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.

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A Variational Graph Partitioning Approach to Modeling Protein Liquid-liquid Phase Separation

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Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs. In this work, we introduce a GNN-based framework (graph-partitioned GNN [GP-GNN]) to partition the GNN graph to focus on the most relevant subgraphs. Our approach jointly learns task-dependent graph partitions and node representations, making it particularly effective when critical features reside within initially unidentified subgraphs. Protein liquid-liquid phase separation (LLPS) is a problem especially well-suited to GP-GNNs because intrinsically disordered regions (IDRs) are known to function as protein subdomains in it, playing a key role in the phase separation process. In this study, we demonstrate how GP-GNN accurately predicts LLPS by partitioning protein graphs into task-relevant subgraphs consistent with known IDRs. Our model achieves state-of-the-art accuracy in predicting LLPS and offers biological insights valuable for downstream investigation.

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Multi-hop Evidence Pursuit Meets the Web: Team Papelo at FEVER 2024

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Separating disinformation from fact on the web has long challenged both the search and the reasoning powers of humans. We show that the reasoning power of large language models (LLMs) and the retrieval power of modern search engines can be combined to automate this process and explainably verify claims. We integrate LLMs and search under a multi-hop evidence pursuit strategy. This strategy generates an initial question based on an input claim using a sequence to sequence model, searches and formulates an answer to the question, and iteratively generates follow-up questions to pursue the evidence that is missing using an LLM. We demonstrate our system on the FEVER 2024 (AVeriTeC) shared task. Compared to a strategy of generating all the questions at once, our method obtains .045 higher label accuracy and .155 higher AVeriTeC score (evaluating the adequacy of the evidence). Through ablations, we show the importance of various design choices, such as the question generation method, medium-sized context, reasoning with one document at a time, adding metadata, paraphrasing, reducing the problem to two classes, and reconsidering the final verdict. Our submitted system achieves .510 AVeriTeC score on the dev set and .477 AVeriTec score on the test set.

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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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Exploring the Role of Reasoning Structures for Constructing Proofs in Multi-Step Natural Language Reasoning with Large Language Models

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When performing complex multi-step reasoning tasks, the ability of Large Language Models (LLMs) to derive structured intermediate proof steps is important for ensuring that the models truly perform the desired reasoning and for improving models’ explainability. This paper is centered around a focused study: whether the current state-of-the-art generalist LLMs can leverage the structures in a few examples to better construct the proof structures with in-context learning. Our study specifically focuses on structure-aware demonstration and structure-aware pruning. We demonstrate that they both help improve performance. A detailed analysis is provided to help understand the results.

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Learning to Localize Actions in Instructional Videos with LLM-Based Multi-Pathway Text-Video Alignment

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Learning to localize temporal boundaries of procedure steps in instructional videos is challenging due to the limited availability of annotated large-scale training videos. Recent works focus on learning the cross-modal alignment between video segments and ASR-transcripted narration texts through contrastive learning. However, these methods fail to account for the alignment noise, i.e., irrelevant narrations to the instructional task in videos and unreliable timestamps in narrations. To address these challenges, this work proposes a novel training framework. Motivated by the strong capabilities of Large Language Models (LLMs) in procedure understanding and text summarization, we first apply an LLM to filter out task-irrelevant information and summarize task-related procedure steps (LLM-steps) from narrations. To further generate reliable pseudo-matching between the LLM-steps and the video for training, we propose the Multi-Pathway Text-Video Alignment (MPTVA) strategy. The key idea is to measure alignment between LLM-steps and videos via multiple pathways, including: (1) step-narration-video alignment using narration timestamps, (2) direct step-to-video alignment based on their long-term semantic similarity, and (3) direct step-to-video alignment focusing on short-term fine-grained semantic similarity learned from general video domains. The results from different pathways are fused to generate reliable pseudo step-video matching. We conducted extensive experiments across various tasks and problem settings to evaluate our proposed method. Our approach surpasses state-of-the-art methods in three downstream tasks: procedure step grounding, step localization, and narration grounding by 5.9%, 3.1%, and 2.8%.

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Predicting Spatially Resolved Gene Expression via Tissue Morphology using Adaptive Spatial GNNs (ECCB)

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Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered with targeted tissues are more affordable and routinely generated in many research and clinical studies. Hence, predicting spatial gene expression from the morphological clues embedded in tissue histological images provides a scalable alternative approach to decoding tissue complexity.

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MCTR: Multi Camera Tracking Transformer

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Multi-camera tracking plays a pivotal role in various real-world applications. While end-to-end methods have gained significant interest in single-camera tracking, multi-camera tracking remains predominantly reliant on heuristic techniques. In response to this gap, this paper introduces Multi-Camera Tracking tRansformer (MCTR), a novel end-to-end approach tailored for multi-object detection and tracking across multiple cameras with overlapping fields of view. MCTR leverages end-to-end detectors like DEtector TRansformer (DETR) to produce detections and detection embeddings independently for each camera view. The framework maintains set of track embeddings that encaplusate global information about the tracked objects, and updates them at every frame by integrating the local information from the view-specific detection embeddings. The track embeddings are probabilistically associated with detections in every camera view and frame to generate consistent object tracks. The soft probabilistic association facilitates the design of differentiable losses that enable end-to-end training of the entire system. To validate our approach, we conduct experiments on MMPTrack and AI City Challenge, two recently introduced large-scale multi-camera multi-object tracking datasets.

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Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma

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We aim to improve the prediction of response or resistance to immunotherapies in patients with melanoma. This goal is based on the hypothesis that current gene signatures predicting immunotherapy outcomes show only modest accuracy due to the lack of spatial information about cellular functions and molecular processes within tumors and their microenvironment.

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zeta-QVAE: 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 compressing the original data to manageable dimensions while still representing essential information for downstream analysis. In classical machine learning, variational autoencoders (VAEs) facilitate efficient data compression, representation learning for subsequent tasks, and novel data generation. However, no model has been proposed that exactly captures all of these features for direct application to quantum data on quantum computers. Some existing quantum models for data compression lack regularization of latent representations, thus preventing direct use for generation and control of generalization. Others are hybrid models with only some internal quantum components, impeding direct training on quantum data. To bridge this gap, we present a fully quantum framework, ?-QVAE, which encompasses all the capabilities of classical VAEs and can be directly applied for both classical and quantum data compression. Our model utilizes regularized mixed states to attain optimal latent representations. It accommodates various divergences for reconstruction and regularization. Furthermore, by accommodating mixed states at every stage, it can utilize the full-data density matrix and allow for a “global” training objective. Doing so, in turn, makes efficient optimization possible and has potential implications for private and federated learning. In addition to exploring the theoretical properties of ?-QVAE, we demonstrate its performance on representative genomics and synthetic data. Our results consistently indicate that ?-QVAE exhibits similar or better performance compared to matched classical models.

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Monitoring AI-Modified Content at Scale: A Case Study on the Impact of ChatGPT on AI Conference Peer Reviews

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We present an approach for estimating the fraction of text in a large corpus which is likely to be substantially modified or produced by a large language model (LLM). Our maximum likelihood model leverages expert-written and AI-generated reference texts to accurately and efficiently examine real-world LLM-use at the corpus level. We apply this approach to a case study of scientific peer review in AI conferences that took place after the release of ChatGPT: ICLR 2024, NeurIPS 2023, CoRL 2023 and EMNLP 2023. Our results suggest that between 6.5% and 16.9% of text submitted as peer reviews to these conferences could have been substantially modified by LLMs, i.e. beyond spell-checking or minor writing updates. The circumstances in which generated text occurs offer insight into user behavior: the estimated fraction of LLM-generated text is higher in reviews which report lower confidence, were submitted close to the deadline, and from reviewers who are less likely to respond to author rebuttals. We also observe corpus-level trends in generated text which may be too subtle to detect at the individual level, and discuss the implications of such trends on peer review. We call for future interdisciplinary work to examine how LLM use is changing our information and knowledge practices.

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