Prototypical Information Bottlenecking and Disentangling for Multimodal Cancer Survival Prediction

Multimodal learning significantly benefits cancer survival prediction, especially the integration of pathological images and genomic data. Despite advantages of multimodal learning for cancer survival prediction, massive redundancy in multimodal data prevents it from extracting discriminative and compact information: (1) An extensive amount of intra-modal task-unrelated information blurs discriminability, especially for gigapixel whole slide images (WSIs) with many patches in pathology and thousands of pathways in genomic data, leading to an ``intra-modal redundancy" issue. (2) Duplicated information among modalities dominates the representation of multimodal data, which makes modality-specific information prone to being ignored, resulting in an ``inter-modal redundancy" issue. To address these, we propose a new framework, Prototypical Information Bottlenecking and Disentangling (PIBD), consisting of Prototypical Information Bottleneck (PIB) module for intra-modal redundancy and Prototypical Information Disentanglement (PID) module for inter-modal redundancy. Specifically, a variant of information bottleneck, PIB, is proposed to model prototypes approximating a bunch of instances for different risk levels, which can be used for selection of discriminative instances within modality. PID module decouples entangled multimodal data into compact distinct components: modality-common and modality-specific knowledge, under the guidance of the joint prototypical distribution. Extensive experiments on five cancer benchmark datasets demonstrated our superiority over other methods.

A Comparative Analysis of Conversational Large Language Models in Knowledge-Based Text Generation

Generating natural language text from graph-structured data is essential for conversational information seeking. Semantic triples derived from knowledge graphs can serve as a valuable source for grounding responses from conversational agents by providing a factual basis for the information they communicate. This is especially relevant in the context of large language models, which offer great potential for conversational interaction but are prone to hallucinating, omitting, or producing conflicting information. In this study, we conduct an empirical analysis of conversational large language models in generating natural language text from semantic triples. We compare four large language models of varying sizes with different prompting techniques. Through a series of benchmark experiments on the WebNLG dataset, we analyze the models' performance and identify the most common issues in the generated predictions. Our findings show that the capabilities of large language models in triple verbalization can be significantly improved through few-shot prompting, post-processing, and efficient fine-tuning techniques, particularly for smaller models that exhibit lower zero-shot performance.

Bi-CryptoNets: Leveraging Different-Level Privacy for Encrypted Inference

Privacy-preserving neural networks have attracted increasing attention in recent years, and various algorithms have been developed to keep the balance between accuracy, computational complexity and information security from the cryptographic view. This work takes a different view from the input data and structure of neural networks. We decompose the input data (e.g., some images) into sensitive and insensitive segments according to importance and privacy. The sensitive segment includes some important and private information such as human faces and we take strong homomorphic encryption to keep security, whereas the insensitive one contains some background and we add perturbations. We propose the bi-CryptoNets, i.e., plaintext and ciphertext branches, to deal with two segments, respectively, and ciphertext branch could utilize the information from plaintext branch by unidirectional connections. We adopt knowledge distillation for our bi-CryptoNets by transferring representations from a well-trained teacher neural network. Empirical studies show the effectiveness and decrease of inference latency for our bi-CryptoNets.

Swin-UMamba: Mamba-based UNet with ImageNet-based pretraining

Accurate medical image segmentation demands the integration of multi-scale information, spanning from local features to global dependencies. However, it is challenging for existing methods to model long-range global information, where convolutional neural networks (CNNs) are constrained by their local receptive fields, and vision transformers (ViTs) suffer from high quadratic complexity of their attention mechanism. Recently, Mamba-based models have gained great attention for their impressive ability in long sequence modeling. Several studies have demonstrated that these models can outperform popular vision models in various tasks, offering higher accuracy, lower memory consumption, and less computational burden. However, existing Mamba-based models are mostly trained from scratch and do not explore the power of pretraining, which has been proven to be quite effective for data-efficient medical image analysis. This paper introduces a novel Mamba-based model, Swin-UMamba, designed specifically for medical image segmentation tasks, leveraging the advantages of ImageNet-based pretraining. Our experimental results reveal the vital role of ImageNet-based training in enhancing the performance of Mamba-based models. Swin-UMamba demonstrates superior performance with a large margin compared to CNNs, ViTs, and latest Mamba-based models. Notably, on AbdomenMRI, Encoscopy, and Microscopy datasets, Swin-UMamba outperforms its closest counterpart U-Mamba by an average score of 3.58%. The code and models of Swin-UMamba are publicly available at: https://github.com/JiarunLiu/Swin-UMamba

Domain Adaptation of Multilingual Semantic Search -- Literature Review

This literature review gives an overview of current approaches to perform domain adaptation in a low-resource and approaches to perform multilingual semantic search in a low-resource setting. We developed a new typology to cluster domain adaptation approaches based on the part of dense textual information retrieval systems, which they adapt, focusing on how to combine them efficiently. We also explore the possibilities of combining multilingual semantic search with domain adaptation approaches for dense retrievers in a low-resource setting.

A Paradigm for Potential Model Performance Improvement in Classification and Regression Problems. A Proof of Concept

A methodology that seeks to enhance model prediction performance is presented. The method involves generating multiple auxiliary models that capture relationships between attributes as a function of each other. Such information serves to generate additional informative columns in the dataset that can potentially enhance target prediction. A proof of case and related code is provided.

Privacy Leakage on DNNs: A Survey of Model Inversion Attacks and Defenses

Model Inversion (MI) attacks aim to disclose private information about the training data by abusing access to the pre-trained models. These attacks enable adversaries to reconstruct high-fidelity data that closely aligns with the private training data, which has raised significant privacy concerns. Despite the rapid advances in the field, we lack a comprehensive overview of existing MI attacks and defenses. To fill this gap, this paper thoroughly investigates this field and presents a holistic survey. Firstly, our work briefly reviews the traditional MI on machine learning scenarios. We then elaborately analyze and compare numerous recent attacks and defenses on \textbf{D}eep \textbf{N}eural \textbf{N}etworks (DNNs) across multiple modalities and learning tasks.

Effective Protein-Protein Interaction Exploration with PPIretrieval

Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the challenge has shifted towards effectively navigating the vast complex universe to identify potential PPIs. Herein, we propose PPIretrieval, the first deep learning-based model for protein-protein interaction exploration, which leverages existing PPI data to effectively search for potential PPIs in an embedding space, capturing rich geometric and chemical information of protein surfaces. When provided with an unseen query protein with its associated binding site, PPIretrieval effectively identifies a potential binding partner along with its corresponding binding site in an embedding space, facilitating the formation of protein-protein complexes.

A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Modified K-means with Cluster Assignment -- Application to COVID-19 Data

Text extraction is a highly subjective problem which depends on the dataset that one is working on and the kind of summarization details that needs to be extracted out. All the steps ranging from preprocessing of the data, to the choice of an optimal model for predictions, depends on the problem and the corpus at hand. In this paper, we describe a text extraction model where the aim is to extract word specified information relating to the semantics such that we can get all related and meaningful information about that word in a succinct format. This model can obtain meaningful results and can augment ubiquitous search model or a normal clustering or topic modelling algorithms. By utilizing new technique called two cluster assignment technique with K-means model, we improved the ontology of the retrieved text. We further apply the vector average damping technique for flexible movement of clusters. Our experimental results on a recent corpus of Covid-19 shows that we obtain good results based on main keywords.