Developing ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering

ChatGPT explores a strategic blueprint of question answering (QA) in delivering medical diagnosis, treatment recommendations, and other healthcare support. This is achieved through the increasing incorporation of medical domain data via natural language processing (NLP) and multimodal paradigms. By transitioning the distribution of text, images, videos, and other modalities from the general domain to the medical domain, these techniques have expedited the progress of medical domain question answering (MDQA). They bridge the gap between human natural language and sophisticated medical domain knowledge or expert manual annotations, handling large-scale, diverse, unbalanced, or even unlabeled data analysis scenarios in medical contexts. Central to our focus is the utilizing of language models and multimodal paradigms for medical question answering, aiming to guide the research community in selecting appropriate mechanisms for their specific medical research requirements. Specialized tasks such as unimodal-related question answering, reading comprehension, reasoning, diagnosis, relation extraction, probability modeling, and others, as well as multimodal-related tasks like vision question answering, image caption, cross-modal retrieval, report summarization, and generation, are discussed in detail. Each section delves into the intricate specifics of the respective method under consideration. This paper highlights the structures and advancements of medical domain explorations against general domain methods, emphasizing their applications across different tasks and datasets. It also outlines current challenges and opportunities for future medical domain research, paving the way for continued innovation and application in this rapidly evolving field.

GPAvatar: Generalizable and Precise Head Avatar from Image(s)

Head avatar reconstruction, crucial for applications in virtual reality, online meetings, gaming, and film industries, has garnered substantial attention within the computer vision community. The fundamental objective of this field is to faithfully recreate the head avatar and precisely control expressions and postures. Existing methods, categorized into 2D-based warping, mesh-based, and neural rendering approaches, present challenges in maintaining multi-view consistency, incorporating non-facial information, and generalizing to new identities. In this paper, we propose a framework named GPAvatar that reconstructs 3D head avatars from one or several images in a single forward pass. The key idea of this work is to introduce a dynamic point-based expression field driven by a point cloud to precisely and effectively capture expressions. Furthermore, we use a Multi Tri-planes Attention (MTA) fusion module in the tri-planes canonical field to leverage information from multiple input images. The proposed method achieves faithful identity reconstruction, precise expression control, and multi-view consistency, demonstrating promising results for free-viewpoint rendering and novel view synthesis.

DiffSHEG: A Diffusion-Based Approach for Real-Time Speech-driven Holistic 3D Expression and Gesture Generation

We propose DiffSHEG, a Diffusion-based approach for Speech-driven Holistic 3D Expression and Gesture generation with arbitrary length. While previous works focused on co-speech gesture or expression generation individually, the joint generation of synchronized expressions and gestures remains barely explored. To address this, our diffusion-based co-speech motion generation transformer enables uni-directional information flow from expression to gesture, facilitating improved matching of joint expression-gesture distributions. Furthermore, we introduce an outpainting-based sampling strategy for arbitrary long sequence generation in diffusion models, offering flexibility and computational efficiency. Our method provides a practical solution that produces high-quality synchronized expression and gesture generation driven by speech. Evaluated on two public datasets, our approach achieves state-of-the-art performance both quantitatively and qualitatively. Additionally, a user study confirms the superiority of DiffSHEG over prior approaches. By enabling the real-time generation of expressive and synchronized motions, DiffSHEG showcases its potential for various applications in the development of digital humans and embodied agents.

A Survey of Reasoning with Foundation Models

Reasoning, a crucial ability for complex problem-solving, plays a pivotal role in various real-world settings such as negotiation, medical diagnosis, and criminal investigation. It serves as a fundamental methodology in the field of Artificial General Intelligence (AGI). With the ongoing development of foundation models, there is a growing interest in exploring their abilities in reasoning tasks. In this paper, we introduce seminal foundation models proposed or adaptable for reasoning, highlighting the latest advancements in various reasoning tasks, methods, and benchmarks. We then delve into the potential future directions behind the emergence of reasoning abilities within foundation models. We also discuss the relevance of multimodal learning, autonomous agents, and super alignment in the context of reasoning. By discussing these future research directions, we hope to inspire researchers in their exploration of this field, stimulate further advancements in reasoning with foundation models, and contribute to the development of AGI.

MEAOD: Model Extraction Attack against Object Detectors

The widespread use of deep learning technology across various industries has made deep neural network models highly valuable and, as a result, attractive targets for potential attackers. Model extraction attacks, particularly query-based model extraction attacks, allow attackers to replicate a substitute model with comparable functionality to the victim model and present a significant threat to the confidentiality and security of MLaaS platforms. While many studies have explored threats of model extraction attacks against classification models in recent years, object detection models, which are more frequently used in real-world scenarios, have received less attention. In this paper, we investigate the challenges and feasibility of query-based model extraction attacks against object detection models and propose an effective attack method called MEAOD. It selects samples from the attacker-possessed dataset to construct an efficient query dataset using active learning and enhances the categories with insufficient objects. We additionally improve the extraction effectiveness by updating the annotations of the query dataset. According to our gray-box and black-box scenarios experiments, we achieve an extraction performance of over 70% under the given condition of a 10k query budget.

Atlantis: Enabling Underwater Depth Estimation with Stable Diffusion

Monocular depth estimation has experienced significant progress on terrestrial images in recent years, largely due to deep learning advancements. However, it remains inadequate for underwater scenes, primarily because of data scarcity. Given the inherent challenges of light attenuation and backscattering in water, acquiring clear underwater images or precise depth information is notably difficult and costly. Consequently, learning-based approaches often rely on synthetic data or turn to unsupervised or self-supervised methods to mitigate this lack of data. Nonetheless, the performance of these methods is often constrained by the domain gap and looser constraints. In this paper, we propose a novel pipeline for generating photorealistic underwater images using accurate terrestrial depth data. This approach facilitates the training of supervised models for underwater depth estimation, effectively reducing the performance disparity between terrestrial and underwater environments. Contrary to prior synthetic datasets that merely apply style transfer to terrestrial images without altering the scene content, our approach uniquely creates vibrant, non-existent underwater scenes by leveraging terrestrial depth data through the innovative Stable Diffusion model. Specifically, we introduce a unique Depth2Underwater ControlNet, trained on specially prepared \{Underwater, Depth, Text\} data triplets, for this generation task. Our newly developed dataset enables terrestrial depth estimation models to achieve considerable improvements, both quantitatively and qualitatively, on unseen underwater images, surpassing their terrestrial pre-trained counterparts. Moreover, the enhanced depth accuracy for underwater scenes also aids underwater image restoration techniques that rely on depth maps, further demonstrating our dataset's utility. The dataset will be available at https://github.com/zkawfanx/Atlantis.

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model

Signal peptide (SP) is a short peptide located in the N-terminus of proteins. It is essential to target and transfer transmembrane and secreted proteins to correct positions. Compared with traditional experimental methods to identify signal peptides, computational methods are faster and more efficient, which are more practical for analyzing thousands or even millions of protein sequences, especially for metagenomic data. Here we present Unbiased Organism-agnostic Signal Peptide Network (USPNet), a signal peptide classification and cleavage site prediction deep learning method that takes advantage of protein language models. We propose to apply label distribution-aware margin loss to handle data imbalance problems and use evolutionary information of protein to enrich representation and overcome species information dependence.

A Video is Worth 256 Bases: Spatial-Temporal Expectation-Maximization Inversion for Zero-Shot Video Editing

This paper presents a video inversion approach for zero-shot video editing, which aims to model the input video with low-rank representation during the inversion process. The existing video editing methods usually apply the typical 2D DDIM inversion or na\"ive spatial-temporal DDIM inversion before editing, which leverages time-varying representation for each frame to derive noisy latent. Unlike most existing approaches, we propose a Spatial-Temporal Expectation-Maximization (STEM) inversion, which formulates the dense video feature under an expectation-maximization manner and iteratively estimates a more compact basis set to represent the whole video. Each frame applies the fixed and global representation for inversion, which is more friendly for temporal consistency during reconstruction and editing. Extensive qualitative and quantitative experiments demonstrate that our STEM inversion can achieve consistent improvement on two state-of-the-art video editing methods.

InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.