Miracle-dz/UniFAR-FTUs huggingface dataset:
Graph Multi-Similarity Learning for Molecular Property Prediction

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative similarities) between molecules. However, current molecular representation learning methods fall short in exploring multi-similarity and often underestimate the complexity of relationships between molecules. Additionally, previous multi-similarity approaches require the specification of positive and negative pairs to attribute distinct predefined weights to different relative similarities, which can introduce potential bias. In this work, we introduce Graph Multi-Similarity Learning for Molecular Property Prediction (GraphMSL) framework, along with a novel approach to formulate a generalized multi-similarity metric without the need to define positive and negative pairs. In each of the chemical modality spaces (e.g.,molecular depiction image, fingerprint, NMR, and SMILES) under consideration, we first define a self-similarity metric (i.e., similarity between an anchor molecule and another molecule), and then transform it into a generalized multi-similarity metric for the anchor through a pair weighting function. GraphMSL validates the efficacy of the multi-similarity metric across MoleculeNet datasets. Furthermore, these metrics of all modalities are integrated into a multimodal multi-similarity metric, which showcases the potential to improve the performance. Moreover, the focus of the model can be redirected or customized by altering the fusion function. Last but not least, GraphMSL proves effective in drug discovery evaluations through post-hoc analyses of the learnt representations.
Gamifying a Software Testing Course with Continuous Integration

Testing plays a crucial role in software development, and it is essential for software engineering students to receive proper testing education. However, motivating students to write tests and use automated testing during software development can be challenging. To address this issue and enhance student engagement in testing when they write code, we propose to incentivize students to test more by gamifying continuous integration. For this we use Gamekins, a tool that is seamlessly integrated into the Jenkins continuous integration platform and uses game elements based on commits to the source code repository: Developers can earn points by completing test challenges and quests generated by Gamekins, compete with other developers or teams on a leaderboard, and receive achievements for their test-related accomplishments. In this paper, we present our integration of Gamekins into an undergraduate-level course on software testing. We observe a correlation between how students test their code and their use of Gamekins, as well as a significant improvement in the accuracy of their results compared to a previous iteration of the course without gamification. As a further indicator of how this approach improves testing behavior, the students reported enjoyment in writing tests with Gamekins.
Datacube segmentation via Deep Spectral Clustering

Extended Vision techniques are ubiquitous in physics. However, the data cubes steaming from such analysis often pose a challenge in their interpretation, due to the intrinsic difficulty in discerning the relevant information from the spectra composing the data cube. Furthermore, the huge dimensionality of data cube spectra poses a complex task in its statistical interpretation; nevertheless, this complexity contains a massive amount of statistical information that can be exploited in an unsupervised manner to outline some essential properties of the case study at hand, e.g.~it is possible to obtain an image segmentation via (deep) clustering of data-cube's spectra, performed in a suitably defined low-dimensional embedding space. To tackle this topic, we explore the possibility of applying unsupervised clustering methods in encoded space, i.e. perform deep clustering on the spectral properties of datacube pixels. A statistical dimensional reduction is performed by an ad hoc trained (Variational) AutoEncoder, in charge of mapping spectra into lower dimensional metric spaces, while the clustering process is performed by a (learnable) iterative K-Means clustering algorithm. We apply this technique to two different use cases, of different physical origins: a set of Macro mapping X-Ray Fluorescence (MA-XRF) synthetic data on pictorial artworks, and a dataset of simulated astrophysical observations.
Picosecond transfer from short-term to long-term memory in analog antiferromagnetic memory device

Experiments in materials with a compensated ordering of magnetic moments have demonstrated a potential for approaching the thermodynamic limit of the fastest and least-dissipative operation of a digital memory bit. In addition, these materials are very promising for a construction of energy-efficient analog devices with neuromorphic functionalities, which are inspired by computing-in-memory capabilities of the human brain. In this paper, we report on experimental separation of switching-related and heat-related resistance signal dynamics in memory devices microfabricated from CuMnAs antiferromagnetic metal. We show that the memory variable multilevel resistance can be used as a long-term memory (LTM), lasting up to minutes at room temperature. In addition, ultrafast reflectivity change and heat dissipation from nanoscale-thickness CuMnAs films, taking place on picosecond to hundreds of nanoseconds time scales, can be used as a short-term memory (STM). Information about input stimuli, represented by femtosecond laser pulses, can be transferred from STM to LTM after rehearsals at picosecond to nanosecond times in these memory devices, where information can be retrieved at times up to 10^15 longer than the input pulse duration. Our results open a route towards ultra-fast low-power implementations of spiking neuron and synapse functionalities using a resistive analog antiferromagnetic memory.
A Queueing Model for the Ambulance Ramping Problem with an Offload Zone

This work develops a methodology for studying the effect of an offload zone on the ambulance ramping problem using a multi-server, multi-class non-preemptive priority queueing model that can be treated analytically. A prototype model for the ambulance/emergency-department interface is constructed, which is then implemented as a formal discrete event simulation, and is run as a regenerative steady-state simulation for empirical estimation of the ambulance queue-length and waiting-time distributions. The model is also solved by analytical means for explicit and exact representations of these distributions, which are subsequently tested against simulation results. A number of measures of performance is extracted, including the mean and 90th percentiles of the ambulance queue length and waiting time, as well as the average number of ambulance days lost per month due to offload delay (offload delay rate). Various easily computable approximations are proposed and tested. In particular, a closed-form, purely algebraic expression that approximates the dependence of the offload delay rate on the capacity of the offload zone is proposed. It can be evaluated directly from model input parameters and is found to be, for all practical purposes, indistinguishable from the exact result.
Graph Contrastive Learning with Cohesive Subgraph Awareness

Graph contrastive learning (GCL) has emerged as a state-of-the-art strategy for learning representations of diverse graphs including social and biomedical networks. GCL widely uses stochastic graph topology augmentation, such as uniform node dropping, to generate augmented graphs. However, such stochastic augmentations may severely damage the intrinsic properties of a graph and deteriorate the following representation learning process. We argue that incorporating an awareness of cohesive subgraphs during the graph augmentation and learning processes has the potential to enhance GCL performance. To this end, we propose a novel unified framework called CTAug, to seamlessly integrate cohesion awareness into various existing GCL mechanisms. In particular, CTAug comprises two specialized modules: topology augmentation enhancement and graph learning enhancement. The former module generates augmented graphs that carefully preserve cohesion properties, while the latter module bolsters the graph encoder's ability to discern subgraph patterns. Theoretical analysis shows that CTAug can strictly improve existing GCL mechanisms. Empirical experiments verify that CTAug can achieve state-of-the-art performance for graph representation learning, especially for graphs with high degrees. The code is available at https://doi.org/10.5281/zenodo.10594093, or https://github.com/wuyucheng2002/CTAug.
A Ca$^{2+}$ puff model based on integrodifferential equations

The calcium (Ca$^{2+}$) signalling system is important for many cellular processes within the human body. Signals are transmitted within the cell by releasing Ca$^{2+}$ from the endoplasmic reticulum (ER) into the cytosol via clusters of Ca$^{2+}$ channels. Mathematical models of Ca$^{2+}$ release via inositol 1,4,5-trisphosphate receptors (IP$_{3}$R) help with understanding underlying Ca$^{2+}$ dynamics but data-driven modelling of stochastic Ca$^{2+}$ release events, known as Ca$^{2+}$ puffs, is a difficult challenge. Parameterising Markov models for representing the IP$_{3}$R with steady-state single channel data obtained at fixed combinations of the ligands Ca$^{2+}$ and inositol-trisphosphate (IP$_{3}$) has previously been demonstrated to be insufficient. However, by extending an IP$_{3}$R model based on steady-state data with an integral term that incorporates the delayed response of the channel to varying Ca$^{2+}$ concentrations we succeed in generating realistic Ca$^{2+}$ puffs. By interpreting the integral term as a weighted average of Ca$^{2+}$ concentrations that extend over a time interval of length $\tau$ into the past we conclude that the IP$_{3}$R requires a certain amount of memory of past ligand concentrations.
GUMsley: Evaluating Entity Salience in Summarization for 12 English Genres

As NLP models become increasingly capable of understanding documents in terms of coherent entities rather than strings, obtaining the most salient entities for each document is not only an important end task in itself but also vital for Information Retrieval (IR) and other downstream applications such as controllable summarization. In this paper, we present and evaluate GUMsley, the first entity salience dataset covering all named and non-named salient entities for 12 genres of English text, aligned with entity types, Wikification links and full coreference resolution annotations. We promote a strict definition of salience using human summaries and demonstrate high inter-annotator agreement for salience based on whether a source entity is mentioned in the summary. Our evaluation shows poor performance by pre-trained SOTA summarization models and zero-shot LLM prompting in capturing salient entities in generated summaries. We also show that predicting or providing salient entities to several model architectures enhances performance and helps derive higher-quality summaries by alleviating the entity hallucination problem in existing abstractive summarization.
Head and Neck Tumor Segmentation from [18F]F-FDG PET/CT Images Based on 3D Diffusion Model

Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.
Avoiding breakdown in incomplete factorizations in low precision arithmetic

The emergence of low precision floating-point arithmetic in computer hardware has led to a resurgence of interest in the use of mixed precision numerical linear algebra. For linear systems of equations, there has been renewed enthusiasm for mixed precision variants of iterative refinement. We consider the iterative solution of large sparse systems using incomplete factorization preconditioners. The focus is on the robust computation of such preconditioners in half precision arithmetic and employing them to solve symmetric positive definite systems to higher precision accuracy; however, the proposed ideas can be applied more generally. Even for well-conditioned problems, incomplete factorizations can break down when small entries occur on the diagonal during the factorization. When using half precision arithmetic, overflows are an additional possible source of breakdown. We examine how breakdowns can be avoided and we implement our strategies within new half precision Fortran sparse incomplete Cholesky factorization software. Results are reported for a range of problems from practical applications. These demonstrate that, even for highly ill-conditioned problems, half precision preconditioners can potentially replace double precision preconditioners, although unsurprisingly this may be at the cost of additional iterations of a Krylov solver.
The augmented external activity complex of a matroid

For a matroid, we define a new simplicial complex whose facets are indexed by its independent sets. This complex contains the external activity complex as a subcomplex. We call our complex the augmented external activity complex since its definition is motivated by the recently defined augmented tautological classes of matroids. We prove that our complex is shellable and show that our shelling satisfies the stronger property of being an $H$-shelling. This explicates our result that the $h$-vector of our complex is the $f$-vector of the independence complex. We also define an augmented no broken circuit complex, which contains the usual no broken circuit complex as a subcomplex. We prove its shellability and show that our shelling is also an $H$-shelling. The $h$-vector of this complex is the $f$-vector of the no broken circuit complex.
CaMU: Disentangling Causal Effects in Deep Model Unlearning

Machine unlearning requires removing the information of forgetting data while keeping the necessary information of remaining data. Despite recent advancements in this area, existing methodologies mainly focus on the effect of removing forgetting data without considering the negative impact this can have on the information of the remaining data, resulting in significant performance degradation after data removal. Although some methods try to repair the performance of remaining data after removal, the forgotten information can also return after repair. Such an issue is due to the intricate intertwining of the forgetting and remaining data. Without adequately differentiating the influence of these two kinds of data on the model, existing algorithms take the risk of either inadequate removal of the forgetting data or unnecessary loss of valuable information from the remaining data. To address this shortcoming, the present study undertakes a causal analysis of the unlearning and introduces a novel framework termed Causal Machine Unlearning (CaMU). This framework adds intervention on the information of remaining data to disentangle the causal effects between forgetting data and remaining data. Then CaMU eliminates the causal impact associated with forgetting data while concurrently preserving the causal relevance of the remaining data. Comprehensive empirical results on various datasets and models suggest that CaMU enhances performance on the remaining data and effectively minimizes the influences of forgetting data. Notably, this work is the first to interpret deep model unlearning tasks from a new perspective of causality and provide a solution based on causal analysis, which opens up new possibilities for future research in deep model unlearning.
Elephants Do Not Forget: Differential Privacy with State Continuity for Privacy Budget

Current implementations of differentially-private (DP) systems either lack support to track the global privacy budget consumed on a dataset, or fail to faithfully maintain the state continuity of this budget. We show that failure to maintain a privacy budget enables an adversary to mount replay, rollback and fork attacks - obtaining answers to many more queries than what a secure system would allow. As a result the attacker can reconstruct secret data that DP aims to protect - even if DP code runs in a Trusted Execution Environment (TEE). We propose ElephantDP, a system that aims to provide the same guarantees as a trusted curator in the global DP model would, albeit set in an untrusted environment. Our system relies on a state continuity module to provide protection for the privacy budget and a TEE to faithfully execute DP code and update the budget. To provide security, our protocol makes several design choices including the content of the persistent state and the order between budget updates and query answers. We prove that ElephantDP provides liveness (i.e., the protocol can restart from a correct state and respond to queries as long as the budget is not exceeded) and DP confidentiality (i.e., an attacker learns about a dataset as much as it would from interacting with a trusted curator). Our implementation and evaluation of the protocol use Intel SGX as a TEE to run the DP code and a network of TEEs to maintain state continuity. Compared to an insecure baseline, we observe only 1.1-2$\times$ overheads and lower relative overheads for larger datasets and complex DP queries.
Tensor-based process control and monitoring for semiconductor manufacturing with unstable disturbances

With the development and popularity of sensors installed in manufacturing systems, complex data are collected during manufacturing processes, which brings challenges for traditional process control methods. This paper proposes a novel process control and monitoring method for the complex structure of high-dimensional image-based overlay errors (modeled in tensor form), which are collected in semiconductor manufacturing processes. The proposed method aims to reduce overlay errors using limited control recipes. We first build a high-dimensional process model and propose different tensor-on-vector regression algorithms to estimate parameters in the model to alleviate the curse of dimensionality. Then, based on the estimate of tensor parameters, the exponentially weighted moving average (EWMA) controller for tensor data is designed whose stability is theoretically guaranteed. Considering the fact that low-dimensional control recipes cannot compensate for all high-dimensional disturbances on the image, control residuals are monitored to prevent significant drifts of uncontrollable high-dimensional disturbances. Through extensive simulations and real case studies, the performances of parameter estimation algorithms and the EWMA controller in tensor space are evaluated. Compared with existing image-based feedback controllers, the superiority of our method is verified especially when disturbances are not stable.
Singing Voice Data Scaling-up: An Introduction to ACE-Opencpop and KiSing-v2

In singing voice synthesis (SVS), generating singing voices from musical scores faces challenges due to limited data availability, a constraint less common in text-to-speech (TTS). This study proposes a new approach to address this data scarcity. We utilize an existing singing voice synthesizer for data augmentation and apply precise manual tuning to reduce unnatural voice synthesis. Our development of two extensive singing voice corpora, ACE-Opencpop and KiSing-v2, facilitates large-scale, multi-singer voice synthesis. Utilizing pre-trained models derived from these corpora, we achieve notable improvements in voice quality, evident in both in-domain and out-of-domain scenarios. The corpora, pre-trained models, and their related training recipes are publicly available at Muskits-ESPnet (https://github.com/espnet/espnet).
Quantum steering from phase measurements with limited resources

Quantum steering captures the ability of one party, Alice, to control through quantum correlations the state at a distant location, Bob, with superior ability than allowed by a local hidden state model. Verifying the presence of quantum steering has implications for the certification of quantum channels, and its connection to the metrological power of the quantum state has been recently proved. This link is established by means of the violation of a Cram\'er-Rao bound holding for non-steerable states: its direct assessment would then require operation in the asymptotic regime of a large number of repetitions. Here, we extend previous work to account explicitly for the use of a limited number of resources, and put this modified approach to test in a quantum optics experiment. The imperfections in the apparatus demand an adaptation of the original test in the multiparameter setting. Our results provide guidelines to apply such a metrological approach to the validation of quantum channels.
Predicting the Future with Simple World Models

World models can represent potentially high-dimensional pixel observations in compact latent spaces, making it tractable to model the dynamics of the environment. However, the latent dynamics inferred by these models may still be highly complex. Abstracting the dynamics of the environment with simple models can have several benefits. If the latent dynamics are simple, the model may generalize better to novel transitions, and discover useful latent representations of environment states. We propose a regularization scheme that simplifies the world model's latent dynamics. Our model, the Parsimonious Latent Space Model (PLSM), minimizes the mutual information between latent states and the dynamics that arise between them. This makes the dynamics softly state-invariant, and the effects of the agent's actions more predictable. We combine the PLSM with three different model classes used for i) future latent state prediction, ii) video prediction, and iii) planning. We find that our regularization improves accuracy, generalization, and performance in downstream tasks.