Linfeng Zhang

Sihang Li, Jin Huang, Jiaxi Zhuang et al.

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

Yingying Sun, Jun A, Zhiwei Liu et al.

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

Peize He, Zichen Wen, Yubo Wang et al.

Processing long-form audio is a major challenge for Large Audio Language models (LALMs). These models struggle with the quadratic cost of attention ($O(N^2)$) and with modeling long-range temporal dependencies. Existing audio benchmarks are built mostly from short clips and do not evaluate models in realistic long context settings. To address this gap, we introduce AudioMarathon, a benchmark designed to evaluate both understanding and inference efficiency on long-form audio. AudioMarathon provides a diverse set of tasks built upon three pillars: long-context audio inputs with durations ranging from 90.0 to 300.0 seconds, which correspond to encoded sequences of 2,250 to 7,500 audio tokens, respectively, full domain coverage across speech, sound, and music, and complex reasoning that requires multi-hop inference. We evaluate state-of-the-art LALMs and observe clear performance drops as audio length grows. We also study acceleration techniques and analyze the trade-offs of token pruning and KV cache eviction. The results show large gaps across current LALMs and highlight the need for better temporal reasoning and memory-efficient architectures. We believe AudioMarathon will drive the audio and multimodal research community to develop more advanced audio understanding models capable of solving complex audio tasks.