Tabular data from different tables exhibit significant diversity due to varied definitions and types of features, as well as complex inter-feature and feature-target relationships. Cross-dataset pretraining, which learns reusable patterns from upstream data to support downstream tasks, have shown notable success in various fields. Yet, when applied to tabular data prediction, this paradigm faces challenges due to the limited reusable patterns among diverse tabular datasets (tables) and the general scarcity of tabular data available for fine-tuning. In this study, we fill this gap by introducing a cross-table pretrained Transformer, XTFormer, for versatile downstream tabular prediction tasks. Our methodology insight is pretraining XTFormer to establish a "meta-function" space that encompasses all potential feature-target mappings. In pre-training, a variety of potential mappings are extracted from pre-training tabular datasets and are embedded into the "meta-function" space, and suited mappings are extracted from the "meta-function" space for downstream tasks by a specified coordinate positioning approach. Experiments show that, in 190 downstream tabular prediction tasks, our cross-table pretrained XTFormer wins both XGBoost and Catboost on 137 (72%) tasks, and surpasses representative deep learning models FT-Transformer and the tabular pre-training approach XTab on 144 (76%) and 162 (85%) tasks.

We investigate the optimal transport problem between probability measures when the underlying cost function is understood to satisfy a least action principle, also known as a Lagrangian cost. These generalizations are useful when connecting observations from a physical system where the transport dynamics are influenced by the geometry of the system, such as obstacles (e.g., incorporating barrier functions in the Lagrangian), and allows practitioners to incorporate a priori knowledge of the underlying system such as non-Euclidean geometries (e.g., paths must be circular). Our contributions are of computational interest, where we demonstrate the ability to efficiently compute geodesics and amortize spline-based paths, which has not been done before, even in low dimensional problems. Unlike prior work, we also output the resulting Lagrangian optimal transport map without requiring an ODE solver. We demonstrate the effectiveness of our formulation on low-dimensional examples taken from prior work. The source code to reproduce our experiments is available at https://github.com/facebookresearch/lagrangian-ot.

We address the challenge of inferring causal effects in social network data. This results in challenges due to interference -- where a unit's outcome is affected by neighbors' treatments -- and network-induced confounding factors. While there is extensive literature focusing on estimating causal effects in social network setups, a majority of them make prior assumptions about the form of network-induced confounding mechanisms. Such strong assumptions are rarely likely to hold especially in high-dimensional networks. We propose a novel methodology that combines graph machine learning approaches with the double machine learning framework to enable accurate and efficient estimation of direct and peer effects using a single observational social network. We demonstrate the semiparametric efficiency of our proposed estimator under mild regularity conditions, allowing for consistent uncertainty quantification. We demonstrate that our method is accurate, robust, and scalable via an extensive simulation study. We use our method to investigate the impact of Self-Help Group participation on financial risk tolerance.

Background: The aim of this study was to investigate the role of clinical, dosimetric and pretherapeutic magnetic resonance imaging (MRI) features for lesion-specific outcome prediction of stereotactic radiotherapy (SRT) in patients with brain metastases from malignant melanoma (MBM). Methods: In this multicenter, retrospective analysis, we reviewed 517 MBM from 130 patients treated with SRT (single fraction or hypofractionated). For each gross tumor volume (GTV) 1576 radiomic features (RF) were calculated (788 each for the GTV and for a 3 mm margin around the GTV). Clinical parameters, radiation dose and RF from pretherapeutic contrast-enhanced T1-weighted MRI from different institutions were evaluated with a feature processing and elimination pipeline in a nested cross-validation scheme. Results: Seventy-two (72) of 517 lesions (13.9%) showed a local failure (LF) after SRT. The processing pipeline showed clinical, dosimetric and radiomic features providing information for LF prediction. The most prominent ones were the correlation of the gray level co-occurrence matrix of the margin (hazard ratio (HR): 0.37, confidence interval (CI): 0.23-0.58) and systemic therapy before SRT (HR: 0.55, CI: 0.42-0.70). The majority of RF associated with LF was calculated in the margin around the GTV. Conclusions: Pretherapeutic MRI based RF connected with lesion-specific outcome after SRT could be identified, despite multicentric data and minor differences in imaging protocols. Image data analysis of the surrounding metastatic environment may provide therapy-relevant information with the potential to further individualize radiotherapy strategies.

Popular word embedding methods such as GloVe and Word2Vec are related to the factorization of the pointwise mutual information (PMI) matrix. In this paper, we link correspondence analysis (CA) to the factorization of the PMI matrix. CA is a dimensionality reduction method that uses singular value decomposition (SVD), and we show that CA is mathematically close to the weighted factorization of the PMI matrix. In addition, we present variants of CA that turn out to be successful in the factorization of the word-context matrix, i.e. CA applied to a matrix where the entries undergo a square-root transformation (ROOT-CA) and a root-root transformation (ROOTROOT-CA). An empirical comparison among CA- and PMI-based methods shows that overall results of ROOT-CA and ROOTROOT-CA are slightly better than those of the PMI-based methods.

Understanding transition paths between meta-stable states in molecular systems is fundamental for material design and drug discovery. However, sampling these paths via molecular dynamics simulations is computationally prohibitive due to the high-energy barriers between the meta-stable states. Recent machine learning approaches are often restricted to simple systems or rely on collective variables (CVs) extracted from expensive domain knowledge. In this work, we propose to leverage generative flow networks (GFlowNets) to sample transition paths without relying on CVs. We reformulate the problem as amortized energy-based sampling over molecular trajectories and train a bias potential by minimizing the squared log-ratio between the target distribution and the generator, derived from the flow matching objective of GFlowNets. Our evaluation on three proteins (Alanine Dipeptide, Polyproline, and Chignolin) demonstrates that our approach, called TPS-GFN, generates more realistic and diverse transition paths than the previous CV-free machine learning approach.

Research in neural models inspired by mammal's visual cortex has led to many spiking neural networks such as pulse-coupled neural networks (PCNNs). These models are oscillating, spatio-temporal models stimulated with images to produce several time-based responses. This paper reviews PCNN's state of the art, covering its mathematical formulation, variants, and other simplifications found in the literature. We present several applications in which PCNN architectures have successfully addressed some fundamental image processing and computer vision challenges, including image segmentation, edge detection, medical imaging, image fusion, image compression, object recognition, and remote sensing. Results achieved in these applications suggest that the PCNN architecture generates useful perceptual information relevant to a wide variety of computer vision tasks.

Clinical variant classification of pathogenic versus benign genetic variants remains a challenge in clinical genetics. Recently, the proposition of genomic foundation models has improved the generic variant effect prediction (VEP) accuracy via weakly-supervised or unsupervised training. However, these VEPs are not diseasespecific, limiting their adaptation at the point of care. To address this problem, we propose DYNA: Disease-specificity fine-tuning via a Siamese neural network broadly applicable to all genomic foundation models for more effective variant effect predictions in disease-specific contexts. We evaluate DYNA in two distinct diseaserelevant tasks. For coding VEPs, we focus on various cardiovascular diseases, where gene-disease relationships of loss-of-function vs. gain-of-function dictate disease-specific VEP. For non-coding VEPs, we apply DYNA to an essential posttranscriptional regulatory axis of RNA splicing, the most common non-coding pathogenic mechanism in established clinical VEP guidelines. The DYNA fine-tuned models show superior performance in the held-out rare variant testing set and are further replicated in large, clinically-relevant variant annotations in ClinVAR. Thus, DYNA offers a potent disease-specific variant effect prediction method, excelling in intra-gene generalization and generalization to unseen genetic variants, making it particularly valuable for disease associations and clinical applicability. Clinical variant interpretation is transforming precision medicine, yet limitations exist that prevent its further adaptations and utilities [1]. Following a disease diagnosis, the identification and classification of pathogenic vs benign genetic variant has important clinical implications. The outcome of clinical variant interpretation provides a basis for clinical screening [2, 3] and genetic testing of first-degree family members [4], and may serve as a prognostic marker for the affected patient [5, 6]. Currently, the utility of genetic testing is limited by the fact that a substantial proportion (30-50%) of yielded variants are classified as variant of uncertain significance (VUS) according to the ACMG guidelines [7].

Variational Autoencoders for multimodal data hold promise for many tasks in data analysis, such as representation learning, conditional generation, and imputation. Current architectures either share the encoder output, decoder input, or both across modalities to learn a shared representation. Such architectures impose hard constraints on the model. In this work, we show that a better latent representation can be obtained by replacing these hard constraints with a soft constraint. We propose a new mixture-of-experts prior, softly guiding each modality's latent representation towards a shared aggregate posterior. This approach results in a superior latent representation and allows each encoding to preserve information better from its uncompressed original features. In extensive experiments on multiple benchmark datasets and two challenging real-world datasets, we show improved learned latent representations and imputation of missing data modalities compared to existing methods.

Personalized learning is a proposed approach to address the problem of data heterogeneity in collaborative machine learning. In a decentralized setting, the two main challenges of personalization are client clustering and data privacy. In this paper, we address these challenges by developing P4 (Personalized Private Peer-to-Peer) a method that ensures that each client receives a personalized model while maintaining differential privacy guarantee of each client's local dataset during and after the training. Our approach includes the design of a lightweight algorithm to identify similar clients and group them in a private, peer-to-peer (P2P) manner. Once grouped, we develop differentially-private knowledge distillation for clients to co-train with minimal impact on accuracy. We evaluate our proposed method on three benchmark datasets (FEMNIST or Federated EMNIST, CIFAR-10 and CIFAR-100) and two different neural network architectures (Linear and CNN-based networks) across a range of privacy parameters. The results demonstrate the potential of P4, as it outperforms the state-of-the-art of differential private P2P by up to 40 percent in terms of accuracy. We also show the practicality of P4 by implementing it on resource constrained devices, and validating that it has minimal overhead, e.g., about 7 seconds to run collaborative training between two clients.