OpenRaiser/Intern-Atlas huggingface dataset:
Validation of the Practicability of Logical Assessment Formula for Evaluations with Inaccurate Ground-Truth Labels: An Application Study on Tumour Segmentation for Breast Cancer
Venue: arXiv cs.AI 2024
Year: 2024

The logical assessment formula (LAF) is a new theory proposed for evaluations with inaccurate ground-truth labels (IAGTLs) to assess the predictive models for artificial intelligence applications. However, the practicability of LAF for evaluations with IAGTLs has not yet been validated in real-world practice. In this paper, we applied LAF to two tasks of tumour segmentation for breast cancer (TSfBC) in medical histopathology whole slide image analysis (MHWSIA) for evaluations with IAGTLs. Experimental results and analysis show that the LAF-based evaluations with IAGTLs were unable to confidently act like usual evaluations with accurate ground-truth labels on the one easier task of TSfBC while being able to reasonably act like usual evaluations with AGTLs on the other more difficult task of TSfBC. These results and analysis reflect the potential of LAF applied to MHWSIA for evaluations with IAGTLs. This paper presents the first practical validation of LAF for evaluations with IAGTLs in a real-world application.
ValiText -- a unified validation framework for computational text-based measures of social constructs
Venue: arXiv cs.CL 2024
Year: 2024

Guidance on how to validate computational text-based measures of social constructs is fragmented. While researchers generally acknowledge the importance of validating text-based measures, they often lack a shared vocabulary and a unified framework to do so. This paper introduces ValiText, a new validation framework designed to assist scholars in validly measuring social constructs in textual data. The framework is built on a conceptual foundation of validity in the social sciences, strengthened by an empirical review of validation practices in the social sciences and consultations with experts. Ultimately, ValiText prescribes researchers to demonstrate three types of validation evidence: substantive evidence (outlining the theoretical underpinning of the measure), structural evidence (examining the properties of the text model and its output) and external evidence (testing for how the measure relates to independent information). The framework is further supplemented by a checklist of validation steps, offering practical guidance in the form of documentation sheets that guide researchers in the validation process.
DeepOnto: A Python Package for Ontology Engineering with Deep Learning
Venue: arXiv cs.AI 2024
Year: 2024

Integrating deep learning techniques, particularly language models (LMs), with knowledge representation techniques like ontologies has raised widespread attention, urging the need of a platform that supports both paradigms. Although packages such as OWL API and Jena offer robust support for basic ontology processing features, they lack the capability to transform various types of information within ontologies into formats suitable for downstream deep learning-based applications. Moreover, widely-used ontology APIs are primarily Java-based while deep learning frameworks like PyTorch and Tensorflow are mainly for Python programming. To address the needs, we present DeepOnto, a Python package designed for ontology engineering with deep learning. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to incorporate other essential components including reasoning, verbalisation, normalisation, taxonomy, projection, and more. Building on this module, DeepOnto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methods, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of DeepOnto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).
TGRL: An Algorithm for Teacher Guided Reinforcement Learning
Venue: arXiv cs.LG 2024
Year: 2024

Learning from rewards (i.e., reinforcement learning or RL) and learning to imitate a teacher (i.e., teacher-student learning) are two established approaches for solving sequential decision-making problems. To combine the benefits of these different forms of learning, it is common to train a policy to maximize a combination of reinforcement and teacher-student learning objectives. However, without a principled method to balance these objectives, prior work used heuristics and problem-specific hyperparameter searches to balance the two objectives. We present a $\textit{principled}$ approach, along with an approximate implementation for $\textit{dynamically}$ and $\textit{automatically}$ balancing when to follow the teacher and when to use rewards. The main idea is to adjust the importance of teacher supervision by comparing the agent's performance to the counterfactual scenario of the agent learning without teacher supervision and only from rewards. If using teacher supervision improves performance, the importance of teacher supervision is increased and otherwise it is decreased. Our method, $\textit{Teacher Guided Reinforcement Learning}$ (TGRL), outperforms strong baselines across diverse domains without hyper-parameter tuning.
STG-MTL: Scalable Task Grouping for Multi-Task Learning Using Data Map
Venue: arXiv cs.LG 2024
Year: 2024

Multi-Task Learning (MTL) is a powerful technique that has gained popularity due to its performance improvement over traditional Single-Task Learning (STL). However, MTL is often challenging because there is an exponential number of possible task groupings, which can make it difficult to choose the best one because some groupings might produce performance degradation due to negative interference between tasks. That is why existing solutions are severely suffering from scalability issues, limiting any practical application. In our paper, we propose a new data-driven method that addresses these challenges and provides a scalable and modular solution for classification task grouping based on a re-proposed data-driven features, Data Maps, which capture the training dynamics for each classification task during the MTL training. Through a theoretical comparison with other techniques, we manage to show that our approach has the superior scalability. Our experiments show a better performance and verify the method's effectiveness, even on an unprecedented number of tasks (up to 100 tasks on CIFAR100). Being the first to work on such number of tasks, our comparisons on the resulting grouping shows similar grouping to the mentioned in the dataset, CIFAR100. Finally, we provide a modular implementation for easier integration and testing, with examples from multiple datasets and tasks.
Exploring the Potential of Large Language Models (LLMs) in Learning on Graphs
Venue: arXiv cs.LG 2024
Year: 2024

Learning on Graphs has attracted immense attention due to its wide real-world applications. The most popular pipeline for learning on graphs with textual node attributes primarily relies on Graph Neural Networks (GNNs), and utilizes shallow text embedding as initial node representations, which has limitations in general knowledge and profound semantic understanding. In recent years, Large Language Models (LLMs) have been proven to possess extensive common knowledge and powerful semantic comprehension abilities that have revolutionized existing workflows to handle text data. In this paper, we aim to explore the potential of LLMs in graph machine learning, especially the node classification task, and investigate two possible pipelines: LLMs-as-Enhancers and LLMs-as-Predictors. The former leverages LLMs to enhance nodes' text attributes with their massive knowledge and then generate predictions through GNNs. The latter attempts to directly employ LLMs as standalone predictors. We conduct comprehensive and systematical studies on these two pipelines under various settings. From comprehensive empirical results, we make original observations and find new insights that open new possibilities and suggest promising directions to leverage LLMs for learning on graphs. Our codes and datasets are available at https://github.com/CurryTang/Graph-LLM.
Leveraging text data for causal inference using electronic health records
Venue: arXiv cs.CL 2024
Year: 2024

In studies that rely on data from electronic health records (EHRs), unstructured text data such as clinical progress notes offer a rich source of information about patient characteristics and care that may be missing from structured data. Despite the prevalence of text in clinical research, these data are often ignored for the purposes of quantitative analysis due their complexity. This paper presents a unified framework for leveraging text data to support causal inference with electronic health data at multiple stages of analysis. In particular, we consider how natural language processing and statistical text analysis can be combined with standard inferential techniques to address common challenges due to missing data, confounding bias, and treatment effect heterogeneity. Through an application to a recent EHR study investigating the effects of a non-randomized medical intervention on patient outcomes, we show how incorporating text data in a traditional matching analysis can help strengthen the validity of an estimated treatment effect and identify patient subgroups that may benefit most from treatment. We believe these methods have the potential to expand the scope of secondary analysis of clinical data to domains where structured EHR data is limited, such as in developing countries. To this end, we provide code and open-source replication materials to encourage adoption and broader exploration of these techniques in clinical research.
A Combinatorial Characterization of Supervised Online Learnability
Venue: arXiv cs.LG 2024
Year: 2024

We study the online learnability of hypothesis classes with respect to arbitrary, but bounded loss functions. No characterization of online learnability is known at this level of generality. We give a new scale-sensitive combinatorial dimension, named the sequential minimax dimension, and show that it gives a tight quantitative characterization of online learnability. In addition, we show that the sequential minimax dimension subsumes most existing combinatorial dimensions in online learning theory.
Probabilistic Test-Time Generalization by Variational Neighbor-Labeling
Venue: arXiv cs.LG 2024
Year: 2024

This paper strives for domain generalization, where models are trained exclusively on source domains before being deployed on unseen target domains. We follow the strict separation of source training and target testing, but exploit the value of the unlabeled target data itself during inference. We make three contributions. First, we propose probabilistic pseudo-labeling of target samples to generalize the source-trained model to the target domain at test time. We formulate the generalization at test time as a variational inference problem, by modeling pseudo labels as distributions, to consider the uncertainty during generalization and alleviate the misleading signal of inaccurate pseudo labels. Second, we learn variational neighbor labels that incorporate the information of neighboring target samples to generate more robust pseudo labels. Third, to learn the ability to incorporate more representative target information and generate more precise and robust variational neighbor labels, we introduce a meta-generalization stage during training to simulate the generalization procedure. Experiments on seven widely-used datasets demonstrate the benefits, abilities, and effectiveness of our proposal.
Optimization-based Learning for Dynamic Load Planning in Trucking Service Networks
Venue: arXiv cs.AI 2024
Year: 2024

The load planning problem is a critical challenge in service network design for parcel carriers: it decides how many trailers to assign for dispatch over time between pairs of terminals. Another key challenge is to determine a flow plan, which specifies how parcel volumes are assigned to planned loads. This paper considers the Outbound Load Planning Problem (OLPP) that considers flow and load planning challenges jointly in order to adjust loads and flows as the demand forecast changes over time before the day of operations in a terminal. The paper aims at developing a decision-support tool to inform planners making these decisions at terminals across the network. The paper formulates the OLPP as a mixed-integer programming model and shows that it admits a large number of symmetries in a network where each commodity can be routed through primary and alternate terminals. As a result, an optimization solver may return fundamentally different solutions to closely related problems, confusing planners and reducing trust in optimization. To remedy this limitation, this paper proposes a lexicographical optimization approach that eliminates those symmetries by generating optimal solutions staying close to a reference plan. Moreover, this paper designs an optimization proxy that addresses the computational challenges of the optimization model. The optimization proxy combines a machine-learning model and a repair procedure to find near-optimal solutions that satisfy real-time constraints imposed by planners in the loop. An extensive computational study on industrial instances shows that the optimization proxy is orders of magnitude faster for generating solutions that are consistent with each other. The proposed approach also demonstrates the benefits of the OLPP for load consolidation and the significant savings obtained from combining machine learning and optimization.
DEDUCE: Multi-head attention decoupled contrastive learning to discover cancer subtypes based on multi-omics data
Venue: arXiv cs.LG 2024
Year: 2024

Background and Objective: Given the high heterogeneity and clinical diversity of cancer, substantial variations exist in multi-omics data and clinical features across different cancer subtypes. Methods: We propose a model, named DEDUCE, based on a symmetric multi-head attention encoders (SMAE), for unsupervised contrastive learning to analyze multi-omics cancer data, with the aim of identifying and characterizing cancer subtypes. This model adopts a unsupervised SMAE that can deeply extract contextual features and long-range dependencies from multi-omics data, thereby mitigating the impact of noise. Importantly, DEDUCE introduces a subtype decoupled contrastive learning method based on a multi-head attention mechanism to simultaneously learn features from multi-omics data and perform clustering for identifying cancer subtypes. Subtypes are clustered by calculating the similarity between samples in both the feature space and sample space of multi-omics data. The fundamental concept involves decoupling various attributes of multi-omics data features and learning them as contrasting terms. A contrastive loss function is constructed to quantify the disparity between positive and negative examples, and the model minimizes this difference, thereby promoting the acquisition of enhanced feature representation. Results: The DEDUCE model undergoes extensive experiments on simulated multi-omics datasets, single-cell multi-omics datasets, and cancer multi-omics datasets, outperforming 10 deep learning models. The DEDUCE model outperforms state-of-the-art methods, and ablation experiments demonstrate the effectiveness of each module in the DEDUCE model. Finally, we applied the DEDUCE model to identify six cancer subtypes of AML.
Interpreting and generalizing deep learning in physics-based problems with functional linear models
Venue: arXiv cs.LG 2024
Year: 2024

Although deep learning has achieved remarkable success in various scientific machine learning applications, its opaque nature poses concerns regarding interpretability and generalization capabilities beyond the training data. Interpretability is crucial and often desired in modeling physical systems. Moreover, acquiring extensive datasets that encompass the entire range of input features is challenging in many physics-based learning tasks, leading to increased errors when encountering out-of-distribution (OOD) data. In this work, motivated by the field of functional data analysis (FDA), we propose generalized functional linear models as an interpretable surrogate for a trained deep learning model. We demonstrate that our model could be trained either based on a trained neural network (post-hoc interpretation) or directly from training data (interpretable operator learning). A library of generalized functional linear models with different kernel functions is considered and sparse regression is used to discover an interpretable surrogate model that could be analytically presented. We present test cases in solid mechanics, fluid mechanics, and transport. Our results demonstrate that our model can achieve comparable accuracy to deep learning and can improve OOD generalization while providing more transparency and interpretability. Our study underscores the significance of interpretable representation in scientific machine learning and showcases the potential of functional linear models as a tool for interpreting and generalizing deep learning.
A Semi-Automated Solution Approach Recommender for a Given Use Case: a Case Study for AI/ML in Oncology via Scopus and OpenAI
Venue: arXiv cs.AI 2024
Year: 2024

Nowadays, literature review is a necessary task when trying to solve a given problem. However, an exhaustive literature review is very time-consuming in today's vast literature landscape. It can take weeks, even if looking only for abstracts or surveys. Moreover, choosing a method among others, and targeting searches within relevant problem and solution domains, are not easy tasks. These are especially true for young researchers or engineers starting to work in their field. Even if surveys that provide methods used to solve a specific problem already exist, an automatic way to do it for any use case is missing, especially for those who don't know the existing literature. Our proposed tool, SARBOLD-LLM, allows discovering and choosing among methods related to a given problem, providing additional information about their uses in the literature to derive decision-making insights, in only a few hours. The SARBOLD-LLM comprises three modules: (1: Scopus search) paper selection using a keyword selection scheme to query Scopus API; (2: Scoring and method extraction) relevancy and popularity scores calculation and solution method extraction in papers utilizing OpenAI API (GPT 3.5); (3: Analyzes) sensitivity analysis and post-analyzes which reveals trends, relevant papers and methods. Comparing the SARBOLD-LLM to manual ground truth using precision, recall, and F1-score metrics, the performance results of AI in the oncology case study are 0.68, 0.9, and 0.77, respectively. SARBOLD-LLM demonstrates successful outcomes across various domains, showcasing its robustness and effectiveness. The SARBOLD-LLM addresses engineers more than researchers, as it proposes methods and trends without adding pros and cons. It is a useful tool to select which methods to investigate first and comes as a complement to surveys. This can limit the global search and accumulation of knowledge for the end user. However...
Distill-SODA: Distilling Self-Supervised Vision Transformer for Source-Free Open-Set Domain Adaptation in Computational Pathology
Venue: arXiv cs.CV 2024
Year: 2024

Developing computational pathology models is essential for reducing manual tissue typing from whole slide images, transferring knowledge from the source domain to an unlabeled, shifted target domain, and identifying unseen categories. We propose a practical setting by addressing the above-mentioned challenges in one fell swoop, i.e., source-free open-set domain adaptation. Our methodology focuses on adapting a pre-trained source model to an unlabeled target dataset and encompasses both closed-set and open-set classes. Beyond addressing the semantic shift of unknown classes, our framework also deals with a covariate shift, which manifests as variations in color appearance between source and target tissue samples. Our method hinges on distilling knowledge from a self-supervised vision transformer (ViT), drawing guidance from either robustly pre-trained transformer models or histopathology datasets, including those from the target domain. In pursuit of this, we introduce a novel style-based adversarial data augmentation, serving as hard positives for self-training a ViT, resulting in highly contextualized embeddings. Following this, we cluster semantically akin target images, with the source model offering weak pseudo-labels, albeit with uncertain confidence. To enhance this process, we present the closed-set affinity score (CSAS), aiming to correct the confidence levels of these pseudo-labels and to calculate weighted class prototypes within the contextualized embedding space. Our approach establishes itself as state-of-the-art across three public histopathological datasets for colorectal cancer assessment. Notably, our self-training method seamlessly integrates with open-set detection methods, resulting in enhanced performance in both closed-set and open-set recognition tasks.
Learning Fine Pinch-Grasp Skills using Tactile Sensing from A Few Real-world Demonstrations
Venue: arXiv cs.RO 2024
Year: 2024

Imitation learning for robot dexterous manipulation, especially with a real robot setup, typically requires a large number of demonstrations. In this paper, we present a data-efficient learning from demonstration framework which exploits the use of rich tactile sensing data and achieves fine bimanual pinch grasping. Specifically, we employ a convolutional autoencoder network that can effectively extract and encode high-dimensional tactile information. Further, We develop a framework that achieves efficient multi-sensor fusion for imitation learning, allowing the robot to learn contact-aware sensorimotor skills from demonstrations. Our comparision study against the framework without using encoded tactile features highlighted the effectiveness of incorporating rich contact information, which enabled dexterous bimanual grasping with active contact searching. Extensive experiments demonstrated the robustness of the fine pinch grasp policy directly learned from few-shot demonstration, including grasping of the same object with different initial poses, generalizing to ten unseen new objects, robust and firm grasping against external pushes, as well as contact-aware and reactive re-grasping in case of dropping objects under very large perturbations. Furthermore, the saliency map analysis method is used to describe weight distribution across various modalities during pinch grasping, confirming the effectiveness of our framework at leveraging multimodal information.