ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

Visual Agents as Fast and Slow Thinkers

Achieving human-level intelligence requires refining cognitive distinctions between System 1 and System 2 thinking. While contemporary AI, driven by large language models, demonstrates human-like traits, it falls short of genuine cognition. Transitioning from structured benchmarks to real-world scenarios presents challenges for visual agents, often leading to inaccurate and overly confident responses. To address the challenge, we introduce FaST, which incorporates the Fast and Slow Thinking mechanism into visual agents. FaST employs a switch adapter to dynamically select between System 1/2 modes, tailoring the problem-solving approach to different task complexity. It tackles uncertain and unseen objects by adjusting model confidence and integrating new contextual data. With this novel design, we advocate a flexible system, hierarchical reasoning capabilities, and a transparent decision-making pipeline, all of which contribute to its ability to emulate human-like cognitive processes in visual intelligence. Empirical results demonstrate that FaST outperforms various well-known baselines, achieving 80.8% accuracy over VQA^{v2} for visual question answering and 48.7% GIoU score over ReasonSeg for reasoning segmentation, demonstrate FaST's superior performance. Extensive testing validates the efficacy and robustness of FaST's core components, showcasing its potential to advance the development of cognitive visual agents in AI systems.

W-RAG: Weakly Supervised Dense Retrieval in RAG for Open-domain Question Answering

In knowledge-intensive tasks such as open-domain question answering (OpenQA), Large Language Models (LLMs) often struggle to generate factual answers relying solely on their internal (parametric) knowledge. To address this limitation, Retrieval-Augmented Generation (RAG) systems enhance LLMs by retrieving relevant information from external sources, thereby positioning the retriever as a pivotal component. Although dense retrieval demonstrates state-of-the-art performance, its training poses challenges due to the scarcity of ground-truth evidence, largely attributed to the high costs of human annotation. In this paper, we propose W-RAG by utilizing the ranking capabilities of LLMs to create weakly labeled data for training dense retrievers. Specifically, we rerank the top-$K$ passages retrieved via BM25 by assessing the probability that LLMs will generate the correct answer based on the question and each passage. The highest-ranking passages are then used as positive training examples for dense retrieval. Our comprehensive experiments across four publicly available OpenQA datasets demonstrate that our approach enhances both retrieval and OpenQA performance compared to baseline models.

Radiance Field Learners As UAV First-Person Viewers

First-Person-View (FPV) holds immense potential for revolutionizing the trajectory of Unmanned Aerial Vehicles (UAVs), offering an exhilarating avenue for navigating complex building structures. Yet, traditional Neural Radiance Field (NeRF) methods face challenges such as sampling single points per iteration and requiring an extensive array of views for supervision. UAV videos exacerbate these issues with limited viewpoints and significant spatial scale variations, resulting in inadequate detail rendering across diverse scales. In response, we introduce FPV-NeRF, addressing these challenges through three key facets: (1) Temporal consistency. Leveraging spatio-temporal continuity ensures seamless coherence between frames; (2) Global structure. Incorporating various global features during point sampling preserves space integrity; (3) Local granularity. Employing a comprehensive framework and multi-resolution supervision for multi-scale scene feature representation tackles the intricacies of UAV video spatial scales. Additionally, due to the scarcity of publicly available FPV videos, we introduce an innovative view synthesis method using NeRF to generate FPV perspectives from UAV footage, enhancing spatial perception for drones. Our novel dataset spans diverse trajectories, from outdoor to indoor environments, in the UAV domain, differing significantly from traditional NeRF scenarios. Through extensive experiments encompassing both interior and exterior building structures, FPV-NeRF demonstrates a superior understanding of the UAV flying space, outperforming state-of-the-art methods in our curated UAV dataset. Explore our project page for further insights: https://fpv-nerf.github.io/.

Uncertainty is Fragile: Manipulating Uncertainty in Large Language Models

Large Language Models (LLMs) are employed across various high-stakes domains, where the reliability of their outputs is crucial. One commonly used method to assess the reliability of LLMs' responses is uncertainty estimation, which gauges the likelihood of their answers being correct. While many studies focus on improving the accuracy of uncertainty estimations for LLMs, our research investigates the fragility of uncertainty estimation and explores potential attacks. We demonstrate that an attacker can embed a backdoor in LLMs, which, when activated by a specific trigger in the input, manipulates the model's uncertainty without affecting the final output. Specifically, the proposed backdoor attack method can alter an LLM's output probability distribution, causing the probability distribution to converge towards an attacker-predefined distribution while ensuring that the top-1 prediction remains unchanged. Our experimental results demonstrate that this attack effectively undermines the model's self-evaluation reliability in multiple-choice questions. For instance, we achieved a 100 attack success rate (ASR) across three different triggering strategies in four models. Further, we investigate whether this manipulation generalizes across different prompts and domains. This work highlights a significant threat to the reliability of LLMs and underscores the need for future defenses against such attacks. The code is available at https://github.com/qcznlp/uncertainty_attack.

Inertial Confinement Fusion Forecasting via LLMs

Controlled fusion energy is deemed pivotal for the advancement of human civilization. In this study, we introduce $\textbf{Fusion-LLM}$, a novel integration of Large Language Models (LLMs) with classical reservoir computing paradigms tailored to address challenges in Inertial Confinement Fusion ($\texttt{ICF}$). Our approach offers several key contributions: Firstly, we propose the $\textit{LLM-anchored Reservoir}$, augmented with a fusion-specific prompt, enabling accurate forecasting of hot electron dynamics during implosion. Secondly, we develop $\textit{Signal-Digesting Channels}$ to temporally and spatially describe the laser intensity across time, capturing the unique characteristics of $\texttt{ICF}$ inputs. Lastly, we design the $\textit{Confidence Scanner}$ to quantify the confidence level in forecasting, providing valuable insights for domain experts to design the $\texttt{ICF}$ process. Extensive experiments demonstrate the superior performance of our method, achieving 1.90 CAE, 0.14 $\texttt{top-1}$ MAE, and 0.11 $\texttt{top-5}$ MAE in predicting Hard X-ray ($\texttt{HXR}$) energies of $\texttt{ICF}$ tasks, which presents state-of-the-art comparisons against concurrent best systems. Additionally, we present $\textbf{Fusion4AI}$, the first $\texttt{ICF}$ benchmark based on physical experiments, aimed at fostering novel ideas in plasma physics research and enhancing the utility of LLMs in scientific exploration. Overall, our work strives to forge an innovative synergy between AI and plasma science for advancing fusion energy.

AMD: Automatic Multi-step Distillation of Large-scale Vision Models

Transformer-based architectures have become the de-facto standard models for diverse vision tasks owing to their superior performance. As the size of the models continues to scale up, model distillation becomes extremely important in various real applications, particularly on devices limited by computational resources. However, prevailing knowledge distillation methods exhibit diminished efficacy when confronted with a large capacity gap between the teacher and the student, e.g, 10x compression rate. In this paper, we present a novel approach named Automatic Multi-step Distillation (AMD) for large-scale vision model compression. In particular, our distillation process unfolds across multiple steps. Initially, the teacher undergoes distillation to form an intermediate teacher-assistant model, which is subsequently distilled further to the student. An efficient and effective optimization framework is introduced to automatically identify the optimal teacher-assistant that leads to the maximal student performance. We conduct extensive experiments on multiple image classification datasets, including CIFAR-10, CIFAR-100, and ImageNet. The findings consistently reveal that our approach outperforms several established baselines, paving a path for future knowledge distillation methods on large-scale vision models.

Lateralization LoRA: Interleaved Instruction Tuning with Modality-Specialized Adaptations

Recent advancements in Vision-Language Models (VLMs) have led to the development of Vision-Language Generalists (VLGs) capable of understanding and generating interleaved images and text. Despite these advances, VLGs still struggle to follow user instructions for interleaved text and image generation. To address this issue, we introduce LeafInstruct, the first open-sourced interleaved instruction tuning data with over 30,000 high-quality instances across more than 10 domains. Due to the extensive size of existing VLGs, we opt for parameter-efficient tuning. However, we observe that VLGs tuned with a standard LoRA typically exhibit inferior performance in interleaved text-image generation. We attribute this problem to modality interference and the lack of modality-specialized adaptation design. Hence, we propose Lateralization LoRA, a novel modality-specialized adaptation method inspired by the concept of brain lateralization. Lateralization LoRA employs a hybrid approach, combining the traditional linear LoRA and a Convolutional LoRA for generating text and images, enabling the generation of high-quality text and images by leveraging modality-specific structures and parameter sets. We perform instruction tuning of the VLG (i.e., EMU2) using Lateralization LoRA on the LeafInstruct dataset. Extensive experiments demonstrate that EMU2 tuned with Lateralization LoRA achieve state-of-the-art performance, significantly surpassing baseline models in complex interleaved tasks.

Direct Multi-Turn Preference Optimization for Language Agents

Adapting Large Language Models (LLMs) for agent tasks is critical in developing language agents. Direct Preference Optimization (DPO) is a promising technique for this adaptation with the alleviation of compounding errors, offering a means to directly optimize Reinforcement Learning (RL) objectives. However, applying DPO to multi-turn tasks presents challenges due to the inability to cancel the partition function. Overcoming this obstacle involves making the partition function independent of the current state and addressing length disparities between preferred and dis-preferred trajectories. In this light, we replace the policy constraint with the state-action occupancy measure constraint in the RL objective and add length normalization to the Bradley-Terry model, yielding a novel loss function named DMPO for multi-turn agent tasks with theoretical explanations. Extensive experiments on three multi-turn agent task datasets confirm the effectiveness and superiority of the DMPO loss.

CrAM: Credibility-Aware Attention Modification in LLMs for Combating Misinformation in RAG

Retrieval-Augmented Generation (RAG) can alleviate hallucinations of Large Language Models (LLMs) by referencing external documents. However, the misinformation in external documents may mislead LLMs' generation. To address this issue, we explore the task of "credibility-aware RAG", in which LLMs automatically adjust the influence of retrieved documents based on their credibility scores to counteract misinformation. To this end, we introduce a plug-and-play method named $\textbf{Cr}$edibility-aware $\textbf{A}$ttention $\textbf{M}$odification (CrAM). CrAM identifies influential attention heads in LLMs and adjusts their attention scores based on the credibility of the documents, thereby reducing the impact of low-credibility documents. Experiments on Natual Questions and TriviaQA using Llama2-13B, Llama3-8B, and Qwen-7B show that CrAM improves the RAG performance of LLMs against misinformation pollution by over 20%, even surpassing supervised fine-tuning methods.