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The ability of Large Language Models (LLMs) to critique and refine their reasoning is crucial for their application in evaluation, feedback provision, and self-improvement. This paper introduces CriticBench, a comprehensive benchmark designed to assess LLMs' abilities to critique and rectify their reasoning across a variety of tasks. CriticBench encompasses five reasoning domains: mathematical, commonsense, symbolic, coding, and algorithmic. It compiles 15 datasets and incorporates responses from three LLM families. Utilizing CriticBench, we evaluate and dissect the performance of 17 LLMs in generation, critique, and correction reasoning, i.e., GQC reasoning. Our findings reveal: (1) a linear relationship in GQC capabilities, with critique-focused training markedly enhancing performance; (2) a task-dependent variation in correction effectiveness, with logic-oriented tasks being more amenable to correction; (3) GQC knowledge inconsistencies that decrease as model size increases; and (4) an intriguing inter-model critiquing dynamic, where stronger models are better at critiquing weaker ones, while weaker models can surprisingly surpass stronger ones in their self-critique. We hope these insights into the nuanced critique-correct reasoning of LLMs will foster further research in LLM critique and self-improvement.

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. Here, we develop BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function. Moreover, BioDiscoveryAgent achieves an average of 18% improvement in detecting desired phenotypes across five datasets, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' capabilities.

Large language models (LLMs) have shown impressive capabilities across diverse settings, but still struggle as the length and complexity of the context increases. To address this challenge, we propose Thinking Recursively and Dynamically (ThReaD). THREAD frames model generation as a thread of execution that, based on the context, can run to completion or dynamically spawn new threads. By spawning, threads can offload work (e.g., thinking, retrieving information) to child threads, which only return tokens needed for the parent thread to do its work. In effect, this enables the model to adapt, as needed, the amount of intermediate work used to produce tokens. We apply THREAD in the settings of LLM task solving and question answering, where the dynamic threading allows the model to recursively decompose the given task or question into progressively simpler sub-problems that can be solved by separate child threads. We test THREAD, implemented using a few-shot learning approach, on diverse benchmarks for agent tasks and data-grounded question answering. THREAD achieves state-of-the-art performance with GPT-4 and GPT-3.5 on these benchmarks, including ALFWorld, TextCraft, and WebShop, along with two new benchmarks, DataCommons QA and MIMIC-III ICU QA. In addition, THREAD outperforms existing frameworks by 10% to 50% absolute points with smaller models, including Llama-3-8b and CodeLlama-7b.

The introduction of transformers has been an important breakthrough for AI research and application as transformers are the foundation behind Generative AI. A promising application domain for transformers is cybersecurity, in particular the malware domain analysis. The reason is the flexibility of the transformer models in handling long sequential features and understanding contextual relationships. However, as the use of transformers for malware analysis is still in the infancy stage, it is critical to evaluate, systematize, and contextualize existing literature to foster future research. This Systematization of Knowledge (SoK) paper aims to provide a comprehensive analysis of transformer-based approaches designed for malware analysis. Based on our systematic analysis of existing knowledge, we structure and propose taxonomies based on: (a) how different transformers are adapted, organized, and modified across various use cases; and (b) how diverse feature types and their representation capabilities are reflected. We also provide an inventory of datasets used to explore multiple research avenues in the use of transformers for malware analysis and discuss open challenges with future research directions. We believe that this SoK paper will assist the research community in gaining detailed insights from existing work and will serve as a foundational resource for implementing novel research using transformers for malware analysis.

Utilizing large language models (LLMs) for transforming natural language questions into SQL queries (text-to-SQL) is a promising yet challenging approach, particularly when applied to real-world databases with complex and extensive schemas. In particular, effectively incorporating data catalogs and database values for SQL generation remains an obstacle, leading to suboptimal solutions. We address this problem by proposing a new pipeline that effectively retrieves relevant data and context, selects an efficient schema, and synthesizes correct and efficient SQL queries. To increase retrieval precision, our pipeline introduces a hierarchical retrieval method leveraging model-generated keywords, locality-sensitive hashing indexing, and vector databases. Additionally, we have developed an adaptive schema pruning technique that adjusts based on the complexity of the problem and the model's context size. Our approach generalizes to both frontier proprietary models like GPT-4 and open-source models such as Llama-3-70B. Through a series of ablation studies, we demonstrate the effectiveness of each component of our pipeline and its impact on the end-to-end performance. Our method achieves new state-of-the-art performance on the cross-domain challenging BIRD dataset.

Recent knowledge editing methods have primarily focused on modifying structured knowledge in large language models, heavily relying on the assumption that structured knowledge is stored as key-value pairs locally in MLP layers or specific neurons. However, this task setting overlooks the fact that a significant portion of real-world knowledge is stored in an unstructured format, characterized by long-form content, noise, and a complex yet comprehensive nature. The "knowledge locating" and "term-driven optimization" techniques conducted from the assumption used in previous methods (e.g., MEMIT) are ill-suited for unstructured knowledge. To address these challenges, we propose a novel unstructured knowledge editing method, namely UnKE, which extends previous assumptions in the layer dimension and token dimension. Firstly, in the layer dimension, we discard the "knowledge locating" step and treat first few layers as the key, which expand knowledge storage through layers to break the "knowledge stored locally" assumption. Next, we replace "term-driven optimization" with "cause-driven optimization" across all inputted tokens in the token dimension, directly optimizing the last layer of the key generator to perform editing to generate the required key vectors. By utilizing key-value pairs at the layer level, UnKE effectively represents and edits complex and comprehensive unstructured knowledge, leveraging the potential of both the MLP and attention layers. Results on newly proposed unstructure knowledge editing dataset (UnKEBench) and traditional structured datasets demonstrate that UnKE achieves remarkable performance, surpassing strong baselines.

We propose the Data Contamination Quiz (DCQ), a simple and effective approach to detect data contamination in large language models (LLMs) and estimate the amount of it. Specifically, we frame data contamination detection as a series of multiple-choice questions and devise a quiz format wherein three perturbed versions of each subsampled instance from a specific dataset partition (e.g., GSM8k test set) are created. These changes only include word-level perturbations. The generated perturbations, along with the original dataset instance, form the options in the DCQ, with an extra option accommodating the possibility of selecting none of the provided options. Given that the only distinguishing signal among the options is the exact wording with respect to the original dataset instance, an LLM, when tasked with identifying the original dataset instance, gravitates towards selecting the original one if it has been exposed to it in its pre-training phase -- a trait intrinsic to LLMs. While accounting for positional biases in LLMs, the quiz performance reveals the contamination level for the model being examined with the dataset partition to which the quiz pertains. Applied to various datasets with GPT-4 and GPT-3.5, our findings -- while fully lacking access to pre-training data and model parameters -- suggest that DCQ achieves state-of-the-art results and uncovers greater contamination/memorization levels compared to existing methods and proficiently bypasses more safety filters, especially those set to avoid generating copyrighted contents.

Large language models (LLMs) have demonstrated impressive capabilities in natural language processing. However, their internal mechanisms are still unclear and this lack of transparency poses unwanted risks for downstream applications. Therefore, understanding and explaining these models is crucial for elucidating their behaviors, limitations, and social impacts. In this paper, we introduce a taxonomy of explainability techniques and provide a structured overview of methods for explaining Transformer-based language models. We categorize techniques based on the training paradigms of LLMs: traditional fine-tuning-based paradigm and prompting-based paradigm. For each paradigm, we summarize the goals and dominant approaches for generating local explanations of individual predictions and global explanations of overall model knowledge. We also discuss metrics for evaluating generated explanations, and discuss how explanations can be leveraged to debug models and improve performance. Lastly, we examine key challenges and emerging opportunities for explanation techniques in the era of LLMs in comparison to conventional machine learning models.

Interpretability methods are developed to understand the working mechanisms of black-box models, which is crucial to their responsible deployment. Fulfilling this goal requires both that the explanations generated by these methods are correct and that people can easily and reliably understand them. While the former has been addressed in prior work, the latter is often overlooked, resulting in informal model understanding derived from a handful of local explanations. In this paper, we introduce explanation summary (ExSum), a mathematical framework for quantifying model understanding, and propose metrics for its quality assessment. On two domains, ExSum highlights various limitations in the current practice, helps develop accurate model understanding, and reveals easily overlooked properties of the model. We also connect understandability to other properties of explanations such as human alignment, robustness, and counterfactual minimality and plausibility.

Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.