Machine LearningRead the latest publications from our world-class team of researchers from our Machine Learning team who have been at the forefront of machine learning developments, including deep learning, support vector machines, and semantic analysis, for over a decade. We develop innovative technologies integrated into NEC’s products and services. Machine learning is the critical technology for data analytics and artificial intelligence. Recent progress in this field opens opportunities for various new applications.

Posts

Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations

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Cell fate decisions are highly coordinated processes governed bycomplex interactions among numerous regulatory genes, whiledisruptions in these mechanisms can lead to developmental abnormalitiesand disease. Traditional methods often fail to capture suchcombinatorial interactions, limiting their ability to fully model cellfate dynamics. Here, we introduce MetaVelo, a global feature explanationframework for identifying key regulatory gene sets influencingcell fate transitions. MetaVelo models these transitions as ablack-box function and employs a differentiable neural ordinary differentialequation (ODE) surrogate to enable efficient optimization.By reparameterizing the problem as a controllable data generationprocess, MetaVelo overcomes the challenges posed by the nondifferentiablenature of cell fate dynamics. Benchmarking acrossdiverse stand-alone and longitudinal single-cell RNA-seq datasetsand three black-box cell fate models demonstrates its superiorityover 12 baseline methods in predicting developmental trajectoriesand identifying combinatorial regulatory gene sets. MetaVelo furtherdistinguishes independent from synergistic regulatory genes,offering novel insights into the gene interactions governing cellfate. With the growing availability of high-resolution single-celldata, MetaVelo provides a scalable and effective framework fo

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On Synthesizing Data for Context Attribution in Question Answering

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Question Answering (QA) accounts for a significantportion of LLM usage “in the wild”.However, LLMs sometimes produce false ormisleading responses, also known as hallucinations.Therefore, grounding the generatedanswers in contextually provided information—i.e., providing evidence for the generated text—is paramount for LLMs’ trustworthiness. Providingthis information is the task of context attribution.In this paper, we systematically studyLLM-based approaches for this task, namelywe investigate (i) zero-shot inference, (ii) LLMensembling, and (iii) fine-tuning of small LMson synthetic data generated by larger LLMs.Our key contribution is SYNQA: a novel generativestrategy for synthesizing context attributiondata. Given selected context sentences, anLLM generates QA pairs that are supported bythese sentences. This leverages LLMs’ naturalstrengths in text generation while ensuring clearattribution paths in the synthetic training data.We show that the attribution data synthesizedvia SYNQA is highly effective for fine-tuningsmall LMs for context attribution in differentQA tasks and domains. Finally, with a userstudy, we validate the usefulness of small, efficientLMs (fine-tuned on synthetic data fromSYNQA) in context attribution for QA.

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Group Relative Augmentation for Data Efficient Action Detection

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Adapting large Video-Language Models (VLMs) for action detection using only a few examples poses challenges like overfitting and the granularity mismatch between scene-level pre-training and required person-centric understanding. We propose an efficient adaptation strategy combining parameter-efficient tuning (LoRA) with a novel learnable internal feature augmentation. Applied within the frozen VLM backbone using FiLM, these augmentations generate diverse feature variations directly relevant to the task. Additionally, we introduce a group-weighted loss function that dynamically modulates the training contribution of each augmented sample based on its prediction divergence relative to the group average. This promotes robust learning by prioritizing informative yet reasonable augmentations. We demonstrate our method’s effectiveness on complex multi-label, multi-person action detection datasets (AVA, MOMA), achieving strong mAP performance and showcasing significant data efficiency for adapting VLMs from limited examples.

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Quantitative Bounds for Length Generalization in Transformers

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We provide quantitative bounds on the length of sequences required to be observed during training for a transformer to length generalize, e.g., to continue to perform well on sequences unseen during training. Our results improve on Huang et al. [8], who show that there is a finite training length beyond which length generalization is guaranteed, but for which they do not provide quantitative bounds.

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PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Design

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Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets on demand, without extensive rounds of wet-lab testing,remains a significant challenge. Here, we introduce PPDiff, a diffusion model to jointly design the sequence and structure of binders for arbitrary protein targets in a non-autoregressive manner. PPDiff builds upon our developed Sequence Structure Interleaving Network with Causal attention layers (SSINC), which integrates interleaved self-attention layers to capture global amino acid correlations, k-nearest neighbor (kNN) equivariant graph layers to model local interactions in three-dimensional (3D) space, and causal attention layers to simplify the intricate interdependencies within the protein sequence. To assess PPDiff, we curate PPBench, a general protein complex dataset comprising 706,360 complexes from the Protein Data Bank (PDB). The model is pretrained on PPBench and finetuned on two real-world applications: target-protein mini-binder complex design and antigen-antibody complex design. PPDiff consistently surpasses baseline methods, achieving success rates of 50.00%, 23.16%, and 16.89% for the pretraining task and the two downstream applications, respectively.

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Pathologist-Read vs AI-Driven Assessment of Tumor-Infiltrating Lymphocytes in Melanoma

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Tumor-infiltrating lymphocytes (TILs) are a provocative biomarker in melanoma, influencing diagnosis, prognosis, and immunotherapy outcomes; however, traditional pathologistreadTIL assessment on hematoxylin and eosin–stained slides is prone to interobserver variability, leading to inconsistent clinical decisions. Therefore, development of newer TIL scoring approachesthat produce more reliable and consistent readouts is important.

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Solving Inverse Problems via a Score-Based Prior: An Approximation-Free Posterior Sampling Approach

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Diffusion models (DMs) have proven to be effective in modeling high-dimensional distributions, leading to their widespread adoption for representing complex priors in Bayesian inverse problems (BIPs). However, current DM-based posterior sampling methods proposed for solving common BIPs rely on heuristic approximations to the generative process. To exploit the generative capability of DMs and avoid the usage of such approximations, we propose an ensemble-based algorithm that performs posterior sampling without the use of heuristic approximations. Our algorithm is motivated by existing works that combine DM-based methods with the sequential Monte Carlo (SMC) method. By examining how the prior evolves through the diffusion process encoded by the pre-trained score function, we derive a modified partial differential equation (PDE) governing the evolution of the corresponding posterior distribution. This PDE includes a modified diffusion term and a reweighting term, which can be simulated via stochastic weighted particle methods. Theoretically, we prove that the error between the true posterior distribution canbe bounded in terms of the training error of the pre-trained score function and the ]number of particles in the ensemble. Empirically, we validate our algorithm on several inverse problems in imaging to show that our method gives more accurate reconstructions compared to existing DM-based methods.

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A Quantum Variational Autoencoder Utilizing Regularized Mixed-state Latent Representations

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A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves finding low-dimensional representations that preserve essential information for downstream analysis. Inclassical machine learning, variational autoencoders (VAEs) facilitate efficient data compression, representationlearning for subsequent tasks, and novel data generation. However, no quantum model has been proposed thatexactly captures all of these features for direct application to quantum data on quantum computers. Some existingquantum models for data compression lack regularization of latent representations, thus preventing direct use forgeneration and control of generalization. Others are hybrid models with only some internal quantum components,impeding direct training on quantum data. To address this, we present a fully quantum framework, ?-QVAE,which encompasses all the capabilities of classical VAEs and can be directly applied to map both classicaland quantum data to a lower-dimensional space, while effectively reconstructing much of the original statefrom it. Our model utilizes regularized mixed states to attain optimal latent representations. It accommodatesvarious divergences for reconstruction and regularization. Furthermore, by accommodating mixed states at everystage, it can utilize the full data density matrix and allow for a training objective defined on probabilisticmixtures of input data. Doing so, in turn, makes efficient optimization possible and has potential implications forprivate and federated learning. In addition to exploring the theoretical properties of ?-QVAE, we demonstrateits performance on representative genomics and synthetic data. Our results indicate that ?-QVAE consistentlylearns representations that better utilize the capacity of the latent space and exhibits similar or better performancecompared with matched classical models.

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Attribute-Centric Compositional Text-to-Image Generation

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Despite the recent impressive breakthroughs in text-to-image generation, generative models have difficulty in capturing thedata distribution of underrepresented attribute compositions while over-memorizing overrepresented attribute compositions,which raises public concerns about their robustness and fairness. To tackle this challenge, we propose ACTIG, an attributecentriccompositional text-to-image generation framework. We present an attribute-centric feature augmentation and a novelimage-free training scheme, which greatly improves model’s ability to generate images with underrepresented attributes.Wefurther propose an attribute-centric contrastive loss to avoid overfitting to overrepresented attribute compositions.We validateour framework on the CelebA-HQ and CUB datasets. Extensive experiments show that the compositional generalization ofACTIG is outstanding, and our framework outperforms previous works in terms of image quality and text-image consistency

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Learning Disentangled Equivariant Representation for Explicitly Controllable 3D Molecule Generation

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We consider the conditional generation of 3D drug-like molecules with explicit control over molecular properties such as drug-like properties (e.g., Quantitative Estimate of Druglikenessor Synthetic Accessibility score) and effectively binding to specific protein sites. To tackle this problem, we propose an E(3)-equivariant Wasserstein autoencoder and factorize thelatent space of our generative model into two disentangled aspects: molecular properties and the remaining structural context of 3D molecules. Our model ensures explicit control over these molecular attributes while maintaining equivariance of coordinate representation and invariance of data likelihood. Furthermore, we introduce a novel alignment-based coordinate loss to adapt equivariant networks for auto-regressive denovo 3D molecule generation from scratch. Extensive experiments validate our model’s effectiveness on property-guidedand context-guided molecule generation, both for de-novo 3D molecule design and structure-based drug discovery against protein targets.

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