Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis of resonant modes in electromagnetics

Resonant modes determine the response of electromagnetic devices, including dielectric and plasmonic resonators. Relying on the degrees of freedom that metamaterials provide, this contribution shows how to design, at will, the resonant modes of a dielectric object placed in an unbounded space. Specifically, the proposed method returns in analytical form the spatial distribution of the dielectric susceptibility tensor for which the object exhibits resonances at prescribed frequencies and spatial distribution of the polarization. Together with the synthesis of the material, two key concepts are introduced: the controlled tunability of the resonant modes and the number of essential modes, i.e. the number of modes that uniquely characterize the spatial distribution of the dielectric susceptibility. Moreover, this approach can be applied to design the resonant modes of any system where the constitutive relationship is linear and local.
Fairness and Diversity in Recommender Systems: A Survey

Recommender systems are effective tools for mitigating information overload and have seen extensive applications across various domains. However, the single focus on utility goals proves to be inadequate in addressing real-world concerns, leading to increasing attention to fairness-aware and diversity-aware recommender systems. While most existing studies explore fairness and diversity independently, we identify strong connections between these two domains. In this survey, we first discuss each of them individually and then dive into their connections. Additionally, motivated by the concepts of user-level and item-level fairness, we broaden the understanding of diversity to encompass not only the item level but also the user level. With this expanded perspective on user and item-level diversity, we re-interpret fairness studies from the viewpoint of diversity. This fresh perspective enhances our understanding of fairness-related work and paves the way for potential future research directions. Papers discussed in this survey along with public code links are available at https://github.com/YuyingZhao/Awesome-Fairness-and-Diversity-Papers-in-Recommender-Systems .
Moire-enabled artificial topological superconductivity in twisted bilayer graphene

Twisted van der Waals materials have risen as highly tunable platform for realizing unconventional superconductivity. Here we demonstrate how a topological superconducting state can be driven in a twisted graphene multilayer at a twist angle of approximately 1.6 degrees proximitized to other 2D materials. We show that an encapsulated twisted bilayer subject to induced Rashba spin-orbit coupling, s-wave superconductivity and exchange field generates a topological superconducting state enabled by the moire pattern. We demonstrate a variety of topological states with different Chern numbers highly tunable through doping, strain and bias voltage. Our proposal does not depend on a fine tuning of the twist angle, but solely on the emergence of moire minibands and is applicable for twist angles between 1.3 and 3 degrees. Our results establish the potential of twisted graphene bilayers to create artificial topological superconductivity without requiring ultraflat dispersions.
Berezinskii-Kosterlitz-Thouless phase transitions in a kagome spin ice by a quantifying Monte Carlo process: Distribution of Hamming distances

We reinvestigate the phase transitions of the Ising model on the Kagome lattice with antiferromagnetic nearest-neighbor and ferromagnetic next-nearest-neighbor interactions, which has a six-state-clock spin ice ground state and two consecutive Berezinskii-Kosterlitz-Thouless (BKT) phase transitions. Employing the classical Monte Carlo (MC) simulations, the phases are characterized by the magnetic order parameter, and the critical temperatures are obtained by the finite-size scaling of related physical quantities. Moreover, we attempt to gain general information on the phase transitions from the MC process instead of MC results and successfully extract the correct transition points with surprisingly high accuracy. Specifically, we focus on the selected data set of uncorrelated MC configurations and quantify the MC process using the distribution of two-configuration Hamming distances in this small data collection. This distribution is more than a quantity that features different behaviors in different phases but also nicely supports the same BKT scaling form as the order parameter, from which we successfully determine the two BKT transition points with surprisingly high accuracy. We also discuss the connection between the phase transitions and the intrinsic dimension extracted from the Hamming distances, which is widely used in the growing field of machine learning and is reported to be able to detect critical points. Our findings provide a new understanding of the spin ice transitions in the Kagome lattice and can hopefully be used similarly to identify transitions in the quantum system on the same lattice with strong frustrations.
ReviewRanker: A Semi-Supervised Learning Based Approach for Code Review Quality Estimation

Code review is considered a key process in the software industry for minimizing bugs and improving code quality. Inspection of review process effectiveness and continuous improvement can boost development productivity. Such inspection is a time-consuming and human-bias-prone task. We propose a semi-supervised learning based system ReviewRanker which is aimed at assigning each code review a confidence score which is expected to resonate with the quality of the review. Our proposed method is trained based on simple and and well defined labels provided by developers. The labeling task requires little to no effort from the developers and has an indirect relation to the end goal (assignment of review confidence score). ReviewRanker is expected to improve industry-wide code review quality inspection through reducing human bias and effort required for such task. The system has the potential of minimizing the back-and-forth cycle existing in the development and review process. Usable code and dataset for this research can be found at: https://github.com/saifarnab/code_review
MD-HIT: Machine learning for materials property prediction with dataset redundancy control

Materials datasets are usually featured by the existence of many redundant (highly similar) materials due to the tinkering material design practice over the history of materials research. For example, the materials project database has many perovskite cubic structure materials similar to SrTiO$_3$. This sample redundancy within the dataset makes the random splitting of machine learning model evaluation to fail so that the ML models tend to achieve over-estimated predictive performance which is misleading for the materials science community. This issue is well known in the field of bioinformatics for protein function prediction, in which a redundancy reduction procedure (CD-Hit) is always applied to reduce the sample redundancy by ensuring no pair of samples has a sequence similarity greater than a given threshold. This paper surveys the overestimated ML performance in the literature for both composition based and structure based material property prediction. We then propose a material dataset redundancy reduction algorithm called MD-HIT and evaluate it with several composition and structure based distance threshold sfor reducing data set sample redundancy. We show that with this control, the predicted performance tends to better reflect their true prediction capability. Our MD-hit code can be freely accessed at https://github.com/usccolumbia/MD-HIT
Vocal Tract Area Estimation by Gradient Descent

Articulatory features can provide interpretable and flexible controls for the synthesis of human vocalizations by allowing the user to directly modify parameters like vocal strain or lip position. To make this manipulation through resynthesis possible, we need to estimate the features that result in a desired vocalization directly from audio recordings. In this work, we propose a white-box optimization technique for estimating glottal source parameters and vocal tract shapes from audio recordings of human vowels. The approach is based on inverse filtering and optimizing the frequency response of a wave\-guide model of the vocal tract with gradient descent, propagating error gradients through the mapping of articulatory features to the vocal tract area function. We apply this method to the task of matching the sound of the Pink Trombone, an interactive articulatory synthesizer, to a given vocalization. We find that our method accurately recovers control functions for audio generated by the Pink Trombone itself. We then compare our technique against evolutionary optimization algorithms and a neural network trained to predict control parameters from audio. A subjective evaluation finds that our approach outperforms these black-box optimization baselines on the task of reproducing human vocalizations.
Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering

In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific image data. In many cases, tremendous effort has been spent to package these new advances into usable software tools and, as a result, users can nowadays routinely apply cutting-edge methods to their analysis problems using software tools such as ilastik [1], cellprofiler [2], Fiji/ImageJ2 [3,4] and its many modern plugins that build on the BigDataViewer ecosystem [5], and many others. Such software tools have now become part of a critical infrastructure for science [6]. Unfortunately, overshadowed by the few exceptions that have had long-lasting impact, many other potentially useful tools fail to find their way into the hands of users. While there are many reasons for this, we believe that at least some of the underlying problems, which we discuss in more detail below, can be mitigated. In this opinion piece, we specifically argue that embedding teams of research software engineers (RSEs) within imaging and image analysis core facilities would be a major step towards sustainable bioimage analysis software.
Where to Drop Sensors from Aerial Robots to Monitor a Surface-Level Phenomenon?

We consider the problem of routing a team of energy-constrained Unmanned Aerial Vehicles (UAVs) to drop unmovable sensors for monitoring a task area in the presence of stochastic wind disturbances. In prior work on mobile sensor routing problems, sensors and their carrier are one integrated platform, and sensors are assumed to be able to take measurements at exactly desired locations. By contrast, airdropping the sensors onto the ground can introduce stochasticity in the landing locations of the sensors. We focus on addressing this stochasticity in sensor locations from the path-planning perspective. Specifically, we formulate the problem (Multi-UAV Sensor Drop) as a variant of the Submodular Team Orienteering Problem with one additional constraint on the number of sensors on each UAV. The objective is to maximize the Mutual Information between the phenomenon at Points of Interest (PoIs) and the measurements that sensors will take at stochastic locations. We show that such an objective is computationally expensive to evaluate. To tackle this challenge, we propose a surrogate objective with a closed-form expression based on the expected mean and expected covariance of the Gaussian Process. We propose a heuristic algorithm to solve the optimization problem with the surrogate objective. The formulation and the algorithms are validated through extensive simulations.
Interpreting and generalizing deep learning in physics-based problems with functional linear models

Although deep learning has achieved remarkable success in various scientific machine learning applications, its black-box nature poses concerns regarding interpretability and generalization capabilities beyond the training data. Interpretability is crucial and often desired in modeling physical systems. Moreover, acquiring extensive datasets that encompass the entire range of input features is challenging in many physics-based learning tasks, leading to increased errors when encountering out-of-distribution (OOD) data. In this work, motivated by the field of functional data analysis (FDA), we propose generalized functional linear models as an interpretable surrogate for a trained deep learning model. We demonstrate that our model could be trained either based on a trained neural network (post-hoc interpretation) or directly from training data (interpretable operator learning). A library of generalized functional linear models with different kernel functions is considered and sparse regression is used to discover an interpretable surrogate model that could be analytically presented. We present test cases in solid mechanics, fluid mechanics, and transport. Our results demonstrate that our model can achieve comparable accuracy to deep learning and can improve OOD generalization while providing more transparency and interpretability. Our study underscores the significance of interpretability in scientific machine learning and showcases the potential of functional linear models as a tool for interpreting and generalizing deep learning.
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Our implementation is available at https://github.com/DeepGraphLearning/SiamDiff.
SparseVSR: Lightweight and Noise Robust Visual Speech Recognition

Recent advances in deep neural networks have achieved unprecedented success in visual speech recognition. However, there remains substantial disparity between current methods and their deployment in resource-constrained devices. In this work, we explore different magnitude-based pruning techniques to generate a lightweight model that achieves higher performance than its dense model equivalent, especially under the presence of visual noise. Our sparse models achieve state-of-the-art results at 10% sparsity on the LRS3 dataset and outperform the dense equivalent up to 70% sparsity. We evaluate our 50% sparse model on 7 different visual noise types and achieve an overall absolute improvement of more than 2% WER compared to the dense equivalent. Our results confirm that sparse networks are more resistant to noise than dense networks.
CMDFusion: Bidirectional Fusion Network With Cross-Modality Knowledge Distillation for LiDAR Semantic Segmentation

2D RGB images and 3D LIDAR point clouds provide complementary knowledge for the perception system of autonomous vehicles. Several 2D and 3D fusion methods have been explored for the LIDAR semantic segmentation task, but they suffer from different problems. 2D-to-3D fusion methods require strictly paired data during inference, which may not be available in real-world scenarios, while 3D-to-2D fusion methods cannot explicitly make full use of the 2D information. Therefore, we propose a Bidirectional Fusion Network with Cross-Modality Knowledge Distillation (CMDFusion) in this work. Our method has two contributions. First, our bidirectional fusion scheme explicitly and implicitly enhances the 3D feature via 2D-to-3D fusion and 3D-to-2D fusion, respectively, which surpasses either one of the single fusion schemes. Second, we distillate the 2D knowledge from a 2D network (Camera branch) to a 3D network (2D knowledge branch) so that the 3D network can generate 2D information even for those points not in the FOV (field of view) of the camera. In this way, RGB images are not required during inference anymore since the 2D knowledge branch provides 2D information according to the 3D LIDAR input. We show that our CMDFusion achieves the best performance among all fusion-based methods on SemanticKITTI and nuScenes datasets.
Extending the Forward Forward Algorithm

The Forward Forward algorithm, proposed by Geoffrey Hinton in November 2022, is a novel method for training neural networks as an alternative to backpropagation. In this project, we replicate Hinton's experiments on the MNIST dataset, and subsequently extend the scope of the method with two significant contributions. First, we establish a baseline performance for the Forward Forward network on the IMDb movie reviews dataset. As far as we know, our results on this sentiment analysis task marks the first instance of the algorithm's extension beyond computer vision. Second, we introduce a novel pyramidal optimization strategy for the loss threshold - a hyperparameter specific to the Forward Forward method. Our pyramidal approach shows that a good thresholding strategy causes a difference of up to 8% in test error. Lastly, we perform visualizations of the trained parameters and derived several significant insights, such as a notably larger (10-20x) mean and variance in the weights acquired by the Forward Forward network. Repository: https://github.com/Ads-cmu/ForwardForward
Enhancing Cross-lingual Transfer via Phonemic Transcription Integration

Previous cross-lingual transfer methods are restricted to orthographic representation learning via textual scripts. This limitation hampers cross-lingual transfer and is biased towards languages sharing similar well-known scripts. To alleviate the gap between languages from different writing scripts, we propose PhoneXL, a framework incorporating phonemic transcriptions as an additional linguistic modality beyond the traditional orthographic transcriptions for cross-lingual transfer. Particularly, we propose unsupervised alignment objectives to capture (1) local one-to-one alignment between the two different modalities, (2) alignment via multi-modality contexts to leverage information from additional modalities, and (3) alignment via multilingual contexts where additional bilingual dictionaries are incorporated. We also release the first phonemic-orthographic alignment dataset on two token-level tasks (Named Entity Recognition and Part-of-Speech Tagging) among the understudied but interconnected Chinese-Japanese-Korean-Vietnamese (CJKV) languages. Our pilot study reveals phonemic transcription provides essential information beyond the orthography to enhance cross-lingual transfer and bridge the gap among CJKV languages, leading to consistent improvements on cross-lingual token-level tasks over orthographic-based multilingual PLMs.
CORE-GPT: Combining Open Access research and large language models for credible, trustworthy question answering

In this paper, we present CORE-GPT, a novel question-answering platform that combines GPT-based language models and more than 32 million full-text open access scientific articles from CORE. We first demonstrate that GPT3.5 and GPT4 cannot be relied upon to provide references or citations for generated text. We then introduce CORE-GPT which delivers evidence-based answers to questions, along with citations and links to the cited papers, greatly increasing the trustworthiness of the answers and reducing the risk of hallucinations. CORE-GPT's performance was evaluated on a dataset of 100 questions covering the top 20 scientific domains in CORE, resulting in 100 answers and links to 500 relevant articles. The quality of the provided answers and and relevance of the links were assessed by two annotators. Our results demonstrate that CORE-GPT can produce comprehensive and trustworthy answers across the majority of scientific domains, complete with links to genuine, relevant scientific articles.
Automatic diagnosis of knee osteoarthritis severity using Swin transformer

Knee osteoarthritis (KOA) is a widespread condition that can cause chronic pain and stiffness in the knee joint. Early detection and diagnosis are crucial for successful clinical intervention and management to prevent severe complications, such as loss of mobility. In this paper, we propose an automated approach that employs the Swin Transformer to predict the severity of KOA. Our model uses publicly available radiographic datasets with Kellgren and Lawrence scores to enable early detection and severity assessment. To improve the accuracy of our model, we employ a multi-prediction head architecture that utilizes multi-layer perceptron classifiers. Additionally, we introduce a novel training approach that reduces the data drift between multiple datasets to ensure the generalization ability of the model. The results of our experiments demonstrate the effectiveness and feasibility of our approach in predicting KOA severity accurately.
Back to Optimization: Diffusion-based Zero-Shot 3D Human Pose Estimation

Learning-based methods have dominated the 3D human pose estimation (HPE) tasks with significantly better performance in most benchmarks than traditional optimization-based methods. Nonetheless, 3D HPE in the wild is still the biggest challenge for learning-based models, whether with 2D-3D lifting, image-to-3D, or diffusion-based methods, since the trained networks implicitly learn camera intrinsic parameters and domain-based 3D human pose distributions and estimate poses by statistical average. On the other hand, the optimization-based methods estimate results case-by-case, which can predict more diverse and sophisticated human poses in the wild. By combining the advantages of optimization-based and learning-based methods, we propose the \textbf{Ze}ro-shot \textbf{D}iffusion-based \textbf{O}ptimization (\textbf{ZeDO}) pipeline for 3D HPE to solve the problem of cross-domain and in-the-wild 3D HPE. Our multi-hypothesis \textit{\textbf{ZeDO}} achieves state-of-the-art (SOTA) performance on Human3.6M, with minMPJPE $51.4$mm, without training with any 2D-3D or image-3D pairs. Moreover, our single-hypothesis \textit{\textbf{ZeDO}} achieves SOTA performance on 3DPW dataset with PA-MPJPE $40.3$mm on cross-dataset evaluation, which even outperforms learning-based methods trained on 3DPW.