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Oct 31

Dynamic Perceiver for Efficient Visual Recognition

Early exiting has become a promising approach to improving the inference efficiency of deep networks. By structuring models with multiple classifiers (exits), predictions for ``easy'' samples can be generated at earlier exits, negating the need for executing deeper layers. Current multi-exit networks typically implement linear classifiers at intermediate layers, compelling low-level features to encapsulate high-level semantics. This sub-optimal design invariably undermines the performance of later exits. In this paper, we propose Dynamic Perceiver (Dyn-Perceiver) to decouple the feature extraction procedure and the early classification task with a novel dual-branch architecture. A feature branch serves to extract image features, while a classification branch processes a latent code assigned for classification tasks. Bi-directional cross-attention layers are established to progressively fuse the information of both branches. Early exits are placed exclusively within the classification branch, thus eliminating the need for linear separability in low-level features. Dyn-Perceiver constitutes a versatile and adaptable framework that can be built upon various architectures. Experiments on image classification, action recognition, and object detection demonstrate that our method significantly improves the inference efficiency of different backbones, outperforming numerous competitive approaches across a broad range of computational budgets. Evaluation on both CPU and GPU platforms substantiate the superior practical efficiency of Dyn-Perceiver. Code is available at https://www.github.com/LeapLabTHU/Dynamic_Perceiver.

  • 10 authors
·
Jun 19, 2023

PromptMRG: Diagnosis-Driven Prompts for Medical Report Generation

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

  • 4 authors
·
Aug 24, 2023

Similarity-Distance-Magnitude Universal Verification

We address the neural network robustness problem by adding Similarity (i.e., correctly predicted depth-matches into training)-awareness and Distance-to-training-distribution-awareness to the existing output Magnitude (i.e., decision-boundary)-awareness of the softmax function. The resulting SDM activation function provides strong signals of the relative epistemic (reducible) predictive uncertainty. We use this novel behavior to further address the complementary HCI problem of mapping the output to human-interpretable summary statistics over relevant partitions of a held-out calibration set. Estimates of prediction-conditional uncertainty are obtained via a parsimonious learned transform over the class-conditional empirical CDFs of the output of a final-layer SDM activation function. For decision-making and as an intrinsic model check, estimates of class-conditional accuracy are obtained by further partitioning the high-probability regions of this calibrated output into class-conditional, region-specific CDFs. The uncertainty estimates from SDM calibration are remarkably robust to test-time distribution shifts and out-of-distribution inputs; incorporate awareness of the effective sample size; provide estimates of uncertainty from the learning and data splitting processes; and are well-suited for selective classification and conditional branching for additional test-time compute based on the predictive uncertainty, as for selective LLM generation, routing, and composition over multiple models and retrieval. Finally, we construct SDM networks, LLMs with uncertainty-aware verification and interpretability-by-exemplar as intrinsic properties. We provide open-source software implementing these results.

  • 1 authors
·
Feb 27

ProtoECGNet: Case-Based Interpretable Deep Learning for Multi-Label ECG Classification with Contrastive Learning

Deep learning-based electrocardiogram (ECG) classification has shown impressive performance but clinical adoption has been slowed by the lack of transparent and faithful explanations. Post hoc methods such as saliency maps may fail to reflect a model's true decision process. Prototype-based reasoning offers a more transparent alternative by grounding decisions in similarity to learned representations of real ECG segments, enabling faithful, case-based explanations. We introduce ProtoECGNet, a prototype-based deep learning model for interpretable, multi-label ECG classification. ProtoECGNet employs a structured, multi-branch architecture that reflects clinical interpretation workflows: it integrates a 1D CNN with global prototypes for rhythm classification, a 2D CNN with time-localized prototypes for morphology-based reasoning, and a 2D CNN with global prototypes for diffuse abnormalities. Each branch is trained with a prototype loss designed for multi-label learning, combining clustering, separation, diversity, and a novel contrastive loss that encourages appropriate separation between prototypes of unrelated classes while allowing clustering for frequently co-occurring diagnoses. We evaluate ProtoECGNet on all 71 diagnostic labels from the PTB-XL dataset, demonstrating competitive performance relative to state-of-the-art black-box models while providing structured, case-based explanations. To assess prototype quality, we conduct a structured clinician review of the final model's projected prototypes, finding that they are rated as representative and clear. ProtoECGNet shows that prototype learning can be effectively scaled to complex, multi-label time-series classification, offering a practical path toward transparent and trustworthy deep learning models for clinical decision support.

  • 7 authors
·
Apr 11

CrossViT: Cross-Attention Multi-Scale Vision Transformer for Image Classification

The recently developed vision transformer (ViT) has achieved promising results on image classification compared to convolutional neural networks. Inspired by this, in this paper, we study how to learn multi-scale feature representations in transformer models for image classification. To this end, we propose a dual-branch transformer to combine image patches (i.e., tokens in a transformer) of different sizes to produce stronger image features. Our approach processes small-patch and large-patch tokens with two separate branches of different computational complexity and these tokens are then fused purely by attention multiple times to complement each other. Furthermore, to reduce computation, we develop a simple yet effective token fusion module based on cross attention, which uses a single token for each branch as a query to exchange information with other branches. Our proposed cross-attention only requires linear time for both computational and memory complexity instead of quadratic time otherwise. Extensive experiments demonstrate that our approach performs better than or on par with several concurrent works on vision transformer, in addition to efficient CNN models. For example, on the ImageNet1K dataset, with some architectural changes, our approach outperforms the recent DeiT by a large margin of 2\% with a small to moderate increase in FLOPs and model parameters. Our source codes and models are available at https://github.com/IBM/CrossViT.

  • 3 authors
·
Mar 27, 2021

Dual-Branch Network for Portrait Image Quality Assessment

Portrait images typically consist of a salient person against diverse backgrounds. With the development of mobile devices and image processing techniques, users can conveniently capture portrait images anytime and anywhere. However, the quality of these portraits may suffer from the degradation caused by unfavorable environmental conditions, subpar photography techniques, and inferior capturing devices. In this paper, we introduce a dual-branch network for portrait image quality assessment (PIQA), which can effectively address how the salient person and the background of a portrait image influence its visual quality. Specifically, we utilize two backbone networks (i.e., Swin Transformer-B) to extract the quality-aware features from the entire portrait image and the facial image cropped from it. To enhance the quality-aware feature representation of the backbones, we pre-train them on the large-scale video quality assessment dataset LSVQ and the large-scale facial image quality assessment dataset GFIQA. Additionally, we leverage LIQE, an image scene classification and quality assessment model, to capture the quality-aware and scene-specific features as the auxiliary features. Finally, we concatenate these features and regress them into quality scores via a multi-perception layer (MLP). We employ the fidelity loss to train the model via a learning-to-rank manner to mitigate inconsistencies in quality scores in the portrait image quality assessment dataset PIQ. Experimental results demonstrate that the proposed model achieves superior performance in the PIQ dataset, validating its effectiveness. The code is available at https://github.com/sunwei925/DN-PIQA.git.

  • 11 authors
·
May 14, 2024

Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification

In the application of Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) classification, attention mechanisms often focus on a subset of discriminative instances, which are closely linked to overfitting. To mitigate overfitting, we present Attention-Challenging MIL (ACMIL). ACMIL combines two techniques based on separate analyses for attention value concentration. Firstly, UMAP of instance features reveals various patterns among discriminative instances, with existing attention mechanisms capturing only some of them. To remedy this, we introduce Multiple Branch Attention (MBA) to capture more discriminative instances using multiple attention branches. Secondly, the examination of the cumulative value of Top-K attention scores indicates that a tiny number of instances dominate the majority of attention. In response, we present Stochastic Top-K Instance Masking (STKIM), which masks out a portion of instances with Top-K attention values and allocates their attention values to the remaining instances. The extensive experimental results on three WSI datasets with two pre-trained backbones reveal that our ACMIL outperforms state-of-the-art methods. Additionally, through heatmap visualization and UMAP visualization, this paper extensively illustrates ACMIL's effectiveness in suppressing attention value concentration and overcoming the overfitting challenge. The source code is available at https://github.com/dazhangyu123/ACMIL.

  • 6 authors
·
Nov 13, 2023

FER-YOLO-Mamba: Facial Expression Detection and Classification Based on Selective State Space

Facial Expression Recognition (FER) plays a pivotal role in understanding human emotional cues. However, traditional FER methods based on visual information have some limitations, such as preprocessing, feature extraction, and multi-stage classification procedures. These not only increase computational complexity but also require a significant amount of computing resources. Considering Convolutional Neural Network (CNN)-based FER schemes frequently prove inadequate in identifying the deep, long-distance dependencies embedded within facial expression images, and the Transformer's inherent quadratic computational complexity, this paper presents the FER-YOLO-Mamba model, which integrates the principles of Mamba and YOLO technologies to facilitate efficient coordination in facial expression image recognition and localization. Within the FER-YOLO-Mamba model, we further devise a FER-YOLO-VSS dual-branch module, which combines the inherent strengths of convolutional layers in local feature extraction with the exceptional capability of State Space Models (SSMs) in revealing long-distance dependencies. To the best of our knowledge, this is the first Vision Mamba model designed for facial expression detection and classification. To evaluate the performance of the proposed FER-YOLO-Mamba model, we conducted experiments on two benchmark datasets, RAF-DB and SFEW. The experimental results indicate that the FER-YOLO-Mamba model achieved better results compared to other models. The code is available from https://github.com/SwjtuMa/FER-YOLO-Mamba.

  • 4 authors
·
May 2, 2024

MVCNet: Multi-View Contrastive Network for Motor Imagery Classification

Electroencephalography (EEG)-based brain-computer interfaces (BCIs) enable neural interaction by decoding brain activity for external communication. Motor imagery (MI) decoding has received significant attention due to its intuitive mechanism. However, most existing models rely on single-stream architectures and overlook the multi-view nature of EEG signals, leading to limited performance and generalization. We propose a multi-view contrastive network (MVCNet), a dual-branch architecture that parallelly integrates CNN and Transformer models to capture both local spatial-temporal features and global temporal dependencies. To enhance the informativeness of training data, MVCNet incorporates a unified augmentation pipeline across time, frequency, and spatial domains. Two contrastive modules are further introduced: a cross-view contrastive module that enforces consistency of original and augmented views, and a cross-model contrastive module that aligns features extracted from both branches. Final representations are fused and jointly optimized by contrastive and classification losses. Experiments on five public MI datasets across three scenarios demonstrate that MVCNet consistently outperforms seven state-of-the-art MI decoding networks, highlighting its effectiveness and generalization ability. MVCNet provides a robust solution for MI decoding by integrating multi-view information and dual-branch modeling, contributing to the development of more reliable BCI systems.

  • 5 authors
·
Feb 18

Uni4Eye: Unified 2D and 3D Self-supervised Pre-training via Masked Image Modeling Transformer for Ophthalmic Image Classification

A large-scale labeled dataset is a key factor for the success of supervised deep learning in computer vision. However, a limited number of annotated data is very common, especially in ophthalmic image analysis, since manual annotation is time-consuming and labor-intensive. Self-supervised learning (SSL) methods bring huge opportunities for better utilizing unlabeled data, as they do not need massive annotations. With an attempt to use as many as possible unlabeled ophthalmic images, it is necessary to break the dimension barrier, simultaneously making use of both 2D and 3D images. In this paper, we propose a universal self-supervised Transformer framework, named Uni4Eye, to discover the inherent image property and capture domain-specific feature embedding in ophthalmic images. Uni4Eye can serve as a global feature extractor, which builds its basis on a Masked Image Modeling task with a Vision Transformer (ViT) architecture. We employ a Unified Patch Embedding module to replace the origin patch embedding module in ViT for jointly processing both 2D and 3D input images. Besides, we design a dual-branch multitask decoder module to simultaneously perform two reconstruction tasks on the input image and its gradient map, delivering discriminative representations for better convergence. We evaluate the performance of our pre-trained Uni4Eye encoder by fine-tuning it on six downstream ophthalmic image classification tasks. The superiority of Uni4Eye is successfully established through comparisons to other state-of-the-art SSL pre-training methods.

  • 4 authors
·
Mar 9, 2022

Adaptive Dual Uncertainty Optimization: Boosting Monocular 3D Object Detection under Test-Time Shifts

Accurate monocular 3D object detection (M3OD) is pivotal for safety-critical applications like autonomous driving, yet its reliability deteriorates significantly under real-world domain shifts caused by environmental or sensor variations. To address these shifts, Test-Time Adaptation (TTA) methods have emerged, enabling models to adapt to target distributions during inference. While prior TTA approaches recognize the positive correlation between low uncertainty and high generalization ability, they fail to address the dual uncertainty inherent to M3OD: semantic uncertainty (ambiguous class predictions) and geometric uncertainty (unstable spatial localization). To bridge this gap, we propose Dual Uncertainty Optimization (DUO), the first TTA framework designed to jointly minimize both uncertainties for robust M3OD. Through a convex optimization lens, we introduce an innovative convex structure of the focal loss and further derive a novel unsupervised version, enabling label-agnostic uncertainty weighting and balanced learning for high-uncertainty objects. In parallel, we design a semantic-aware normal field constraint that preserves geometric coherence in regions with clear semantic cues, reducing uncertainty from the unstable 3D representation. This dual-branch mechanism forms a complementary loop: enhanced spatial perception improves semantic classification, and robust semantic predictions further refine spatial understanding. Extensive experiments demonstrate the superiority of DUO over existing methods across various datasets and domain shift types.

  • 7 authors
·
Aug 28

Expansion and Shrinkage of Localization for Weakly-Supervised Semantic Segmentation

Generating precise class-aware pseudo ground-truths, a.k.a, class activation maps (CAMs), is essential for weakly-supervised semantic segmentation. The original CAM method usually produces incomplete and inaccurate localization maps. To tackle with this issue, this paper proposes an Expansion and Shrinkage scheme based on the offset learning in the deformable convolution, to sequentially improve the recall and precision of the located object in the two respective stages. In the Expansion stage, an offset learning branch in a deformable convolution layer, referred as "expansion sampler" seeks for sampling increasingly less discriminative object regions, driven by an inverse supervision signal that maximizes image-level classification loss. The located more complete object in the Expansion stage is then gradually narrowed down to the final object region during the Shrinkage stage. In the Shrinkage stage, the offset learning branch of another deformable convolution layer, referred as "shrinkage sampler", is introduced to exclude the false positive background regions attended in the Expansion stage to improve the precision of the localization maps. We conduct various experiments on PASCAL VOC 2012 and MS COCO 2014 to well demonstrate the superiority of our method over other state-of-the-art methods for weakly-supervised semantic segmentation. Code will be made publicly available here https://github.com/TyroneLi/ESOL_WSSS.

  • 5 authors
·
Sep 16, 2022

VI-Net: Boosting Category-level 6D Object Pose Estimation via Learning Decoupled Rotations on the Spherical Representations

Rotation estimation of high precision from an RGB-D object observation is a huge challenge in 6D object pose estimation, due to the difficulty of learning in the non-linear space of SO(3). In this paper, we propose a novel rotation estimation network, termed as VI-Net, to make the task easier by decoupling the rotation as the combination of a viewpoint rotation and an in-plane rotation. More specifically, VI-Net bases the feature learning on the sphere with two individual branches for the estimates of two factorized rotations, where a V-Branch is employed to learn the viewpoint rotation via binary classification on the spherical signals, while another I-Branch is used to estimate the in-plane rotation by transforming the signals to view from the zenith direction. To process the spherical signals, a Spherical Feature Pyramid Network is constructed based on a novel design of SPAtial Spherical Convolution (SPA-SConv), which settles the boundary problem of spherical signals via feature padding and realizesviewpoint-equivariant feature extraction by symmetric convolutional operations. We apply the proposed VI-Net to the challenging task of category-level 6D object pose estimation for predicting the poses of unknown objects without available CAD models; experiments on the benchmarking datasets confirm the efficacy of our method, which outperforms the existing ones with a large margin in the regime of high precision.

  • 4 authors
·
Aug 19, 2023

Parameter-Inverted Image Pyramid Networks

Image pyramids are commonly used in modern computer vision tasks to obtain multi-scale features for precise understanding of images. However, image pyramids process multiple resolutions of images using the same large-scale model, which requires significant computational cost. To overcome this issue, we propose a novel network architecture known as the Parameter-Inverted Image Pyramid Networks (PIIP). Our core idea is to use models with different parameter sizes to process different resolution levels of the image pyramid, thereby balancing computational efficiency and performance. Specifically, the input to PIIP is a set of multi-scale images, where higher resolution images are processed by smaller networks. We further propose a feature interaction mechanism to allow features of different resolutions to complement each other and effectively integrate information from different spatial scales. Extensive experiments demonstrate that the PIIP achieves superior performance in tasks such as object detection, segmentation, and image classification, compared to traditional image pyramid methods and single-branch networks, while reducing computational cost. Notably, when applying our method on a large-scale vision foundation model InternViT-6B, we improve its performance by 1%-2% on detection and segmentation with only 40%-60% of the original computation. These results validate the effectiveness of the PIIP approach and provide a new technical direction for future vision computing tasks. Our code and models are available at https://github.com/OpenGVLab/PIIP.

  • 9 authors
·
Jun 6, 2024

Towards Generalizable Forgery Detection and Reasoning

Accurate and interpretable detection of AI-generated images is essential for mitigating risks associated with AI misuse. However, the substantial domain gap among generative models makes it challenging to develop a generalizable forgery detection model. Moreover, since every pixel in an AI-generated image is synthesized, traditional saliency-based forgery explanation methods are not well suited for this task. To address these challenges, we formulate detection and explanation as a unified Forgery Detection and Reasoning task (FDR-Task), leveraging Multi-Modal Large Language Models (MLLMs) to provide accurate detection through reliable reasoning over forgery attributes. To facilitate this task, we introduce the Multi-Modal Forgery Reasoning dataset (MMFR-Dataset), a large-scale dataset containing 120K images across 10 generative models, with 378K reasoning annotations on forgery attributes, enabling comprehensive evaluation of the FDR-Task. Furthermore, we propose FakeReasoning, a forgery detection and reasoning framework with three key components: 1) a dual-branch visual encoder that integrates CLIP and DINO to capture both high-level semantics and low-level artifacts; 2) a Forgery-Aware Feature Fusion Module that leverages DINO's attention maps and cross-attention mechanisms to guide MLLMs toward forgery-related clues; 3) a Classification Probability Mapper that couples language modeling and forgery detection, enhancing overall performance. Experiments across multiple generative models demonstrate that FakeReasoning not only achieves robust generalization but also outperforms state-of-the-art methods on both detection and reasoning tasks.

  • 8 authors
·
Mar 27

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

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

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

A Systematic Literature Review of Automated ICD Coding and Classification Systems using Discharge Summaries

Codification of free-text clinical narratives have long been recognised to be beneficial for secondary uses such as funding, insurance claim processing and research. The current scenario of assigning codes is a manual process which is very expensive, time-consuming and error prone. In recent years, many researchers have studied the use of Natural Language Processing (NLP), related Machine Learning (ML) and Deep Learning (DL) methods and techniques to resolve the problem of manual coding of clinical narratives and to assist human coders to assign clinical codes more accurately and efficiently. This systematic literature review provides a comprehensive overview of automated clinical coding systems that utilises appropriate NLP, ML and DL methods and techniques to assign ICD codes to discharge summaries. We have followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA) guidelines and conducted a comprehensive search of publications from January, 2010 to December 2020 in four academic databases- PubMed, ScienceDirect, Association for Computing Machinery(ACM) Digital Library, and the Association for Computational Linguistics(ACL) Anthology. We reviewed 7,556 publications; 38 met the inclusion criteria. This review identified: datasets having discharge summaries; NLP techniques along with some other data extraction processes, different feature extraction and embedding techniques. To measure the performance of classification methods, different evaluation metrics are used. Lastly, future research directions are provided to scholars who are interested in automated ICD code assignment. Efforts are still required to improve ICD code prediction accuracy, availability of large-scale de-identified clinical corpora with the latest version of the classification system. This can be a platform to guide and share knowledge with the less experienced coders and researchers.

  • 3 authors
·
Jul 11, 2021

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

Profitable Trade-Off Between Memory and Performance In Multi-Domain Chatbot Architectures

Text classification problem is a very broad field of study in the field of natural language processing. In short, the text classification problem is to determine which of the previously determined classes the given text belongs to. Successful studies have been carried out in this field in the past studies. In the study, Bidirectional Encoder Representations for Transformers (BERT), which is a frequently preferred method for solving the classification problem in the field of natural language processing, is used. By solving classification problems through a single model to be used in a chatbot architecture, it is aimed to alleviate the load on the server that will be created by more than one model used for solving more than one classification problem. At this point, with the masking method applied during the estimation of a single BERT model, which was created for classification in more than one subject, the estimation of the model was provided on a problem-based basis. Three separate data sets covering different fields from each other are divided by various methods in order to complicate the problem, and classification problems that are very close to each other in terms of field are also included in this way. The dataset used in this way consists of five classification problems with 154 classes. A BERT model containing all classification problems and other BERT models trained specifically for the problems were compared with each other in terms of performance and the space they occupied on the server.

  • 7 authors
·
Nov 6, 2021

Upper Limb Movement Recognition utilising EEG and EMG Signals for Rehabilitative Robotics

Upper limb movement classification, which maps input signals to the target activities, is a key building block in the control of rehabilitative robotics. Classifiers are trained for the rehabilitative system to comprehend the desires of the patient whose upper limbs do not function properly. Electromyography (EMG) signals and Electroencephalography (EEG) signals are used widely for upper limb movement classification. By analysing the classification results of the real-time EEG and EMG signals, the system can understand the intention of the user and predict the events that one would like to carry out. Accordingly, it will provide external help to the user. However, the noise in the real-time EEG and EMG data collection process contaminates the effectiveness of the data, which undermines classification performance. Moreover, not all patients process strong EMG signals due to muscle damage and neuromuscular disorder. To address these issues, this paper explores different feature extraction techniques and machine learning and deep learning models for EEG and EMG signals classification and proposes a novel decision-level multisensor fusion technique to integrate EEG signals with EMG signals. This system retrieves effective information from both sources to understand and predict the desire of the user, and thus aid. By testing out the proposed technique on a publicly available WAY-EEG-GAL dataset, which contains EEG and EMG signals that were recorded simultaneously, we manage to conclude the feasibility and effectiveness of the novel system.

  • 2 authors
·
Jul 18, 2022

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.

  • 6 authors
·
Aug 11 2

TONE: A 3-Tiered ONtology for Emotion analysis

Emotions have played an important part in many sectors, including psychology, medicine, mental health, computer science, and so on, and categorizing them has proven extremely useful in separating one emotion from another. Emotions can be classified using the following two methods: (1) The supervised method's efficiency is strongly dependent on the size and domain of the data collected. A categorization established using relevant data from one domain may not work well in another. (2) An unsupervised method that uses either domain expertise or a knowledge base of emotion types already exists. Though this second approach provides a suitable and generic categorization of emotions and is cost-effective, the literature doesn't possess a publicly available knowledge base that can be directly applied to any emotion categorization-related task. This pushes us to create a knowledge base that can be used for emotion classification across domains, and ontology is often used for this purpose. In this study, we provide TONE, an emotion-based ontology that effectively creates an emotional hierarchy based on Dr. Gerrod Parrot's group of emotions. In addition to ontology development, we introduce a semi-automated vocabulary construction process to generate a detailed collection of terms for emotions at each tier of the hierarchy. We also demonstrate automated methods for establishing three sorts of dependencies in order to develop linkages between different emotions. Our human and automatic evaluation results show the ontology's quality. Furthermore, we describe three distinct use cases that demonstrate the applicability of our ontology.

  • 3 authors
·
Jan 10, 2024

Towards MLOps: A DevOps Tools Recommender System for Machine Learning System

Applying DevOps practices to machine learning system is termed as MLOps and machine learning systems evolve on new data unlike traditional systems on requirements. The objective of MLOps is to establish a connection between different open-source tools to construct a pipeline that can automatically perform steps to construct a dataset, train the machine learning model and deploy the model to the production as well as store different versions of model and dataset. Benefits of MLOps is to make sure the fast delivery of the new trained models to the production to have accurate results. Furthermore, MLOps practice impacts the overall quality of the software products and is completely dependent on open-source tools and selection of relevant open-source tools is considered as challenged while a generalized method to select an appropriate open-source tools is desirable. In this paper, we present a framework for recommendation system that processes the contextual information (e.g., nature of data, type of the data) of the machine learning project and recommends a relevant toolchain (tech-stack) for the operationalization of machine learning systems. To check the applicability of the proposed framework, four different approaches i.e., rule-based, random forest, decision trees and k-nearest neighbors were investigated where precision, recall and f-score is measured, the random forest out classed other approaches with highest f-score value of 0.66.

  • 3 authors
·
Feb 20, 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

Towards Human-Guided, Data-Centric LLM Co-Pilots

Machine learning (ML) has the potential to revolutionize various domains, but its adoption is often hindered by the disconnect between the needs of domain experts and translating these needs into robust and valid ML tools. Despite recent advances in LLM-based co-pilots to democratize ML for non-technical domain experts, these systems remain predominantly focused on model-centric aspects while overlooking critical data-centric challenges. This limitation is problematic in complex real-world settings where raw data often contains complex issues, such as missing values, label noise, and domain-specific nuances requiring tailored handling. To address this we introduce CliMB-DC, a human-guided, data-centric framework for LLM co-pilots that combines advanced data-centric tools with LLM-driven reasoning to enable robust, context-aware data processing. At its core, CliMB-DC introduces a novel, multi-agent reasoning system that combines a strategic coordinator for dynamic planning and adaptation with a specialized worker agent for precise execution. Domain expertise is then systematically incorporated to guide the reasoning process using a human-in-the-loop approach. To guide development, we formalize a taxonomy of key data-centric challenges that co-pilots must address. Thereafter, to address the dimensions of the taxonomy, we integrate state-of-the-art data-centric tools into an extensible, open-source architecture, facilitating the addition of new tools from the research community. Empirically, using real-world healthcare datasets we demonstrate CliMB-DC's ability to transform uncurated datasets into ML-ready formats, significantly outperforming existing co-pilot baselines for handling data-centric challenges. CliMB-DC promises to empower domain experts from diverse domains -- healthcare, finance, social sciences and more -- to actively participate in driving real-world impact using ML.

  • 5 authors
·
Jan 17

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

LADDER: Language Driven Slice Discovery and Error Rectification

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate domain knowledge, limiting their usage in specialized fields \eg radiology. We propose\ladder (Language-Driven Discovery and Error Rectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent domain knowledge and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

BostonU Boston University
·
Jul 31, 2024

Varifocal-Net: A Chromosome Classification Approach using Deep Convolutional Networks

Chromosome classification is critical for karyotyping in abnormality diagnosis. To expedite the diagnosis, we present a novel method named Varifocal-Net for simultaneous classification of chromosome's type and polarity using deep convolutional networks. The approach consists of one global-scale network (G-Net) and one local-scale network (L-Net). It follows three stages. The first stage is to learn both global and local features. We extract global features and detect finer local regions via the G-Net. By proposing a varifocal mechanism, we zoom into local parts and extract local features via the L-Net. Residual learning and multi-task learning strategies are utilized to promote high-level feature extraction. The detection of discriminative local parts is fulfilled by a localization subnet of the G-Net, whose training process involves both supervised and weakly-supervised learning. The second stage is to build two multi-layer perceptron classifiers that exploit features of both two scales to boost classification performance. The third stage is to introduce a dispatch strategy of assigning each chromosome to a type within each patient case, by utilizing the domain knowledge of karyotyping. Evaluation results from 1909 karyotyping cases showed that the proposed Varifocal-Net achieved the highest accuracy per patient case (%) 99.2 for both type and polarity tasks. It outperformed state-of-the-art methods, demonstrating the effectiveness of our varifocal mechanism, multi-scale feature ensemble, and dispatch strategy. The proposed method has been applied to assist practical karyotype diagnosis.

  • 9 authors
·
Oct 13, 2018

DNA Sequence Classification with Compressors

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

  • 1 authors
·
Jan 25, 2024

Zero-Shot ECG Classification with Multimodal Learning and Test-time Clinical Knowledge Enhancement

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets. Code and models are available at https://github.com/cheliu-computation/MERL

  • 6 authors
·
Mar 11, 2024

Priority prediction of Asian Hornet sighting report using machine learning methods

As infamous invaders to the North American ecosystem, the Asian giant hornet (Vespa mandarinia) is devastating not only to native bee colonies, but also to local apiculture. One of the most effective way to combat the harmful species is to locate and destroy their nests. By mobilizing the public to actively report possible sightings of the Asian giant hornet, the governmentcould timely send inspectors to confirm and possibly destroy the nests. However, such confirmation requires lab expertise, where manually checking the reports one by one is extremely consuming of human resources. Further given the limited knowledge of the public about the Asian giant hornet and the randomness of report submission, only few of the numerous reports proved positive, i.e. existing nests. How to classify or prioritize the reports efficiently and automatically, so as to determine the dispatch of personnel, is of great significance to the control of the Asian giant hornet. In this paper, we propose a method to predict the priority of sighting reports based on machine learning. We model the problem of optimal prioritization of sighting reports as a problem of classification and prediction. We extracted a variety of rich features in the report: location, time, image(s), and textual description. Based on these characteristics, we propose a classification model based on logistic regression to predict the credibility of a certain report. Furthermore, our model quantifies the impact between reports to get the priority ranking of the reports. Extensive experiments on the public dataset from the WSDA (the Washington State Department of Agriculture) have proved the effectiveness of our method.

  • 5 authors
·
Jun 28, 2021

Enquire One's Parent and Child Before Decision: Fully Exploit Hierarchical Structure for Self-Supervised Taxonomy Expansion

Taxonomy is a hierarchically structured knowledge graph that plays a crucial role in machine intelligence. The taxonomy expansion task aims to find a position for a new term in an existing taxonomy to capture the emerging knowledge in the world and keep the taxonomy dynamically updated. Previous taxonomy expansion solutions neglect valuable information brought by the hierarchical structure and evaluate the correctness of merely an added edge, which downgrade the problem to node-pair scoring or mini-path classification. In this paper, we propose the Hierarchy Expansion Framework (HEF), which fully exploits the hierarchical structure's properties to maximize the coherence of expanded taxonomy. HEF makes use of taxonomy's hierarchical structure in multiple aspects: i) HEF utilizes subtrees containing most relevant nodes as self-supervision data for a complete comparison of parental and sibling relations; ii) HEF adopts a coherence modeling module to evaluate the coherence of a taxonomy's subtree by integrating hypernymy relation detection and several tree-exclusive features; iii) HEF introduces the Fitting Score for position selection, which explicitly evaluates both path and level selections and takes full advantage of parental relations to interchange information for disambiguation and self-correction. Extensive experiments show that by better exploiting the hierarchical structure and optimizing taxonomy's coherence, HEF vastly surpasses the prior state-of-the-art on three benchmark datasets by an average improvement of 46.7% in accuracy and 32.3% in mean reciprocal rank.

  • 5 authors
·
Jan 27, 2021

TransICD: Transformer Based Code-wise Attention Model for Explainable ICD Coding

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

  • 3 authors
·
Mar 28, 2021

An Automatic SOAP Classification System Using Weakly Supervision And Transfer Learning

In this paper, we introduce a comprehensive framework for developing a machine learning-based SOAP (Subjective, Objective, Assessment, and Plan) classification system without manually SOAP annotated training data or with less manually SOAP annotated training data. The system is composed of the following two parts: 1) Data construction, 2) A neural network-based SOAP classifier, and 3) Transfer learning framework. In data construction, since a manual construction of a large size training dataset is expensive, we propose a rule-based weak labeling method utilizing the structured information of an EHR note. Then, we present a SOAP classifier composed of a pre-trained language model and bi-directional long-short term memory with conditional random field (Bi-LSTM-CRF). Finally, we propose a transfer learning framework that re-uses the trained parameters of the SOAP classifier trained with the weakly labeled dataset for datasets collected from another hospital. The proposed weakly label-based learning model successfully performed SOAP classification (89.99 F1-score) on the notes collected from the target hospital. Otherwise, in the notes collected from other hospitals and departments, the performance dramatically decreased. Meanwhile, we verified that the transfer learning framework is advantageous for inter-hospital adaptation of the model increasing the models' performance in every cases. In particular, the transfer learning approach was more efficient when the manually annotated data size was smaller. We showed that SOAP classification models trained with our weakly labeling algorithm can perform SOAP classification without manually annotated data on the EHR notes from the same hospital. The transfer learning framework helps SOAP classification model's inter-hospital migration with a minimal size of the manually annotated dataset.

  • 3 authors
·
Nov 26, 2022

NCL-SM: A Fully Annotated Dataset of Images from Human Skeletal Muscle Biopsies

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

  • 7 authors
·
Nov 25, 2023

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

LegalVis: Exploring and Inferring Precedent Citations in Legal Documents

To reduce the number of pending cases and conflicting rulings in the Brazilian Judiciary, the National Congress amended the Constitution, allowing the Brazilian Supreme Court (STF) to create binding precedents (BPs), i.e., a set of understandings that both Executive and lower Judiciary branches must follow. The STF's justices frequently cite the 58 existing BPs in their decisions, and it is of primary relevance that judicial experts could identify and analyze such citations. To assist in this problem, we propose LegalVis, a web-based visual analytics system designed to support the analysis of legal documents that cite or could potentially cite a BP. We model the problem of identifying potential citations (i.e., non-explicit) as a classification problem. However, a simple score is not enough to explain the results; that is why we use an interpretability machine learning method to explain the reason behind each identified citation. For a compelling visual exploration of documents and BPs, LegalVis comprises three interactive visual components: the first presents an overview of the data showing temporal patterns, the second allows filtering and grouping relevant documents by topic, and the last one shows a document's text aiming to interpret the model's output by pointing out which paragraphs are likely to mention the BP, even if not explicitly specified. We evaluated our identification model and obtained an accuracy of 96%; we also made a quantitative and qualitative analysis of the results. The usefulness and effectiveness of LegalVis were evaluated through two usage scenarios and feedback from six domain experts.

  • 4 authors
·
Mar 3, 2022

Challenges and Barriers of Using Low Code Software for Machine Learning

As big data grows ubiquitous across many domains, more and more stakeholders seek to develop Machine Learning (ML) applications on their data. The success of an ML application usually depends on the close collaboration of ML experts and domain experts. However, the shortage of ML engineers remains a fundamental problem. Low-code Machine learning tools/platforms (aka, AutoML) aim to democratize ML development to domain experts by automating many repetitive tasks in the ML pipeline. This research presents an empirical study of around 14k posts (questions + accepted answers) from Stack Overflow (SO) that contained AutoML-related discussions. We examine how these topics are spread across the various Machine Learning Life Cycle (MLLC) phases and their popularity and difficulty. This study offers several interesting findings. First, we find 13 AutoML topics that we group into four categories. The MLOps topic category (43% questions) is the largest, followed by Model (28% questions), Data (27% questions), Documentation (2% questions). Second, Most questions are asked during Model training (29%) (i.e., implementation phase) and Data preparation (25%) MLLC phase. Third, AutoML practitioners find the MLOps topic category most challenging, especially topics related to model deployment & monitoring and Automated ML pipeline. These findings have implications for all three AutoML stakeholders: AutoML researchers, AutoML service vendors, and AutoML developers. Academia and Industry collaboration can improve different aspects of AutoML, such as better DevOps/deployment support and tutorial-based documentation.

  • 2 authors
·
Nov 8, 2022

Learning Support and Trivial Prototypes for Interpretable Image Classification

Prototypical part network (ProtoPNet) methods have been designed to achieve interpretable classification by associating predictions with a set of training prototypes, which we refer to as trivial prototypes because they are trained to lie far from the classification boundary in the feature space. Note that it is possible to make an analogy between ProtoPNet and support vector machine (SVM) given that the classification from both methods relies on computing similarity with a set of training points (i.e., trivial prototypes in ProtoPNet, and support vectors in SVM). However, while trivial prototypes are located far from the classification boundary, support vectors are located close to this boundary, and we argue that this discrepancy with the well-established SVM theory can result in ProtoPNet models with inferior classification accuracy. In this paper, we aim to improve the classification of ProtoPNet with a new method to learn support prototypes that lie near the classification boundary in the feature space, as suggested by the SVM theory. In addition, we target the improvement of classification results with a new model, named ST-ProtoPNet, which exploits our support prototypes and the trivial prototypes to provide more effective classification. Experimental results on CUB-200-2011, Stanford Cars, and Stanford Dogs datasets demonstrate that ST-ProtoPNet achieves state-of-the-art classification accuracy and interpretability results. We also show that the proposed support prototypes tend to be better localised in the object of interest rather than in the background region.

  • 8 authors
·
Jan 8, 2023

Wide and Deep Neural Networks Achieve Optimality for Classification

While neural networks are used for classification tasks across domains, a long-standing open problem in machine learning is determining whether neural networks trained using standard procedures are optimal for classification, i.e., whether such models minimize the probability of misclassification for arbitrary data distributions. In this work, we identify and construct an explicit set of neural network classifiers that achieve optimality. Since effective neural networks in practice are typically both wide and deep, we analyze infinitely wide networks that are also infinitely deep. In particular, using the recent connection between infinitely wide neural networks and Neural Tangent Kernels, we provide explicit activation functions that can be used to construct networks that achieve optimality. Interestingly, these activation functions are simple and easy to implement, yet differ from commonly used activations such as ReLU or sigmoid. More generally, we create a taxonomy of infinitely wide and deep networks and show that these models implement one of three well-known classifiers depending on the activation function used: (1) 1-nearest neighbor (model predictions are given by the label of the nearest training example); (2) majority vote (model predictions are given by the label of the class with greatest representation in the training set); or (3) singular kernel classifiers (a set of classifiers containing those that achieve optimality). Our results highlight the benefit of using deep networks for classification tasks, in contrast to regression tasks, where excessive depth is harmful.

  • 3 authors
·
Apr 29, 2022

Microstructure quality control of steels using deep learning

In quality control, microstructures are investigated rigorously to ensure structural integrity, exclude the presence of critical volume defects, and validate the formation of the target microstructure. For quenched, hierarchically-structured steels, the morphology of the bainitic and martensitic microstructures are of major concern to guarantee the reliability of the material under service conditions. Therefore, industries conduct small sample-size inspections of materials cross-sections through metallographers to validate the needle morphology of such microstructures. We demonstrate round-robin test results revealing that this visual grading is afflicted by pronounced subjectivity despite the thorough training of personnel. Instead, we propose a deep learning image classification approach that distinguishes steels based on their microstructure type and classifies their needle length alluding to the ISO 643 grain size assessment standard. This classification approach facilitates the reliable, objective, and automated classification of hierarchically structured steels. Specifically, an accuracy of 96% and roughly 91% is attained for the distinction of martensite/bainite subtypes and needle length, respectively. This is achieved on an image dataset that contains significant variance and labeling noise as it is acquired over more than ten years from multiple plants, alloys, etchant applications, and light optical microscopes by many metallographers (raters). Interpretability analysis gives insights into the decision-making of these models and allows for estimating their generalization capability.

  • 5 authors
·
Jun 1, 2023

A Text Classification Framework for Simple and Effective Early Depression Detection Over Social Media Streams

With the rise of the Internet, there is a growing need to build intelligent systems that are capable of efficiently dealing with early risk detection (ERD) problems on social media, such as early depression detection, early rumor detection or identification of sexual predators. These systems, nowadays mostly based on machine learning techniques, must be able to deal with data streams since users provide their data over time. In addition, these systems must be able to decide when the processed data is sufficient to actually classify users. Moreover, since ERD tasks involve risky decisions by which people's lives could be affected, such systems must also be able to justify their decisions. However, most standard and state-of-the-art supervised machine learning models are not well suited to deal with this scenario. This is due to the fact that they either act as black boxes or do not support incremental classification/learning. In this paper we introduce SS3, a novel supervised learning model for text classification that naturally supports these aspects. SS3 was designed to be used as a general framework to deal with ERD problems. We evaluated our model on the CLEF's eRisk2017 pilot task on early depression detection. Most of the 30 contributions submitted to this competition used state-of-the-art methods. Experimental results show that our classifier was able to outperform these models and standard classifiers, despite being less computationally expensive and having the ability to explain its rationale.

  • 3 authors
·
May 18, 2019

Unraveling the Key Components of OOD Generalization via Diversification

Supervised learning datasets may contain multiple cues that explain the training set equally well, i.e., learning any of them would lead to the correct predictions on the training data. However, many of them can be spurious, i.e., lose their predictive power under a distribution shift and consequently fail to generalize to out-of-distribution (OOD) data. Recently developed "diversification" methods (Lee et al., 2023; Pagliardini et al., 2023) approach this problem by finding multiple diverse hypotheses that rely on different features. This paper aims to study this class of methods and identify the key components contributing to their OOD generalization abilities. We show that (1) diversification methods are highly sensitive to the distribution of the unlabeled data used for diversification and can underperform significantly when away from a method-specific sweet spot. (2) Diversification alone is insufficient for OOD generalization. The choice of the used learning algorithm, e.g., the model's architecture and pretraining, is crucial. In standard experiments (classification on Waterbirds and Office-Home datasets), using the second-best choice leads to an up to 20\% absolute drop in accuracy. (3) The optimal choice of learning algorithm depends on the unlabeled data and vice versa i.e. they are co-dependent. (4) Finally, we show that, in practice, the above pitfalls cannot be alleviated by increasing the number of diverse hypotheses, the major feature of diversification methods. These findings provide a clearer understanding of the critical design factors influencing the OOD generalization abilities of diversification methods. They can guide practitioners in how to use the existing methods best and guide researchers in developing new, better ones.

  • 6 authors
·
Dec 26, 2023