DeepFM-Crispr: Prediction of CRISPR On-Target Effects via Deep Learning

Since the advent of CRISPR-Cas9, a groundbreaking gene-editing technology that enables precise genomic modifications via a short RNA guide sequence, there has been a marked increase in the accessibility and application of this technology across various fields. The success of CRISPR-Cas9 has spurred further investment and led to the discovery of additional CRISPR systems, including CRISPR-Cas13. Distinct from Cas9, which targets DNA, Cas13 targets RNA, offering unique advantages for gene modulation. We focus on Cas13d, a variant known for its collateral activity where it non-specifically cleaves adjacent RNA molecules upon activation, a feature critical to its function. We introduce DeepFM-Crispr, a novel deep learning model developed to predict the on-target efficiency and evaluate the off-target effects of Cas13d. This model harnesses a large language model to generate comprehensive representations rich in evolutionary and structural data, thereby enhancing predictions of RNA secondary structures and overall sgRNA efficacy. A transformer-based architecture processes these inputs to produce a predictive efficacy score. Comparative experiments show that DeepFM-Crispr not only surpasses traditional models but also outperforms recent state-of-the-art deep learning methods in terms of prediction accuracy and reliability.

Eagle: Exploring The Design Space for Multimodal LLMs with Mixture of Encoders

The ability to accurately interpret complex visual information is a crucial topic of multimodal large language models (MLLMs). Recent work indicates that enhanced visual perception significantly reduces hallucinations and improves performance on resolution-sensitive tasks, such as optical character recognition and document analysis. A number of recent MLLMs achieve this goal using a mixture of vision encoders. Despite their success, there is a lack of systematic comparisons and detailed ablation studies addressing critical aspects, such as expert selection and the integration of multiple vision experts. This study provides an extensive exploration of the design space for MLLMs using a mixture of vision encoders and resolutions. Our findings reveal several underlying principles common to various existing strategies, leading to a streamlined yet effective design approach. We discover that simply concatenating visual tokens from a set of complementary vision encoders is as effective as more complex mixing architectures or strategies. We additionally introduce Pre-Alignment to bridge the gap between vision-focused encoders and language tokens, enhancing model coherence. The resulting family of MLLMs, Eagle, surpasses other leading open-source models on major MLLM benchmarks. Models and code: https://github.com/NVlabs/Eagle

Mosaic IT: Enhancing Instruction Tuning with Data Mosaics

Finetuning large language models with a variety of instruction-response pairs has enhanced their capability to understand and follow instructions. Current instruction tuning primarily relies on teacher models or human intervention to generate and refine the instructions and responses, which are costly, non-sustainable, and may lack diversity. In this paper, we introduce Mosaic Instruction Tuning (Mosaic-IT), a human/model-free method that can efficiently create rich and diverse augmentations from existing instruction tuning data to enhance the finetuned LLM.Mosaic-IT randomly concatenates multiple instruction data into one and trains the model to produce the corresponding responses with predefined higher-level meta-instructions to strengthen its multi-step instruction-following and format-following skills. Our extensive evaluations demonstrate a superior performance and training efficiency of Mosaic-IT, which achieves consistent performance improvements over various benchmarks and an 80% reduction in training costs compared with original instruction tuning. Our codes and data are available at https://github.com/tianyi-lab/Mosaic-IT.

Large Language Models and Causal Inference in Collaboration: A Comprehensive Survey

Causal inference has shown potential in enhancing the predictive accuracy, fairness, robustness, and explainability of Natural Language Processing (NLP) models by capturing causal relationships among variables. The emergence of generative Large Language Models (LLMs) has significantly impacted various NLP domains, particularly through their advanced reasoning capabilities. This survey focuses on evaluating and improving LLMs from a causal view in the following areas: understanding and improving the LLMs' reasoning capacity, addressing fairness and safety issues in LLMs, complementing LLMs with explanations, and handling multimodality. Meanwhile, LLMs' strong reasoning capacities can in turn contribute to the field of causal inference by aiding causal relationship discovery and causal effect estimations. This review explores the interplay between causal inference frameworks and LLMs from both perspectives, emphasizing their collective potential to further the development of more advanced and equitable artificial intelligence systems.

On the Safety Concerns of Deploying LLMs/VLMs in Robotics: Highlighting the Risks and Vulnerabilities

In this paper, we highlight the critical issues of robustness and safety associated with integrating large language models (LLMs) and vision-language models (VLMs) into robotics applications. Recent works have focused on using LLMs and VLMs to improve the performance of robotics tasks, such as manipulation, navigation, etc. However, such integration can introduce significant vulnerabilities, in terms of their susceptibility to adversarial attacks due to the language models, potentially leading to catastrophic consequences. By examining recent works at the interface of LLMs/VLMs and robotics, we show that it is easy to manipulate or misguide the robot's actions, leading to safety hazards. We define and provide examples of several plausible adversarial attacks, and conduct experiments on three prominent robot frameworks integrated with a language model, including KnowNo VIMA, and Instruct2Act, to assess their susceptibility to these attacks. Our empirical findings reveal a striking vulnerability of LLM/VLM-robot integrated systems: simple adversarial attacks can significantly undermine the effectiveness of LLM/VLM-robot integrated systems. Specifically, our data demonstrate an average performance deterioration of 21.2% under prompt attacks and a more alarming 30.2% under perception attacks. These results underscore the critical need for robust countermeasures to ensure the safe and reliable deployment of the advanced LLM/VLM-based robotic systems.

MMC: Advancing Multimodal Chart Understanding with Large-scale Instruction Tuning

With the rapid development of large language models (LLMs) and their integration into large multimodal models (LMMs), there has been impressive progress in zero-shot completion of user-oriented vision-language tasks. However, a gap remains in the domain of chart image understanding due to the distinct abstract components in charts. To address this, we introduce a large-scale MultiModal Chart Instruction (MMC-Instruction) dataset comprising 600k instances supporting diverse tasks and chart types. Leveraging this data, we develop MultiModal Chart Assistant (MMCA), an LMM that achieves state-of-the-art performance on existing chart QA benchmarks. Recognizing the need for a comprehensive evaluation of LMM chart understanding, we also propose a MultiModal Chart Benchmark (MMC-Benchmark), a comprehensive human-annotated benchmark with 9 distinct tasks evaluating reasoning capabilities over charts. Extensive experiments on MMC-Benchmark reveal the limitations of existing LMMs on correctly interpreting charts, even for the most recent GPT-4V model. Our work provides an instruction-tuning methodology and benchmark to advance multimodal understanding of charts.

HallusionBench: You See What You Think? Or You Think What You See? An Image-Context Reasoning Benchmark Challenging for GPT-4V, LLaVA-1.5, and Other Multi-modality Models

Large language models (LLMs), after being aligned with vision models and integrated into vision-language models (VLMs), can bring impressive improvement in image reasoning tasks. This was shown by the recently released GPT-4V(ison), LLaVA-1.5, etc. However, the strong language prior in these SOTA LVLMs can be a double-edged sword: they may ignore the image context and solely rely on the (even contradictory) language prior for reasoning. In contrast, the vision modules in VLMs are weaker than LLMs and may result in misleading visual representations, which are then translated to confident mistakes by LLMs. To study these two types of VLM mistakes, i.e., language hallucination and visual illusion, we curated HallusionBench, an image-context reasoning benchmark that is still challenging to even GPT-4V and LLaVA-1.5. We provide a detailed analysis of examples in HallusionBench, which sheds novel insights on the illusion or hallucination of VLMs and how to improve them in the future. The benchmark and codebase will be released at https://github.com/tianyi-lab/HallusionBench.

Driving Policy Prediction based on Deep Learning Models

In this project, we implemented an end-to-end system that takes in combined visual features of video frames from a normal camera and depth information from a cloud points scanner, and predicts driving policies (vehicle speed and steering angle). We verified the safety of our system by comparing the predicted results with standard behaviors by real-world experienced drivers. Our test results show that the predictions can be considered as accurate in at lease half of the testing cases (50% 80%, depending on the model), and using combined features improved the performance in most cases than using video frames only.

Towards Understanding In-Context Learning with Contrastive Demonstrations and Saliency Maps

We investigate the role of various demonstration components in the in-context learning (ICL) performance of large language models (LLMs). Specifically, we explore the impacts of ground-truth labels, input distribution, and complementary explanations, particularly when these are altered or perturbed. We build on previous work, which offers mixed findings on how these elements influence ICL. To probe these questions, we employ explainable NLP (XNLP) methods and utilize saliency maps of contrastive demonstrations for both qualitative and quantitative analysis. Our findings reveal that flipping ground-truth labels significantly affects the saliency, though it's more noticeable in larger LLMs. Our analysis of the input distribution at a granular level reveals that changing sentiment-indicative terms in a sentiment analysis task to neutral ones does not have as substantial an impact as altering ground-truth labels. Finally, we find that the effectiveness of complementary explanations in boosting ICL performance is task-dependent, with limited benefits seen in sentiment analysis tasks compared to symbolic reasoning tasks. These insights are critical for understanding the functionality of LLMs and guiding the development of effective demonstrations, which is increasingly relevant in light of the growing use of LLMs in applications such as ChatGPT. Our research code is publicly available at https://github.com/paihengxu/XICL.

Aligning Large Multi-Modal Model with Robust Instruction Tuning

Despite the promising progress in multi-modal tasks, current large multi-modal models (LMM) are prone to hallucinating inconsistent descriptions with respect to the associated image and human instructions. This paper addresses this issue by introducing the first large and diverse visual instruction tuning dataset, named Large-scale Robust Visual (LRV)-Instruction. Our dataset consists of 120k visual instructions generated by GPT4, covering 16 vision-and-language tasks with open-ended instructions and answers. Unlike existing studies that primarily focus on positive instruction samples, we design LRV-Instruction to include both positive and negative instructions for more robust visual instruction tuning. Our negative instructions are designed at two semantic levels: (i) Nonexistent Element Manipulation and (ii) Existent Element Manipulation. To efficiently measure the hallucination generated by LMMs, we propose GPT4-Assisted Visual Instruction Evaluation (GAVIE), a novel approach to evaluate visual instruction tuning without the need for human-annotated groundtruth answers and can adapt to diverse instruction formats. We conduct comprehensive experiments to investigate the hallucination of LMMs. Our results demonstrate that existing LMMs exhibit significant hallucination when presented with our negative instructions, particularly with Existent Element Manipulation instructions. Moreover, by finetuning MiniGPT4 on LRV-Instruction, we successfully mitigate hallucination while improving performance on public datasets using less training data compared to state-of-the-art methods. Additionally, we observed that a balanced ratio of positive and negative instances in the training data leads to a more robust model. Our project link is available at https://fuxiaoliu.github.io/LRV/.