We develop a 3D equivariant diffusion model that jointly learns the generative process of both fragment poses and the 3D structure of the linker.

Targeted protein degradation techniques, such as PROteolysis TArgeting Chimeras (PROTACs), have emerged as powerful tools for selectively removing disease-causing proteins. One challenging problem in this field is designing a linker to connect different molecular fragments to form a stable drug-candidate molecule. Existing models for linker design assume that the relative positions of the fragments are known, which may not be the case in real scenarios. In this work, we address a more general problem where the poses of the fragments are in 3D space. We develop a 3D equivariant diffusion model that jointly learns the generative process of both fragment poses and the 3D structure of the linker. By viewing fragments as rigid bodies, we design a fragment pose prediction module inspired by the Newton-Euler equations in rigid body mechanics. Empirical studies on ZINC and PROTAC-DB datasets demonstrate that our model can generate chemically valid, synthetically-accessible, and low-energy molecules under both unconstrained and constrained generation settings.

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 {\em atom-level-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 \textsc{D3FG}, a {\em functional-group-based} diffusion model for pocket-specific molecule generation and elaboration.

This paper proposes the RePAIR dataset that represents a challenging benchmark to test modern computational and data driven methods for puzzle-solving and reassembly tasks. Our dataset has unique properties that are uncommon to current benchmarks for 2D and 3D puzzle solving. The fragments and fractures are realistic, caused by a collapse of a fresco during a World War II bombing at the Pompeii archaeological park. The fragments are also eroded and have missing pieces with irregular shapes and different dimensions, challenging further the reassembly algorithms. The dataset is multi-modal providing high resolution images with characteristic pictorial elements, detailed 3D scans of the fragments and meta-data annotated by the archaeologists. Ground truth has been generated through several years of unceasing fieldwork, including the excavation and cleaning of each fragment, followed by manual puzzle solving by archaeologists of a subset of approx.

Model smoothing is of central importance for obtaining a reliable teacher model in the student-teacher framework, where the teacher generates surrogate supervision signals to train the student. A popular model smoothing method is the Temporal Moving Average (TMA), which continuously averages the teacher parameters with the up-to-date student parameters. In this paper, we propose ''Spatial Ensemble'', a novel model smoothing mechanism in parallel with TMA. Spatial Ensemble randomly picks up a small fragment of the student model to directly replace the corresponding fragment of the teacher model.

Haplotype assembly and viral quasispecies reconstruction are challenging tasks concerned with analysis of genomic mixtures using sequencing data. High-throughput sequencing technologies generate enormous amounts of short fragments (reads) which essentially oversample components of a mixture; the representation redundancy enables reconstruction of the components (haplotypes, viral strains). The reconstruction problem, known to be NP-hard, boils down to grouping together reads originating from the same component in a mixture. Existing methods struggle to solve this problem with required level of accuracy and low runtimes; the problem is becoming increasingly more challenging as the number and length of the components increase. This paper proposes a read clustering method based on a convolutional auto-encoder designed to first project sequenced fragments to a low-dimensional space and then estimate the probability of the read origin using learned embedded features. The components are reconstructed by finding consensus sequences that agglomerate reads from the same origin. Mini-batch stochastic gradient descent and dimension reduction of reads allow the proposed method to efficiently deal with massive numbers of long reads. Experiments on simulated, semi-experimental and experimental data demonstrate the ability of the proposed method to accurately reconstruct haplotypes and viral quasispecies, often demonstrating superior performance compared to state-of-the-art methods. Source codes are available at https://github.com/WuLoli/CAECseq.

Cross-domain shifts present a significant challenge for decision transformer (DT) policies. Existing cross-domain policy adaptation methods typically rely on a single simple filtering criterion to select source trajectory fragments and stitch them together. They match either state structure or action feasibility. However, the selected fragments still have poor stitchability: state structures can misalign, the return-to-go (RTG) becomes incomparable when the reward or horizon changes, and actions may jump at trajectory junctions. As a result, RTG tokens lose continuity, which compromises DT's inference ability. To tackle these challenges, we propose Data Fusion-Enhanced Decision Transformer (DFDT), a compact pipeline that restores stitchability. Particularly, DFDT fuses scarce target data with selectively trusted source fragments via a two-level data filter, maximum mean discrepancy (MMD) mismatch for state-structure alignment, and optimal transport (OT) deviation for action feasibility. It then trains on a feasibility-weighted fusion distribution. Furthermore, DFDT replaces RTG tokens with advantage-conditioned tokens, which improves the continuity of the semantics in the token sequence. It also applies a $Q$-guided regularizer to suppress junction value and action jumps. Theoretically, we provide bounds that tie state value and policy performance gaps to the MMD-mismatch and OT-deviation measures, and show that the bounds tighten as these two measures shrink. We show that DFDT improves return and stability over strong offline RL and sequence-model baselines across gravity, kinematic, and morphology shifts on D4RL-style control tasks, and further corroborate these gains with token-stitching and sequence-semantics stability analyses.

The Weighted First-Order Model Counting Problem (WFOMC) asks to compute the weighted sum of models of a given first-order logic sentence over a given domain. Conditioning WFOMC on evidence -- fixing the truth values of a set of ground literals -- has been shown impossible in time polynomial in the domain size (unless $\mathsf{\#P \subseteq FP}$) even for fragments of logic that are otherwise tractable for WFOMC without evidence. In this work, we address the barrier by restricting the binary evidence to the case where the underlying Gaifman graph has bounded treewidth. We present a polynomial-time algorithm in the domain size for computing WFOMC for the two-variable fragments $\text{FO}^2$ and $\text{C}^2$ conditioned on such binary evidence. Furthermore, we show the applicability of our algorithm in combinatorial problems by solving the stable seating arrangement problem on bounded-treewidth graphs of bounded degree, which was an open problem. We also conducted experiments to show the scalability of our algorithm compared to the existing model counting solvers.

Computer vision and robotics applications ranging from augmented reality to robot autonomy in large-scale environments require spatio-temporal memory frameworks that capture both geometric structure for accurate language-grounding as well as semantic detail. Existing methods face a tradeoff, where producing rich open-vocabulary descriptions comes at the expense of real-time performance when these descriptions have to be grounded in 3D. To address these challenges, we propose Describe Anything, Anywhere, at Any Moment (DAAAM), a novel spatio-temporal memory framework for large-scale and real-time 4D scene understanding. DAAAM introduces a novel optimization-based frontend to infer detailed semantic descriptions from localized captioning models, such as the Describe Anything Model (DAM), leveraging batch processing to speed up inference by an order of magnitude for online processing. It leverages such semantic understanding to build a hierarchical 4D scene graph (SG), which acts as an effective globally spatially and temporally consistent memory representation. DAAAM constructs 4D SGs with detailed, geometrically grounded descriptions while maintaining real-time performance. We show that DAAAM's 4D SG interfaces well with a tool-calling agent for inference and reasoning. We thoroughly evaluate DAAAM in the complex task of spatio-temporal question answering on the NaVQA benchmark and show its generalization capabilities for sequential task grounding on the SG3D benchmark. We further curate an extended OC-NaVQA benchmark for large-scale and long-time evaluations. DAAAM achieves state-of-the-art results in both tasks, improving OC-NaVQA question accuracy by 53.6%, position errors by 21.9%, temporal errors by 21.6%, and SG3D task grounding accuracy by 27.8% over the most competitive baselines, respectively. We release our data and code open-source.

We introduce milearn, a Python package for multi-instance learning (MIL) that follows the familiar scikit-learn fit/predict interface while providing a unified framework for both classical and neural-network-based MIL algorithms for regression and classification. The package also includes built-in hyperparameter optimization designed specifically for small MIL datasets, enabling robust model selection in data-scarce scenarios. We demonstrate the versatility of milearn across a broad range of synthetic MIL benchmark datasets, including digit classification and regression, molecular property prediction, and protein-protein interaction (PPI) prediction. Special emphasis is placed on the key instance detection (KID) problem, for which the package provides dedicated support.