The immune checkpoint inhibitors have demonstrated promising clinical efficacy across various tumor types, yet the percentage of patients who benefit from them remains low. The bindings between tumor antigens and HLA-I/TCR molecules determine the antigen presentation and T-cell activation, thereby playing an important role in the immunotherapy response. In this paper, we propose UnifyImmun, a unified cross-attention transformer model designed to simultaneously predict the bindings of peptides to both receptors, providing more comprehensive evaluation of antigen immunogenicity. We devise a two-phase strategy using virtual adversarial training that enables these two tasks to reinforce each other mutually, by compelling the encoders to extract more expressive features. Our method demonstrates superior performance in predicting both pHLA and pTCR binding on multiple independent and external test sets. Notably, on a large-scale COVID-19 pTCR binding test set without any seen peptide in training set, our method outperforms the current state-of-the-art methods by more than 10\%. The predicted binding scores significantly correlate with the immunotherapy response and clinical outcomes on two clinical cohorts. Furthermore, the cross-attention scores and integrated gradients reveal the amino-acid sites critical for peptide binding to receptors. In essence, our approach marks a significant step toward comprehensive evaluation of antigen immunogenicity.

Commenting code is a crucial activity in software development, as it aids in facilitating future maintenance and updates. To enhance the efficiency of writing comments and reduce developers' workload, researchers has proposed various automated code summarization (ACS) techniques to automatically generate comments/summaries for given code units. However, these ACS techniques primarily focus on generating summaries for code units at the method level. There is a significant lack of research on summarizing higher-level code units, such as file-level and module-level code units, despite the fact that summaries of these higher-level code units are highly useful for quickly gaining a macro-level understanding of software components and architecture. To fill this gap, in this paper, we conduct a systematic study on how to use LLMs for commenting higher-level code units, including file level and module level. These higher-level units are significantly larger than method-level ones, which poses challenges in handling long code inputs within LLM constraints and maintaining efficiency. To address these issues, we explore various summarization strategies for ACS of higher-level code units, which can be divided into three types: full code summarization, reduced code summarization, and hierarchical code summarization. The experimental results suggest that for summarizing file-level code units, using the full code is the most effective approach, with reduced code serving as a cost-efficient alternative. However, for summarizing module-level code units, hierarchical code summarization becomes the most promising strategy. In addition, inspired by the research on method-level ACS, we also investigate using the LLM as an evaluator to evaluate the quality of summaries of higher-level code units. The experimental results demonstrate that the LLM's evaluation results strongly correlate with human evaluations.

Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as nutrient bioavailability, antioxidant activity, and therapeutic efficacy. However, these interactions remain challenging due to the structural diversity of polyphenols and the dynamic nature of protein binding. Traditional experimental techniques like nuclear magnetic resonance (NMR) and mass spectrometry (MS), along with computational tools such as molecular docking and molecular dynamics (MD), have offered important insights but face constraints in scalability, throughput, and reproducibility. This review explores how deep learning (DL) is reshaping the study of PhPIs by enabling efficient prediction of binding sites, interaction affinities, and MD using high-dimensional bio- and chem-informatics data. While DL enhances prediction accuracy and reduces experimental redundancy, its effectiveness remains limited by data availability, quality, and representativeness, particularly in the context of natural products. We critically assess current DL frameworks for PhPIs analysis and outline future directions, including multimodal data integration, improved model generalizability, and development of domain-specific benchmark datasets. This synthesis offers guidance for researchers aiming to apply DL in unraveling structure-function relationships of polyphenols, accelerating discovery in nutritional science and therapeutic development.

The output prediction of quantum circuits is a formidably challenging task imperative in developing quantum devices. Motivated by the natural graph representation of quantum circuits, this paper proposes a Graph Neural Networks (GNNs)-based framework to predict the output expectation values of quantum circuits under noisy and noiseless conditions and compare the performance of different parameterized quantum circuits (PQCs). We construct datasets under noisy and noiseless conditions using a non-parameterized quantum gate set to predict circuit expectation values. The node feature vectors for GNNs are specifically designed to include noise information. In our simulations, we compare the prediction performance of GNNs in both noisy and noiseless conditions against Convolutional Neural Networks (CNNs) on the same dataset and their qubit scalability. GNNs demonstrate superior prediction accuracy across diverse conditions. Subsequently, we utilize the parameterized quantum gate set to construct noisy PQCs and compute the ground state energy of hydrogen molecules using the Variational Quantum Eigensolver (VQE). We propose two schemes: the Indirect Comparison scheme, which involves directly predicting the ground state energy and subsequently comparing circuit performances, and the Direct Comparison scheme, which directly predicts the relative performance of the two circuits. Simulation results indicate that the Direct Comparison scheme significantly outperforms the Indirect Comparison scheme by an average of 36.2% on the same dataset, providing a new and effective perspective for using GNNs to predict the overall properties of PQCs, specifically by focusing on their performance differences.

Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of cancer-related death worldwide. Accurate histopathological grading of CRC is essential for prognosis and treatment planning but remains a subjective process prone to observer variability and limited by global shortages of trained pathologists. To promote automated and standardized solutions, we organized the ICIP Grand Challenge on Colorectal Cancer Tumor Grading and Segmentation using the publicly available METU CCTGS dataset. The dataset comprises 103 whole-slide images with expert pixel-level annotations for five tissue classes. Participants submitted segmentation masks via Codalab, evaluated using metrics such as macro F-score and mIoU. Among 39 participating teams, six outperformed the Swin Transformer baseline (62.92 F-score). This paper presents an overview of the challenge, dataset, and the top-performing methods

Predictive learning for spatio-temporal processes (PL-STP) on complex spatial domains plays a critical role in various scientific and engineering fields, with its essence being the construction of operators between infinite-dimensional function spaces. This paper focuses on the unequal-domain mappings in PL-STP and categorising them into increase-domain and decrease-domain mapping. Recent advances in deep learning have revealed the great potential of neural operators (NOs) to learn operators directly from observational data. However, existing NOs require input space and output space to be the same domain, which pose challenges in ensuring predictive accuracy and stability for unequal-domain mappings. To this end, this study presents a general reduced-order neural operator named Reduced-Order Neural Operator on Riemannian Manifolds (RO-NORM), which consists of two parts: the unequal-domain encoder/decoder and the same-domain approximator. Motivated by the variable separation in classical modal decomposition, the unequal-domain encoder/decoder uses the pre-computed bases to reformulate the spatio-temporal function as a sum of products between spatial (or temporal) bases and corresponding temporally (or spatially) distributed weight functions, thus the original unequal-domain mapping can be converted into a same-domain mapping. Consequently, the same-domain approximator NORM is applied to model the transformed mapping. The performance of our proposed method has been evaluated on six benchmark cases, including parametric PDEs, engineering and biomedical applications, and compared with four baseline algorithms: DeepONet, POD-DeepONet, PCA-Net, and vanilla NORM. The experimental results demonstrate the superiority of RO-NORM in prediction accuracy and training efficiency for PL-STP.

Mixed precision quantization (MPQ) is an effective quantization approach to achieve accuracy-complexity trade-off of neural network, through assigning different bit-widths to network activations and weights in each layer. The typical way of existing MPQ methods is to optimize quantization policies (i.e., bit-width allocation) in a gradient descent manner, termed as Differentiable (DMPQ). At the end of the search, the bit-width associated to the quantization parameters which has the largest value will be selected to form the final mixed precision quantization policy, with the implicit assumption that the values of quantization parameters reflect the operation contribution to the accuracy improvement. While much has been discussed about the MPQ improvement, the bit-width selection process has received little attention. We study this problem and argue that the magnitude of quantization parameters does not necessarily reflect the actual contribution of the bit-width to the task performance. Then, we propose a Shapley-based MPQ (SMPQ) method, which measures the bit-width operation direct contribution on the MPQ task. To reduce computation cost, a Monte Carlo sampling-based approximation strategy is proposed for Shapley computation. Extensive experiments on mainstream benchmarks demonstrate that our SMPQ consistently achieves state-of-the-art performance than gradient-based competitors.

Current superconducting quantum devices impose strict connectivity constraints on quantum circuit execution, necessitating circuit transformation before executing quantum circuits on physical hardware. Numerous quantum circuit transformation (QCT) algorithms have been proposed. To enable faithful evaluation of state-of-the-art QCT algorithms, this paper introduces QKNOB (Qubit mapping Benchmark with Known Near-Optimality), a novel benchmark construction method for QCT. QKNOB circuits have built-in transformations with near-optimal (close to the theoretical optimum) SWAP count and depth overhead. QKNOB provides general and unbiased evaluation of QCT algorithms. Using QKNOB, we demonstrate that SABRE, the default Qiskit compiler, consistently achieves the best performance on the 53-qubit IBM Q Rochester and Google Sycamore devices for both SWAP count and depth objectives. Our results also reveal significant performance gaps relative to the near-optimal transformation costs of QKNOB. Our construction algorithm and benchmarks are open-source.

Drug combination therapy has become a increasingly promising method in the treatment of cancer. However, the number of possible drug combinations is so huge that it is hard to screen synergistic drug combinations through wet-lab experiments. Therefore, computational screening has become an important way to prioritize drug combinations. Graph neural network have recently shown remarkable performance in the prediction of compound-protein interactions, but it has not been applied to the screening of drug combinations. In this paper, we proposed a deep learning model based on graph neural networks and attention mechanism to identify drug combinations that can effectively inhibit the viability of specific cancer cells. The feature embeddings of drug molecule structure and gene expression profiles were taken as input to multi-layer feedforward neural network to identify the synergistic drug combinations. We compared DeepDDS with classical machine learning methods and other deep learning-based methods on benchmark data set, and the leave-one-out experimental results showed that DeepDDS achieved better performance than competitive methods. Also, on an independent test set released by well-known pharmaceutical enterprise AstraZeneca, DeepDDS was superior to competitive methods by more than 16\% predictive precision. Furthermore, we explored the interpretability of the graph attention network, and found the correlation matrix of atomic features revealed important chemical substructures of drugs. We believed that DeepDDS is an effective tool that prioritized synergistic drug combinations for further wet-lab experiment validation.

The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises from the immense diversity of TCR repository. However, TCR diversity poses a significant challenge on accurately predicting antigen-TCR bindings. In this study, we introduce a lightweight masked language model, termed tcrLM, to address this challenge. Our approach involves randomly masking segments of TCR sequences and training tcrLM to infer the masked segments, thereby enabling the extraction of expressive features from TCR sequences. To further enhance robustness, we incorporate virtual adversarial training into tcrLM. We construct the largest TCR CDR3 sequence set with more than 100 million distinct sequences, and pretrain tcrLM on these sequences. The pre-trained encoder is subsequently applied to predict TCR-antigen binding specificity. We evaluate model performance on three test datasets: independent, external, and COVID-19 test set. The results demonstrate that tcrLM not only surpasses existing TCR-antigen binding prediction methods, but also outperforms other mainstream protein language models. More interestingly, tcrLM effectively captures the biochemical properties and positional preference of amino acids within TCR sequences. Additionally, the predicted TCR-neoantigen binding scores indicates the immunotherapy responses and clinical outcomes in a melanoma cohort. These findings demonstrate the potential of tcrLM in predicting TCR-antigen binding specificity, with significant implications for advancing immunotherapy and personalized medicine.

During the curing process of composites, the temperature history heavily determines the evolutions of the field of degree of cure as well as the residual stress, which will further influence the mechanical properties of composite, thus it is important to simulate the real temperature history to optimize the curing process of composites. Since thermochemical analysis using Finite Element (FE) simulations requires heavy computational loads and data-driven approaches suffer from the complexity of highdimensional mapping. This paper proposes a Residual Fourier Neural Operator (ResFNO) to establish the direct high-dimensional mapping from any given cure cycle to the corresponding temperature histories. By integrating domain knowledge into a time-resolution independent parameterized neural network, the mapping between cure cycles to temperature histories can be learned using limited number of labelled data. Besides, a novel Fourier residual mapping is designed based on mode decomposition to accelerate the training and boost the performance significantly. Several cases are carried out to evaluate the superior performance and generalizability of the proposed method comprehensively.

Let $R$ be a ring with identity and $J(R)$ be its Jacobson radical. Assume that $a\in R$ is $(b,c)$-invertible and $j_a,j_b,j_c\in J(R)$. This paper provides necessary and sufficient conditions for $a+j_a$ to be $(b+j_b,c+j_c)$-invertible. As an application, corresponding results on generalized inverses of dual matrices are derived.

We introduce an efficient method for learning linear models from uncertain data, where uncertainty is represented as a set of possible variations in the data, leading to predictive multiplicity. Our approach leverages abstract interpretation and zonotopes, a type of convex polytope, to compactly represent these dataset variations, enabling the symbolic execution of gradient descent on all possible worlds simultaneously. We develop techniques to ensure that this process converges to a fixed point and derive closed-form solutions for this fixed point. Our method provides sound over-approximations of all possible optimal models and viable prediction ranges. We demonstrate the effectiveness of our approach through theoretical and empirical analysis, highlighting its potential to reason about model and prediction uncertainty due to data quality issues in training data.

The qubit mapping problem (QMP) focuses on the mapping and routing of qubits in quantum circuits so that the strict connectivity constraints imposed by near-term quantum hardware are satisfied. QMP is a pivotal task for quantum circuit compilation and its decision version is NP-complete. In this study, we present an effective approach called Adaptive Divided-And-Conqure (ADAC) to solve QMP. Our ADAC algorithm adaptively partitions circuits by leveraging subgraph isomorphism and ensuring coherence among subcircuits. Additionally, we employ a heuristic approach to optimise the routing algorithm during circuit partitioning. Through extensive experiments across various NISQ devices and circuit benchmarks, we demonstrate that the proposed ADAC algorithm outperforms the state-of-the-art method. Specifically, ADAC shows an improvement of nearly 50\% on the IBM Tokyo architecture. Furthermore, ADAC exhibits an improvement of around 18\% on pseudo-realistic circuits implemented on grid-like architectures with larger qubit numbers, where the pseudo-realistic circuits are constructed based on the characteristics of widely existing realistic circuits, aiming to investigate the applicability of ADAC. Our findings highlight the potential of ADAC in quantum circuit compilation and the deployment of practical applications on near-term quantum hardware platforms.

The equation of state (EoS) for neutron stars is a crucial topic in astrophysics, nuclear physics, and quantum chromodynamics (QCD), influencing their structure, stability, and observable properties. This review classifies EoS models into hadronic matter, hybrid, and quark matter models, analyzing their assumptions, predictions, and constraints. While hadronic models characterize nucleonic matter, potentially including contributions from hyperons or mesons, hybrid models introduce phase transitions to quark matter, and quark models hypothesize the presence of deconfined quark matter cores or entirely quark-composed stars. By synthesizing results from recent theoretical and observational studies, this review aims to offer a comprehensive understanding of the methodologies used in constructing neutron star EoS, their implications, and future directions.

The advancement of single-cell sequencing technology has promoted the generation of a large amount of single-cell transcriptional profiles, providing unprecedented opportunities to identify drug-resistant cell subpopulations within a tumor. However, few studies have focused on drug response prediction at single-cell level, and their performance remains suboptimal. This paper proposed scAdaDrug, a novel multi-source domain adaptation model powered by adaptive importance-aware representation learning to predict drug response of individual cells. We used a shared encoder to extract domain-invariant features related to drug response from multiple source domains by utilizing adversarial domain adaptation. Particularly, we introduced a plug-and-play module to generate importance-aware and mutually independent weights, which could adaptively modulate the latent representation of each sample in element-wise manner between source and target domains. Extensive experimental results showed that our model achieved state-of-the-art performance in predicting drug response on multiple independent datasets, including single-cell datasets derived from both cell lines and patient-derived xenografts (PDX) models, as well as clinical tumor patient cohorts. Moreover, the ablation experiments demonstrated our model effectively captured the underlying patterns determining drug response from multiple source domains.

Attributed graph clustering is one of the most fundamental tasks among graph learning field, the goal of which is to group nodes with similar representations into the same cluster without human annotations. Recent studies based on graph contrastive learning method have achieved remarkable results when exploit graph-structured data. However, most existing methods 1) do not directly address the clustering task, since the representation learning and clustering process are separated; 2) depend too much on data augmentation, which greatly limits the capability of contrastive learning; 3) ignore the contrastive message for clustering tasks, which adversely degenerate the clustering results. In this paper, we propose a Neighborhood Contrast Framework for Attributed Graph Clustering, namely NCAGC, seeking for conquering the aforementioned limitations. Specifically, by leveraging the Neighborhood Contrast Module, the representation of neighbor nodes will be 'push closer' and become clustering-oriented with the neighborhood contrast loss. Moreover, a Contrastive Self-Expression Module is built by minimizing the node representation before and after the self-expression layer to constraint the learning of self-expression matrix. All the modules of NCAGC are optimized in a unified framework, so the learned node representation contains clustering-oriented messages. Extensive experimental results on four attributed graph datasets demonstrate the promising performance of NCAGC compared with 16 state-of-the-art clustering methods. The code is available at this https URL

Target localization based on frequency diverse array (FDA) radar has lately garnered significant research interest. A linear frequency offset (FO) across FDA antennas yields a range-angle dependent beampattern that allows for joint estimation of range and direction-of-arrival (DoA). Prior works on FDA largely focus on the one-dimensional linear array to estimate only azimuth angle and range while ignoring the elevation and Doppler velocity. However, in many applications, the latter two parameters are also essential for target localization. Further, there is also an interest in radar systems that employ fewer measurements in temporal, Doppler, or spatial signal domains. We address these multiple challenges by proposing a co-prime L-shaped FDA, wherein co-prime FOs are applied across the elements of L-shaped co-prime array and each element transmits at a non-uniform co-prime pulse repetition interval (C$^3$ or C-Cube). This co-pulsing FDA yields significantly large degrees-of-freedom (DoFs) for target localization in the range-azimuth-elevation-Doppler domain while also reducing the time-on-target and transmit spectral usage. By exploiting these DoFs, we develop C-Cube auto-pairing (CCing) algorithm, in which all the parameters are ipso facto paired during a joint estimation. We show that C-Cube FDA requires at least $2\sqrt{Q+1}-1$ antenna elements and $2\sqrt{Q+1}-1$ pulses to guarantee perfect recovery of $Q$ targets as against $Q+1$ elements and $Q+1$ pulses required by both L-shaped uniform linear array and L-shaped linear FO FDA with uniform pulsing. We derive Cramér-Rao bounds (CRBs) for joint angle-range-Doppler estimation errors for C-Cube FDA and provide the conditions under which the CRBs exist. Numerical experiments with our CCing algorithm show great performance improvements in parameter recovery.