Mic-hackathon 2024: Hackathon on Machine Learning for Electron and Scanning Probe Microscopy

Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains difficult due to the lack of standardized code ecosystems, benchmarks, and integration strategies. As a result, data usage is inefficient and analysis time is extensive. In addition to post-acquisition analysis, new APIs from major microscope manufacturers enable real-time, ML-based analytics for automated decision-making and ML-agent-controlled microscope operation. Yet, a gap remains between the ML and microscopy communities, limiting the impact of these methods on physics, materials discovery, and optimization. Hackathons help bridge this divide by fostering collaboration between ML researchers and microscopy experts. They encourage the development of novel solutions that apply ML to microscopy, while preparing a future workforce for instrumentation, materials science, and applied ML. This hackathon produced benchmark datasets and digital twins of microscopes to support community growth and standardized workflows. All related code is available at GitHub: https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1

Cost-Efficient LLM Training with Lifetime-Aware Tensor Offloading via GPUDirect Storage

We present the design and implementation of a new lifetime-aware tensor offloading framework for GPU memory expansion using low-cost PCIe-based solid-state drives (SSDs). Our framework, TERAIO, is developed explicitly for large language model (LLM) training with multiple GPUs and multiple SSDs. Its design is driven by our observation that the active tensors take only a small fraction (1.7% on average) of allocated GPU memory in each LLM training iteration, the inactive tensors are usually large and will not be used for a long period of time, creating ample opportunities for offloading/prefetching tensors to/from slow SSDs without stalling the GPU training process. TERAIO accurately estimates the lifetime (active period of time in GPU memory) of each tensor with the profiling of the first few iterations in the training process. With the tensor lifetime analysis, TERAIO will generate an optimized tensor offloading/prefetching plan and integrate it into the compiled LLM program via PyTorch. TERAIO has a runtime tensor migration engine to execute the offloading/prefetching plan via GPUDirect storage, which allows direct tensor migration between GPUs and SSDs for alleviating the CPU bottleneck and maximizing the SSD bandwidth utilization. In comparison with state-of-the-art studies such as ZeRO-Offload and ZeRO-Infinity, we show that TERAIO improves the training performance of various LLMs by 1.47x on average, and achieves 80.7% of the ideal performance assuming unlimited GPU memory.

Boosting Statistic Learning with Synthetic Data from Pretrained Large Models

The rapid advancement of generative models, such as Stable Diffusion, raises a key question: how can synthetic data from these models enhance predictive modeling? While they can generate vast amounts of datasets, only a subset meaningfully improves performance. We propose a novel end-to-end framework that generates and systematically filters synthetic data through domain-specific statistical methods, selectively integrating high-quality samples for effective augmentation. Our experiments demonstrate consistent improvements in predictive performance across various settings, highlighting the potential of our framework while underscoring the inherent limitations of generative models for data augmentation. Despite the ability to produce large volumes of synthetic data, the proportion that effectively improves model performance is limited.

Soft Reasoning Paths for Knowledge Graph Completion

Reasoning paths are reliable information in knowledge graph completion (KGC) in which algorithms can find strong clues of the actual relation between entities. However, in real-world applications, it is difficult to guarantee that computationally affordable paths exist toward all candidate entities. According to our observation, the prediction accuracy drops significantly when paths are absent. To make the proposed algorithm more stable against the missing path circumstances, we introduce soft reasoning paths. Concretely, a specific learnable latent path embedding is concatenated to each relation to help better model the characteristics of the corresponding paths. The combination of the relation and the corresponding learnable embedding is termed a soft path in our paper. By aligning the soft paths with the reasoning paths, a learnable embedding is guided to learn a generalized path representation of the corresponding relation. In addition, we introduce a hierarchical ranking strategy to make full use of information about the entity, relation, path, and soft path to help improve both the efficiency and accuracy of the model. Extensive experimental results illustrate that our algorithm outperforms the compared state-of-the-art algorithms by a notable margin. The code will be made publicly available after the paper is officially accepted.

K2MUSE: A human lower limb multimodal dataset under diverse conditions for facilitating rehabilitation robotics

The natural interaction and control performance of lower limb rehabilitation robots are closely linked to biomechanical information from various human locomotion activities. Multidimensional human motion data significantly deepen the understanding of the complex mechanisms governing neuromuscular alterations, thereby facilitating the development and application of rehabilitation robots in multifaceted real-world environments. However, currently available lower limb datasets are inadequate for supplying the essential multimodal data and large-scale gait samples necessary for effective data-driven approaches, and they neglect the significant effects of acquisition interference in real applications.To fill this gap, we present the K2MUSE dataset, which includes a comprehensive collection of multimodal data, comprising kinematic, kinetic, amplitude-mode ultrasound (AUS), and surface electromyography (sEMG) measurements. The proposed dataset includes lower limb multimodal data from 30 able-bodied participants walking under different inclines (0$^\circ$, $\pm$5$^\circ$, and $\pm$10$^\circ$), various speeds (0.5 m/s, 1.0 m/s, and 1.5 m/s), and different nonideal acquisition conditions (muscle fatigue, electrode shifts, and inter-day differences). The kinematic and ground reaction force data were collected via a Vicon motion capture system and an instrumented treadmill with embedded force plates, whereas the sEMG and AUS data were synchronously recorded for thirteen muscles on the bilateral lower limbs. This dataset offers a new resource for designing control frameworks for rehabilitation robots and conducting biomechanical analyses of lower limb locomotion. The dataset is available at https://k2muse.github.io/.

Conditional Independence Test Based on Transport Maps

Testing conditional independence between two random vectors given a third is a fundamental and challenging problem in statistics, particularly in multivariate nonparametric settings due to the complexity of conditional structures. We propose a novel framework for testing conditional independence using transport maps. At the population level, we show that two well-defined transport maps can transform the conditional independence test into an unconditional independence test, this substantially simplifies the problem. These transport maps are estimated from data using conditional continuous normalizing flow models. Within this framework, we derive a test statistic and prove its consistency under both the null and alternative hypotheses. A permutation-based procedure is employed to evaluate the significance of the test. We validate the proposed method through extensive simulations and real-data analysis. Our numerical studies demonstrate the practical effectiveness of the proposed method for conditional independence testing.

Knowledge Graph Completion with Relation-Aware Anchor Enhancement

Text-based knowledge graph completion methods take advantage of pre-trained language models (PLM) to enhance intrinsic semantic connections of raw triplets with detailed text descriptions. Typical methods in this branch map an input query (textual descriptions associated with an entity and a relation) and its candidate entities into feature vectors, respectively, and then maximize the probability of valid triples. These methods are gaining promising performance and increasing attention for the rapid development of large language models. According to the property of the language models, the more related and specific context information the input query provides, the more discriminative the resultant embedding will be. In this paper, through observation and validation, we find a neglected fact that the relation-aware neighbors of the head entities in queries could act as effective contexts for more precise link prediction. Driven by this finding, we propose a relation-aware anchor enhanced knowledge graph completion method (RAA-KGC). Specifically, in our method, to provide a reference of what might the target entity be like, we first generate anchor entities within the relation-aware neighborhood of the head entity. Then, by pulling the query embedding towards the neighborhoods of the anchors, it is tuned to be more discriminative for target entity matching. The results of our extensive experiments not only validate the efficacy of RAA-KGC but also reveal that by integrating our relation-aware anchor enhancement strategy, the performance of current leading methods can be notably enhanced without substantial modifications.

MindEye-OmniAssist: A Gaze-Driven LLM-Enhanced Assistive Robot System for Implicit Intention Recognition and Task Execution

A promising effective human-robot interaction in assistive robotic systems is gaze-based control. However, current gaze-based assistive systems mainly help users with basic grasping actions, offering limited support. Moreover, the restricted intent recognition capability constrains the assistive system's ability to provide diverse assistance functions. In this paper, we propose an open implicit intention recognition framework powered by Large Language Model (LLM) and Vision Foundation Model (VFM), which can process gaze input and recognize user intents that are not confined to predefined or specific scenarios. Furthermore, we implement a gaze-driven LLM-enhanced assistive robot system (MindEye-OmniAssist) that recognizes user's intentions through gaze and assists in completing task. To achieve this, the system utilizes open vocabulary object detector, intention recognition network and LLM to infer their full intentions. By integrating eye movement feedback and LLM, it generates action sequences to assist the user in completing tasks. Real-world experiments have been conducted for assistive tasks, and the system achieved an overall success rate of 41/55 across various undefined tasks. Preliminary results show that the proposed method holds the potential to provide a more user-friendly human-computer interaction interface and significantly enhance the versatility and effectiveness of assistive systems by supporting more complex and diverse task.

Real-Time Cell Sorting with Scalable In Situ FPGA-Accelerated Deep Learning

Precise cell classification is essential in biomedical diagnostics and therapeutic monitoring, particularly for identifying diverse cell types involved in various diseases. Traditional cell classification methods such as flow cytometry depend on molecular labeling which is often costly, time-intensive, and can alter cell integrity. To overcome these limitations, we present a label-free machine learning framework for cell classification, designed for real-time sorting applications using bright-field microscopy images. This approach leverages a teacher-student model architecture enhanced by knowledge distillation, achieving high efficiency and scalability across different cell types. Demonstrated through a use case of classifying lymphocyte subsets, our framework accurately classifies T4, T8, and B cell types with a dataset of 80,000 preprocessed images, accessible via an open-source Python package for easy adaptation. Our teacher model attained 98\% accuracy in differentiating T4 cells from B cells and 93\% accuracy in zero-shot classification between T8 and B cells. Remarkably, our student model operates with only 0.02\% of the teacher model's parameters, enabling field-programmable gate array (FPGA) deployment. Our FPGA-accelerated student model achieves an ultra-low inference latency of just 14.5~$\mu$s and a complete cell detection-to-sorting trigger time of 24.7~$\mu$s, delivering 12x and 40x improvements over the previous state-of-the-art real-time cell analysis algorithm in inference and total latency, respectively, while preserving accuracy comparable to the teacher model. This framework provides a scalable, cost-effective solution for lymphocyte classification, as well as a new SOTA real-time cell sorting implementation for rapid identification of subsets using in situ deep learning on off-the-shelf computing hardware.

DeepSuM: Deep Sufficient Modality Learning Framework

Multimodal learning has become a pivotal approach in developing robust learning models with applications spanning multimedia, robotics, large language models, and healthcare. The efficiency of multimodal systems is a critical concern, given the varying costs and resource demands of different modalities. This underscores the necessity for effective modality selection to balance performance gains against resource expenditures. In this study, we propose a novel framework for modality selection that independently learns the representation of each modality. This approach allows for the assessment of each modality's significance within its unique representation space, enabling the development of tailored encoders and facilitating the joint analysis of modalities with distinct characteristics. Our framework aims to enhance the efficiency and effectiveness of multimodal learning by optimizing modality integration and selection.