MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

Self-Supervised Prompt Optimization

Well-designed prompts are crucial for enhancing Large language models' (LLMs) reasoning capabilities while aligning their outputs with task requirements across diverse domains. However, manually designed prompts require expertise and iterative experimentation. While existing prompt optimization methods aim to automate this process, they rely heavily on external references such as ground truth or by humans, limiting their applicability in real-world scenarios where such data is unavailable or costly to obtain. To address this, we propose Self-Supervised Prompt Optimization (SPO), a cost-efficient framework that discovers effective prompts for both closed and open-ended tasks without requiring external reference. Motivated by the observations that prompt quality manifests directly in LLM outputs and LLMs can effectively assess adherence to task requirements, we derive evaluation and optimization signals purely from output comparisons. Specifically, SPO selects superior prompts through pairwise output comparisons evaluated by an LLM evaluator, followed by an LLM optimizer that aligns outputs with task requirements. Extensive experiments demonstrate that SPO outperforms state-of-the-art prompt optimization methods, achieving comparable or superior results with significantly lower costs (e.g., 1.1% to 5.6% of existing methods) and fewer samples (e.g., three samples). The code is available at https://github.com/geekan/MetaGPT.

AFlow: Automating Agentic Workflow Generation

Large language models (LLMs) have demonstrated remarkable potential in solving complex tasks across diverse domains, typically by employing agentic workflows that follow detailed instructions and operational sequences. However, constructing these workflows requires significant human effort, limiting scalability and generalizability. Recent research has sought to automate the generation and optimization of these workflows, but existing methods still rely on initial manual setup and fall short of achieving fully automated and effective workflow generation. To address this challenge, we reformulate workflow optimization as a search problem over code-represented workflows, where LLM-invoking nodes are connected by edges. We introduce AFlow, an automated framework that efficiently explores this space using Monte Carlo Tree Search, iteratively refining workflows through code modification, tree-structured experience, and execution feedback. Empirical evaluations across six benchmark datasets demonstrate AFlow's efficacy, yielding a 5.7% average improvement over state-of-the-art baselines. Furthermore, AFlow enables smaller models to outperform GPT-4o on specific tasks at 4.55% of its inference cost in dollars. The code will be available at https://github.com/geekan/MetaGPT.