Daily Papers

Predicting peptide--major histocompatibility complex I (pMHC-I) binding affinity remains challenging due to extreme allelic diversity (sim30,000 HLA alleles), severe data scarcity for most alleles, and noisy experimental measurements. Current methods particularly struggle with underrepresented alleles and quantitative binding prediction. We test whether domain-specific continued pre-training of protein language models is beneficial for their application to pMHC-I binding affinity prediction. Starting from ESM Cambrian (300M parameters), we perform masked-language modeling (MLM)-based continued pre-training on HLA-associated peptides (epitopes), testing two input formats: epitope sequences alone versus epitopes concatenated with HLA heavy chain sequences. We then fine-tune for functional IC_{50} binding affinity prediction using only high-quality quantitative data, avoiding mass spectrometry biases that are inherited by existing methods.

Cambrian-S aims to take the first steps towards improving video world models with spatial supersensing by introducing (i) two benchmarks, VSI-Super-Recall (VSR) and VSI-Super-Counting (VSC), and (ii) bespoke predictive sensing inference strategies tailored to each benchmark. In this work, we conduct a critical analysis of Cambrian-S across both these fronts. First, we introduce a simple baseline, NoSense, which discards almost all temporal structure and uses only a bag-of-words SigLIP model, yet near-perfectly solves VSR, achieving 95% accuracy even on 4-hour videos. This shows benchmarks like VSR can be nearly solved without spatial cognition, world modeling or spatial supersensing. Second, we hypothesize that the tailored inference methods proposed by Cambrian-S likely exploit shortcut heuristics in the benchmark. We illustrate this with a simple sanity check on the VSC benchmark, called VSC-Repeat: We concatenate each video with itself 1-5 times, which does not change the number of unique objects. However, this simple perturbation entirely collapses the mean relative accuracy of Cambrian-S from 42% to 0%. A system that performs spatial supersensing and integrates information across experiences should recognize views of the same scene and keep object-count predictions unchanged; instead, Cambrian-S inference algorithm relies largely on a shortcut in the VSC benchmark that rooms are never revisited. Taken together, our findings suggest that (i) current VSI-Super benchmarks do not yet reliably measure spatial supersensing, and (ii) predictive-sensing inference recipes used by Cambrian-S improve performance by inadvertently exploiting shortcuts rather than from robust spatial supersensing. We include the response from the Cambrian-S authors (in Appendix A) to provide a balanced perspective alongside our claims. We release our code at: https://github.com/bethgelab/supersanity

Multimodal large language models (MLLMs) have made significant strides, yet they face challenges in the medical domain due to limited specialized knowledge. While recent medical MLLMs demonstrate strong performance in lab settings, they often struggle in real-world applications, highlighting a substantial gap between research and practice. In this paper, we seek to address this gap at various stages of the end-to-end learning pipeline, including data collection, model fine-tuning, and evaluation. At the data collection stage, we introduce SemiHVision, a dataset that combines human annotations with automated augmentation techniques to improve both medical knowledge representation and diagnostic reasoning. For model fine-tuning, we trained PMC-Cambrian-8B-AN over 2400 H100 GPU hours, resulting in performance that surpasses public medical models like HuatuoGPT-Vision-34B (79.0% vs. 66.7%) and private general models like Claude3-Opus (55.7%) on traditional benchmarks such as SLAKE and VQA-RAD. In the evaluation phase, we observed that traditional benchmarks cannot accurately reflect realistic clinical task capabilities. To overcome this limitation and provide more targeted guidance for model evaluation, we introduce the JAMA Clinical Challenge, a novel benchmark specifically designed to evaluate diagnostic reasoning. On this benchmark, PMC-Cambrian-AN achieves state-of-the-art performance with a GPT-4 score of 1.29, significantly outperforming HuatuoGPT-Vision-34B (1.13) and Claude3-Opus (1.17), demonstrating its superior diagnostic reasoning abilities.

We introduce Cambrian-1, a family of multimodal LLMs (MLLMs) designed with a vision-centric approach. While stronger language models can enhance multimodal capabilities, the design choices for vision components are often insufficiently explored and disconnected from visual representation learning research. This gap hinders accurate sensory grounding in real-world scenarios. Our study uses LLMs and visual instruction tuning as an interface to evaluate various visual representations, offering new insights into different models and architectures -- self-supervised, strongly supervised, or combinations thereof -- based on experiments with over 20 vision encoders. We critically examine existing MLLM benchmarks, addressing the difficulties involved in consolidating and interpreting results from various tasks, and introduce a new vision-centric benchmark, CV-Bench. To further improve visual grounding, we propose the Spatial Vision Aggregator (SVA), a dynamic and spatially-aware connector that integrates high-resolution vision features with LLMs while reducing the number of tokens. Additionally, we discuss the curation of high-quality visual instruction-tuning data from publicly available sources, emphasizing the importance of data source balancing and distribution ratio. Collectively, Cambrian-1 not only achieves state-of-the-art performance but also serves as a comprehensive, open cookbook for instruction-tuned MLLMs. We provide model weights, code, supporting tools, datasets, and detailed instruction-tuning and evaluation recipes. We hope our release will inspire and accelerate advancements in multimodal systems and visual representation learning.