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byAK and the research community

Jul 29

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.

Pangu Pro MoE: Mixture of Grouped Experts for Efficient Sparsity

The surgence of Mixture of Experts (MoE) in Large Language Models promises a small price of execution cost for a much larger model parameter count and learning capacity, because only a small fraction of parameters are activated for each input token. However, it is commonly observed that some experts are activated far more often than others, leading to system inefficiency when running the experts on different devices in parallel. Therefore, we introduce Mixture of Grouped Experts (MoGE), which groups the experts during selection and balances the expert workload better than MoE in nature. It constrains tokens to activate an equal number of experts within each predefined expert group. When a model execution is distributed on multiple devices, this architectural design ensures a balanced computational load across devices, significantly enhancing throughput, particularly for the inference phase. Further, we build Pangu Pro MoE on Ascend NPUs, a sparse model based on MoGE with 72 billion total parameters, 16 billion of which are activated for each token. The configuration of Pangu Pro MoE is optimized for Ascend 300I Duo and 800I A2 through extensive system simulation studies. Our experiments indicate that MoGE indeed leads to better expert load balancing and more efficient execution for both model training and inference on Ascend NPUs. The inference performance of Pangu Pro MoE achieves 1148 tokens/s per card and can be further improved to 1528 tokens/s per card by speculative acceleration, outperforming comparable 32B and 72B Dense models. Furthermore, we achieve an excellent cost-to-performance ratio for model inference on Ascend 300I Duo. Our studies show that Ascend NPUs are capable of training Pangu Pro MoE with massive parallelization to make it a leading model within the sub-100B total parameter class, outperforming prominent open-source models like GLM-Z1-32B and Qwen3-32B.

Performance Scaling via Optimal Transport: Enabling Data Selection from Partially Revealed Sources

Traditionally, data selection has been studied in settings where all samples from prospective sources are fully revealed to a machine learning developer. However, in practical data exchange scenarios, data providers often reveal only a limited subset of samples before an acquisition decision is made. Recently, there have been efforts to fit scaling laws that predict model performance at any size and data source composition using the limited available samples. However, these scaling functions are black-box, computationally expensive to fit, highly susceptible to overfitting, or/and difficult to optimize for data selection. This paper proposes a framework called <projektor>, which predicts model performance and supports data selection decisions based on partial samples of prospective data sources. Our approach distinguishes itself from existing work by introducing a novel *two-stage* performance inference process. In the first stage, we leverage the Optimal Transport distance to predict the model's performance for any data mixture ratio within the range of disclosed data sizes. In the second stage, we extrapolate the performance to larger undisclosed data sizes based on a novel parameter-free mapping technique inspired by neural scaling laws. We further derive an efficient gradient-based method to select data sources based on the projected model performance. Evaluation over a diverse range of applications demonstrates that <projektor> significantly improves existing performance scaling approaches in terms of both the accuracy of performance inference and the computation costs associated with constructing the performance predictor. Also, <projektor> outperforms by a wide margin in data selection effectiveness compared to a range of other off-the-shelf solutions.

Cheaply Evaluating Inference Efficiency Metrics for Autoregressive Transformer APIs

Large language models (LLMs) power many state-of-the-art systems in natural language processing. However, these models are extremely computationally expensive, even at inference time, raising the natural question: when is the extra cost of deploying a larger model worth the anticipated boost in capabilities? Better understanding this tradeoff fundamentally could benefit from an inference efficiency metric that is both (i) easily comparable across models from different providers, and (ii) representative of the true cost of running queries in an isolated performance environment. Unfortunately, access to LLMs today is largely restricted to black-box text generation APIs and raw runtimes measured through this interface do not satisfy these desiderata: model providers can apply various software and hardware optimizations orthogonal to the model, and models served on shared infrastructure are susceptible to performance contention. To circumvent these problems, we propose a new metric for comparing inference efficiency across models. This metric puts models on equal footing as though they were served (i) on uniform hardware and software, and (ii) without performance contention. We call this metric the idealized runtime, and we propose a methodology to efficiently estimate this metric for autoregressive Transformer models. We also propose cost-aware variants that incorporate the number of accelerators needed to serve the model. Using these metrics, we compare ten state-of-the-art LLMs to provide the first analysis of inference efficiency-capability tradeoffs; we make several observations from this analysis, including the fact that the superior inference runtime performance of certain APIs is often a byproduct of optimizations within the API rather than the underlying model. Our methodology also facilitates the efficient comparison of different software and hardware stacks.