Thalamus‑Reasoning is a 9B multimodal large language model that embeds bulk or single‑cell transcriptomes as continuous vectors, allowing them to be interleaved with natural‑language instructions and other samples. The model is trained on a large corpus that links experimental measurements to biological knowledge and task supervision, covering 157 task groups and 5.21 million conversations. It outperforms competing models on several held‑out annotation tasks, the GEO‑OmicsQA benchmark, and PerturbQA perturbation‑response prediction, demonstrating the benefit of continuous omics representations over text‑only gene lists.
By Maciej Sypetkowski, {\L}ukasz Smoli\'nski, Remigiusz Kinas, Joanna Krawczyk, Bart{\l}omiej Hofman, Aleksandra Mo\.zwi{\l}{\l}o, Micha{\l} Pikusa, Tomasz Jetka, Rafa{\l} Powalski
arXiv:2606. 00432v1 Announce Type: new Abstract: As retrieval-augmented generation (RAG) systems scale, it becomes increasingly challenging to ensure faithful grounding in external evidence.
By Ibne Farabi Shihab, Fariya Afrin, Sanjeda Akter, Anuj Sharma
arXiv:2605.06728v2 Announce Type: replace-cross
Abstract: Large language models can reason over biological knowledge, but they are not naturally equipped to work with quantitative omics measurements....
By Maciej Sypetkowski, {\L}ukasz Smoli{\'n}ski, Remigiusz Kinas, Joanna Krawczyk, Bart{\l}omiej Hofman, Aleksandra Mo{\.z}wi{\l}{\l}o, Micha{\l} Pikusa, Tomasz Jetka, Rafa{\l} Powalski
ShiftRAG is a new retrieval‑augmented generation framework that decouples discriminative retrieval learning from autoregressive generation while still using a single LLM backbone. It addresses the textual bottleneck of existing RAG pipelines by projecting retrieval alignments into continuous soft tokens, creating a high‑bandwidth interface that feeds retrieval signals into the generator. The approach also introduces a soft orthogonality objective to reduce rank collapse and layer‑wise relevance dynamics to preserve fine‑grained latent space, resulting in significant improvements in retrieval and question‑answering performance over state‑of‑the‑art baselines.
By Youmin Ko, Jihong Jeong, Hyunjoon Kim
BioMol-MQA is a new question‑answering dataset focused on polypharmacy that combines a multimodal knowledge graph—containing both text and molecular structure—with challenging questions designed to test large language models’ ability to retrieve and reason over this diverse information. The dataset highlights the limitations of current retrieval‑augmented generation systems, which typically handle only single‑modality text, by demonstrating that existing LLMs perform poorly unless provided with the necessary multimodal background data. This underscores the need for more robust RAG frameworks capable of integrating multiple data types for accurate responses.
By Saptarshi Sengupta, Shuhua Yang, Paul Kwong Yu, Fali Wang, Suhang Wang
The paper presents the first large‑scale benchmark for uncertainty quantification (UQ) calibration in long‑form scientific question answering, evaluating four UQ methods on 685,000 responses from up to 20 large language models across seven datasets. It shows that instruction tuning leads to token‑level probability polarization, undermining token‑level uncertainty signals, while reasoning model families differ in how they handle this effect. Only semantic consistency—consistency of the final answer—provides well‑calibrated outputs, demonstrating that semantic calibration remains robust in multi‑step, dependency‑rich reasoning.
By Philip M\"uller, Nicholas Popovi\v{c}, Michael F\"arber, Peter Steinbach
The paper introduces CoT-Interpretability Alignment (CIA), a metric that quantifies how well a large language model’s chain-of-thought (CoT) explanations match its internal reasoning processes. Evaluated on two-hop question answering, hint intervention, and integer multiplication across three LLMs, the study finds limited alignment (44.8–75.9%) and demonstrates that post‑training with a reward combining task accuracy and parametric faithfulness can substantially improve CoT faithfulness without sacrificing accuracy. The authors provide a framework for auditing CoT faithfulness and a pathway to making explicit reasoning more trustworthy, with code and data publicly available.
By Yihuai Hong, Shauli Ravfogel, Chen Zhao, Eunsol Choi
arXiv:2607. 25947v1 Announce Type: new Abstract: Question answering (QA) over irregular clinical time series (ICTS) plays a pivotal role in a wide range of healthcare applications.
By Frank Nie, Ethan B Liu, Yuan Zhu, Wei Fan, Jindong Han
arXiv:2606.27786v2 Announce Type: replace-cross
Abstract: Retrieval-augmented generation (RAG) enhances the faithfulness of large language models (LLMs) by incorporating external knowledge into the g...
By Ruochang Li, Pengcheng Huang, Zhenghao Liu, Yukun Yan, Huiyuan Xie, Yu Gu, Ge Yu, Maosong Sun
arXiv:2511.21075v4 Announce Type: replace-cross
Abstract: Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text...
By Zhenchao Tang, Fang Wang, Haohuai He, Jiale Zhou, Tianxu Lv, Jun Zhu, Shouzhi Chen, Minghao Yang, Yu Wang, Jiayang Wu, Yidong Song, Yaokun Li, Jiehui Huang, Jun Zhou, Bing He, Jianhua Yao
arXiv:2609.07093v2 Announce Type: replace
Abstract: Retrieval-augmented generation (RAG) enables large language models (LLMs) to answer questions by accessing external knowledge and has been widely a...
By Yifan Wang, Xinkui Lin, Yongxiu Xu, Shen Gao, Ruochen Yang, Kun Huang, Yubin Wang, Jie Wu, Wei Liu, Jian Luan, Hongbo Xu, Shuo Shang
arXiv:2604.08974v2 Announce Type: replace
Abstract: Uncertainty quantification techniques measure confidence in language model outputs to support critical applications like hallucination detection an...
By Lorenzo Jaime Yu Flores, Cesare Spinoso di-Piano, Jackie Chi Kit Cheung