Clustering for Protein Representation Learning

Protein representation learning is a challenging task that aims to capture the structure and function of proteins from their amino acid sequences. Previous methods largely ignored the fact that not all amino acids are equally important for protein folding and activity. In this article, we propose a neural clustering framework that can automatically discover the critical components of a protein by considering both its primary and tertiary structure information. Our framework treats a protein as a graph, where each node represents an amino acid and each edge represents a spatial or sequential connection between amino acids. We then apply an iterative clustering strategy to group the nodes into clusters based on their 1D and 3D positions and assign scores to each cluster. We select the highest-scoring clusters and use their medoid nodes for the next iteration of clustering, until we obtain a hierarchical and informative representation of the protein. We evaluate on four protein-related tasks: protein fold classification, enzyme reaction classification, gene ontology term prediction, and enzyme commission number prediction. Experimental results demonstrate that our method achieves state-of-the-art performance.

Psychometry: An Omnifit Model for Image Reconstruction from Human Brain Activity

Reconstructing the viewed images from human brain activity bridges human and computer vision through the Brain-Computer Interface. The inherent variability in brain function between individuals leads existing literature to focus on acquiring separate models for each individual using their respective brain signal data, ignoring commonalities between these data. In this article, we devise Psychometry, an omnifit model for reconstructing images from functional Magnetic Resonance Imaging (fMRI) obtained from different subjects. Psychometry incorporates an omni mixture-of-experts (Omni MoE) module where all the experts work together to capture the inter-subject commonalities, while each expert associated with subject-specific parameters copes with the individual differences. Moreover, Psychometry is equipped with a retrieval-enhanced inference strategy, termed Ecphory, which aims to enhance the learned fMRI representation via retrieving from prestored subject-specific memories. These designs collectively render Psychometry omnifit and efficient, enabling it to capture both inter-subject commonality and individual specificity across subjects. As a result, the enhanced fMRI representations serve as conditional signals to guide a generation model to reconstruct high-quality and realistic images, establishing Psychometry as state-of-the-art in terms of both high-level and low-level metrics.

Ghost Sentence: A Tool for Everyday Users to Copyright Data from Large Language Models

Web user data plays a central role in the ecosystem of pre-trained large language models (LLMs) and their fine-tuned variants. Billions of data are crawled from the web and fed to LLMs. How can \textit{\textbf{everyday web users}} confirm if LLMs misuse their data without permission? In this work, we suggest that users repeatedly insert personal passphrases into their documents, enabling LLMs to memorize them. These concealed passphrases in user documents, referred to as \textit{ghost sentences}, once they are identified in the generated content of LLMs, users can be sure that their data is used for training. To explore the effectiveness and usage of this copyrighting tool, we define the \textit{user training data identification} task with ghost sentences. Multiple datasets from various sources at different scales are created and tested with LLMs of different sizes. For evaluation, we introduce a last $k$ words verification manner along with two metrics: document and user identification accuracy. In the specific case of instruction tuning of a 3B LLaMA model, 11 out of 16 users with ghost sentences identify their data within the generation content. These 16 users contribute 383 examples to $\sim$1.8M training documents. For continuing pre-training of a 1.1B TinyLlama model, 61 out of 64 users with ghost sentences identify their data within the LLM output. These 64 users contribute 1156 examples to $\sim$10M training documents.

ProtChatGPT: Towards Understanding Proteins with Large Language Models

Protein research is crucial in various fundamental disciplines, but understanding their intricate structure-function relationships remains challenging. Recent Large Language Models (LLMs) have made significant strides in comprehending task-specific knowledge, suggesting the potential for ChatGPT-like systems specialized in protein to facilitate basic research. In this work, we introduce ProtChatGPT, which aims at learning and understanding protein structures via natural languages. ProtChatGPT enables users to upload proteins, ask questions, and engage in interactive conversations to produce comprehensive answers. The system comprises protein encoders, a Protein-Language Pertaining Transformer (PLP-former), a projection adapter, and an LLM. The protein first undergoes protein encoders and PLP-former to produce protein embeddings, which are then projected by the adapter to conform with the LLM. The LLM finally combines user questions with projected embeddings to generate informative answers. Experiments show that ProtChatGPT can produce promising responses to proteins and their corresponding questions. We hope that ProtChatGPT could form the basis for further exploration and application in protein research. Code and our pre-trained model will be publicly available.

Action Sensitivity Learning for the Ego4D Episodic Memory Challenge 2023

This report presents ReLER submission to two tracks in the Ego4D Episodic Memory Benchmark in CVPR 2023, including Natural Language Queries and Moment Queries. This solution inherits from our proposed Action Sensitivity Learning framework (ASL) to better capture discrepant information of frames. Further, we incorporate a series of stronger video features and fusion strategies. Our method achieves an average mAP of 29.34, ranking 1st in Moment Queries Challenge, and garners 19.79 mean R1, ranking 2nd in Natural Language Queries Challenge. Our code will be released.

Action Sensitivity Learning for Temporal Action Localization

Temporal action localization (TAL), which involves recognizing and locating action instances, is a challenging task in video understanding. Most existing approaches directly predict action classes and regress offsets to boundaries, while overlooking the discrepant importance of each frame. In this paper, we propose an Action Sensitivity Learning framework (ASL) to tackle this task, which aims to assess the value of each frame and then leverage the generated action sensitivity to recalibrate the training procedure. We first introduce a lightweight Action Sensitivity Evaluator to learn the action sensitivity at the class level and instance level, respectively. The outputs of the two branches are combined to reweight the gradient of the two sub-tasks. Moreover, based on the action sensitivity of each frame, we design an Action Sensitive Contrastive Loss to enhance features, where the action-aware frames are sampled as positive pairs to push away the action-irrelevant frames. The extensive studies on various action localization benchmarks (i.e., MultiThumos, Charades, Ego4D-Moment Queries v1.0, Epic-Kitchens 100, Thumos14 and ActivityNet1.3) show that ASL surpasses the state-of-the-art in terms of average-mAP under multiple types of scenarios, e.g., single-labeled, densely-labeled and egocentric.

Efficient Multimodal Fusion via Interactive Prompting

Large-scale pre-training has brought unimodal fields such as computer vision and natural language processing to a new era. Following this trend, the size of multi-modal learning models constantly increases, leading to an urgent need to reduce the massive computational cost of finetuning these models for downstream tasks. In this paper, we propose an efficient and flexible multimodal fusion method, namely PMF, tailored for fusing unimodally pre-trained transformers. Specifically, we first present a modular multimodal fusion framework that exhibits high flexibility and facilitates mutual interactions among different modalities. In addition, we disentangle vanilla prompts into three types in order to learn different optimizing objectives for multimodal learning. It is also worth noting that we propose to add prompt vectors only on the deep layers of the unimodal transformers, thus significantly reducing the training memory usage. Experiment results show that our proposed method achieves comparable performance to several other multimodal finetuning methods with less than 3% trainable parameters and up to 66% saving of training memory usage.

Auto-ReID: Searching for a Part-aware ConvNet for Person Re-Identification

Prevailing deep convolutional neural networks (CNNs) for person re-IDentification (reID) are usually built upon the ResNet or VGG backbones, which were originally designed for classification. Because reID has certain differences from classification, the architecture should be modified accordingly. We propose to search for a CNN architecture that is specifically suitable for the reID task. There are three main problems. First, body structural information plays an important role in reID but is not encoded in backbones. Part-based reID models incorporate structure information at the tail of a CNN. Performance relies heavily on human experts and the models are backbone-dependent, requiring extensive human effort when a different backbone is used. Second, Neural Architecture Search (NAS) automates the process of architecture design without human effort, but no existing NAS methods incorporate the structure information of input images. Third, reID is essentially a retrieval task but current NAS algorithms are merely designed for classification. To solve these problems, we propose a retrieval-based search algorithm over a specifically designed reID search space, named Auto-ReID. Our Auto-ReID enables the automated approach to find an efficient and effective CNN architecture that is specifically suitable for reID. Extensive experiments indicate that the searched architecture achieves state-of-the-art performance while requiring less than about 50% parameters and 53% FLOPs compared to others.