#01Nov 5, 2026
cs.AI
Benchmarking Large Language Models on Heterogeneous Cognitive and Biomedical Knowledge Graphs: The Role of Graph Grounding in Multi-Hop Reasoning and Hallucination Mitigation
Ali Sarabadani, Kheirolah Rahsepar Fard, Tahereh Jeirani
Large language models (LLMs) are increasingly used in biomedical and cognitive neuroscience, but their ability to reason reliably over heterogeneous knowledge graphs (KGs) remains unclear. We benchmark five LLMs (GPT-5.1, Gemini 2.0 Pro, Llama 3, Qwen, and BioGPT) across five KGs: DrugBank, NeuroSynth, Cognitive Atlas, Brain Map, and GDPKG. We introduce a multitier query dataset to evaluate reasoning depth and factual accuracy under KG-aware (graph-grounded) and KG-agnostic conditions. Inter-annotator agreement was substantial, with Cohen's kappa of 0.781 (range: 0.753-0.807) and Fleiss' kappa of 0.77. Results show that general-purpose models, particularly GPT-5.1 and Gemini 2.0 Pro, generally outperform domain-specific models on multi-hop and high-level reasoning tasks, although performance declines as query complexity increases. KG grounding reduces hallucination rates across all evaluated models. Contrary to our initial hypothesis, domain-specific models do not consistently outperform general-purpose models on specialized tasks without graph grounding. These findings highlight the value of combining broad language-model capabilities with structured domain knowledge. We provide practical guidance for selecting LLM-KG integration strategies based on task complexity and computational constraints, and discuss hybrid neurosymbolic architectures for personalized medicine, cognitive disorder diagnosis, and explainable AI.
#02Nov 5, 2026
cs.LG
On the limitations of molecular representations
Acer Blake, Fergus Imrie, Charlotte M. Deane
Molecular representations such as fingerprints and learned embeddings play a central role in cheminformatics and small-molecule machine learning. They serve as the primary input for a diverse array of tasks, including clustering, dataset splitting, and virtual screening, yet their evaluation is often limited to downstream model performance on narrow benchmark tasks. We carried out a systematic investigation of the quality of molecular representations, finding that none of the state-of-the-art molecular embedding models capture graph structure, 3D shape, or ADMET endpoint similarity better than fingerprints or physicochemical descriptors. However, classical fingerprints also revealed their own material limitations. For example, we show that depending on the representation, between 225M and $\sim$4B molecules have non-unique representations in the 10.8B Enamine REAL database, with implications for virtual screening. Our findings provide an insight into the current limitations of molecular representations, outlining future research directions for the development of more robust encodings of small molecules.
#03Nov 5, 2026
cs.LG
Spectral and Subspace Dynamics of LoRA in Supervised Fine-Tuning and Reinforcement Learning
Chenruo Liu, Zihan Wang, Yijun Dong and 1 more
Low-rank adaptation (LoRA) is commonly used in both supervised fine-tuning (SFT) and reinforcement learning (RL), often under similar optimizer settings. Yet, how the different dynamics of the two stages manifest in the low-rank increment that LoRA optimizes remains unclear. Tracking the singular spectrum and subspaces of LoRA updates on mathematical reasoning tasks, we find that RL concentrates the spectrum at every learning rate, while SFT expands it at moderate learning rates; moreover, RL rotates the singular subspaces much faster than SFT at small learning rates. Interpolating between SFT and RL one ingredient at a time, we pinpoint group-mean baseline subtraction as the source of both contrasts. A quadratic multi-index model updated via LoRA unveils the underlying mechanism: group-mean baseline subtraction tilts the balance between two competing forces, coherent fitting and gradient noise, toward spectral concentration and faster subspace rotation, while forcing the risk-favorable learning rate to be low. Guided by these dynamics, we tailor LoRA updates to each stage: in SFT, we flatten the spectrum of the full update to spread adaptation across singular directions, whereas in RL, we flatten the part of the update outside the current LoRA increment span to promote subspace rotation. Experiments on mathematical reasoning tasks across multiple models show that the respective configurations for SFT and RL yield the best performance among the compared methods in most evaluated settings.
#04Nov 5, 2026
cs.LG
Towards interpreting any residual stream direction by scaling activation inversion
Celeste De Schamphelaere, Juan J. Vazquez, Ari Spiesberger and 4 more
To interpret a direction in a language model's residual stream, we can look for text that strongly activates it. But when such text is found by scanning a corpus, it is limited to what that corpus contains. We develop Maximally-Activating Example Metamodels (MAEMs), language models which map residual stream directions from a subject model to text exemplars that strongly activate those directions. Our objective is to maximise the cosine similarity of a supplied residual stream direction with the activations of the text generated by the MAEM. This label-free RL objective helps to scale MAEMs on diverse sources of residual stream directions. Empirically, we find the resultant metamodel produces informative exemplars: a Qwen3.6-27B MAEM inverts held-out activations better than corpus search or a natural-language autoencoder (NLA), beats corpus search (at 10M tokens) on a majority of held-out languages/domains, and activates 89% of held-out SAE features. It also identifies concepts behind steering vectors about as well as NLAs, recovers the payloads of LoRA backdoors more often than corpus search, and can even verbalise some model workspace inner monologue. Unlike explanations produced by other metamodels (e.g. NLAs), MAEM exemplars can be verified with a forward pass on the subject model, making the MAEM objective a grounded alternative for scaling the training of metamodels.
#05Nov 5, 2026
cs.LG
Unpacking the Compute Efficiency of Strong-to-Weak OPD against GRPO
Zeyu Leo Liu, Yang Li, Bo Pang and 7 more
On-policy distillation (OPD) trains a student on its own rollouts under a frozen teacher's per-token supervision. Does this dense signal reduce the training FLOPs needed to reach a target accuracy compared with reinforcement learning? We systematically compare vanilla reverse-KL OPD with Group Relative Policy Optimization (GRPO) across task difficulty, student and teacher size, domain, and optimization choices, measuring held-out accuracy against training FLOPs. With an external post-trained teacher, OPD generally loses to GRPO in accuracy per training FLOP at matched settings, even when the teacher is further trained with GRPO, and often suffers response-length inflation. Yet a different teacher changes the picture: when the teacher is the student's own GRPO checkpoint, OPD recovers that checkpoint's accuracy on math with $50\times$ fewer distillation FLOPs than GRPO needs to reach the same accuracy. Following the same teacher setting, we consistently observe this high efficiency with a larger student, on code, and in a second model family. On a single domain, however, the GRPO checkpoint is already the desired model, so distilling it adds to total compute. Across domains, separate GRPO checkpoints hold different capabilities, and no single checkpoint serves every domain. Multi-teacher OPD (DeepSeek-AI, 2026) consolidates per-domain GRPO experts into a single student that matches each expert's accuracy, with the distillation stage costing only 5.2% (on 2 domains) and 8.0% (on 4 domains) of the specialist training FLOPs. Counting specialist training and distillation together, this pipeline reaches joint GRPO's performance on the 2-domain mix with 42.0% fewer total FLOPs.