Personalized treatment outcome prediction based on trial data for small-sample and rare patient groups is a critical task in precision medicine. However, the high cost and scarcity of trial data limit the prediction performance. To address this issue, we propose a cross-fidelity knowledge distillation and adaptive fusion network (CFKD-AFN), which leverages abundant but low-fidelity simulation data to enhance the prediction on scarce but high-fidelity trial data. CFKD-AFN incorporates a dual-channel knowledge distillation module to extract complementary knowledge from the low-fidelity model, along with an attention-guided fusion module to adaptively integrate multi-source information. Experiments on chronic obstructive pulmonary disease show that CFKD-AFN reduces the mean squared error by 6.67% ~ 74.55% and the mean absolute percentage error by 1.43% ~ 51.54% compared to the evaluated competing methods and remains robust to varying high-fidelity dataset sizes. Furthermore, we extend the CFKD-AFN framework to an interpretable variant for exploratory analysis of feature-attribution patterns associated with treatment outcomes.
Wenjie Chen, Li Zhuang, Ziying Luo et al.· 0 citations
Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with submolecular instances (atoms and bonds). While molecular pre-training approaches incorporate such knowledge into their pre-training objectives, they typically employ designs tailored to a specific type of knowledge, lacking the flexibility to integrate diverse knowledge present in molecules. Hence, reusing widely available and well-validated pre-trained 2D encoders, while incorporating molecular domain knowledge during downstream adaptation, offers a more practical alternative. In this work, we propose MolGA, which adapts pre-trained 2D graph encoders to downstream molecular applications by flexibly incorporating diverse molecular domain knowledge. First, we propose a molecular alignment strategy that bridge the gap between pre-trained topological representations with domain-knowledge representations. Second, we introduce a conditional adaptation mechanism that generates instance-specific tokens to enable fine-grained integration of molecular domain knowledge for downstream tasks. Finally, we conduct extensive experiments on eleven public datasets, demonstrating the effectiveness of MolGA.
Xingtong Yu, Chang Zhou, Xinming Zhang et al.· 0 citations
Learning the dynamics of a process given sampled observations at several time points is an important but difficult task in many scientific applications. When no ground-truth trajectories are available, but one has only snapshots of data taken at discrete time steps, the problem of modelling the dynamics, and thus inferring the underlying trajectories, can be solved by multi-marginal generalisations of flow matching algorithms. This paper proposes a novel flow matching method that overcomes the limitations of existing multi-marginal trajectory inference algorithms. Our proposed method, ALI-CFM, uses a GAN-inspired adversarial loss to fit neurally parametrised interpolant curves between source and target points such that the marginal distributions at intermediate time points are close to the observed distributions. The resulting interpolants are smooth trajectories that, as we show, are unique under mild assumptions. These interpolants are subsequently marginalised by a flow matching algorithm, yielding a trained vector field for the underlying dynamics. We showcase the versatility and scalability of our method by outperforming the existing baselines on spatial transcriptomics and cell tracking datasets, while performing on par with them on single-cell trajectory prediction.
Code: https://github.com/mmacosha/adversarially-learned-interpolants.
Oskar Kviman, Kirill Tamogashev, Nicola Branchini et al.· 0 citations
The Schr\"odinger bridge problem is concerned with finding a stochastic dynamical system bridging two marginal distributions that minimises a certain transportation cost. This problem, which represents a generalisation of optimal transport to the stochastic case, has received attention due to its connections to diffusion models and flow matching, as well as its applications in the natural sciences. However, all existing algorithms allow to infer such dynamics only for cases where samples from both distributions are available. In this paper, we propose the first general method for modelling Schr\"odinger bridges when one (or both) distributions are given by their unnormalised densities, with no access to data samples. Our algorithm relies on a generalisation of the iterative proportional fitting (IPF) procedure to the data-free case, inspired by recent developments in off-policy reinforcement learning for training of diffusion samplers. We demonstrate the efficacy of the proposed data-to-energy IPF on synthetic problems, finding that it can successfully learn transports between multimodal distributions. As a secondary consequence of our reinforcement learning formulation, which assumes a fixed time discretisation scheme for the dynamics, we find that existing data-to-data Schr\"odinger bridge algorithms can be substantially improved by learning the diffusion coefficient of the dynamics. Finally, we apply the newly developed algorithm to the problem of sampling posterior distributions in latent spaces of generative models, thus creating a data-free image-to-image translation method. Code: https://github.com/mmacosha/d2e-stochastic-dynamics
Kirill Tamogashev, Esmeralda S. Whitammer· 0 citations
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Graph Neural Networks (GNNs) have achieved remarkable success across a range of learning tasks. However, scaling GNNs to large graphs remains a significant challenge, especially for graph-level tasks. In this work, we introduce SHAKE-GNN, a novel scalable graph-level GNN framework based on a hierarchy of Kirchhoff Forests, a class of random spanning forests used to construct stochastic multi-resolution decompositions of graphs. SHAKE-GNN produces multi-scale representations, enabling flexible trade-offs between efficiency and performance. We introduce an improved, data-driven strategy for selecting the trade-off parameter and analyse the time-complexity of SHAKE-GNN. Experimental results on multiple large-scale graph classification benchmarks demonstrate that SHAKE-GNN achieves competitive performance while offering improved scalability.
Recent advances in self-supervised learning for EEG representation have largely relied on masked reconstruction, where models are trained to recover randomly masked signal segments. While effective at modeling local dependencies, the training objective of masked reconstruction does not compel the model to capture global generative constraints essential for characterizing neural activity. To address this limitation, we propose EEGDM, a novel self-supervised framework that leverages latent diffusion models to generate EEG signals as an objective. Unlike masked reconstruction, diffusion-based generation progressively denoises signals from noise to realism, compelling the model to capture holistic temporal patterns and cross-channel relationships. Specifically, EEGDM incorporates an EEG encoder that distills raw signals and their channel augmentations into a compact representation, which serves as conditional information to guide the diffusion denoising process, thereby enabling the encoder and diffusion model to be jointly optimized through the generative objective. This design endows EEGDM with a compact latent space, which not only offers ample control over the generative process but also can be leveraged for downstream tasks. Experimental results show that EEGDM (1) reconstructs high-quality EEG signals, (2) learns robust representations, and (3) achieves competitive performance across diverse downstream tasks, thus exploring a new direction for self-supervised EEG representation learning.
Shaocong Wang, Tong Liu, Yihan Li et al.· 0 citations
The attention mechanism lies at the core of the transformer architecture, providing an interpretable model-internal signal that has motivated a growing interest in attention-based model explanations. Although attention weights do not directly determine model outputs, they reflect patterns of token influence that can inform and complement established explainability techniques. This work studies the potential of utilising the information encoded in attention weights to provide meaningful model explanations by integrating them into explainable AI (XAI) frameworks that target fundamentally different aspects of model behaviour. To this end, we develop two novel explanation methods applicable to both natural language processing and computer vision tasks. The first integrates attention weights into the Shapley value decomposition by redefining the characteristic function in terms of pairwise token interactions via attention weights, thus adapting this widely used game-theoretic solution concept to provide attention-driven attributions for local explanations. The second incorporates attention weights into token-level directional derivatives defined through concept activation vectors to measure concept sensitivity for global explanations. Our empirical evaluations on standard benchmarks and in a comparison study with widely used explanation methods show that attention weights can be meaningfully incorporated into the studied XAI frameworks, highlighting their value in enriching transformer explainability.
Marte Eggen, Jacob Lysn{\ae}s-Larsen, Inga Str\"umke· 0 citations
Large language models (LLMs) already excel at writing code in high-resource languages such as Python and JavaScript, yet stumble on low-resource languages that remain essential to science and engineering. Besides the obvious shortage of pre-training data, post-training itself is a bottleneck: every new language seems to require new datasets, test harnesses, and reinforcement-learning (RL) infrastructure.
We introduce Agnostics, a language-agnostic post-training pipeline that eliminates this per-language engineering. The key idea is to judge code solely by its externally observable behavior, so a single verifier can test solutions written in any language. Concretely, we (i) use an LLM to rewrite existing unit-test datasets into an I/O format, (ii) supply a short configuration that tells the verifier how to compile and run a target language, and (iii) apply reinforcement learning with verifiable rewards (RLVR) in a robust code execution environment.
Applied to five low-resource languages--Lua, Julia, R, OCaml, and Fortran--Agnostics (1) improves Qwen-3 4B to performance that rivals other 16B-70B open-weight models; (2) scales cleanly to larger and diverse model families (Qwen-3 8B, DeepSeek Coder 6.7B Instruct, Phi 4 Mini); and (3) for ${\le} 16$B parameter models, sets new state-of-the-art pass@1 results on MultiPL-E and a new multi-language version of LiveCodeBench that we introduce.
We release the language-agnostic training datasets (Ag-MBPP-X, Ag-Codeforces-X, Ag-LiveCodeBench-X), training code, and ready-to-use configurations, making RL post-training in any programming language as simple as editing a short YAML file.
Aleksander Boruch-Gruszecki, Yangtian Zi, Zixuan Wu et al.· 0 citations
Tabular data derives its value from inter-feature dependencies, yet preserving them during synthesis is fragile when samples are scarce. Existing approaches either learn dependencies implicitly through distribution fitting, rely on statistical graph learning that becomes unstable with few samples, or encode structure through flat text serialization. Recent graph-aware methods use dependency graphs as attention biases or as backbones for non-LLM samplers, but they do not use the graph as a prompt-level plan for organizing the LLM's own generation process. We introduce StructSynth, a framework that treats a dependency graph as a generation plan---determining the generation order, conditioning context, and scope of each black-box LLM call. In Evidence-Grounded Graph Induction, LLM reasoning and statistical association cues jointly construct a Directed Acyclic Graph (DAG) from limited samples. In Graph-Planned Conditional Synthesis, this DAG drives autoregressive synthesis in topological order, conditioning each feature on previously generated values with graph-specified parent structure guiding each step, making the conditioning schedule explicit throughout synthesis. Experiments show that StructSynth achieves state-of-the-art downstream utility and the best privacy-risk ranking among fourteen compared generators in low-data settings.
Siyi Liu, Yujia Zheng, Haoyang Li et al.· 0 citations
The tabular form constitutes the standard way of representing data in relational database systems and spreadsheets. But, similarly to other forms, tabular data suffers from class imbalance, a problem that causes serious performance degradation in a wide variety of machine learning tasks. One of the most effective solutions dictates the usage of Generative Adversarial Networks (GANs) in order to synthesize artificial data instances for the under-represented classes. Despite their good performance, most of the proposed GAN models do not take into account the vector subspaces of the input samples in the real data space, leading to data generation in arbitrary locations. In addition, the class labels are handled in the same manner as the other categorical variables, so conditional sampling by class is rendered less effective. To overcome these problems, this study presents ctdGAN, a conditional GAN for alleviating class imbalance in tabular datasets. Initially, ctdGAN executes a space partitioning step to assign cluster labels to the input samples. Subsequently, it utilizes these labels to synthesize samples via a novel probabilistic sampling strategy and a new loss function that penalizes both cluster and class mis-predictions. In this way, ctdGAN generates samples in subspaces that resemble those of the original data distribution. We also introduce several other improvements, including a simple, yet effective cluster-wise scaling technique that captures multiple feature modes without affecting data dimensionality. The evaluation of ctdGAN with 14 imbalanced datasets demonstrated its strong ability in generating high fidelity samples and improving classification accuracy.
To address the challenges posed by the heavy reliance of multi-output models on preset probability distributions and embedded prior knowledge in non-injective regression tasks, this paper proposes a cycle consistency-based data-driven training framework. The method jointly optimizes a forward model {\Phi}: X to Y and a backward model {\Psi}: Y to X, where the cycle consistency loss is defined as L _cycleb equal L(Y reduce {\Phi}({\Psi}(Y))) (and vice versa). By minimizing this loss, the framework establishes a closed-loop mechanism integrating generation and validation phases, eliminating the need for manual rule design or prior distribution assumptions. Experiments on normalized synthetic and simulated datasets demonstrate that the proposed method achieves a cycle reconstruction error below 0.003, achieving an improvement of approximately 30% in evaluation metrics compared to baseline models without cycle consistency. Furthermore, the framework supports unsupervised learning and significantly reduces reliance on manual intervention, demonstrating potential advantages in non-injective regression tasks.
Learning from multi-variate time-series with heterogeneous channel configurations remains a fundamental challenge for deep neural networks, particularly in clinical domains such as intracranial electroencephalography (iEEG), where channel setups vary widely across subjects. In this work, we introduce multi-variate parallel attention (MVPA), a novel self-attention mechanism that disentangles content, temporal, and spatial attention, enabling flexible, generalizable, and efficient modeling of time-series data with varying channel counts and configurations. We use MVPA to build MVPFormer, a generative foundation model for human electrophysiology, trained to predict the evolution of iEEG signals across subjects. To support this and future efforts by the community, we release the SWEC iEEG dataset, the largest publicly available iEEG dataset to date, comprising nearly 10,000 hours of recordings from heterogeneous clinical sources. MVPFormer leverages MVPA to achieve strong generalization across subjects, demonstrating expert-level performance in several iEEG tasks. MVPFormer surpasses state-of-the-art (SOTA) Transformer baselines in seizure detection across the SWEC, the MAYO, and the FNUSA datasets, while also achieving SOTA performance on four Brain TreeBank iEEG decoding tasks (volume, pitch, onset, and speech). We further validate MVPA on standard time-series forecasting and classification tasks, where it matches or exceeds the performance of existing attention-based models. Together, our contributions establish MVPA as a general-purpose attention mechanism for heterogeneous time-series and MVPFormer as the first open-source, open-weights, and open-data iEEG foundation model with SOTA clinical performance. The code is available at https://github.com/IBM/multi-variate-parallel-transformer. The SWEC iEEG dataset is available at https://huggingface.co/datasets/NeuroTec/SWEC_iEEG_Dataset.
Francesco Carzaniga, Michael Hersche, Abu Sebastian et al.· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
MIT News · Artificial Intelligence· news.mit.eduAug 24, 2026
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
