Computational Protein Science in the Era of Large Language Models (LLMs)

Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In the last few decades, Artificial Intelligence (AI) has made significant impacts in computational protein science, leading to notable successes in specific protein modeling tasks. However, those previous AI models still meet limitations, such as the difficulty in comprehending the semantics of protein sequences, and the inability to generalize across a wide range of protein modeling tasks. Recently, LLMs have emerged as a milestone in AI due to their unprecedented language processing & generalization capability. They can promote comprehensive progress in fields rather than solving individual tasks. As a result, researchers have actively introduced LLM techniques in computational protein science, developing protein Language Models (pLMs) that skillfully grasp the foundational knowledge of proteins and can be effectively generalized to solve a diversity of sequence-structure-function reasoning problems. While witnessing prosperous developments, it's necessary to present a systematic overview of computational protein science empowered by LLM techniques. First, we summarize existing pLMs into categories based on their mastered protein knowledge, i.e., underlying sequence patterns, explicit structural and functional information, and external scientific languages. Second, we introduce the utilization and adaptation of pLMs, highlighting their remarkable achievements in promoting protein structure prediction, protein function prediction, and protein design studies. Then, we describe the practical application of pLMs in antibody design, enzyme design, and drug discovery. Finally, we specifically discuss the promising future directions in this fast-growing field.

Knowledge Graph Retrieval-Augmented Generation for LLM-based Recommendation

Recommender systems have become increasingly vital in our daily lives, helping to alleviate the problem of information overload across various user-oriented online services. The emergence of Large Language Models (LLMs) has yielded remarkable achievements, demonstrating their potential for the development of next-generation recommender systems. Despite these advancements, LLM-based recommender systems face inherent limitations stemming from their LLM backbones, particularly issues of hallucinations and the lack of up-to-date and domain-specific knowledge. Recently, Retrieval-Augmented Generation (RAG) has garnered significant attention for addressing these limitations by leveraging external knowledge sources to enhance the understanding and generation of LLMs. However, vanilla RAG methods often introduce noise and neglect structural relationships in knowledge, limiting their effectiveness in LLM-based recommendations. To address these limitations, we propose to retrieve high-quality and up-to-date structure information from the knowledge graph (KG) to augment recommendations. Specifically, our approach develops a retrieval-augmented framework, termed K-RagRec, that facilitates the recommendation generation process by incorporating structure information from the external KG. Extensive experiments have been conducted to demonstrate the effectiveness of our proposed method.

MotiF: Making Text Count in Image Animation with Motion Focal Loss

Text-Image-to-Video (TI2V) generation aims to generate a video from an image following a text description, which is also referred to as text-guided image animation. Most existing methods struggle to generate videos that align well with the text prompts, particularly when motion is specified. To overcome this limitation, we introduce MotiF, a simple yet effective approach that directs the model's learning to the regions with more motion, thereby improving the text alignment and motion generation. We use optical flow to generate a motion heatmap and weight the loss according to the intensity of the motion. This modified objective leads to noticeable improvements and complements existing methods that utilize motion priors as model inputs. Additionally, due to the lack of a diverse benchmark for evaluating TI2V generation, we propose TI2V Bench, a dataset consists of 320 image-text pairs for robust evaluation. We present a human evaluation protocol that asks the annotators to select an overall preference between two videos followed by their justifications. Through a comprehensive evaluation on TI2V Bench, MotiF outperforms nine open-sourced models, achieving an average preference of 72%. The TI2V Bench is released in https://wang-sj16.github.io/motif/.

Score-based Generative Diffusion Models for Social Recommendations

With the prevalence of social networks on online platforms, social recommendation has become a vital technique for enhancing personalized recommendations. The effectiveness of social recommendations largely relies on the social homophily assumption, which presumes that individuals with social connections often share similar preferences. However, this foundational premise has been recently challenged due to the inherent complexity and noise present in real-world social networks. In this paper, we tackle the low social homophily challenge from an innovative generative perspective, directly generating optimal user social representations that maximize consistency with collaborative signals. Specifically, we propose the Score-based Generative Model for Social Recommendation (SGSR), which effectively adapts the Stochastic Differential Equation (SDE)-based diffusion models for social recommendations. To better fit the recommendation context, SGSR employs a joint curriculum training strategy to mitigate challenges related to missing supervision signals and leverages self-supervised learning techniques to align knowledge across social and collaborative domains. Extensive experiments on real-world datasets demonstrate the effectiveness of our approach in filtering redundant social information and improving recommendation performance.

RAG-Star: Enhancing Deliberative Reasoning with Retrieval Augmented Verification and Refinement

Existing large language models (LLMs) show exceptional problem-solving capabilities but might struggle with complex reasoning tasks. Despite the successes of chain-of-thought and tree-based search methods, they mainly depend on the internal knowledge of LLMs to search over intermediate reasoning steps, limited to dealing with simple tasks involving fewer reasoning steps. In this paper, we propose \textbf{RAG-Star}, a novel RAG approach that integrates the retrieved information to guide the tree-based deliberative reasoning process that relies on the inherent knowledge of LLMs. By leveraging Monte Carlo Tree Search, RAG-Star iteratively plans intermediate sub-queries and answers for reasoning based on the LLM itself. To consolidate internal and external knowledge, we propose an retrieval-augmented verification that utilizes query- and answer-aware reward modeling to provide feedback for the inherent reasoning of LLMs. Our experiments involving Llama-3.1-8B-Instruct and GPT-4o demonstrate that RAG-Star significantly outperforms previous RAG and reasoning methods.

Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution

We present the Qwen2-VL Series, an advanced upgrade of the previous Qwen-VL models that redefines the conventional predetermined-resolution approach in visual processing. Qwen2-VL introduces the Naive Dynamic Resolution mechanism, which enables the model to dynamically process images of varying resolutions into different numbers of visual tokens. This approach allows the model to generate more efficient and accurate visual representations, closely aligning with human perceptual processes. The model also integrates Multimodal Rotary Position Embedding (M-RoPE), facilitating the effective fusion of positional information across text, images, and videos. We employ a unified paradigm for processing both images and videos, enhancing the model's visual perception capabilities. To explore the potential of large multimodal models, Qwen2-VL investigates the scaling laws for large vision-language models (LVLMs). By scaling both the model size-with versions at 2B, 8B, and 72B parameters-and the amount of training data, the Qwen2-VL Series achieves highly competitive performance. Notably, the Qwen2-VL-72B model achieves results comparable to leading models such as GPT-4o and Claude3.5-Sonnet across various multimodal benchmarks, outperforming other generalist models. Code is available at \url{https://github.com/QwenLM/Qwen2-VL}.

Do Pre-trained Vision-Language Models Encode Object States?

For a vision-language model (VLM) to understand the physical world, such as cause and effect, a first step is to capture the temporal dynamics of the visual world, for example how the physical states of objects evolve over time (e.g. a whole apple into a sliced apple). Our paper aims to investigate if VLMs pre-trained on web-scale data learn to encode object states, which can be extracted with zero-shot text prompts. We curate an object state recognition dataset ChangeIt-Frames, and evaluate nine open-source VLMs, including models trained with contrastive and generative objectives. We observe that while these state-of-the-art vision-language models can reliably perform object recognition, they consistently fail to accurately distinguish the objects' physical states. Through extensive experiments, we identify three areas for improvements for VLMs to better encode object states, namely the quality of object localization, the architecture to bind concepts to objects, and the objective to learn discriminative visual and language encoders on object states. Data and code are released.

Development of Occupancy Prediction Algorithm for Underground Parking Lots

The core objective of this study is to address the perception challenges faced by autonomous driving in adverse environments like basements. Initially, this paper commences with data collection in an underground garage. A simulated underground garage model is established within the CARLA simulation environment, and SemanticKITTI format occupancy ground truth data is collected in this simulated setting. Subsequently, the study integrates a Transformer-based Occupancy Network model to complete the occupancy grid prediction task within this scenario. A comprehensive BEV perception framework is designed to enhance the accuracy of neural network models in dimly lit, challenging autonomous driving environments. Finally, experiments validate the accuracy of the proposed solution's perception performance in basement scenarios. The proposed solution is tested on our self-constructed underground garage dataset, SUSTech-COE-ParkingLot, yielding satisfactory results.

Exploring Personality-Driven Personalization in XAI: Enhancing User Trust in Gameplay

Tailoring XAI methods to individual needs is crucial for intuitive Human-AI interactions. While context and task goals are vital, factors like user personality traits could also influence method selection. Our study investigates using personality traits to predict user preferences among decision trees, texts, and factor graphs. We trained a Machine Learning model on responses to the Big Five personality test to predict preferences. Deploying these predicted preferences in a navigation game (n=6), we found users more receptive to personalized XAI recommendations, enhancing trust in the system. This underscores the significance of customization in XAI interfaces, impacting user engagement and confidence.

Learning Visual Grounding from Generative Vision and Language Model

Visual grounding tasks aim to localize image regions based on natural language references. In this work, we explore whether generative VLMs predominantly trained on image-text data could be leveraged to scale up the text annotation of visual grounding data. We find that grounding knowledge already exists in generative VLM and can be elicited by proper prompting. We thus prompt a VLM to generate object-level descriptions by feeding it object regions from existing object detection datasets. We further propose attribute modeling to explicitly capture the important object attributes, and spatial relation modeling to capture inter-object relationship, both of which are common linguistic pattern in referring expression. Our constructed dataset (500K images, 1M objects, 16M referring expressions) is one of the largest grounding datasets to date, and the first grounding dataset with purely model-generated queries and human-annotated objects. To verify the quality of this data, we conduct zero-shot transfer experiments to the popular RefCOCO benchmarks for both referring expression comprehension (REC) and segmentation (RES) tasks. On both tasks, our model significantly outperform the state-of-the-art approaches without using human annotated visual grounding data. Our results demonstrate the promise of generative VLM to scale up visual grounding in the real world. Code and models will be released.