Abstract--T cell receptor (TCR) repertoires encode critical immunological signatures for autoimmune diseases, yet their clinical application remains limited by sequence sparsity and low witness rates. We developed EAMil, a multi-instance deep learning framework that leverages TCR sequencing data to diagnose systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) with exceptional accuracy. By integrating Prime-Seq feature extraction with ESMonehot encoding and enhanced gate attention mechanisms, our model achieved state-of-the-art performance with AUCs of 98.95% for SLE and 97.76% for RA. EAMIL successfully identified disease-associated genes with over 90% concordance with established differential analyses and effectively distinguished disease-specific TCR genes. The model demonstrated robustness in classifying multiple disease categories, utilizing the SLEDAI score to stratify SLE patients by disease severity as well as to diagnose the site of damage in SLE patients, and effectively controlling for confounding factors such as age and gender . This interpretable framework for immune receptor analysis provides new insights for autoimmune disease detection and classification with broad potential clinical applications across immune-mediated conditions.

In e-commerce advertising, selecting the most compelling combination of creative elements -- such as titles, images, and highlights -- is critical for capturing user attention and driving conversions. However, existing methods often evaluate creative components individually, failing to navigate the exponentially large search space of possible combinations. To address this challenge, we propose a novel framework named GenCO that integrates generative modeling with multi-instance reward learning. Our unified two-stage architecture first employs a generative model to efficiently produce a diverse set of creative combinations. This generative process is optimized with reinforcement learning, enabling the model to effectively explore and refine its selections. Next, to overcome the challenge of sparse user feedback, a multi-instance learning model attributes combination-level rewards, such as clicks, to the individual creative elements. This allows the reward model to provide a more accurate feedback signal, which in turn guides the generative model toward creating more effective combinations. Deployed on a leading e-commerce platform, our approach has significantly increased advertising revenue, demonstrating its practical value. Additionally, we are releasing a large-scale industrial dataset to facilitate further research in this important domain.

Automated interpretation of ultrasound imaging of the heart (echocardiograms) could improve the detection and treatment of aortic stenosis (AS), a deadly heart disease. However, existing deep learning pipelines for assessing AS from echocardiograms have two key limitations. First, most methods rely on limited 2D cineloops, thereby ignoring widely available Doppler imaging that contains important complementary information about pressure gradients and blood flow abnormalities associated with AS. Second, obtaining labeled data is difficult. There are often far more unlabeled echocardiogram recordings available, but these remain underutilized by existing methods. To overcome these limitations, we introduce Semi-supervised Multimodal Multiple-Instance Learning (SMMIL), a new deep learning framework for automatic interpretation for structural heart diseases like AS. When deployed, SMMIL can combine information from two input modalities, spectral Dopplers and 2D cineloops, to produce a study-level AS diagnosis. During training, SMMIL can combine a smaller labeled set and an abundant unlabeled set of both modalities to improve its classifier. Experiments demonstrate that SMMIL outperforms recent alternatives at 3-level AS severity classification as well as several clinically relevant AS detection tasks.

Multi-instance learning (MIL) is a widely-applied technique in practical applications that involve complex data structures. MIL can be broadly categorized into two types: traditional methods and those based on deep learning. These approaches have yielded significant results, especially with regards to their problem-solving strategies and experimental validation, providing valuable insights for researchers in the MIL field. However, a considerable amount of knowledge is often trapped within the algorithm, leading to subsequent MIL algorithms that solely rely on the model's data fitting to predict unlabeled samples. This results in a significant loss of knowledge and impedes the development of more intelligent models. In this paper, we propose a novel data-driven knowledge fusion for deep multi-instance learning (DKMIL) algorithm. DKMIL adopts a completely different idea from existing deep MIL methods by analyzing the decision-making of key samples in the data set (referred to as the data-driven) and using the knowledge fusion module designed to extract valuable information from these samples to assist the model's training. In other words, this module serves as a new interface between data and the model, providing strong scalability and enabling the use of prior knowledge from existing algorithms to enhance the learning ability of the model. Furthermore, to adapt the downstream modules of the model to more knowledge-enriched features extracted from the data-driven knowledge fusion module, we propose a two-level attention module that gradually learns shallow- and deep-level features of the samples to achieve more effective classification. We will prove the scalability of the knowledge fusion module while also verifying the efficacy of the proposed architecture by conducting experiments on 38 data sets across 6 categories.

Multi-Instance Learning (MIL) is a recent machine learning paradigm which is immensely useful in various real-life applications, like image analysis, video anomaly detection, text classification, etc. It is well known that most of the existing machine learning classifiers are highly vulnerable to adversarial perturbations. Since MIL is a weakly supervised learning, where information is available for a set of instances, called bag and not for every instances, adversarial perturbations can be fatal. In this paper, we have proposed two adversarial perturbation methods to analyze the effect of adversarial perturbations to interpret the vulnerability of MIL methods. Out of the two algorithms, one can be customized for every bag, and the other is a universal one, which can affect all bags in a given data set and thus has some generalizability. Through simulations, we have also shown the effectiveness of the proposed algorithms to fool the state-of-the-art (SOTA) MIL methods. Finally, we have discussed through experiments, about taking care of these kind of adversarial perturbations through a simple strategy. Source codes are available at https://github.com/InkiInki/MI-UAP.

In multi-instance learning, there are two kinds of prediction failure, i.e., false negative and false positive. Current research mainly focus on avoding the former. We attempt to utilize the geometric distribution of instances inside positive bags to avoid both the former and the latter. Based on kernel principal component analysis, we define a projection constraint for each positive bag to classify its constituent instances far away from the separating hyperplane while place positive instances and negative instances at opposite sides. We apply the Constrained Concave-Convex Procedure to solve the resulted problem.

Relation Extraction (RE) is a foundational task of natural language processing. RE seeks to transform raw, unstructured text into structured knowledge by identifying relational information between entity pairs found in text. RE has numerous uses, such as knowledge graph completion, text summarization, question-answering, and search querying. The history of RE methods can be roughly organized into four phases: pattern-based RE, statistical-based RE, neural-based RE, and large language model-based RE. This survey begins with an overview of a few exemplary works in the earlier phases of RE, highlighting limitations and shortcomings to contextualize progress. Next, we review popular benchmarks and critically examine metrics used to assess RE performance. We then discuss distant supervision, a paradigm that has shaped the development of modern RE methods. Lastly, we review recent RE works focusing on denoising and pre-training methods.

Multi-instance learning is a type of weakly supervised learning. It deals with tasks where the data is a set of bags and each bag is a set of instances. Only the bag labels are observed whereas the labels for the instances are unknown. An important advantage of multi-instance learning is that by representing objects as a bag of instances, it is able to preserve the inherent dependencies among parts of the objects. Unfortunately, most existing algorithms assume all instances to be \textit{identically and independently distributed}, which violates real-world scenarios since the instances within a bag are rarely independent. In this work, we propose the Multi-Instance Variational Auto-Encoder (MIVAE) algorithm which explicitly models the dependencies among the instances for predicting both bag labels and instance labels. Experimental results on several multi-instance benchmarks and end-to-end medical imaging datasets demonstrate that MIVAE performs better than state-of-the-art algorithms for both instance label and bag label prediction tasks.

In multi-instance learning, there are two kinds of prediction failure, i.e., false negative and false positive. Current research mainly focus on avoding the former. We attempt to utilize the geometric distribution of instances inside positive bags to avoid both the former and the latter. Based on kernel principal component analysis, we define a projection constraint for each positive bag to classify its constituent instances far away from the separating hyperplane while place positive instances and negative instances at opposite sides. We apply the Constrained Concave-Convex Procedure to solve the resulted problem.

The automatic detection of critical findings in chest X-rays (CXR), such as pneumothorax, is important for assisting radiologists in their clinical workflow like triaging time-sensitive cases and screening for incidental findings. While deep learning (DL) models has become a promising predictive technology with near-human accuracy, they commonly suffer from a lack of explainability, which is an important aspect for clinical deployment of DL models in the highly regulated healthcare industry. For example, localizing critical findings in an image is useful for explaining the predictions of DL classification algorithms. While there have been a host of joint classification and localization methods for computer vision, the state-of-the-art DL models require locally annotated training data in the form of pixel level labels or bounding box coordinates. In the medical domain, this requires an expensive amount of manual annotation by medical experts for each critical finding. This requirement becomes a major barrier for training models that can rapidly scale to various findings. In this work, we address these shortcomings with an interpretable DL algorithm based on multi-instance learning that jointly classifies and localizes critical findings in CXR without the need for local annotations. We show competitive classification results on three different critical findings (pneumothorax, pneumonia, and pulmonary edema) from three different CXR datasets.