Daily Papers

The integration of Multimodal Large Language Models (MLLMs) into chemistry promises to revolutionize scientific discovery, yet their ability to comprehend the dense, graphical language of reactions within authentic literature remains underexplored. Here, we introduce RxnBench, a multi-tiered benchmark designed to rigorously evaluate MLLMs on chemical reaction understanding from scientific PDFs. RxnBench comprises two tasks: Single-Figure QA (SF-QA), which tests fine-grained visual perception and mechanistic reasoning using 1,525 questions derived from 305 curated reaction schemes, and Full-Document QA (FD-QA), which challenges models to synthesize information from 108 articles, requiring cross-modal integration of text, schemes, and tables. Our evaluation of MLLMs reveals a critical capability gap: while models excel at extracting explicit text, they struggle with deep chemical logic and precise structural recognition. Notably, models with inference-time reasoning significantly outperform standard architectures, yet none achieve 50\% accuracy on FD-QA. These findings underscore the urgent need for domain-specific visual encoders and stronger reasoning engines to advance autonomous AI chemists.

In this work, we provide a thorough investigation of gist-based context compression methods to improve long-context processing in large language models. We focus on two key questions: (1) How well can these methods replace full attention models? and (2) What potential failure patterns arise due to compression? Through extensive experiments, we show that while gist-based compression can achieve near-lossless performance on tasks like retrieval-augmented generation and long-document QA, it faces challenges in tasks like synthetic recall. Furthermore, we identify three key failure patterns: lost by the boundary, lost if surprise, and lost along the way. To mitigate these issues, we propose two effective strategies: fine-grained autoencoding, which enhances the reconstruction of original token information, and segment-wise token importance estimation, which adjusts optimization based on token dependencies. Our work provides valuable insights into the understanding of gist token-based context compression and offers practical strategies for improving compression capabilities.

To enable building and testing models on long-document comprehension, we introduce QuALITY, a multiple-choice QA dataset with context passages in English that have an average length of about 5,000 tokens, much longer than typical current models can process. Unlike in prior work with passages, our questions are written and validated by contributors who have read the entire passage, rather than relying on summaries or excerpts. In addition, only half of the questions are answerable by annotators working under tight time constraints, indicating that skimming and simple search are not enough to consistently perform well. Our baseline models perform poorly on this task (55.4%) and significantly lag behind human performance (93.5%).

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model's ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, 'target' segments selectively attend only to the KV-caches of their designated 'source' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings. Code and the Graph-KV data are publicly available.

Retrieval augmented generation (RAG) has become the standard in long context question answering (QA) systems. However, typical implementations of RAG rely on a rather naive retrieval mechanism, in which texts whose embeddings are most similar to that of the query are deemed most relevant. This has consequences in subjective QA tasks, where the most relevant text may not directly contain the answer. In this work, we propose a novel extension to RAG systems, which we call Retrieval from AI Derived Documents (RAIDD). RAIDD leverages the full power of the LLM in the retrieval process by deriving inferred features, such as summaries and example questions, from the documents at ingest. We demonstrate that this approach significantly improves the performance of RAG systems on long-context QA tasks.