images and their corresponding captions. Experiments show that the average top-1 accuracy of KenyanFC is 99% over 10,400 tested Instagram images and of KenyanFTR is 81% over 8,174 tested data points. Ablation studies show that three of the 13 food types are particularly difficult to categorize based on image content only and that adding analysis of captions to the image analysis yields a classifier that is 9 percent points more accurate than a classifier that relies only on images. Our food trend analysis revealed that cakes and roasted meats were the most popular foods in photographs on Instagram in Kenya in March 2019.

  • 6 authors
·
Aug 31, 2019

FEAST: Retrieval-Augmented Multi-Hierarchical Food Classification for the FoodEx2 System

Hierarchical text classification (HTC) and extreme multi-label classification (XML) tasks face compounded challenges from complex label interdependencies, data sparsity, and extreme output dimensions. These challenges are exemplified in the European Food Safety Authority's FoodEx2 system-a standardized food classification framework essential for food consumption monitoring and contaminant exposure assessment across Europe. FoodEx2 coding transforms natural language food descriptions into a set of codes from multiple standardized hierarchies, but faces implementation barriers due to its complex structure. Given a food description (e.g., "organic yogurt''), the system identifies its base term ("yogurt''), all the applicable facet categories (e.g., "production method''), and then, every relevant facet descriptors to each category (e.g., "organic production''). While existing models perform adequately on well-balanced and semantically dense hierarchies, no work has been applied on the practical constraints imposed by the FoodEx2 system. The limited literature addressing such real-world scenarios further compounds these challenges. We propose FEAST (Food Embedding And Semantic Taxonomy), a novel retrieval-augmented framework that decomposes FoodEx2 classification into a three-stage approach: (1) base term identification, (2) multi-label facet prediction, and (3) facet descriptor assignment. By leveraging the system's hierarchical structure to guide training and performing deep metric learning, FEASTlearns discriminative embeddings that mitigate data sparsity and improve generalization on rare and fine-grained labels. Evaluated on the multilingual FoodEx2 benchmark, FEAST outperforms the prior European's CNN baseline F1 scores by 12-38 % on rare classes.

  • 6 authors
·
Mar 2

NutriGen: Personalized Meal Plan Generator Leveraging Large Language Models to Enhance Dietary and Nutritional Adherence

Maintaining a balanced diet is essential for overall health, yet many individuals struggle with meal planning due to nutritional complexity, time constraints, and lack of dietary knowledge. Personalized food recommendations can help address these challenges by tailoring meal plans to individual preferences, habits, and dietary restrictions. However, existing dietary recommendation systems often lack adaptability, fail to consider real-world constraints such as food ingredient availability, and require extensive user input, making them impractical for sustainable and scalable daily use. To address these limitations, we introduce NutriGen, a framework based on large language models (LLM) designed to generate personalized meal plans that align with user-defined dietary preferences and constraints. By building a personalized nutrition database and leveraging prompt engineering, our approach enables LLMs to incorporate reliable nutritional references like the USDA nutrition database while maintaining flexibility and ease-of-use. We demonstrate that LLMs have strong potential in generating accurate and user-friendly food recommendations, addressing key limitations in existing dietary recommendation systems by providing structured, practical, and scalable meal plans. Our evaluation shows that Llama 3.1 8B and GPT-3.5 Turbo achieve the lowest percentage errors of 1.55\% and 3.68\%, respectively, producing meal plans that closely align with user-defined caloric targets while minimizing deviation and improving precision. Additionally, we compared the performance of DeepSeek V3 against several established models to evaluate its potential in personalized nutrition planning.

  • 4 authors
·
Feb 27, 2025

NGQA: A Nutritional Graph Question Answering Benchmark for Personalized Health-aware Nutritional Reasoning

Diet plays a critical role in human health, yet tailoring dietary reasoning to individual health conditions remains a major challenge. Nutrition Question Answering (QA) has emerged as a popular method for addressing this problem. However, current research faces two critical limitations. On one hand, the absence of datasets involving user-specific medical information severely limits personalization. This challenge is further compounded by the wide variability in individual health needs. On the other hand, while large language models (LLMs), a popular solution for this task, demonstrate strong reasoning abilities, they struggle with the domain-specific complexities of personalized healthy dietary reasoning, and existing benchmarks fail to capture these challenges. To address these gaps, we introduce the Nutritional Graph Question Answering (NGQA) benchmark, the first graph question answering dataset designed for personalized nutritional health reasoning. NGQA leverages data from the National Health and Nutrition Examination Survey (NHANES) and the Food and Nutrient Database for Dietary Studies (FNDDS) to evaluate whether a food is healthy for a specific user, supported by explanations of the key contributing nutrients. The benchmark incorporates three question complexity settings and evaluates reasoning across three downstream tasks. Extensive experiments with LLM backbones and baseline models demonstrate that the NGQA benchmark effectively challenges existing models. In sum, NGQA addresses a critical real-world problem while advancing GraphQA research with a novel domain-specific benchmark.

  • 12 authors
·
Dec 19, 2024

MetaFood3D: Large 3D Food Object Dataset with Nutrition Values

Food computing is both important and challenging in computer vision (CV). It significantly contributes to the development of CV algorithms due to its frequent presence in datasets across various applications, ranging from classification and instance segmentation to 3D reconstruction. The polymorphic shapes and textures of food, coupled with high variation in forms and vast multimodal information, including language descriptions and nutritional data, make food computing a complex and demanding task for modern CV algorithms. 3D food modeling is a new frontier for addressing food-related problems, due to its inherent capability to deal with random camera views and its straightforward representation for calculating food portion size. However, the primary hurdle in the development of algorithms for food object analysis is the lack of nutrition values in existing 3D datasets. Moreover, in the broader field of 3D research, there is a critical need for domain-specific test datasets. To bridge the gap between general 3D vision and food computing research, we propose MetaFood3D. This dataset consists of 637 meticulously labeled 3D food objects across 108 categories, featuring detailed nutrition information, weight, and food codes linked to a comprehensive nutrition database. The dataset emphasizes intra-class diversity and includes rich modalities such as textured mesh files, RGB-D videos, and segmentation masks. Experimental results demonstrate our dataset's significant potential for improving algorithm performance, highlight the challenging gap between video captures and 3D scanned data, and show the strength of the MetaFood3D dataset in high-quality data generation, simulation, and augmentation.

  • 13 authors
·
Sep 3, 2024

A Named Entity Based Approach to Model Recipes

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

  • 3 authors
·
Apr 25, 2020

GlucoLens: Explainable Postprandial Blood Glucose Prediction from Diet and Physical Activity

Postprandial hyperglycemia, marked by the blood glucose level exceeding the normal range after meals, is a critical indicator of progression toward type 2 diabetes in prediabetic and healthy individuals. A key metric for understanding blood glucose dynamics after eating is the postprandial area under the curve (PAUC). Predicting PAUC in advance based on a person's diet and activity level and explaining what affects postprandial blood glucose could allow an individual to adjust their lifestyle accordingly to maintain normal glucose levels. In this paper, we propose GlucoLens, an explainable machine learning approach to predict PAUC and hyperglycemia from diet, activity, and recent glucose patterns. We conducted a five-week user study with 10 full-time working individuals to develop and evaluate the computational model. Our machine learning model takes multimodal data including fasting glucose, recent glucose, recent activity, and macronutrient amounts, and provides an interpretable prediction of the postprandial glucose pattern. Our extensive analyses of the collected data revealed that the trained model achieves a normalized root mean squared error (NRMSE) of 0.123. On average, GlucoLense with a Random Forest backbone provides a 16% better result than the baseline models. Additionally, GlucoLens predicts hyperglycemia with an accuracy of 74% and recommends different options to help avoid hyperglycemia through diverse counterfactual explanations. Code available: https://github.com/ab9mamun/GlucoLens.

  • 7 authors
·
Mar 5, 2025

MozzaVID: Mozzarella Volumetric Image Dataset

Influenced by the complexity of volumetric imaging, there is a shortage of established datasets useful for benchmarking volumetric deep-learning models. As a consequence, new and existing models are not easily comparable, limiting the development of architectures optimized specifically for volumetric data. To counteract this trend, we introduce MozzaVID - a large, clean, and versatile volumetric classification dataset. Our dataset contains X-ray computed tomography (CT) images of mozzarella microstructure and enables the classification of 25 cheese types and 149 cheese samples. We provide data in three different resolutions, resulting in three dataset instances containing from 591 to 37,824 images. While being general-purpose, the dataset also facilitates investigating mozzarella structure properties. The structure of food directly affects its functional properties and thus its consumption experience. Understanding food structure helps tune the production and mimicking it enables sustainable alternatives to animal-derived food products. The complex and disordered nature of food structures brings a unique challenge, where a choice of appropriate imaging method, scale, and sample size is not trivial. With this dataset we aim to address these complexities, contributing to more robust structural analysis models. The dataset can be downloaded from: https://archive.compute.dtu.dk/files/public/projects/MozzaVID/.

  • 7 authors
·
Dec 6, 2024

Large Scale Visual Food Recognition

Food recognition plays an important role in food choice and intake, which is essential to the health and well-being of humans. It is thus of importance to the computer vision community, and can further support many food-oriented vision and multimodal tasks. Unfortunately, we have witnessed remarkable advancements in generic visual recognition for released large-scale datasets, yet largely lags in the food domain. In this paper, we introduce Food2K, which is the largest food recognition dataset with 2,000 categories and over 1 million images.Compared with existing food recognition datasets, Food2K bypasses them in both categories and images by one order of magnitude, and thus establishes a new challenging benchmark to develop advanced models for food visual representation learning. Furthermore, we propose a deep progressive region enhancement network for food recognition, which mainly consists of two components, namely progressive local feature learning and region feature enhancement. The former adopts improved progressive training to learn diverse and complementary local features, while the latter utilizes self-attention to incorporate richer context with multiple scales into local features for further local feature enhancement. Extensive experiments on Food2K demonstrate the effectiveness of our proposed method. More importantly, we have verified better generalization ability of Food2K in various tasks, including food recognition, food image retrieval, cross-modal recipe retrieval, food detection and segmentation. Food2K can be further explored to benefit more food-relevant tasks including emerging and more complex ones (e.g., nutritional understanding of food), and the trained models on Food2K can be expected as backbones to improve the performance of more food-relevant tasks. We also hope Food2K can serve as a large scale fine-grained visual recognition benchmark.

  • 8 authors
·
Mar 30, 2021

An Algorithm for Recommending Groceries Based on an Item Ranking Method

This research proposes a new recommender system algorithm for online grocery shopping. The algorithm is based on the perspective that, since the grocery items are usually bought in bulk, a grocery recommender system should be capable of recommending the items in bulk. The algorithm figures out the possible dishes a user may cook based on the items added to the basket and recommends the ingredients accordingly. Our algorithm does not depend on the user ratings. Customers usually do not have the patience to rate the groceries they purchase. Therefore, algorithms that are not dependent on user ratings need to be designed. Instead of using a brute force search, this algorithm limits the search space to a set of only a few probably food categories. Each food category consists of several food subcategories. For example, "fried rice" and "biryani" are food subcategories that belong to the food category "rice". For each food category, items are ranked according to how well they can differentiate a food subcategory. To each food subcategory in the activated search space, this algorithm attaches a score. The score is calculated based on the rank of the items added to the basket. Once the score exceeds a threshold value, its corresponding subcategory gets activated. The algorithm then uses a basket-to-recipe similarity measure to identify the best recipe matches within the activated subcategories only. This reduces the search space to a great extent. We may argue that this algorithm is similar to the content-based recommender system in some sense, but it does not suffer from the limitations like limited content, over-specialization, or the new user problem.

  • 2 authors
·
May 3, 2021

CaLoRAify: Calorie Estimation with Visual-Text Pairing and LoRA-Driven Visual Language Models

The obesity phenomenon, known as the heavy issue, is a leading cause of preventable chronic diseases worldwide. Traditional calorie estimation tools often rely on specific data formats or complex pipelines, limiting their practicality in real-world scenarios. Recently, vision-language models (VLMs) have excelled in understanding real-world contexts and enabling conversational interactions, making them ideal for downstream tasks such as ingredient analysis. However, applying VLMs to calorie estimation requires domain-specific data and alignment strategies. To this end, we curated CalData, a 330K image-text pair dataset tailored for ingredient recognition and calorie estimation, combining a large-scale recipe dataset with detailed nutritional instructions for robust vision-language training. Built upon this dataset, we present CaLoRAify, a novel VLM framework aligning ingredient recognition and calorie estimation via training with visual-text pairs. During inference, users only need a single monocular food image to estimate calories while retaining the flexibility of agent-based conversational interaction. With Low-rank Adaptation (LoRA) and Retrieve-augmented Generation (RAG) techniques, our system enhances the performance of foundational VLMs in the vertical domain of calorie estimation. Our code and data are fully open-sourced at https://github.com/KennyYao2001/16824-CaLORAify.

  • 4 authors
·
Dec 13, 2024

V-Nutri: Dish-Level Nutrition Estimation from Egocentric Cooking Videos

Nutrition estimation of meals from visual data is an important problem for dietary monitoring and computational health, but existing approaches largely rely on single images of the finally completed dish. This setting is fundamentally limited because many nutritionally relevant ingredients and transformations, such as oils, sauces, and mixed components, become visually ambiguous after cooking, making accurate calorie and macronutrient estimation difficult. In this paper, we investigate whether the cooking process information from egocentric cooking videos can contribute to dish-level nutrition estimation. First, we further manually annotated the HD-EPIC dataset and established the first benchmark for video-based nutrition estimation. Most importantly, we propose V-Nutri, a staged framework that combines Nutrition5K-pretrained visual backbones with a lightweight fusion module that aggregates features from the final dish frame and cooking process keyframes extracted from the egocentric videos. V-Nutri also includes a cooking keyframes selection module, a VideoMamba-based event-detection model that targets ingredient-addition moments. Experiments on the HD-EPIC dataset show that process cues can provide complementary nutritional evidence, improving nutrition estimation under controlled conditions. Our results further indicate that the benefit of process keyframes depends strongly on backbone representation capacity and event detection quality. Our code and annotated dataset is available at https://github.com/K624-YCK/V-Nutri.

  • 3 authors
·
Apr 12

A Large-Scale Benchmark for Food Image Segmentation

Food image segmentation is a critical and indispensible task for developing health-related applications such as estimating food calories and nutrients. Existing food image segmentation models are underperforming due to two reasons: (1) there is a lack of high quality food image datasets with fine-grained ingredient labels and pixel-wise location masks -- the existing datasets either carry coarse ingredient labels or are small in size; and (2) the complex appearance of food makes it difficult to localize and recognize ingredients in food images, e.g., the ingredients may overlap one another in the same image, and the identical ingredient may appear distinctly in different food images. In this work, we build a new food image dataset FoodSeg103 (and its extension FoodSeg154) containing 9,490 images. We annotate these images with 154 ingredient classes and each image has an average of 6 ingredient labels and pixel-wise masks. In addition, we propose a multi-modality pre-training approach called ReLeM that explicitly equips a segmentation model with rich and semantic food knowledge. In experiments, we use three popular semantic segmentation methods (i.e., Dilated Convolution based, Feature Pyramid based, and Vision Transformer based) as baselines, and evaluate them as well as ReLeM on our new datasets. We believe that the FoodSeg103 (and its extension FoodSeg154) and the pre-trained models using ReLeM can serve as a benchmark to facilitate future works on fine-grained food image understanding. We make all these datasets and methods public at https://xiongweiwu.github.io/foodseg103.html.

  • 6 authors
·
May 11, 2021

HealthGenie: Empowering Users with Healthy Dietary Guidance through Knowledge Graph and Large Language Models

Seeking dietary guidance often requires navigating complex professional knowledge while accommodating individual health conditions. Knowledge Graphs (KGs) offer structured and interpretable nutritional information, whereas Large Language Models (LLMs) naturally facilitate conversational recommendation delivery. In this paper, we present HealthGenie, an interactive system that combines the strengths of LLMs and KGs to provide personalized dietary recommendations along with hierarchical information visualization for a quick and intuitive overview. Upon receiving a user query, HealthGenie performs query refinement and retrieves relevant information from a pre-built KG. The system then visualizes and highlights pertinent information, organized by defined categories, while offering detailed, explainable recommendation rationales. Users can further tailor these recommendations by adjusting preferences interactively. Our evaluation, comprising a within-subject comparative experiment and an open-ended discussion, demonstrates that HealthGenie effectively supports users in obtaining personalized dietary guidance based on their health conditions while reducing interaction effort and cognitive load. These findings highlight the potential of LLM-KG integration in supporting decision-making through explainable and visualized information. We examine the system's usefulness and effectiveness with an N=12 within-subject study and provide design considerations for future systems that integrate conversational LLM and KG.

  • 9 authors
·
Apr 20, 2025

Calorie Aware Automatic Meal Kit Generation from an Image

Calorie and nutrition research has attained increased interest in recent years. But, due to the complexity of the problem, literature in this area focuses on a limited subset of ingredients or dish types and simple convolutional neural networks or traditional machine learning. Simultaneously, estimation of ingredient portions can help improve calorie estimation and meal re-production from a given image. In this paper, given a single cooking image, a pipeline for calorie estimation and meal re-production for different servings of the meal is proposed. The pipeline contains two stages. In the first stage, a set of ingredients associated with the meal in the given image are predicted. In the second stage, given image features and ingredients, portions of the ingredients and finally the total meal calorie are simultaneously estimated using a deep transformer-based model. Portion estimation introduced in the model helps improve calorie estimation and is also beneficial for meal re-production in different serving sizes. To demonstrate the benefits of the pipeline, the model can be used for meal kits generation. To evaluate the pipeline, the large scale dataset Recipe1M is used. Prior to experiments, the Recipe1M dataset is parsed and explicitly annotated with portions of ingredients. Experiments show that using ingredients and their portions significantly improves calorie estimation. Also, a visual interface is created in which a user can interact with the pipeline to reach accurate calorie estimations and generate a meal kit for cooking purposes.

  • 2 authors
·
Dec 17, 2021

Knowledge distillation to effectively attain both region-of-interest and global semantics from an image where multiple objects appear

Models based on convolutional neural networks (CNN) and transformers have steadily been improved. They also have been applied in various computer vision downstream tasks. However, in object detection tasks, accurately localizing and classifying almost infinite categories of foods in images remains challenging. To address these problems, we first segmented the food as the region-of-interest (ROI) by using the segment-anything model (SAM) and masked the rest of the region except ROI as black pixels. This process simplified the problems into a single classification for which annotation and training were much simpler than object detection. The images in which only the ROI was preserved were fed as inputs to fine-tune various off-the-shelf models that encoded their own inductive biases. Among them, Data-efficient image Transformers (DeiTs) had the best classification performance. Nonetheless, when foods' shapes and textures were similar, the contextual features of the ROI-only images were not enough for accurate classification. Therefore, we introduced a novel type of combined architecture, RveRNet, which consisted of ROI, extra-ROI, and integration modules that allowed it to account for both the ROI's and global contexts. The RveRNet's F1 score was 10% better than other individual models when classifying ambiguous food images. If the RveRNet's modules were DeiT with the knowledge distillation from the CNN, performed the best. We investigated how architectures can be made robust against input noise caused by permutation and translocation. The results indicated that there was a trade-off between how much the CNN teacher's knowledge could be distilled to DeiT and DeiT's innate strength. Code is publicly available at: https://github.com/Seonwhee-Genome/RveRNet.

  • 1 authors
·
Jul 11, 2024

NutriOrion: A Hierarchical Multi-Agent Framework for Personalized Nutrition Intervention Grounded in Clinical Guidelines

Personalized nutrition intervention for patients with multimorbidity is critical for improving health outcomes, yet remains challenging because it requires the simultaneous integration of heterogeneous clinical conditions, medications, and dietary guidelines. Single-agent large language models (LLMs) often suffer from context overload and attention dilution when processing such high-dimensional patient profiles. We introduce NutriOrion, a hierarchical multi-agent framework with a parallel-then-sequential reasoning topology. NutriOrion decomposes nutrition planning into specialized domain agents with isolated contexts to mitigate anchoring bias, followed by a conditional refinement stage. The framework includes a multi-objective prioritization algorithm to resolve conflicting dietary requirements and a safety constraint mechanism that injects pharmacological contraindications as hard negative constraints during synthesis, ensuring clinical validity by construction rather than post-hoc filtering. For clinical interoperability, NutriOrion maps synthesized insights into the ADIME standard and FHIR R4 resources. Evaluated on 330 stroke patients with multimorbidity, NutriOrion outperforms multiple baselines, including GPT-4.1 and alternative multi-agent architectures. It achieves a 12.1 percent drug-food interaction violation rate, demonstrates strong personalization with negative correlations (-0.26 to -0.35) between patient biomarkers and recommended risk nutrients, and yields clinically meaningful dietary improvements, including a 167 percent increase in fiber and a 27 percent increase in potassium, alongside reductions in sodium (9 percent) and sugars (12 percent).

  • 10 authors
·
Feb 20

The Dataset Nutrition Label: A Framework To Drive Higher Data Quality Standards

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

  • 5 authors
·
May 9, 2018

Llama Guard: LLM-based Input-Output Safeguard for Human-AI Conversations

We introduce Llama Guard, an LLM-based input-output safeguard model geared towards Human-AI conversation use cases. Our model incorporates a safety risk taxonomy, a valuable tool for categorizing a specific set of safety risks found in LLM prompts (i.e., prompt classification). This taxonomy is also instrumental in classifying the responses generated by LLMs to these prompts, a process we refer to as response classification. For the purpose of both prompt and response classification, we have meticulously gathered a dataset of high quality. Llama Guard, a Llama2-7b model that is instruction-tuned on our collected dataset, albeit low in volume, demonstrates strong performance on existing benchmarks such as the OpenAI Moderation Evaluation dataset and ToxicChat, where its performance matches or exceeds that of currently available content moderation tools. Llama Guard functions as a language model, carrying out multi-class classification and generating binary decision scores. Furthermore, the instruction fine-tuning of Llama Guard allows for the customization of tasks and the adaptation of output formats. This feature enhances the model's capabilities, such as enabling the adjustment of taxonomy categories to align with specific use cases, and facilitating zero-shot or few-shot prompting with diverse taxonomies at the input. We are making Llama Guard model weights available and we encourage researchers to further develop and adapt them to meet the evolving needs of the community for AI safety.

  • 11 authors
·
Dec 7, 2023 1

Food Pairing Unveiled: Exploring Recipe Creation Dynamics through Recommender Systems

In the early 2000s, renowned chef Heston Blumenthal formulated his "food pairing" hypothesis, positing that if foods share many flavor compounds, then they tend to taste good when eaten together. In 2011, Ahn et al. conducted a study using a dataset of recipes, ingredients, and flavor compounds, finding that, in Western cuisine, ingredients in recipes often share more flavor compounds than expected by chance, indicating a natural tendency towards food pairing. Building upon Ahn's research, our work applies state-of-the-art collaborative filtering techniques to the dataset, providing a tool that can recommend new foods to add in recipes, retrieve missing ingredients and advise against certain combinations. We create our recommender in two ways, by taking into account ingredients appearances in recipes or shared flavor compounds between foods. While our analysis confirms the existence of food pairing, the recipe-based recommender performs significantly better than the flavor-based one, leading to the conclusion that food pairing is just one of the principles to take into account when creating recipes. Furthermore, and more interestingly, we find that food pairing in data is mostly due to trivial couplings of very similar ingredients, leading to a reconsideration of its current role in recipes, from being an already existing feature to a key to open up new scenarios in gastronomy. Our flavor-based recommender can thus leverage this novel concept and provide a new tool to lead culinary innovation.

  • 3 authors
·
Jun 21, 2024

Automated Chronotyping from a Daily Calendar using Machine Learning

Chronotype compares individuals' circadian phase to others. It contextualizes mental health risk assessments and detection of social jet lag, which can hamper mental health and cognitive performance. Existing ways of determining chronotypes, such as Dim Light Melatonin Onset (DLMO) or the Morningness-Eveningness Questionnaire (MEQ), are limited by being discrete in time and time-intensive to update, meaning they rarely capture real-world variability across time. Chronotyping users based on a daily planner app might augment existing methods to enable assessment continuously and at scale. This paper reports the construction of a supervised binary classifier that attempts to demonstrate the feasibility of this approach. 1,460 registered users from the Owaves app opted in by filling out the MEQ survey between July 14, 2022, and May 1, 2023. 142 met the eligibility criteria. We used multimodal app data from individuals identified as morning and evening types from MEQ data, basing the classifier on app time series data. This included daily timing for 8 main lifestyle activity types: exercise, sleep, social interactions, meal times, relaxation, work, play, and miscellaneous, as defined in the app. The timing of activities showed substantial change across time, as well as heterogeneity by activity type. Our novel chronotyping classifier was able to predict the morningness and eveningness of its users with an ROC AUC of 0.70. Our findings demonstrate the feasibility of chronotype classification from multimodal, real-world app data, while highlighting fundamental challenges to applying discrete and fixed labels to complex, dynamic, multimodal behaviors. Our findings suggest a potential for real-time monitoring of shifts in chronotype specific to different causes (i.e. types of activity), which could feasibly be used to support future, prospective mental health support research.

  • 7 authors
·
Jul 8, 2024

Review GIDE -- Restaurant Review Gastrointestinal Illness Detection and Extraction with Large Language Models

Foodborne gastrointestinal (GI) illness is a common cause of ill health in the UK. However, many cases do not interact with the healthcare system, posing significant challenges for traditional surveillance methods. The growth of publicly available online restaurant reviews and advancements in large language models (LLMs) present potential opportunities to extend disease surveillance by identifying public reports of GI illness. In this study, we introduce a novel annotation schema, developed with experts in GI illness, applied to the Yelp Open Dataset of reviews. Our annotations extend beyond binary disease detection, to include detailed extraction of information on symptoms and foods. We evaluate the performance of open-weight LLMs across these three tasks: GI illness detection, symptom extraction, and food extraction. We compare this performance to RoBERTa-based classification models fine-tuned specifically for these tasks. Our results show that using prompt-based approaches, LLMs achieve micro-F1 scores of over 90% for all three of our tasks. Using prompting alone, we achieve micro-F1 scores that exceed those of smaller fine-tuned models. We further demonstrate the robustness of LLMs in GI illness detection across three bias-focused experiments. Our results suggest that publicly available review text and LLMs offer substantial potential for public health surveillance of GI illness by enabling highly effective extraction of key information. While LLMs appear to exhibit minimal bias in processing, the inherent limitations of restaurant review data highlight the need for cautious interpretation of results.

  • 8 authors
·
Mar 12, 2025

Evaluating the Feasibility of Inferring Dietary Behavior Change Receptivity from Egocentric Images of Eating Environment

Accurately assessing dietary behavior change receptivity is essential for designing effective just-in-time adaptive interventions (JITAIs) that promote healthier eating habits. However, self-report-based assessment of behavior change receptivity is sparse and delayed, limiting its practical use in continuous monitoring. To explore whether passive sensing may help address this challenge, this study conducts a pilot investigation of inferring participants' self-reported behavior change receptivity from egocentric eating images collected by a wearable camera. We use pilot data obtained from free-living eating episodes using the Automatic Ingestion Monitor v2 (AIM-2). The data included egocentric image sequences captured during eating and paired with responses to questions assessing specific dimensions of behavior change receptivity (awareness, interaction capability, and motivation). To examine whether visual information contained any relevancy to these responses, we evaluated a transfer-learning-assisted framework that combines a pre-trained Contrastive Language-Image Pre-Training (CLIP) vision encoder with a lightweight transformer classifier. The model processes eating episode image sequences to extract potential semantic and temporal cues related to behavior change receptivity. Preliminary experimental results show promising improvements over simple baseline models for behavior change receptivity indicators. These early findings suggest that egocentric eating episode images may contain cues related to dietary behavior change receptivity, and warrant further investigation with larger and more comprehensive datasets.

  • 6 authors
·
May 26

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

  • 7 authors
·
May 23, 2025

Periodical embeddings uncover hidden interdisciplinary patterns in the subject classification scheme of science

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

  • 2 authors
·
Dec 27, 2025

Lightweight Fish Classification Model for Sustainable Marine Management: Indonesian Case

The enormous demand for seafood products has led to exploitation of marine resources and near-extinction of some species. In particular, overfishing is one the main issues in sustainable marine development. In alignment with the protection of marine resources and sustainable fishing, this study proposes to advance fish classification techniques that support identifying protected fish species using state-of-the-art machine learning. We use a custom modification of the MobileNet model to design a lightweight classifier called M-MobileNet that is capable of running on limited hardware. As part of the study, we compiled a labeled dataset of 37,462 images of fish found in the waters of the Indonesian archipelago. The proposed model is trained on the dataset to classify images of the captured fish into their species and give recommendations on whether they are consumable or not. Our modified MobileNet model uses only 50\% of the top layer parameters with about 42% GTX 860M utility and achieves up to 97% accuracy in fish classification and determining its consumability. Given the limited computing capacity available on many fishing vessels, the proposed model provides a practical solution to on-site fish classification. In addition, synchronized implementation of the proposed model on multiple vessels can supply valuable information about the movement and location of different species of fish.

  • 3 authors
·
Jan 4, 2024 1

iBitter-Stack: A Multi-Representation Ensemble Learning Model for Accurate Bitter Peptide Identification

The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key roles in physiological and pharmacological processes. However, experimental methods for identifying bitter peptides are time-consuming and expensive. With the rapid expansion of peptide sequence databases in the post-genomic era, the demand for efficient computational approaches to distinguish bitter from non-bitter peptides has become increasingly significant. In this study, we propose a novel stacking-based ensemble learning framework aimed at enhancing the accuracy and reliability of bitter peptide classification. Our method integrates diverse sequence-based feature representations and leverages a broad set of machine learning classifiers. The first stacking layer comprises multiple base classifiers, each trained on distinct feature encoding schemes, while the second layer employs logistic regression to refine predictions using an eight-dimensional probability vector. Extensive evaluations on a carefully curated dataset demonstrate that our model significantly outperforms existing predictive methods, providing a robust and reliable computational tool for bitter peptide identification. Our approach achieves an accuracy of 96.09\% and a Matthews Correlation Coefficient (MCC) of 0.9220 on the independent test set, underscoring its effectiveness and generalizability. To facilitate real-time usage and broader accessibility, we have also developed a user-friendly web server based on the proposed method, which is freely accessible at https://ibitter-stack-webserver.streamlit.app/. This tool enables researchers and practitioners to conveniently screen peptide sequences for bitterness in real-time applications.

  • 5 authors
·
May 21, 2025

Machine Learning Applied to the Detection of Mycotoxin in Food: A Review

Mycotoxins, toxic secondary metabolites produced by certain fungi, pose significant threats to global food safety and public health. These compounds can contaminate a variety of crops, leading to economic losses and health risks to both humans and animals. Traditional lab analysis methods for mycotoxin detection can be time-consuming and may not always be suitable for large-scale screenings. However, in recent years, machine learning (ML) methods have gained popularity for use in the detection of mycotoxins and in the food safety industry in general, due to their accurate and timely predictions. We provide a systematic review on some of the recent ML applications for detecting/predicting the presence of mycotoxin on a variety of food ingredients, highlighting their advantages, challenges, and potential for future advancements. We address the need for reproducibility and transparency in ML research through open access to data and code. An observation from our findings is the frequent lack of detailed reporting on hyperparameters in many studies as well as a lack of open source code, which raises concerns about the reproducibility and optimisation of the ML models used. The findings reveal that while the majority of studies predominantly utilised neural networks for mycotoxin detection, there was a notable diversity in the types of neural network architectures employed, with convolutional neural networks being the most popular.

  • 4 authors
·
Apr 23, 2024

Choosing an Appropriate Platform and Workflow for Processing Camera Trap Data using Artificial Intelligence

Camera traps have transformed how ecologists study wildlife species distributions, activity patterns, and interspecific interactions. Although camera traps provide a cost-effective method for monitoring species, the time required for data processing can limit survey efficiency. Thus, the potential of Artificial Intelligence (AI), specifically Deep Learning (DL), to process camera-trap data has gained considerable attention. Using DL for these applications involves training algorithms, such as Convolutional Neural Networks (CNNs), to automatically detect objects and classify species. To overcome technical challenges associated with training CNNs, several research communities have recently developed platforms that incorporate DL in easy-to-use interfaces. We review key characteristics of four AI-powered platforms -- Wildlife Insights (WI), MegaDetector (MD), Machine Learning for Wildlife Image Classification (MLWIC2), and Conservation AI -- including data management tools and AI features. We also provide R code in an open-source GitBook, to demonstrate how users can evaluate model performance, and incorporate AI output in semi-automated workflows. We found that species classifications from WI and MLWIC2 generally had low recall values (animals that were present in the images often were not classified to the correct species). Yet, the precision of WI and MLWIC2 classifications for some species was high (i.e., when classifications were made, they were generally accurate). MD, which classifies images using broader categories (e.g., "blank" or "animal"), also performed well. Thus, we conclude that, although species classifiers were not accurate enough to automate image processing, DL could be used to improve efficiencies by accepting classifications with high confidence values for certain species or by filtering images containing blanks.

  • 6 authors
·
Feb 4, 2022

Introducing Three New Benchmark Datasets for Hierarchical Text Classification

Hierarchical Text Classification (HTC) is a natural language processing task with the objective to classify text documents into a set of classes from a structured class hierarchy. Many HTC approaches have been proposed which attempt to leverage the class hierarchy information in various ways to improve classification performance. Machine learning-based classification approaches require large amounts of training data and are most-commonly compared through three established benchmark datasets, which include the Web Of Science (WOS), Reuters Corpus Volume 1 Version 2 (RCV1-V2) and New York Times (NYT) datasets. However, apart from the RCV1-V2 dataset which is well-documented, these datasets are not accompanied with detailed description methodologies. In this paper, we introduce three new HTC benchmark datasets in the domain of research publications which comprise the titles and abstracts of papers from the Web of Science publication database. We first create two baseline datasets which use existing journal-and citation-based classification schemas. Due to the respective shortcomings of these two existing schemas, we propose an approach which combines their classifications to improve the reliability and robustness of the dataset. We evaluate the three created datasets with a clustering-based analysis and show that our proposed approach results in a higher quality dataset where documents that belong to the same class are semantically more similar compared to the other datasets. Finally, we provide the classification performance of four state-of-the-art HTC approaches on these three new datasets to provide baselines for future studies on machine learning-based techniques for scientific publication classification.

  • 3 authors
·
Nov 28, 2024

Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

  • 2 authors
·
Nov 27, 2020

Meta-information-aware Dual-path Transformer for Differential Diagnosis of Multi-type Pancreatic Lesions in Multi-phase CT

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

  • 8 authors
·
Mar 1, 2023

F4-ITS: Fine-grained Feature Fusion for Food Image-Text Search

The proliferation of digital food content has intensified the need for robust and accurate systems capable of fine-grained visual understanding and retrieval. In this work, we address the challenging task of food image-to-text matching, a critical component in applications such as dietary monitoring, smart kitchens, and restaurant automation. We propose F4-ITS: Fine-grained Feature Fusion for Food Image-Text Search, a training-free, vision-language model (VLM)-guided framework that significantly improves retrieval performance through enhanced multi-modal feature representations. Our approach introduces two key contributions: (1) a uni-directional(and bi-directional) multi-modal fusion strategy that combines image embeddings with VLM-generated textual descriptions to improve query expressiveness, and (2) a novel feature-based re-ranking mechanism for top-k retrieval, leveraging predicted food ingredients to refine results and boost precision. Leveraging open-source image-text encoders, we demonstrate substantial gains over standard baselines - achieving ~10% and ~7.7% improvements in top-1 retrieval under dense and sparse caption scenarios, and a ~28.6% gain in top-k ingredient-level retrieval. Additionally, we show that smaller models (e.g., ViT-B/32) can match or outperform larger counterparts (e.g., ViT-H, ViT-G, ViT-bigG) when augmented with textual fusion, highlighting the effectiveness of our method in resource-constrained settings. Code and test datasets will be made publicly available at: https://github.com/mailcorahul/f4-its

  • 1 authors
·
Aug 23, 2025

Accelerometry-Derived Digital Biomarkers for Cardiometabolic Risk: A Population-Representative Tabular Benchmark with Uncertainty Quantification

Structured tabular data dominates clinical medicine, yet existing benchmarks fail to reflect real-world properties like complex survey sampling, demographic oversampling, and subgroup fairness. We introduce the NHANES Accelerometry Cardiometabolic Benchmark, derived from NHANES 2003-2006, comprising 1,381 adults with hip-worn accelerometry, fasting laboratory biomarkers, dietary intake, and anthropometrics. We evaluate three tabular learning methods -- ridge regression, XGBoost, and the foundation model TabPFN v2 -- to predict glycated haemoglobin (HbA1c), fasting triglycerides, and C-reactive protein (CRP) from activity phenotypes and lifestyle covariates. TabPFN v2 achieves the best overall performance (HbA1c R^2=0.156, CRP R^2=0.383), while triglycerides remain largely unpredictable (R^2 < 0.05), consistent with known genetic dominance. We apply split conformal prediction to generate distribution-free 90% prediction intervals and evaluate demographic coverage equity across sex and race/ethnicity subgroups. Marginal coverage aligns with the 90% target for CRP and HbA1c but falls below for triglycerides. At the subgroup level, we observe localized undercoverage (e.g., HbA1c for Mexican American participants), illustrating the gap between marginal guarantees and the conditional coverage required for clinical fairness. Code and data are at https://github.com/felizzi/nhanes-accel-cardiometabolic-benchmark.

  • 1 authors
·
Jun 28

A Unified Three-Stage Machine Learning Framework for Diabetes Detection, Subtype Discrimination, and Cognitive-Metabolic Hypothesis Testing

Diabetes mellitus affects over 537 million adults worldwide and remains a major challenge in preventive healthcare. Existing machine-learning studies primarily formulate diabetes prediction as a binary classification problem, while subtype-oriented analysis and glycaemic-cognitive associations remain comparatively underexplored. We present a reproducible three-stage machine learning framework for diabetes detection, subtype-oriented clustering, and metabolic-cognitive association analysis. In Stage 1, five supervised classifiers together with a stacking ensemble are benchmarked on the NCSU Diabetes Dataset using stratified five-fold cross-validation and evaluation metrics including ROC-AUC, balanced accuracy, recall, and F1-score. SVM-RBF and Logistic Regression achieve the highest ROC-AUC (0.825 pm 0.026), while Random Forest achieves the highest accuracy (0.762 pm 0.030). SHAP explainability identifies Glucose, BMI, and Age as the dominant predictive biomarkers. In Stage 2, silhouette-validated K-Means clustering (k=2, silhouette approx 0.116) is applied to confirmed diabetic cases using Glucose, Insulin, and Age, recovering clinically plausible subtype-oriented partitions without requiring ground-truth subtype labels. In Stage 3, statistical analysis of the Ohio Longitudinal Cognitive Dataset (n=373) reveals a significant positive association between glycaemic control and cognitive function (ρ_s = 0.208, p = 5.29 times 10^{-5}), which survives Holm correction. The findings support the utility of statistically grounded and interpretable ML pipelines for reproducible diabetes analytics and subtype-aware exploratory analysis.

  • 3 authors
·
May 12

Revisiting MLLMs: An In-Depth Analysis of Image Classification Abilities

With the rapid advancement of Multimodal Large Language Models (MLLMs), a variety of benchmarks have been introduced to evaluate their capabilities. While most evaluations have focused on complex tasks such as scientific comprehension and visual reasoning, little attention has been given to assessing their fundamental image classification abilities. In this paper, we address this gap by thoroughly revisiting the MLLMs with an in-depth analysis of image classification. Specifically, building on established datasets, we examine a broad spectrum of scenarios, from general classification tasks (e.g., ImageNet, ObjectNet) to more fine-grained categories such as bird and food classification. Our findings reveal that the most recent MLLMs can match or even outperform CLIP-style vision-language models on several datasets, challenging the previous assumption that MLLMs are bad at image classification VLMClassifier. To understand the factors driving this improvement, we conduct an in-depth analysis of the network architecture, data selection, and training recipe used in public MLLMs. Our results attribute this success to advancements in language models and the diversity of training data sources. Based on these observations, we further analyze and attribute the potential reasons to conceptual knowledge transfer and enhanced exposure of target concepts, respectively. We hope our findings will offer valuable insights for future research on MLLMs and their evaluation in image classification tasks.

  • 7 authors
·
Dec 20, 2024

MV-MLM: Bridging Multi-View Mammography and Language for Breast Cancer Diagnosis and Risk Prediction

Large annotated datasets are essential for training robust Computer-Aided Diagnosis (CAD) models for breast cancer detection or risk prediction. However, acquiring such datasets with fine-detailed annotation is both costly and time-consuming. Vision-Language Models (VLMs), such as CLIP, which are pre-trained on large image-text pairs, offer a promising solution by enhancing robustness and data efficiency in medical imaging tasks. This paper introduces a novel Multi-View Mammography and Language Model for breast cancer classification and risk prediction, trained on a dataset of paired mammogram images and synthetic radiology reports. Our MV-MLM leverages multi-view supervision to learn rich representations from extensive radiology data by employing cross-modal self-supervision across image-text pairs. This includes multiple views and the corresponding pseudo-radiology reports. We propose a novel joint visual-textual learning strategy to enhance generalization and accuracy performance over different data types and tasks to distinguish breast tissues or cancer characteristics(calcification, mass) and utilize these patterns to understand mammography images and predict cancer risk. We evaluated our method on both private and publicly available datasets, demonstrating that the proposed model achieves state-of-the-art performance in three classification tasks: (1) malignancy classification, (2) subtype classification, and (3) image-based cancer risk prediction. Furthermore, the model exhibits strong data efficiency, outperforming existing fully supervised or VLM baselines while trained on synthetic text reports and without the need for actual radiology reports.

  • 4 authors
·
Oct 30, 2025

GLiClass: Generalist Lightweight Model for Sequence Classification Tasks

Classification is one of the most widespread tasks in AI applications, serving often as the first step in filtering, sorting, and categorizing data. Since modern AI systems must handle large volumes of input data and early pipeline stages can propagate errors downstream, achieving high efficiency and accuracy is critical. Moreover, classification requirements can change dynamically based on user needs, necessitating models with strong zero-shot capabilities. While generative LLMs have become mainstream for zero-shot classification due to their versatility, they suffer from inconsistent instruction following and computational inefficiency. Cross-encoders, commonly used as rerankers in RAG pipelines, face a different bottleneck: they must process text-label pairs sequentially, significantly reducing efficiency with large label sets. Embedding-based approaches offer good efficiency but struggle with complex scenarios involving logical and semantic constraints. We propose GLiClass, a novel method that adapts the GLiNER architecture for sequence classification tasks. Our approach achieves strong accuracy and efficiency comparable to embedding-based methods, while maintaining the flexibility needed for zero-shot and few-shot learning scenarios. Additionally, we adapted proximal policy optimization (PPO) for multi-label text classification, enabling training classifiers in data-sparse conditions or from human feedback.

CLOC: Contrastive Learning for Ordinal Classification with Multi-Margin N-pair Loss

In ordinal classification, misclassifying neighboring ranks is common, yet the consequences of these errors are not the same. For example, misclassifying benign tumor categories is less consequential, compared to an error at the pre-cancerous to cancerous threshold, which could profoundly influence treatment choices. Despite this, existing ordinal classification methods do not account for the varying importance of these margins, treating all neighboring classes as equally significant. To address this limitation, we propose CLOC, a new margin-based contrastive learning method for ordinal classification that learns an ordered representation based on the optimization of multiple margins with a novel multi-margin n-pair loss (MMNP). CLOC enables flexible decision boundaries across key adjacent categories, facilitating smooth transitions between classes and reducing the risk of overfitting to biases present in the training data. We provide empirical discussion regarding the properties of MMNP and show experimental results on five real-world image datasets (Adience, Historical Colour Image Dating, Knee Osteoarthritis, Indian Diabetic Retinopathy Image, and Breast Carcinoma Subtyping) and one synthetic dataset simulating clinical decision bias. Our results demonstrate that CLOC outperforms existing ordinal classification methods and show the interpretability and controllability of CLOC in learning meaningful, ordered representations that align with clinical and practical needs.

  • 3 authors
·
Jan 11

Mycorrhiza: Genotype Assignment usingPhylogenetic Networks

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

  • 3 authors
·
Oct 13, 2020

Toward Automated Cognitive Assessment in Parkinson's Disease Using Pretrained Language Models

Understanding how individuals with Parkinson's disease (PD) describe cognitive experiences in their daily lives can offer valuable insights into disease-related cognitive and emotional changes. However, extracting such information from unstructured patient narratives is challenging due to the subtle, overlapping nature of cognitive constructs. This study developed and evaluated natural language processing (NLP) models to automatically identify categories that reflect various cognitive processes from de-identified first-person narratives. Three model families, a Bio_ClinicalBERT-based span categorization model for nested entity recognition, a fine-tuned Meta-Llama-3-8B-Instruct model using QLoRA for instruction following, and GPT-4o mini evaluated under zero- and few-shot settings, were compared on their performance on extracting seven categories. Our findings indicated that model performance varied substantially across categories and model families. The fine-tuned Meta-Llama-3-8B-Instruct achieved the highest overall F1-scores (0.74 micro-average and 0.59 macro-average), particularly excelling in context-dependent categories such as thought and social interaction. Bio_ClinicalBERT exhibited high precision but low recall and performed comparable to Llama for some category types such as location and time but failed on other categories such as thought, emotion and social interaction. Compared to conventional information extraction tasks, this task presents a greater challenge due to the abstract and overlapping nature of narrative accounts of complex cognitive processes. Nonetheless, with continued refinement, these NLP systems hold promise for enabling low-burden, longitudinal monitoring of cognitive function and serving as a valuable complement to formal neuropsychological assessments in PD.

  • 7 authors
·
Nov 10, 2025

Personality Style Recognition via Machine Learning: Identifying Anaclitic and Introjective Personality Styles from Patients' Speech

In disentangling the heterogeneity observed in psychopathology, personality of the patients is considered crucial. While it has been demonstrated that personality traits are reflected in the language used by a patient, we hypothesize that this enables automatic inference of the personality type directly from speech utterances, potentially more accurately than through a traditional questionnaire-based approach explicitly designed for personality classification. To validate this hypothesis, we adopt natural language processing (NLP) and standard machine learning tools for classification. We test this on a dataset of recorded clinical diagnostic interviews (CDI) on a sample of 79 patients diagnosed with major depressive disorder (MDD) -- a condition for which differentiated treatment based on personality styles has been advocated -- and classified into anaclitic and introjective personality styles. We start by analyzing the interviews to see which linguistic features are associated with each style, in order to gain a better understanding of the styles. Then, we develop automatic classifiers based on (a) standardized questionnaire responses; (b) basic text features, i.e., TF-IDF scores of words and word sequences; (c) more advanced text features, using LIWC (linguistic inquiry and word count) and context-aware features using BERT (bidirectional encoder representations from transformers); (d) audio features. We find that automated classification with language-derived features (i.e., based on LIWC) significantly outperforms questionnaire-based classification models. Furthermore, the best performance is achieved by combining LIWC with the questionnaire features. This suggests that more work should be put into developing linguistically based automated techniques for characterizing personality, however questionnaires still to some extent complement such methods.

  • 6 authors
·
Nov 7, 2023

Improving Prototypical Parts Abstraction for Case-Based Reasoning Explanations Designed for the Kidney Stone Type Recognition

The in-vivo identification of the kidney stone types during an ureteroscopy would be a major medical advance in urology, as it could reduce the time of the tedious renal calculi extraction process, while diminishing infection risks. Furthermore, such an automated procedure would make possible to prescribe anti-recurrence treatments immediately. Nowadays, only few experienced urologists are able to recognize the kidney stone types in the images of the videos displayed on a screen during the endoscopy. Thus, several deep learning (DL) models have recently been proposed to automatically recognize the kidney stone types using ureteroscopic images. However, these DL models are of black box nature whicl limits their applicability in clinical settings. This contribution proposes a case-based reasoning DL model which uses prototypical parts (PPs) and generates local and global descriptors. The PPs encode for each class (i.e., kidney stone type) visual feature information (hue, saturation, intensity and textures) similar to that used by biologists. The PPs are optimally generated due a new loss function used during the model training. Moreover, the local and global descriptors of PPs allow to explain the decisions ("what" information, "where in the images") in an understandable way for biologists and urologists. The proposed DL model has been tested on a database including images of the six most widespread kidney stone types. The overall average classification accuracy was 90.37. When comparing this results with that of the eight other DL models of the kidney stone state-of-the-art, it can be seen that the valuable gain in explanability was not reached at the expense of accuracy which was even slightly increased with respect to that (88.2) of the best method of the literature. These promising and interpretable results also encourage urologists to put their trust in AI-based solutions.

  • 8 authors
·
Sep 19, 2024

Natural Language Processing in Electronic Health Records in Relation to Healthcare Decision-making: A Systematic Review

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

  • 8 authors
·
Jun 22, 2023

FOLD-SE: An Efficient Rule-based Machine Learning Algorithm with Scalable Explainability

We present FOLD-SE, an efficient, explainable machine learning algorithm for classification tasks given tabular data containing numerical and categorical values. FOLD-SE generates a set of default rules-essentially a stratified normal logic program-as an (explainable) trained model. Explainability provided by FOLD-SE is scalable, meaning that regardless of the size of the dataset, the number of learned rules and learned literals stay quite small while good accuracy in classification is maintained. A model with smaller number of rules and literals is easier to understand for human beings. FOLD-SE is competitive with state-of-the-art machine learning algorithms such as XGBoost and Multi-Layer Perceptrons (MLP) wrt accuracy of prediction. However, unlike XGBoost and MLP, the FOLD-SE algorithm is explainable. The FOLD-SE algorithm builds upon our earlier work on developing the explainable FOLD-R++ machine learning algorithm for binary classification and inherits all of its positive features. Thus, pre-processing of the dataset, using techniques such as one-hot encoding, is not needed. Like FOLD-R++, FOLD-SE uses prefix sum to speed up computations resulting in FOLD-SE being an order of magnitude faster than XGBoost and MLP in execution speed. The FOLD-SE algorithm outperforms FOLD-R++ as well as other rule-learning algorithms such as RIPPER in efficiency, performance and scalability, especially for large datasets. A major reason for scalable explainability of FOLD-SE is the use of a literal selection heuristics based on Gini Impurity, as opposed to Information Gain used in FOLD-R++. A multi-category classification version of FOLD-SE is also presented.

  • 2 authors
·
Aug 16, 2022 1