Boltzmann Attention Sampling for Image Analysis with Small Objects

Detecting and segmenting small objects, such as lung nodules and tumor lesions, remains a critical challenge in image analysis. These objects often occupy less than 0.1% of an image, making traditional transformer architectures inefficient and prone to performance degradation due to redundant attention computations on irrelevant regions. Existing sparse attention mechanisms rely on rigid hierarchical structures, which are poorly suited for detecting small, variable, and uncertain object locations. In this paper, we propose BoltzFormer, a novel transformer-based architecture designed to address these challenges through dynamic sparse attention. BoltzFormer identifies and focuses attention on relevant areas by modeling uncertainty using a Boltzmann distribution with an annealing schedule. Initially, a higher temperature allows broader area sampling in early layers, when object location uncertainty is greatest. As the temperature decreases in later layers, attention becomes more focused, enhancing efficiency and accuracy. BoltzFormer seamlessly integrates into existing transformer architectures via a modular Boltzmann attention sampling mechanism. Comprehensive evaluations on benchmark datasets demonstrate that BoltzFormer significantly improves segmentation performance for small objects while reducing attention computation by an order of magnitude compared to previous state-of-the-art methods.

Universal Abstraction: Harnessing Frontier Models to Structure Real-World Data at Scale

The vast majority of real-world patient information resides in unstructured clinical text, and the process of medical abstraction seeks to extract and normalize structured information from this unstructured input. However, traditional medical abstraction methods can require significant manual efforts that can include crafting rules or annotating training labels, limiting scalability. In this paper, we propose UniMedAbstractor (UMA), a zero-shot medical abstraction framework leveraging Large Language Models (LLMs) through a modular and customizable prompt template. We refer to our approach as universal abstraction as it can quickly scale to new attributes through its universal prompt template without curating attribute-specific training labels or rules. We evaluate UMA for oncology applications, focusing on fifteen key attributes representing the cancer patient journey, from short-context attributes (e.g., performance status, treatment) to complex long-context attributes requiring longitudinal reasoning (e.g., tumor site, histology, TNM staging). Experiments on real-world data show UMA's strong performance and generalizability. Compared to supervised and heuristic baselines, UMA with GPT-4o achieves on average an absolute 2-point F1/accuracy improvement for both short-context and long-context attribute abstraction. For pathologic T staging, UMA even outperforms the supervised model by 20 points in accuracy.

BLOOM: A 176B-Parameter Open-Access Multilingual Language Model

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.

BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical