We present a data-adaptive method for parameter-efficient fine-tuning of large neural networks. Standard low-rank adaptation methods improve efficiency by restricting each layer update to a fixed low-rank form, but this static parameterization can be too rigid when the appropriate correction depends on the input and on the evolving depth-wise computation of the network. Our approach replaces a purely layer-local adapter with a shared queryable memory of low-rank update atoms. For each block of layers, the model forms a query from the current low-rank state and a running summary of previous blocks, uses this query to retrieve a content-dependent combination of shared update components via attention, and applies the resulting routed operator within the low-rank bottleneck. In this way, the method retains the efficiency and scalability of low-rank adaptation while allowing the effective update to vary across inputs and to share reusable structure across layers. The resulting architecture provides a principled middle ground between static LoRA-style updates and fully generated parameter updates: it remains compact and parameter-efficient while supporting dynamic, context-sensitive adaptation. Further, we incorporate instruction-regularization by augmenting routing logits with a language-induced prior over update atoms, thereby biasing the selection of low-rank transformations toward semantically relevant directions without generating unconstrained parameter updates. Experiments on noisy non-linear regression tasks and LLM fine-tuning suggest that this queryable update-memory formulation can improve final test performance and training stability compared to standard low-rank adaptation, while using a comparable number of trainable parameters.

In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are atomlevel-based methods, which consider atoms as basic components and generate atom positions and types. In this way, however, it is hard to generate realistic fragments with complicated structures. To solve this, we propose D3FG, a functional-groupbased diffusion model for pocket-specific molecule generation and elaboration. D3FG decomposes molecules into two categories of components: functional groups defined as rigid bodies and linkers as mass points. And the two kinds of components can together form complicated fragments that enhance ligand-protein interactions. To be specific, in the diffusion process, D3FG diffuses the data distribution of the positions, orientations, and types of the components into a prior distribution; In the generative process, the noise is gradually removed from the three variables by denoisers parameterized with designed equivariant graph neural networks. In the experiments, our method can generate molecules with more realistic 3D structures, competitive affinities toward the protein targets, and better drug properties. Besides, D3FG as a solution to a new task of molecule elaboration, could generate molecules with high affinities based on existing ligands and the hotspots of target proteins.

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes for this task, overtaking classical methods based on fixed molecular kernels. However, they still appear very limited from a theoretical perspective, since regular GNNs cannot distinguish certain types of graphs. In this work we close this gap between theory and practice. We show that GNNs with directed edge embeddings and two-hop message passing are indeed universal approximators for predictions that are invariant to translation, and equivariant to permutation and rotation. We then leverage these insights and multiple structural improvements to propose the geometric message passing neural network (GemNet). We demonstrate the benefits of the proposed changes in multiple ablation studies. GemNet outperforms previous models on the COLL, MD17, and OC20 datasets by 34 %, 41 %, and 20 %, respectively, and performs especially well on the most challenging molecules. Our implementation is available online. 1

A.1 Molecule Design We present more examples of generated molecules by our method and the CNN baseline liGAN. We select 6 molecules with highest binding affinity for each method and each binding site. The 3 additional binding sites are selected randomly from the testing set. By comparing the samples from two methods, we can find that the 3D molecules generated by our method are generally more realistic, while molecules generated by the baseline have more erroneous structures, such as bonds that are too short and angles that are too sharp. Besides, molecules generated by our method are more diverse, while the 3D atom configurations generated by the baseline are often similar.

In this paper, we introduce spatiotemporal joint filter decomposition to decouple spatial and temporal learning, while preserving spatiotemporal dependency in a video. A 3D convolutional filter is now jointly decomposed over a set of spatial and temporal filter atoms respectively. In this way, a 3D convolutional layer becomes three: a temporal atom layer, a spatial atom layer, and a joint coefficient layer, all three remaining convolutional. One obvious arithmetic manipulation allowed in our joint decomposition is to swap spatial or temporal atoms with a set of atoms that have the same number but different sizes, while keeping the remaining unchanged. For example, as shown later, we can now achieve tempo-invariance by simply dilating temporal atoms only. To illustrate this useful atom-swapping property, we further demonstrate how such a decomposition permits the direct learning of 3DCNNs with full-size videos through iterations of two consecutive sub-stages of learning: In the temporal stage, full-temporal downsampled-spatial data are used to learn temporal atoms and joint coefficients while fixing spatial atoms. In the spatial stage, full-spatial downsampled-temporal data are used for spatial atoms and joint coefficients while fixing temporal atoms. We show empirically on multiple action recognition datasets that, the decoupled spatiotemporal learning significantly reduces the model memory footprints, and allows deep 3DCNNs to model high-spatial long-temporal dependency with limited computational resources while delivering comparable performance.