arXiv subjects

Benjamin Warner

Publications and source records attributed to Benjamin Warner.

4 recordsLinked to original sources

arXiv2026

Medmarks: A Comprehensive Open-Source LLM Benchmark Suite for Medical Tasks

Evaluating large language models (LLMs) for medical applications remains challenging due to benchmark saturation, limited data accessibility, and insufficient coverage of relevant tasks. Existing suites have either saturated, heavily depend on restricted datasets, or lack comprehensive model coverage. We introduce Medmarks, a fully open-source evaluation suite with 30 benchmarks spanning question answering, information extraction, medical calculations, and open-ended clinical reasoning. We perform a systematic evaluation of 61 models across 71 configurations using verifiable metrics and LLM-as-a-Judge. Our results show that frontier reasoning models (Gemini 3 Pro Preview, GPT-5.1, & GPT-5.2) achieve the highest performance across both benchmarks, most frontier proprietary models are significantly more token efficient than open-weight alternatives, medically fine-tuned models outperform their generalist counterparts, and that models are susceptible to answer-order bias (particularly smaller models and Grok 4). A subset of our evals (Medmarks-T) can be directly used as reinforcement learning environments to post-train LLMs for medical reasoning. Code is available at https://github.com/MedARC-AI/Medmarks

cs.CL↗

arXiv2025

Scaling Vision Transformers for Functional MRI with Flat Maps

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

cs.CV↗

arXiv2025

It's All in The [MASK]: Simple Instruction-Tuning Enables BERT-like Masked Language Models As Generative Classifiers

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language models (LLMs). In this work, we introduce ModernBERT-Large-Instruct, a 0.4B-parameter encoder model that leverages its masked language modelling (MLM) head for generative classification. Our approach employs an intentionally simple training loop and inference mechanism that requires no heavy pre-processing, heavily engineered prompting, or architectural modifications. ModernBERT-Large-Instruct exhibits strong zero-shot performance on both classification and knowledge-based tasks, outperforming similarly sized LLMs on MMLU and achieving 93% of Llama3-1B's MMLU performance with 60% less parameters. We also demonstrate that, when fine-tuned, the generative approach using the MLM head matches or even surpasses traditional classification-head methods across diverse NLU tasks.This capability emerges specifically in models trained on contemporary, diverse data mixes, with models trained on lower volume, less-diverse data yielding considerably weaker performance. Although preliminary, these results demonstrate the potential of using the original generative masked language modelling head over traditional task-specific heads for downstream tasks. Our work suggests that further exploration into this area is warranted, highlighting many avenues for future improvements.

cs.CL↗

arXiv2024

Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference

Encoder-only transformer models such as BERT offer a great performance-size tradeoff for retrieval and classification tasks with respect to larger decoder-only models. Despite being the workhorse of numerous production pipelines, there have been limited Pareto improvements to BERT since its release. In this paper, we introduce ModernBERT, bringing modern model optimizations to encoder-only models and representing a major Pareto improvement over older encoders. Trained on 2 trillion tokens with a native 8192 sequence length, ModernBERT models exhibit state-of-the-art results on a large pool of evaluations encompassing diverse classification tasks and both single and multi-vector retrieval on different domains (including code). In addition to strong downstream performance, ModernBERT is also the most speed and memory efficient encoder and is designed for inference on common GPUs.

cs.CL↗