Scientific discovery is a catalyst for human intellectual advances, driven by the cycle of hypothesis generation, experimental design, data evaluation, and iterative assumption refinement. This process, while crucial, is expensive and heavily dependent on the domain knowledge of scientists to generate hypotheses and navigate the scientific cycle. Central to this is causality, the ability to establish the relationship between the cause and the effect. Motivated by the scientific discovery process, in this work, we formulate a novel task where the input is a partial causal graph with missing variables, and the output is a hypothesis about the missing variables to complete the partial graph. We design a benchmark with varying difficulty levels and knowledge assumptions about the causal graph. With the growing interest in using Large Language Models (LLMs) to assist in scientific discovery, we benchmark open-source and closed models on our testbed. We show the strong ability of LLMs to hypothesize the mediation variables between a cause and its effect. In contrast, they underperform in hypothesizing the cause and effect variables themselves. We also observe surprising results where some of the open-source models outperform the closed GPT-4 model.

Graphs are pervasive in the real-world, such as social network analysis, bioinformatics, and knowledge graphs. Graph neural networks (GNNs) have great ability in node classification, a fundamental task on graphs. Unfortunately, conventional GNNs still face challenges in scenarios with few labeled nodes, despite the prevalence of few-shot node classification tasks in real-world applications. To address this challenge, various approaches have been proposed, including graph meta-learning, transfer learning, and methods based on Large Language Models (LLMs). However, traditional meta-learning and transfer learning methods often require prior knowledge from base classes or fail to exploit the potential advantages of unlabeled nodes. Meanwhile, LLM-based methods may overlook the zero-shot capabilities of LLMs and rely heavily on the quality of generated contexts. In this paper, we propose a novel approach that integrates LLMs and GNNs, leveraging the zero-shot inference and reasoning capabilities of LLMs and employing a Graph-LLM-based active learning paradigm to enhance GNNs' performance. Extensive experiments demonstrate the effectiveness of our model in improving node classification accuracy with considerably limited labeled data, surpassing state-of-the-art baselines by significant margins.

Large Language Models (LLMs) have demonstrated remarkable proficiency in various natural language generation (NLG) tasks. Previous studies suggest that LLMs' generation process involves uncertainty. However, existing approaches to uncertainty estimation mainly focus on sequence-level uncertainty, overlooking individual pieces of information within sequences. These methods fall short in separately assessing the uncertainty of each component in a sequence. In response, we propose a novel framework for Concept-Level Uncertainty Estimation (CLUE) for LLMs. We leverage LLMs to convert output sequences into concept-level representations, breaking down sequences into individual concepts and measuring the uncertainty of each concept separately. We conduct experiments to demonstrate that CLUE can provide more interpretable uncertainty estimation results compared with sentence-level uncertainty, and could be a useful tool for various tasks such as hallucination detection and story generation.

Effective collaboration of dual-arm robots and their tool use capabilities are increasingly important areas in the advancement of robotics. These skills play a significant role in expanding robots' ability to operate in diverse real-world environments. However, progress is impeded by the scarcity of specialized training data. This paper introduces RoboTwin, a novel benchmark dataset combining real-world teleoperated data with synthetic data from digital twins, designed for dual-arm robotic scenarios. Using the COBOT Magic platform, we have collected diverse data on tool usage and human-robot interaction. We present a innovative approach to creating digital twins using AI-generated content, transforming 2D images into detailed 3D models. Furthermore, we utilize large language models to generate expert-level training data and task-specific pose sequences oriented toward functionality. Our key contributions are: 1) the RoboTwin benchmark dataset, 2) an efficient real-to-simulation pipeline, and 3) the use of language models for automatic expert-level data generation. These advancements are designed to address the shortage of robotic training data, potentially accelerating the development of more capable and versatile robotic systems for a wide range of real-world applications. The project page is available at https://robotwin-benchmark.github.io/early-version/

We present a prototype for a Bioinformatics Retrieval Augmentation Data (BRAD) digital assistant. BRAD integrates a suite of tools to handle a wide range of bioinformatics tasks, from code execution to online search. We demonstrate BRAD's capabilities through (1) improved question-and-answering with retrieval augmented generation (RAG), (2) BRAD's ability to run and write complex software pipelines, and (3) BRAD's ability to organize and distribute tasks across individual and teams of agents. We use BRAD for automation of bioinformatics workflows, performing tasks ranging from gene enrichment and searching the archive to automatic code generation and running biomarker identification pipelines. BRAD is a step toward the ultimate goal to develop a digital twin of laboratories driven by self-contained loops for hypothesis generation and testing of digital biology experiments.

Momentum based optimizers are central to a wide range of machine learning applications. These typically rely on an Exponential Moving Average (EMA) of gradients, which decays exponentially the present contribution of older gradients. This accounts for gradients being local linear approximations which lose their relevance as the iterate moves along the loss landscape. This work questions the use of a single EMA to accumulate past gradients and empirically demonstrates how this choice can be sub-optimal: a single EMA cannot simultaneously give a high weight to the immediate past, and a non-negligible weight to older gradients. Building on this observation, we propose AdEMAMix, a simple modification of the Adam optimizer with a mixture of two EMAs to better take advantage of past gradients. Our experiments on language modeling and image classification show -- quite surprisingly -- that gradients can stay relevant for tens of thousands of steps. They help to converge faster, and often to lower minima: e.g., a $1.3$B parameter AdEMAMix LLM trained on $101$B tokens performs comparably to an AdamW model trained on $197$B tokens ($+95\%$). Moreover, our method significantly slows-down model forgetting during training. Our work motivates further exploration of different types of functions to leverage past gradients, beyond EMAs.

This study investigates the automated classification of Calls to Action (CTAs) within the 2021 German Instagram election campaign to advance the understanding of mobilization in social media contexts. We analyzed over 2,208 Instagram stories and 712 posts using fine-tuned BERT models and OpenAI's GPT-4 models. The fine-tuned BERT model incorporating synthetic training data achieved a macro F1 score of 0.93, demonstrating a robust classification performance. Our analysis revealed that 49.58% of Instagram posts and 10.64% of stories contained CTAs, highlighting significant differences in mobilization strategies between these content types. Additionally, we found that FDP and the Greens had the highest prevalence of CTAs in posts, whereas CDU and CSU led in story CTAs.

Background and Aims: This study evaluates the medical reasoning performance of large language models (LLMs) and vision language models (VLMs) in gastroenterology. Methods: We used 300 gastroenterology board exam-style multiple-choice questions, 138 of which contain images to systematically assess the impact of model configurations and parameters and prompt engineering strategies utilizing GPT-3.5. Next, we assessed the performance of proprietary and open-source LLMs (versions), including GPT (3.5, 4, 4o, 4omini), Claude (3, 3.5), Gemini (1.0), Mistral, Llama (2, 3, 3.1), Mixtral, and Phi (3), across different interfaces (web and API), computing environments (cloud and local), and model precisions (with and without quantization). Finally, we assessed accuracy using a semiautomated pipeline. Results: Among the proprietary models, GPT-4o (73.7%) and Claude3.5-Sonnet (74.0%) achieved the highest accuracy, outperforming the top open-source models: Llama3.1-405b (64%), Llama3.1-70b (58.3%), and Mixtral-8x7b (54.3%). Among the quantized open-source models, the 6-bit quantized Phi3-14b (48.7%) performed best. The scores of the quantized models were comparable to those of the full-precision models Llama2-7b, Llama2--13b, and Gemma2-9b. Notably, VLM performance on image-containing questions did not improve when the images were provided and worsened when LLM-generated captions were provided. In contrast, a 10% increase in accuracy was observed when images were accompanied by human-crafted image descriptions. Conclusion: In conclusion, while LLMs exhibit robust zero-shot performance in medical reasoning, the integration of visual data remains a challenge for VLMs. Effective deployment involves carefully determining optimal model configurations, encouraging users to consider either the high performance of proprietary models or the flexible adaptability of open-source models.

Model extraction attacks (MEAs) on large language models (LLMs) have received increasing research attention lately. Existing attack methods on LLMs inherit the extraction strategies from those designed for deep neural networks (DNNs) yet neglect the inconsistency of training tasks between MEA and LLMs' alignments. As such, they result in poor attack performances. To tackle this issue, we present Locality Reinforced Distillation (LoRD), a novel model extraction attack algorithm specifically for LLMs. In particular, we design a policy-gradient-style training task, which utilizes victim models' responses as a signal to guide the crafting of preference for the local model. Theoretical analysis has shown that i) LoRD's convergence procedure in MEAs is consistent with the alignments of LLMs, and ii) LoRD can reduce query complexity while mitigating watermark protection through exploration-based stealing. Extensive experiments on domain-specific extractions demonstrate the superiority of our method by examining the extraction of various state-of-the-art commercial LLMs.

Foundational Large Language Models (LLMs) have changed the way we perceive technology. They have been shown to excel in tasks ranging from poem writing and coding to essay generation and puzzle solving. With the incorporation of image generation capability, they have become more comprehensive and versatile AI tools. At the same time, researchers are striving to identify the limitations of these tools to improve them further. Currently identified flaws include hallucination, biases, and bypassing restricted commands to generate harmful content. In the present work, we have identified a fundamental limitation related to the image generation ability of LLMs, and termed it The NO Syndrome. This negation blindness refers to LLMs inability to correctly comprehend NO related natural language prompts to generate the desired images. Interestingly, all tested LLMs including GPT-4, Gemini, and Copilot were found to be suffering from this syndrome. To demonstrate the generalization of this limitation, we carried out simulation experiments and conducted entropy-based and benchmark statistical analysis tests on various LLMs in multiple languages, including English, Hindi, and French. We conclude that the NO syndrome is a significant flaw in current LLMs that needs to be addressed. A related finding of this study showed a consistent discrepancy between image and textual responses as a result of this NO syndrome. We posit that the introduction of a negation context-aware reinforcement learning based feedback loop between the LLMs textual response and generated image could help ensure the generated text is based on both the LLMs correct contextual understanding of the negation query and the generated visual output.