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Quantifying Cross-Attention Interaction in Transformers for Interpreting TCR-pMHC Binding
Li, Jiarui, Yin, Zixiang, Smith, Haley, Ding, Zhengming, Landry, Samuel J., Mettu, Ramgopal R.
CD8+ "killer" T cells and CD4+ "helper" T cells play a central role in the adaptive immune system by recognizing antigens presented by Major Histocompatibility Complex (pMHC) molecules via T Cell Receptors (TCRs). Modeling binding between T cells and the pMHC complex is fundamental to understanding basic mechanisms of human immune response as well as in developing therapies. While transformer-based models such as TULIP have achieved impressive performance in this domain, their black-box nature precludes interpretability and thus limits a deeper mechanistic understanding of T cell response. Most existing post-hoc explainable AI (xAI) methods are confined to encoder-only, co-attention, or model-specific architectures and cannot handle encoder-decoder transformers used in TCR-pMHC modeling. To address this gap, we propose Quantifying Cross-Attention Interaction (QCAI), a new post-hoc method designed to interpret the cross-attention mechanisms in transformer decoders. Quantitative evaluation is a challenge for XAI methods; we have compiled TCR-XAI, a benchmark consisting of 274 experimentally determined TCR-pMHC structures to serve as ground truth for binding. Using these structures we compute physical distances between relevant amino acid residues in the TCR-pMHC interaction region and evaluate how well our method and others estimate the importance of residues in this region across the dataset. We show that QCAI achieves state-of-the-art performance on both interpretability and prediction accuracy under the TCR-XAI benchmark. T cells play a pivotal role in the adaptive immune system by identifying and responding to antigenic proteins, both from pathogens such as viruses, bacteria and cancer cells (Joglekar & Li, 2021) as well as in the context of autoimmunity. The final and arguably most critical component of T cell response is binding between the peptide Major Histocompatibility Complex (pMHC) which contains an antigenic peptide bound to a MHC molecule and the surface receptor on T cells (TCR). The specificity of this interaction underpins T cell-mediated immunity and is an intense area of research in both the development of therapies and fundamental understanding of immune response. Understanding T cell response is the key to vaccines that confer long-lasting immunity, and can also enable effective personalized cancer therapies (Rojas et al., 2023; Poorebrahim et al., 2021). Transformer models have recently been use to analyze T cell immunity (Hudson et al., 2023; Li et al., 2023; Karthikeyan et al., 2023; Driessen et al., 2024; Cornwall et al., 2023).
AI reconstruction of European weather from the Euro-Atlantic regimes
Camilletti, A., Franch, G., Tomasi, E., Cristoforetti, M.
We present a non-linear AI-model designed to reconstruct monthly mean anomalies of the European temperature and precipitation based on the Euro-Atlantic Weather regimes (WR) indices. WR represent recurrent, quasi-stationary, and persistent states of the atmospheric circulation that exert considerable influence over the European weather, therefore offering an opportunity for sub-seasonal to seasonal forecasting. While much research has focused on studying the correlation and impacts of the WR on European weather, the estimation of ground-level climate variables, such as temperature and precipitation, from Euro-Atlantic WR remains largely unexplored and is currently limited to linear methods. The presented AI model can capture and introduce complex non-linearities in the relation between the WR indices, describing the state of the Euro-Atlantic atmospheric circulation and the corresponding surface temperature and precipitation anomalies in Europe. We discuss the AI-model performance in reconstructing the monthly mean two-meter temperature and total precipitation anomalies in the European winter and summer, also varying the number of WR used to describe the monthly atmospheric circulation. We assess the impact of errors on the WR indices in the reconstruction and show that a mean absolute relative error below 80% yields improved seasonal reconstruction compared to the ECMWF operational seasonal forecast system, SEAS5. As a demonstration of practical applicability, we evaluate the model using WR indices predicted by SEAS5, finding slightly better or comparable skill relative to the SEAS5 forecast itself. Our findings demonstrate that WR-based anomaly reconstruction, powered by AI tools, offers a promising pathway for sub-seasonal and seasonal forecasting.
LLM Meeting Decision Trees on Tabular Data
Ye, Hangting, Li, Jinmeng, Zhao, He, Guo, Dandan, Chang, Yi
Tabular data have been playing a vital role in diverse real-world fields, including healthcare, finance, etc. With the recent success of Large Language Models (LLMs), early explorations of extending LLMs to the domain of tabular data have been developed. Most of these LLM-based methods typically first serialize tabular data into natural language descriptions, and then tune LLMs or directly infer on these serialized data. However, these methods suffer from two key inherent issues: (i) data perspective: existing data serialization methods lack universal applicability for structured tabular data, and may pose privacy risks through direct textual exposure, and (ii) model perspective: LLM fine-tuning methods struggle with tabular data, and in-context learning scalability is bottle-necked by input length constraints (suitable for few-shot learning). This work explores a novel direction of integrating LLMs into tabular data throughough logical decision tree rules as intermediaries, proposes a decision tree enhancer with LLM-derived rule for tabular prediction, DeLTa. The proposed DeLTa avoids tabular data serialization, and can be applied to full data learning setting without LLM fine-tuning. Specifically, we leverage the reasoning ability of LLMs to redesign an improved rule given a set of decision tree rules. Furthermore, we provide a calibration method for original decision trees via new generated rule by LLM, which approximates the error correction vector to steer the original decision tree predictions in the direction of ``errors'' reducing. Finally, extensive experiments on diverse tabular benchmarks show that our method achieves state-of-the-art performance.
The emergence of sparse attention: impact of data distribution and benefits of repetition
Zucchet, Nicolas, d'Angelo, Francesco, Lampinen, Andrew K., Chan, Stephanie C. Y.
Emergence is a fascinating property of large language models and neural networks more broadly: as models scale and train for longer, they sometimes develop new abilities in sudden ways. Despite initial studies, we still lack a comprehensive understanding of how and when these abilities emerge. To address this gap, we study the emergence over training of sparse attention, a critical and frequently observed attention pattern in Transformers. By combining theoretical analysis of a toy model with empirical observations on small Transformers trained on a linear regression variant, we uncover the mechanics driving sparse attention emergence and reveal that emergence timing follows power laws based on task structure, architecture, and optimizer choice. We additionally find that repetition can greatly speed up emergence. Finally, we confirm these results on a well-studied in-context associative recall task. Our findings provide a simple, theoretically grounded framework for understanding how data distributions and model design influence the learning dynamics behind one form of emergence.
A Network Science Approach to Granular Time Series Segmentation
Kesiฤ, Ivana, Fortuna, Carolina, Mohorฤiฤ, Mihael, Bertalaniฤ, Blaลพ
Time series segmentation (TSS) is one of the time series (TS) analysis techniques, that has received considerably less attention compared to other TS related tasks. In recent years, deep learning architectures have been introduced for TSS, however their reliance on sliding windows limits segmentation granularity due to fixed window sizes and strides. To overcome these challenges, we propose a new more granular TSS approach that utilizes the Weighted Dual Perspective Visbility Graph (WDPVG) TS into a graph and combines it with a Graph Attention Network (GAT). By transforming TS into graphs, we are able to capture different structural aspects of the data that would otherwise remain hidden. By utilizing the representation learning capabilities of Graph Neural Networks, our method is able to effectively identify meaningful segments within the TS. To better understand the potential of our approach, we also experimented with different TS-to-graph transformations and compared their performance. Our contributions include: a) formulating the TSS as a node classification problem on graphs; b) conducting an extensive analysis of various TS-to-graph transformations applied to TSS using benchmark datasets from the TSSB repository; c) providing the first detailed study on utilizing GNNs for analyzing graph representations of TS in the context of TSS; d) demonstrating the effectiveness of our method, which achieves an average F1 score of 0.97 across 59 diverse TSS benchmark datasets; e) outperforming the seq2point baseline method by 0.05 in terms of F1 score; and f) reducing the required training data compared to the baseline methods.
Global Convergence for Average Reward Constrained MDPs with Primal-Dual Actor Critic Algorithm
Xu, Yang, Ganesh, Swetha, Mondal, Washim Uddin, Bai, Qinbo, Aggarwal, Vaneet
This paper investigates infinite-horizon average reward Constrained Markov Decision Processes (CMDPs) with general parametrization. We propose a Primal-Dual Natural Actor-Critic algorithm that adeptly manages constraints while ensuring a high convergence rate. In particular, our algorithm achieves global convergence and constraint violation rates of $\tilde{\mathcal{O}}(1/\sqrt{T})$ over a horizon of length $T$ when the mixing time, $ฯ_{\mathrm{mix}}$, is known to the learner. In absence of knowledge of $ฯ_{\mathrm{mix}}$, the achievable rates change to $\tilde{\mathcal{O}}(1/T^{0.5-ฮต})$ provided that $T \geq \tilde{\mathcal{O}}\left(ฯ_{\mathrm{mix}}^{2/ฮต}\right)$. Our results match the theoretical lower bound for Markov Decision Processes and establish a new benchmark in the theoretical exploration of average reward CMDPs.
Benchmarking data encoding methods in Quantum Machine Learning
Zang, Orlane, Barruรฉ, Grรฉgoire, Quertier, Tony
Quantum Machine Learning (QML) is a research area that focuses on the development of Machine Learning (ML) algorithms that can be executed by a quantum computer. Taking advantage of quantum phenomena such as quantum superposition and quantum entanglement, the incorporation of quantum computing in ML aims to leverage the power of the quantum computer to improve existing classical ML algorithms [1]. The process of manipulating the states of qubits by arbitrarily changing the gate parameters for the desired result is closely related to the training process of machine learning algorithms. For solving any specific problem, QML algorithms can be designed as a quantum circuit with a sequence of different quantum gate operations [2][3]. However, Noisy Intermediate Scale Quantum (NISQ) computers are limited in resources and subject to sources of error, such as noise induced by each quantum operation [4][5]. This makes it difficult to develop QML algorithms that perform as well as or better than conventional ones. Hence, developing QML algorithms with good performance, despite today's limited resources, has become a major challenge. To achieve this, it is important to look at several aspects of a QML task, such that the data encoding part. Quantum encoding involves the conversion of classical information into quantum states, enabling QML algorithms to operate efficiently.
C*: A Coverage Path Planning Algorithm for Unknown Environments using Rapidly Covering Graphs
Shen, Zongyuan, Wilson, James P., Gupta, Shalabh
The paper presents a novel sample-based algorithm, called C*, for real-time coverage path planning (CPP) of unknown environments. C* is built upon the concept of a Rapidly Covering Graph (RCG), which is incrementally constructed during robot navigation via progressive sampling of the search space. By using efficient sampling and pruning techniques, the RCG is constructed to be a minimum-sufficient graph, where its nodes and edges form the potential waypoints and segments of the coverage trajectory, respectively. The RCG tracks the coverage progress, generates the coverage trajectory and helps the robot to escape from the dead-end situations. To minimize coverage time, C* produces the desired back-and-forth coverage pattern, while adapting to the TSP-based optimal coverage of local isolated regions, called coverage holes, which are surrounded by obstacles and covered regions. It is analytically proven that C* provides complete coverage of unknown environments. The algorithmic simplicity and low computational complexity of C* make it easy to implement and suitable for real-time on-board applications. The performance of C* is validated by 1) extensive high-fidelity simulations and 2) laboratory experiments using an autonomous robot. C* yields near optimal trajectories, and a comparative evaluation with seven existing CPP methods demonstrates significant improvements in performance in terms of coverage time, number of turns, trajectory length, and overlap ratio, while preventing the formation of coverage holes. Finally, C* is comparatively evaluated on two different CPP applications using 1) energy-constrained robots and 2) multi-robot teams.
Revealing economic facts: LLMs know more than they say
Buckmann, Marcus, Nguyen, Quynh Anh, Hill, Edward
During training, generative large language models (LLMs) are exposed to vast amounts of information, including data relevant to economic modelling, such as geospatial statistics and firm-level financial metrics. If LLMs can effectively retrieve and utilise this knowledge, they could reduce dependence on external data sources that are time-consuming to access, clean, and merge, or that incur financial costs. Moreover, if LLMs accurately represent data, they could support downstream tasks like data imputation and outlier detection. In this study, we evaluate whether and how LLMs can be used for typical economic data processes. Not all knowledge within an LLM may be explicit and retrievable in natural language by prompting the model.
ConsDreamer: Advancing Multi-View Consistency for Zero-Shot Text-to-3D Generation
Zhou, Yuan, Jin, Shilong, Hua, Litao, Lv, Wanjun, Duan, Haoran, Han, Jungong
Abstract--Recent advances in zero-shot text-to-3D generation have revolutionised 3D content creation by enabling direct synthesis from textual descriptions. While state-of-the-art methods leverage 3D Gaussian Splatting with score distillation to enhance multi-view rendering through pre-trained text-to-image (T2I) models, they suffer from inherent prior view biases in T2I Models. These biases lead to inconsistent 3D generation, particularly manifesting as the multi-face Janus problem, where objects exhibit conflicting features across views. T o address this fundamental challenge, we propose ConsDreamer, a novel method that mitigates view bias by refining both the conditional and unconditional terms in the score distillation process: (1) a View Disentanglement Module (VDM) that eliminates viewpoint biases in conditional prompts by decoupling irrelevant view components and injecting precise view control; and (2) a similarity-based partial order loss that enforces geometric consistency in the unconditional term by aligning cosine similarities with azimuth relationships. Extensive experiments demonstrate that ConsDreamer can be seamlessly integrated into various 3D representations and score distillation paradigms, effectively mitigating the multi-face Janus problem. GENERA TION technology plays a crucial role in various fields such as innovative industrial design, game development, and virtual reality. In particular, zero-shot text-to-3D generation [1], [2], [3], [4], [5] aims to generate 3D content without 3D training data, enabling the conversion from concept to reality. However, zero-shot text-to-3D generation tasks [6], [7], [8], [9] are constrained by the inherent complexity of the wild world and the scarcity of 3D data, unlike text-to-image (T2I) tasks [10], [11]. From this perspective, generating high-quality 3D content from text is still a significant challenge.