BioResearcher: Scenario-Guided Multi-Agent for Translational Medicine

Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable provenance. General-purpose foundation models and off-the-shelf tool-augmented or multi-agent systems are not built for this: they tend to produce single-shot answers or run open-endedly, and fall short on the auditable, scenario-specific workflows that heterogeneous biomedical sources demand. This paper introduces Ingenix BioResearcher, a scenario-guided multi-agent system that maps queries to versioned research playbooks, delegates to specialized subagents over 30+ tools and machine-learning endpoints, mixes structured database access with sandboxed code for genome-scale analyses, and applies claim-level multi-model reconciliation before editorial assembly. We evaluate BioResearcher across unit-level capabilities, open-ended biomedical reasoning, and end-to-end clinical discovery. It leads evaluated baselines on 109 single-step tests (83.49% pass rate; 0.892 average score), achieves strong biomedical benchmark performance (89.33% on BixBench-Verified-50 and the top 0.758 mean score on BaisBench Scientific Discovery), and leads on a 30-query clinical end-to-end benchmark with the highest positive hit rate (74.7% $\pm$ 3.3%) and negative clear rate (96.8% $\pm$ 0.2%). These results show broad, competitive performance across unit-level, open-ended, and end-to-end clinical evaluations.

Document Understanding Dataset and Evaluation (DUDE)

We call on the Document AI (DocAI) community to reevaluate current methodologies and embrace the challenge of creating more practically-oriented benchmarks. Document Understanding Dataset and Evaluation (DUDE) seeks to remediate the halted research progress in understanding visually-rich documents (VRDs). We present a new dataset with novelties related to types of questions, answers, and document layouts based on multi-industry, multi-domain, and multi-page VRDs of various origins, and dates. Moreover, we are pushing the boundaries of current methods by creating multi-task and multi-domain evaluation setups that more accurately simulate real-world situations where powerful generalization and adaptation under low-resource settings are desired. DUDE aims to set a new standard as a more practical, long-standing benchmark for the community, and we hope that it will lead to future extensions and contributions that address real-world challenges. Finally, our work illustrates the importance of finding more efficient ways to model language, images, and layout in DocAI.

Going Full-TILT Boogie on Document Understanding with Text-Image-Layout Transformer

We address the challenging problem of Natural Language Comprehension beyond plain-text documents by introducing the TILT neural network architecture which simultaneously learns layout information, visual features, and textual semantics. Contrary to previous approaches, we rely on a decoder capable of unifying a variety of problems involving natural language. The layout is represented as an attention bias and complemented with contextualized visual information, while the core of our model is a pretrained encoder-decoder Transformer. Our novel approach achieves state-of-the-art results in extracting information from documents and answering questions which demand layout understanding (DocVQA, CORD, WikiOps, SROIE). At the same time, we simplify the process by employing an end-to-end model.

LAMBERT: Layout-Aware language Modeling using BERT for information extraction

In this paper we introduce a novel approach to the problem of understanding documents where the local semantics is influenced by non-trivial layout. Namely, we modify the Transformer architecture in a way that allows it to use the graphical features defined by the layout, without the need to re-learn the language semantics from scratch, thanks to starting the training process from a model pretrained on classical language modeling tasks.