#01Jul 20, 2026
cs.LG
Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints
Thomas MacDougall, Maksim Kuznetsov, Roman Schutski and 5 more
Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules. While diffusion models have dominated as a leading paradigm for high-quality 3D molecule generation, LLM-based methods are rapidly emerging in molecular design and have shown competitive performance in pocket-conditioned molecular generation. However, their ability to reason about physics and 3D spatial environments is largely underexplored. In this work, we systematically analyze whether current general-purpose LLMs are capable of navigating complex 3D constraints compared to established baselines such as specialized diffusion models. We consider 3D ligand generation conditioned on protein pockets together with ligand- and interaction-derived spatial constraints, including anchor fragments, pharmacophore points, and mandatory pocket-ligand interactions. To enable this evaluation, we introduce 3D-Fit - a token-efficient benchmarking strategy for assessing LLM performance on multi-conditioned spatial molecule generation. Our findings reveal a clear pattern in LLM spatial capabilities: while they still lag behind state-of-the-art approaches, they are promising and can handle multiple spatial constraints simultaneously, enabling scaling to heterogeneous setups.
#02Jul 20, 2026
cs.LG
Sobek: Streaming Equivariant Tensor Product Convolutions
Vladimir Chorošajev, Cédric Bény
Equivariant graph neural networks repeatedly apply edge-conditioned tensor-product convolutions over graph edges. Conventional implementations materialize edge-specific weights, messages, and adjoints, causing tensor-product workspace and memory traffic to grow rapidly with graph size and operator width. This limits feasible workloads and can prevent larger problems from fully utilizing the GPU. We show that these edge-sized intermediates are artifacts of the execution schedule, not requirements of the equivariant operator. By reassociating radial projection, spherical-harmonic coupling, and graph aggregation, edge-local products can be consumed directly into bounded receiver-side state. The resulting streaming formulation preserves fully connected multiplicity mixing and extends through forward, backward, and double backward. We implement this formulation in Sobek, a generated-CUDA backend, and evaluate it across edge-scaling regimes and varied feature structures. Across two operator families and all three differentiation orders, Sobek is faster in all 75 capacity-matched comparisons, with speedups ranging from $1.2\times$ to $49.7\times$, and reduces peak allocated memory by up to 99\%. It also executes workloads up to two orders of magnitude beyond OpenEquivariance's capacity while retaining near-peak throughput. These results show that edge-scaled tensor-product workspace is a property of the conventional schedule, not of equivariant convolution itself.
#03Jul 20, 2026
cs.CV
SciForma: Structure-Faithful Generation of Scientific Diagrams
Yuxuan Luo, Peng Zhang, Xinjie Zhang and 3 more
Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.
#04Jul 20, 2026
cs.LG
Three-Body Scattering for Generative Modeling
Peng Sun, Zhenglin Cheng, Deyuan Liu and 3 more
Modern generative models typically rely on an adversarial critic, a prescribed noise-to-data path, or an autoregressive factorization. Instead, we show that a proper distributional energy can induce sample-level motion and provide direct regression supervision for a one-step generator. Three-Body Scattering Modeling (TBSM) for generation turns the energy distance into a constant-size per-projectile interaction: each projectile is attracted toward one real source and repelled from one independently generated source. Conditioned on the projectile and its condition, its expectation equals the $2$-Wasserstein gradient-flow velocity of $\frac12D_E^2(P_θ,Q)$. A batch of $B$ frozen-target events yields $O(B)$ sample-level losses, each using one reference for its condition instead of the minibatch-wide all-pairs field used by methods such as Drifting Models. Tracking this conditional expectation online can reduce field noise. Using scattering in frozen image features, TBSM trains one-step generators on ImageNet-256, achieving FID${}=2.23$ with pixel-space PixelDiT-XL and FID${}=1.63$ with latent-space DiT-XL at NFE${}=1$. We provide a design map relating diffusion-related supervision, Drift-like dynamics, and GAN-like objectives. These results establish tracked scattering as a route to high-dimensional one-step generation. Code: https://github.com/sp12138/TBSM.
#05Jul 20, 2026
cs.CV
The Many Senses of Visual Similarity: A Text-Prompted Image Perceptual Metric
Sheng-Yu Wang, Yotam Nitzan, Aaron Hertzmann and 4 more
Human visual similarity judgments are context-dependent. For example, two images may be similar in shape but distinct in color. Existing perceptual similarity metrics, however, collapse these nuances into a single scalar value, offering no mechanism to condition on specific aspects. To bridge this gap, we introduce a large-scale dataset of human similarity judgments over image triplets, where each triplet is annotated across multiple, free-form semantic aspects of similarity. Benchmarking a broad range of frontier vision-language models (VLMs) reveals a considerable performance gap compared to human annotators' consensus. Leveraging our data, we fine-tune a VLM to produce our Text-Prompted Image Perceptual Similarity (TPIPS) metric, capturing multiple senses of visual similarity depending on the specified text prompt. We demonstrate that TPIPS aligns more closely with human perception and generalizes reliably beyond the training distribution. Finally, we show that TPIPS unlocks new capabilities in text-guided retrieval, compositional search, and the fine-grained evaluation of generative models. Our code, data, and trained models are at https://peterwang512.github.io/TPIPS