Designing proteins that satisfy natural language functional requirements is a central goal in protein engineering. A straightforward baseline is to fine-tune generic instruction-tuned LLMs as direct text-to-sequence generators, but this is data- and compute-hungry. With limited supervision, LLMs can produce coherent plans in text yet fail to reliably realize them as sequences. This plan–execute gap motivates ProtoCycle, an agentic framework for protein design that uses LLMs primarily to drive a multi-round, feedback-driven decision cycle. ProtoCycle couples an LLM planner with a lightweight tool environment designed to emulate the iterative workflow of human protein engineers and uses LLM-driven reflection on tool feedback to revise plans. Trained with supervised trajectories and online reinforcement learning, ProtoCycle achieves strong language alignment while maintaining competitive foldability, and ablations show that reflection substantially improves sequence quality.

Test-Time Scaling (TTS) has emerged as an effective paradigm for improving the reasoning performance of large language models (LLMs). However, existing methods — most notably majority voting and heuristic token-level scoring — treat reasoning traces or tokens equally, thereby being susceptible to substantial variations in trajectory quality and localized logical failures. In this work, we introduce **Chronos**, a lightweight and plug-and-play chronological reasoning scorer that models each trajectory as a time series. Specifically, Chronos learns to capture trajectory features of token probabilities, assigns quality scores accordingly, and employs a weighted voting mechanism. Extensive evaluations on both in-domain and out-of-domain benchmarks demonstrate that Chronos consistently delivers substantial gains across a variety of models, with negligible computational overhead. Notably, Chronos@128 achieves relative improvements of 34.21% over Pass@1 and 22.70% over Maj@128 on HMMT25 using Qwen3-4B-Thinking-2507, highlighting its effectiveness.

Unmanned Aerial Vehicle (UAV) Vision-and-Language Navigation (VLN) is vital for applications such as disaster response, logistics delivery, and urban inspection. However, existing methods often struggle with insufficient multimodal fusion, weak generalization, and poor interpretability. To address these challenges, we propose FlightGPT, a novel UAV VLN framework built upon Vision-Language Models (VLMs) with powerful multimodal perception capabilities. We design a two-stage training pipeline: first, Supervised Fine-Tuning (SFT) using high-quality demonstrations to improve initialization and structured reasoning; then, Group Relative Policy Optimization (GRPO) algorithm, guided by a composite reward that considers goal accuracy, reasoning quality, and format compliance, to enhance generalization and adaptability. Furthermore, FlightGPT introduces a Chain-of-Thought (CoT)-based reasoning mechanism to improve decision interpretability. Extensive experiments on the city-scale dataset CityNav demonstrate that FlightGPT achieves state-of-the-art performance across all scenarios, with a 9.22% higher success rate than the strongest baseline in unseen environments. Our implementation is publicly available.

Recent breakthroughs in Large Language Models (LLMs) have revolutionized scientific literature analysis. However, existing benchmarks fail to adequately evaluate the proficiency of LLMs in this domain, particularly in scenarios requiring higher-level abilities beyond mere memorization and the handling of multimodal data.In response to this gap, we introduce SciAssess, a benchmark specifically designed for the comprehensive evaluation of LLMs in scientific literature analysis. It aims to thoroughly assess the efficacy of LLMs by evaluating their capabilities in Memorization (L1), Comprehension (L2), and Analysis & Reasoning (L3). It encompasses a variety of tasks drawn from diverse scientific fields, including biology, chemistry, material, and medicine.To ensure the reliability of SciAssess, rigorous quality control measures have been implemented, ensuring accuracy, anonymization, and compliance with copyright standards. SciAssess evaluates 11 LLMs, highlighting their strengths and areas for improvement. We hope this evaluation supports the ongoing development of LLM applications in scientific literature analysis.SciAssess and its resources are available at https://github.com/sci-assess/SciAssess.

Mechanistic interpretability of large language models (LLMs) aims to uncover the internal processes of information propagation and reasoning. Sparse autoencoders (SAEs) have demonstrated promise in this domain by extracting interpretable and monosemantic features. However, prior works primarily focus on feature extraction from a single layer, failing to effectively capture activations that span multiple layers. In this paper, we introduce Route Sparse Autoencoder (RouteSAE), a new framework that integrates a routing mechanism with a shared SAE to efficiently extract features from multiple layers. It dynamically assigns weights to activations from different layers, incurring minimal parameter overhead while achieving high interpretability and flexibility for targeted feature manipulation. We evaluate RouteSAE through extensive experiments on Llama-3.2-1B-Instruct. Specifically, under the same sparsity constraint of 64, RouteSAE extracts 22.5% more features than baseline SAEs while achieving a 22.3% higher interpretability score. These results underscore the potential of RouteSAE as a scalable and effective method for LLM interpretability, with applications in feature discovery and model intervention. Our codes are available at https://github.com/swei2001/RouteSAEs.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling – experimental procedure prediction – is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of insufficient data exploitation, as it hinders the sharing of interaction mechanism learned across various datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for molecular interaction modeling following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. To train this integrated framework efficiently, we introduce a *multi-hierarchical CoT theory* to refine its training paradigm, and conduct a comprehensive *Molecular Interactive Instructions* dataset for the development of biochemical LLMs involving MRL.Our experiments,conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception — a critical ability of human professionals in comprehending molecules’ topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (i.e., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder’s representation space and an LM’s text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM’s efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM’s ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines.