NEC Laboratories Europe conducts applied research in 5G, AI, cybersecurity, and IoT. Based in Germany, it collaborates with industry and academia to solve real-world problems using future-ready technologies. We collaborate with NEC Laboratories Europe on research in artificial intelligence, networking, and cybersecurity. Together, we’ve advanced graph learning, privacy-preserving AI, and optical networking systems that support innovation across NEC’s global research network. Please read about our latest news and collaborative publications with NEC Laboratories Europe.

Posts

On Synthesizing Data for Context Attribution in Question Answering

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Question Answering (QA) accounts for a significant portion of LLM usage “in the wild”. However, LLMs sometimes produce false or misleading responses, also known as “hallucinations”. Therefore, grounding the generated answers in contextually provided information — i.e., providing evidence for the generated text — is paramount for LLMs’ trustworthiness. Providing this information is the task of context attribution. In this paper, we systematically study LLM-based approaches for this task, namely we investigate (i) zero-shot inference, (ii) LLM ensembling, and (iii) fine-tuning of small LMs on synthetic data generated by larger LLMs. Our key contribution is SynQA: a novel generative strategy for synthesizing context attribution data. Given selected context sentences, an LLM generates QA pairs that are supported by these sentences. This leverages LLMs’ natural strengths in text generation while ensuring clear attribution paths in the synthetic training data. We show that the attribution data synthesized via SynQA is highly effective for fine-tuning small LMs for context attribution in different QA tasks and domains. Finally, with a user study, we validate the usefulness of small LMs (fine-tuned on synthetic data from SynQA) in context attribution for QA.

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Discrete-Continuous Variational Optimization with Local Gradients

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Variational optimization (VO) offers a general approach for handling objectives which may involve discontinuities, or whose gradients are difficult to calculate. By introducing a variational distribution over the parameter space, such objectives are smoothed, and rendered amenable to VO methods. Local gradient information, though, may be available in certain problems, which is neglected by such an approach. We therefore consider a general method for incorporating local information via an augmented VO objective function to accelerate convergence and improve accuracy. We show how our augmented objective can be viewed as an instance of multilevel optimization. Finally, we show our method can train a genetic algorithm simulator, using a recursive Wasserstein distance objective

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Variational methods for Learning Multilevel Genetic Algorithms using the Kantorovich Monad

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Levels of selection and multilevel evolutionary processes are essential concepts in evolutionary theory, and yet there is a lack of common mathematical models for these core ideas. Here, we propose a unified mathematical framework for formulating and optimizing multilevel evolutionary processes and genetic algorithms over arbitrarily many levels based on concepts from category theory and population genetics. We formulate a multilevel version of the Wright-Fisher process using this approach, and we show that this model can be analyzed to clarify key features of multilevel selection. Particularly, we derive an extended multilevel probabilistic version of Price’s Equation via the Kantorovich Monad, and we use this to characterize regimes of parameter space within which selection acts antagonistically or cooperatively across levels. Finally, we show how our framework can provide a unified setting for learning genetic algorithms (GAs), and we show how we can use a Variational Optimization and a multi-level analogue of coalescent analysis to fit multilevel GAs to simulated data.

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LLMs and MI Bring Innovation to Material Development Platforms

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In this paper, we introduce efforts to apply large language models (LLMs) to the field of material development. NEC is advancing the development of a material development platform. By applying core technologies corresponding to two material development steps, namely investigation activities (Read paper/patent) and experimental planning (Design Experiment Plan), the platform organizes documents such as papers and reports as well as data such as experimental results and then presents in an interactive way to users. In addition, with techniquesthat reflect physical and chemical principles into machine learning models, AI can learn even with limited data and accurately predict material properties. Through this platform, we aim to achieve the seamless integration of materials informatics (MI) with a vast body of industry literature and knowledge, thereby bringing innovation to the material development process.

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Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering

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In protein biophysics, the separation between the functionally important residues (forming the active site or binding surface) and those that create the overall structure (the fold) is a well-established and fundamental concept. Identifying and modifying those functional sites is critical for protein engineering but computationally nontrivial, and requires significant domain knowledge. To automate this process from a data-driven perspective, we propose a disentangled Wasserstein autoencoder with an auxiliary classifier, which isolates the function-related patterns from the rest with theoretical guarantees. This enables one-pass protein sequence editing and improves the understanding of the resulting sequences and editing actionsinvolved. To demonstrate its effectiveness, we apply it to T-cell receptors (TCRs), a well-studied structure-function case. We show that our method can be used to alterthe function of TCRs without changing the structural backbone, outperforming several competing methods in generation quality and efficiency, and requiring only 10% of the running time needed by baseline models. To our knowledge, this is the first approach that utilizes disentangled representations for TCR engineering.

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On TCR Binding Predictors Failing to Generalize to Unseen Peptides

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Several recent studies investigate TCR-peptide/-pMHC binding prediction using machine learning or deep learning approaches. Many of these methods achieve impressive results on test sets, which include peptide sequences that are also included in the training set. In this work, we investigate how state of the-art deep learning models for TCR-peptide/-pMHC binding prediction generalize to unseen peptides. We create a dataset including positive samples from IEDB, VDJdb, McPAS-TCR, and the MIRA set, as well as negative samples from both randomization and 10X Genomics assays. We name this collection of samples TChard. We propose the hard split, a simple heuristic for training/test split, which ensures that test samples exclusively present peptides that do not belong to the training set. We investigate the effect of different training/test splitting techniques on the models’ test performance, as well as the effect of training and testing the models using mismatched negative samples generated randomly, in addition to the negative samples derived from assays. Our results show that modern deep learning methods fail to generalize to unseen peptides. We provide an explanation why this happens and verify our hypothesis on the TChard dataset. We then conclude that robust prediction of TCR recognition is still far for being solved.

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Attentive Variational Information Bottleneck for TCR–peptide interaction prediction

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We present a multi-sequence generalization of Variational Information Bottleneck and call the resulting model Attentive Variational Information Bottleneck (AVIB). Our AVIB model leverages multi-head self-attention to implicitly approximate a posterior distribution over latent encodings conditioned on multiple input sequences. We apply AVIB to a fundamental immuno-oncology problem: predicting the interactions between T-cell receptors (TCRs) and peptides.ResultsExperimental results on various datasets show that AVIB significantly outperforms state-of-the-art methods for TCR–peptide interaction prediction. Additionally, we show that the latent posterior distribution learned by AVIB is particularly effective for the unsupervised detection of out-of-distribution amino acid sequences.

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KGxBoard: Explainable and Interactive Leaderboard for Evaluation of Knowledge Graph Completion Models

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Knowledge Graphs (KGs) store information in the form of (head, predicate, tail)-triples. To augment KGs with new knowledge, researchers proposed models for KG Completion (KGC) tasks such as link prediction, i.e., answering (h, p, ?) or (?, p, t) queries. Such models are usually evaluated with averaged metrics on a held-out test set. While useful for tracking progress, averaged single-score metrics cannotreveal what exactly a model has learned — or failed to learn. To address this issue, we propose KGxBoard: an interactive framework for performing fine-grained evaluation on meaningful subsets of the data, each of which tests individual and interpretable capabilities of a KGC model. In our experiments, we highlight the findings that we discovered with the use of KGxBoard, which would have been impossible to detect with standard averaged single-score metrics.

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