Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of efficacy and toxicity according to etoposide and cytarabine dosing in BEAM conditioning followed by autologous stem cell transplantation in Hodgkin lymphoma

Abstract The combination of carmustine, etoposide, cytarabine, and melphalan (BEAM) followed by autologous stem cell transplantation (ASCT) is a commonly used intensification regimen for patients with Hodgkin lymphoma. As etoposide and cytarabine dosing are not defined, we conducted a retrospective, multicenter study, to compare efficacy and toxicity in 130 patients with Hodgkin lymphoma receiving etoposide and cytarabine at either 200 mg/m2/d (n = 50), 400 mg/m2/d (n = 35), or etoposide 200 mg/m2/d and cytarabine 400 mg/m2/d (n = 45). Progression-free survival and overall survival were not associated with the intensity of conditioning. Increased conditioning intensity was associated with longer duration of thrombocytopenia, a higher number of transfused RBC and platelet units and a higher frequency of mucositis, but serious adverse events or infectious complications were not increased. The intensity of BEAM regimen was not associated with survival but with the rate of cytopenia and mucositis advocating for the use of lower dosing in frail patients.
Cross-Video Contextual Knowledge Exploration and Exploitation for Ambiguity Reduction in Weakly Supervised Temporal Action Localization

Weakly supervised temporal action localization (WSTAL) aims to localize actions in untrimmed videos using video-level labels. Despite recent advances, existing approaches mainly follow a localization-by-classification pipeline, generally processing each segment individually, thereby exploiting only limited contextual information. As a result, the model will lack a comprehensive understanding (e.g. appearance and temporal structure) of various action patterns, leading to ambiguity in classification learning and temporal localization. Our work addresses this from a novel perspective, by exploring and exploiting the cross-video contextual knowledge within the dataset to recover the dataset-level semantic structure of action instances via weak labels only, thereby indirectly improving the holistic understanding of fine-grained action patterns and alleviating the aforementioned ambiguities. Specifically, an end-to-end framework is proposed, including a Robust Memory-Guided Contrastive Learning (RMGCL) module and a Global Knowledge Summarization and Aggregation (GKSA) module. First, the RMGCL module explores the contrast and consistency of cross-video action features, assisting in learning more structured and compact embedding space, thus reducing ambiguity in classification learning. Further, the GKSA module is used to efficiently summarize and propagate the cross-video representative action knowledge in a learnable manner to promote holistic action patterns understanding, which in turn allows the generation of high-confidence pseudo-labels for self-learning, thus alleviating ambiguity in temporal localization. Extensive experiments on THUMOS14, ActivityNet1.3, and FineAction demonstrate that our method outperforms the state-of-the-art methods, and can be easily plugged into other WSTAL methods.
Ground-to-Aerial Person Search: Benchmark Dataset and Approach

In this work, we construct a large-scale dataset for Ground-to-Aerial Person Search, named G2APS, which contains 31,770 images of 260,559 annotated bounding boxes for 2,644 identities appearing in both of the UAVs and ground surveillance cameras. To our knowledge, this is the first dataset for cross-platform intelligent surveillance applications, where the UAVs could work as a powerful complement for the ground surveillance cameras. To more realistically simulate the actual cross-platform Ground-to-Aerial surveillance scenarios, the surveillance cameras are fixed about 2 meters above the ground, while the UAVs capture videos of persons at different location, with a variety of view-angles, flight attitudes and flight modes. Therefore, the dataset has the following unique characteristics: 1) drastic view-angle changes between query and gallery person images from cross-platform cameras; 2) diverse resolutions, poses and views of the person images under 9 rich real-world scenarios. On basis of the G2APS benchmark dataset, we demonstrate detailed analysis about current two-step and end-to-end person search methods, and further propose a simple yet effective knowledge distillation scheme on the head of the ReID network, which achieves state-of-the-art performances on both of the G2APS and the previous two public person search datasets, i.e., PRW and CUHK-SYSU. The dataset and source code available on https://github.com/yqc123456/HKD_for_person_search.
Gaussian Process-based Bayesian Quantum Characterization

We present a Bayesian quantum characterization framework that takes into account uncertainties from both experimental data and the dynamical modeling of the experiment. We demonstrate that ignoring dynamical model uncertainty may lead to predictions that are inconsistent with the uncertainty present in quantum data. A Bayesian framework is proposed and applied to characterize a tantalum-based transmon device at Lawrence Livermore National Laboratory. We demonstrate how modeling uncertainty can be represented by a Gaussian process within the Bayesian framework, and how this approach improves the predictive capability of Lindblad's master equations applied to the Ramsey measurement protocol.
kTrans: Knowledge-Aware Transformer for Binary Code Embedding

Binary Code Embedding (BCE) has important applications in various reverse engineering tasks such as binary code similarity detection, type recovery, control-flow recovery and data-flow analysis. Recent studies have shown that the Transformer model can comprehend the semantics of binary code to support downstream tasks. However, existing models overlooked the prior knowledge of assembly language. In this paper, we propose a novel Transformer-based approach, namely kTrans, to generate knowledge-aware binary code embedding. By feeding explicit knowledge as additional inputs to the Transformer, and fusing implicit knowledge with a novel pre-training task, kTrans provides a new perspective to incorporating domain knowledge into a Transformer framework. We inspect the generated embeddings with outlier detection and visualization, and also apply kTrans to 3 downstream tasks: Binary Code Similarity Detection (BCSD), Function Type Recovery (FTR) and Indirect Call Recognition (ICR). Evaluation results show that kTrans can generate high-quality binary code embeddings, and outperforms state-of-the-art (SOTA) approaches on downstream tasks by 5.2%, 6.8%, and 12.6% respectively. kTrans is publicly available at: https://github.com/Learner0x5a/kTrans-release
The motility-matrix production switch in Bacillus subtilis—a modeling perspective

ABSTRACT Phenotype switching can be triggered by external stimuli and by intrinsic stochasticity. Here, we focus on the motility-matrix production switch in Bacillus subtilis. We use modeling to describe the SinR-SlrR bistable switch and its regulation by SinI and to distinguish different sources of stochasticity. Our simulations indicate that intrinsic fluctuations in the synthesis of SinI are insufficient to drive spontaneous switching and suggest that switching is triggered by upstream noise from the Spo0A phosphorelay. IMPORTANCE The switch from motility to matrix production is the first step toward biofilm formation and, thus, to multicellular behavior in Bacillus subtilis. The transition is governed by a bistable switch based on the interplay of the regulators SinR and SlrR, while SinI transmits upstream signals to that switch. Quantitative modeling can be used to study the switching dynamics. Here, we build such a model step by step to describe the dynamics of the switch and its regulation and to study how spontaneous switching is triggered by upstream noise from the Spo0A phosphorelay. The switch from motility to matrix production is the first step toward biofilm formation and, thus, to multicellular behavior in Bacillus subtilis. The transition is governed by a bistable switch based on the interplay of the regulators SinR and SlrR, while SinI transmits upstream signals to that switch. Quantitative modeling can be used to study the switching dynamics. Here, we build such a model step by step to describe the dynamics of the switch and its regulation and to study how spontaneous switching is triggered by upstream noise from the Spo0A phosphorelay.
Simulation of tumor ablation in hyperthermia cancer treatment: A parametric study

A holistic simulation framework is established on magnetic hyperthermia modeling to solve the treatment process of tumor, which is surrounded by a healthy tissue block. The interstitial tissue fluid, MNP distribution, temperature profile, and nanofluids are involved in the simulation. Study evaluates the cancer treatment efficacy by cumulative-equivalent-minutes-at-43 centigrade (CEM43), a widely accepted thermal dose coming from the cell death curve. Results are separated into the conditions of with or without gravity effect in the computational domain, where two baseline case are investigated and compared. An optimal treatment time 46.55 min happens in the baseline case without gravity, but the situation deteriorates with gravity effect where the time for totally killing tumor cells prolongs 36.11% and meanwhile causing 21.32% ablation in healthy tissue. For the cases without gravity, parameter study of Lewis number and Heat source number are conducted and the variation of optimal treatment time are both fitting to the inverse functions. For the case considering the gravity, parameters Buoyancy ratio and Darcy ratio are investigated and their influence on totally killing tumor cells and the injury on healthy tissue are matching with the parabolic functions. The results are beneficial to the prediction of various conditions, and provides useful guide to the magnetic hyperthermia treatment.
Disentanglement Learning via Topology

We propose TopDis (Topological Disentanglement), a method for learning disentangled representations via adding multi-scale topological loss term. Disentanglement is a crucial property of data representations substantial for the explainability and robustness of deep learning models and a step towards high-level cognition. The state-of-the-art method based on VAE minimizes the total correlation of the joint distribution of latent variables. We take a different perspective on disentanglement by analyzing topological properties of data manifolds. In particular, we optimize the topological similarity for data manifolds traversals. To the best of our knowledge, our paper is the first one to propose a differentiable topological loss for disentanglement. Our experiments have shown that the proposed topological loss improves disentanglement scores such as MIG, FactorVAE score, SAP score and DCI disentanglement score with respect to state-of-the-art results. Our method works in an unsupervised manner, permitting to apply it for problems without labeled factors of variation. Additionally, we show how to use the proposed topological loss to find disentangled directions in a trained GAN.
BaDExpert: Extracting Backdoor Functionality for Accurate Backdoor Input Detection

We present a novel defense, against backdoor attacks on Deep Neural Networks (DNNs), wherein adversaries covertly implant malicious behaviors (backdoors) into DNNs. Our defense falls within the category of post-development defenses that operate independently of how the model was generated. The proposed defense is built upon a novel reverse engineering approach that can directly extract backdoor functionality of a given backdoored model to a backdoor expert model. The approach is straightforward -- finetuning the backdoored model over a small set of intentionally mislabeled clean samples, such that it unlearns the normal functionality while still preserving the backdoor functionality, and thus resulting in a model (dubbed a backdoor expert model) that can only recognize backdoor inputs. Based on the extracted backdoor expert model, we show the feasibility of devising highly accurate backdoor input detectors that filter out the backdoor inputs during model inference. Further augmented by an ensemble strategy with a finetuned auxiliary model, our defense, BaDExpert (Backdoor Input Detection with Backdoor Expert), effectively mitigates 17 SOTA backdoor attacks while minimally impacting clean utility. The effectiveness of BaDExpert has been verified on multiple datasets (CIFAR10, GTSRB and ImageNet) across various model architectures (ResNet, VGG, MobileNetV2 and Vision Transformer).
Explicit separations between randomized and deterministic Number-on-Forehead communication

We study the power of randomness in the Number-on-Forehead (NOF) model in communication complexity. We construct an explicit 3-player function $f:[N]^3 \to \{0,1\}$, such that: (i) there exist a randomized NOF protocol computing it that sends a constant number of bits; but (ii) any deterministic or nondeterministic NOF protocol computing it requires sending about $(\log N)^{1/3}$ many bits. This exponentially improves upon the previously best-known such separation. At the core of our proof is an extension of a recent result of the first and third authors on sets of integers without 3-term arithmetic progressions into a non-arithmetic setting.
Masked Feature Modelling: Feature Masking for the Unsupervised Pre-training of a Graph Attention Network Block for Bottom-up Video Event Recognition

In this paper, we introduce Masked Feature Modelling (MFM), a novel approach for the unsupervised pre-training of a Graph Attention Network (GAT) block. MFM utilizes a pretrained Visual Tokenizer to reconstruct masked features of objects within a video, leveraging the MiniKinetics dataset. We then incorporate the pre-trained GAT block into a state-of-the-art bottom-up supervised video-event recognition architecture, ViGAT, to improve the model's starting point and overall accuracy. Experimental evaluations on the YLI-MED dataset demonstrate the effectiveness of MFM in improving event recognition performance.
Machine Learning Small Molecule Properties in Drug Discovery

Machine learning (ML) is a promising approach for predicting small molecule properties in drug discovery. Here, we provide a comprehensive overview of various ML methods introduced for this purpose in recent years. We review a wide range of properties, including binding affinities, solubility, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity). We discuss existing popular datasets and molecular descriptors and embeddings, such as chemical fingerprints and graph-based neural networks. We highlight also challenges of predicting and optimizing multiple properties during hit-to-lead and lead optimization stages of drug discovery and explore briefly possible multi-objective optimization techniques that can be used to balance diverse properties while optimizing lead candidates. Finally, techniques to provide an understanding of model predictions, especially for critical decision-making in drug discovery are assessed. Overall, this review provides insights into the landscape of ML models for small molecule property predictions in drug discovery. So far, there are multiple diverse approaches, but their performances are often comparable. Neural networks, while more flexible, do not always outperform simpler models. This shows that the availability of high-quality training data remains crucial for training accurate models and there is a need for standardized benchmarks, additional performance metrics, and best practices to enable richer comparisons between the different techniques and models that can shed a better light on the differences between the many techniques.
ARF-Plus: Controlling Perceptual Factors in Artistic Radiance Fields for 3D Scene Stylization

The radiance fields style transfer is an emerging field that has recently gained popularity as a means of 3D scene stylization, thanks to the outstanding performance of neural radiance fields in 3D reconstruction and view synthesis. We highlight a research gap in radiance fields style transfer, the lack of sufficient perceptual controllability, motivated by the existing concept in the 2D image style transfer. In this paper, we present ARF-Plus, a 3D neural style transfer framework offering manageable control over perceptual factors, to systematically explore the perceptual controllability in 3D scene stylization. Four distinct types of controls - color preservation control, (style pattern) scale control, spatial (selective stylization area) control, and depth enhancement control - are proposed and integrated into this framework. Results from real-world datasets, both quantitative and qualitative, show that the four types of controls in our ARF-Plus framework successfully accomplish their corresponding perceptual controls when stylizing 3D scenes. These techniques work well for individual style inputs as well as for the simultaneous application of multiple styles within a scene. This unlocks a realm of limitless possibilities, allowing customized modifications of stylization effects and flexible merging of the strengths of different styles, ultimately enabling the creation of novel and eye-catching stylistic effects on 3D scenes.
A-PSRO: A Unified Strategy Learning Method with Advantage Function for Normal-form Games

Solving Nash equilibrium is the key challenge in normal-form games with large strategy spaces, where open-ended learning frameworks offer an efficient approach. In this work, we propose an innovative unified open-ended learning framework A-PSRO, i.e., Advantage Policy Space Response Oracle, as a comprehensive framework for both zero-sum and general-sum games. In particular, we introduce the advantage function as an enhanced evaluation metric for strategies, enabling a unified learning objective for agents engaged in normal-form games. We prove that the advantage function exhibits favorable properties and is connected with the Nash equilibrium, which can be used as an objective to guide agents to learn strategies efficiently. Our experiments reveal that A-PSRO achieves a considerable decrease in exploitability in zero-sum games and an escalation in rewards in general-sum games, significantly outperforming previous PSRO algorithms.
Evolutionary Dynamic Optimization Laboratory: A MATLAB Optimization Platform for Education and Experimentation in Dynamic Environments

Many real-world optimization problems possess dynamic characteristics. Evolutionary dynamic optimization algorithms (EDOAs) aim to tackle the challenges associated with dynamic optimization problems. Looking at the existing works, the results reported for a given EDOA can sometimes be considerably different. This issue occurs because the source codes of many EDOAs, which are usually very complex algorithms, have not been made publicly available. Indeed, the complexity of components and mechanisms used in many EDOAs makes their re-implementation error-prone. In this paper, to assist researchers in performing experiments and comparing their algorithms against several EDOAs, we develop an open-source MATLAB platform for EDOAs, called Evolutionary Dynamic Optimization LABoratory (EDOLAB). This platform also contains an education module that can be used for educational purposes. In the education module, the user can observe a) a 2-dimensional problem space and how its morphology changes after each environmental change, b) the behaviors of individuals over time, and c) how the EDOA reacts to environmental changes and tries to track the moving optimum. In addition to being useful for research and education purposes, EDOLAB can also be used by practitioners to solve their real-world problems. The current version of EDOLAB includes 25 EDOAs and three fully-parametric benchmark generators. The MATLAB source code for EDOLAB is publicly available and can be accessed from [https://github.com/EDOLAB-platform/EDOLAB-MATLAB].
DS4DH at #SMM4H 2023: Zero-Shot Adverse Drug Events Normalization using Sentence Transformers and Reciprocal-Rank Fusion

This paper outlines the performance evaluation of a system for adverse drug event normalization, developed by the Data Science for Digital Health (DS4DH) group for the Social Media Mining for Health Applications (SMM4H) 2023 shared task 5. Shared task 5 targeted the normalization of adverse drug event mentions in Twitter to standard concepts of the Medical Dictionary for Regulatory Activities terminology. Our system hinges on a two-stage approach: BERT fine-tuning for entity recognition, followed by zero-shot normalization using sentence transformers and reciprocal-rank fusion. The approach yielded a precision of 44.9%, recall of 40.5%, and an F1-score of 42.6%. It outperformed the median performance in shared task 5 by 10% and demonstrated the highest performance among all participants. These results substantiate the effectiveness of our approach and its potential application for adverse drug event normalization in the realm of social media text mining.
Vision Transformer Adapters for Generalizable Multitask Learning

We introduce the first multitasking vision transformer adapters that learn generalizable task affinities which can be applied to novel tasks and domains. Integrated into an off-the-shelf vision transformer backbone, our adapters can simultaneously solve multiple dense vision tasks in a parameter-efficient manner, unlike existing multitasking transformers that are parametrically expensive. In contrast to concurrent methods, we do not require retraining or fine-tuning whenever a new task or domain is added. We introduce a task-adapted attention mechanism within our adapter framework that combines gradient-based task similarities with attention-based ones. The learned task affinities generalize to the following settings: zero-shot task transfer, unsupervised domain adaptation, and generalization without fine-tuning to novel domains. We demonstrate that our approach outperforms not only the existing convolutional neural network-based multitasking methods but also the vision transformer-based ones. Our project page is at https://ivrl.github. io/VTAGML.
Mutual-Guided Dynamic Network for Image Fusion

Image fusion aims to generate a high-quality image from multiple images captured under varying conditions. The key problem of this task is to preserve complementary information while filtering out irrelevant information for the fused result. However, existing methods address this problem by leveraging static convolutional neural networks (CNNs), suffering two inherent limitations during feature extraction,i.e., being unable to handle spatial-variant contents and lacking guidance from multiple inputs. In this paper, we propose a novel mutual-guided dynamic network (MGDN) for image fusion, which allows for effective information utilization across different locations and inputs. Specifically, we design a mutual-guided dynamic filter (MGDF) for adaptive feature extraction, composed of a mutual-guided cross-attention (MGCA) module and a dynamic filter predictor, where the former incorporates additional guidance from different inputs and the latter generates spatial-variant kernels for different locations. In addition, we introduce a parallel feature fusion (PFF) module to effectively fuse local and global information of the extracted features. To further reduce the redundancy among the extracted features while simultaneously preserving their shared structural information, we devise a novel loss function that combines the minimization of normalized mutual information (NMI) with an estimated gradient mask. Experimental results on five benchmark datasets demonstrate that our proposed method outperforms existing methods on four image fusion tasks. The code and model are publicly available at: https://github.com/Guanys-dar/MGDN.