Compositional reasoning is a critical capability for multimodal models, enabling systematic understanding of complex scenes through structured combinations of objects, attributes, and relations. However, existing research on this ability primarily focuses on vision-language models (VLMs, e.g., CLIP and SigLIP), with limited exploration of multimodal large language models (MLLMs). To address this gap, we introduce CR³, a novel framework that enhances compositional reasoning abilities of MLLMs via rule-based reinforcement learning. CR³ leverages rule-based rewards to optimize the MLLM's policy on systematically curated multimodal instruction-following tasks, guided by a model-adaptive dynamic task mixing strategy. Our approach boosts performance by over 19% on three compositional reasoning benchmarks, significantly outperforming supervised fine-tuning (SFT) by at least 12%. Crucially, CR³ demonstrates superior generalization by improving performance on out-of-domain benchmarks where SFT methods degrade, highlighting its effectiveness and data efficiency.

Distinguishing spatial relations is a basic part of human cognition which requires fine-grained perception on cross-instance. Although benchmarks like MME, MMBench and SEED comprehensively have evaluated various capabilities which already include visual spatial reasoning(VSR). There is still a lack of sufficient quantity and quality evaluation and optimization datasets for Vision Large Language Models(VLLMs) specifically targeting visual positional reasoning. To handle this, we first diagnosed current VLLMs with the VSR dataset and proposed a unified test set. We found current VLLMs to exhibit a contradiction of over-sensitivity to language instructions and under-sensitivity to visual positional information. By expanding the original benchmark from two aspects of tunning data and model structure, we mitigated this phenomenon. To our knowledge, we expanded spatially positioned image data controllably using diffusion models for the first time and integrated original visual encoding(CLIP) with other 3 powerful visual encoders(SigLIP, SAM and DINO). After conducting combination experiments on scaling data and models, we obtained a VLLM VSR Expert(VSRE) that not only generalizes better to different instructions but also accurately distinguishes differences in visual positional information. VSRE achieved over a 27% increase in accuracy on the VSR test set. It becomes a performant VLLM on the position reasoning of both the VSR dataset and relevant subsets of other evaluation benchmarks. We hope it will accelerate advancements in VLLM on VSR learning.

The drug-target binding affinity(DTA) indicates the strength of the drug-target interaction; therefore, predicting DTA by computational approaches can considerably benefit drug discovery by narrowing down the searching space and pruning those drug-target pairs with low binding affinity scores. In the computational methods, feature representation of proteins is one of the most important parts due to its strong influence on the following regression task. This paper introduces the BERT-based language representation to embed the gene ontology annotations, combined with the raw sequence to characterize a protein by fusing its physical structure and human knowledge. We exploit CNN network stacked over full connected layers to learn the prediction of DTA scores in a supervised manner. This framework enhances the feature representation ability, leading to the improvement of the DTA prediction precision. The evaluation on the Davis and KIBA datasets compared to the state-of-the-art baselines demonstrates our feature representation's superiority.