A common step at the core of many RNA transcript assembly tools is to find a set of weighted paths that best explain the weights of a DAG. While such problems easily become NP-hard, scalable solvers exist only for a basic error-free version of this problem, namely minimally decomposing a network flow into weighted paths. The main result of this paper is to show that we can achieve speedups of two orders of magnitude also for path-finding problems in the realistic setting (i.e., the weights do not induce a flow). We obtain these by employing the safety information that is encoded in the graph structure inside Integer Linear Programming (ILP) solvers for these problems. We first characterize the paths that appear in all path covers of the DAG, generalizing a graph reduction commonly used in the error-free setting (e.g. by Kloster et al. [ALENEX~2018]). Secondly, following the work of Ma, Zheng and Kingsford [RECOMB 2021], we characterize the \emph{sequences} of arcs that appear in all path covers of the DAG. We experiment with a path-finding ILP model (least squares) and with a more recent and accurate one. We use a variety of datasets originally created by Shao and Kingsford [TCBB, 2017], as well as graphs built from sequencing reads by the state-of-the-art tool for long-read transcript discovery, IsoQuant [Prjibelski et al., Nat.~Biotechnology~2023]. The ILPs armed with safe paths or sequences exhibit significant speed-ups over the original ones. On graphs with a large width, average speed-ups are in the range $50-160\times$ in the latter ILP model and in the range $100-1000\times$ in the least squares model. Our scaling techniques apply to any ILP whose solution paths are a path cover of the arcs of the DAG. As such, they can become a scalable building block of practical RNA transcript assembly tools, avoiding heuristic trade-offs currently needed on complex graphs.
Object detection is a critical task in computer vision, with applications in various domains such as autonomous driving and urban scene monitoring. However, deep learning-based approaches often demand large volumes of annotated data, which are costly and difficult to acquire, particularly in complex and unpredictable real-world environments. This dependency significantly hampers the generalization capability of existing object detection techniques. To address this issue, we introduce a novel single-domain object detection generalization method, named GoDiff, which leverages a pre-trained model to enhance generalization in unseen domains. Central to our approach is the Pseudo Target Data Generation (PTDG) module, which employs a latent diffusion model to generate pseudo-target domain data that preserves source domain characteristics while introducing stylistic variations. By integrating this pseudo data with source domain data, we diversify the training dataset. Furthermore, we introduce a cross-style instance normalization technique to blend style features from different domains generated by the PTDG module, thereby increasing the detector's robustness. Experimental results demonstrate that our method not only enhances the generalization ability of existing detectors but also functions as a plug-and-play enhancement for other single-domain generalization methods, achieving state-of-the-art performance in autonomous driving scenarios.
Weighted Timed Games (WTG for short) are the most widely used model to describe controller synthesis problems involving real-time issues. Unfortunately, they are notoriously difficult, and undecidable in general. As a consequence, one-clock WTGs have attracted a lot of attention, especially because they are known to be decidable when only non-negative weights are allowed. However, when arbitrary weights are considered, despite several recent works, their decidability status was still unknown. In this paper, we solve this problem positively and show that the value function can be computed in exponential time (if weights are encoded in unary).
Large language models (LLMs) have transformed the way computers understand and process human language, but using them effectively across different organizations remains still difficult. When organizations work together to improve LLMs, they face several main challenges. First, organizations hesitate to share their valuable data with others. Second, competition between organizations creates trust problems during collaboration. Third, new privacy laws require organizations to be able to delete specific data when requested, which is especially difficult when multiple organizations are learning from shared data. Traditional federated learning approaches do not address these interconnected challenges, particularly in scenarios where participants cannot fully trust each other or the central aggregator. To overcome these limitations, we propose a hybrid blockchain-based federated learning framework that uniquely combines public and private blockchain architectures with multi-agent reinforcement learning. Our framework enables transparent sharing of model update through the public blockchain while protecting sensitive computations in private chains. Each organization operates as an intelligent agent, using Q-learning to optimize its participation strategy and resource allocation, thus aligning individual incentives with collective goals. Notably, we introduce an efficient unlearning mechanism based on Low-Rank Adaptation (LoRA) that enables selective removal of specific data contributions without compromising the model's overall performance. Through extensive experimentation on real-world datasets, we demonstrate that our framework effectively balances privacy protection, trust establishment, and regulatory compliance while maintaining high model performance.
We study the Dominating set problem and Independent Set Problem for dynamic graphs in the vertex-arrival model. We say that a dynamic algorithm for one of these problems is $k$-stable when it makes at most $k$ changes to its output independent set or dominating set upon the arrival of each vertex. We study trade-offs between the stability parameter $k$ of the algorithm and the approximation ratio it achieves. We obtain the following results. 1. We show that there is a constant $\varepsilon^*>0$ such that any dynamic $(1+\varepsilon^*)$-approximation algorithm the for Dominating set problem has stability parameter $\Omega(n)$, even for bipartite graphs of maximum degree 4. 2. We present algorithms with very small stability parameters for the Dominating set problem in the setting where the arrival degree of each vertex is upper bounded by $d$. In particular, we give a $1$-stable $(d+1)^2$-approximation algorithm, a $3$-stable $(9d/2)$-approximation algorithm, and an $O(d)$-stable $O(1)$-approximation algorithm. 3. We show that there is a constant $\varepsilon^*>0$ such that any dynamic $(1+\varepsilon^*)$-approximation algorithm for the Independent Set Problem has stability parameter $\Omega(n)$, even for bipartite graphs of maximum degree $3$. 4. Finally, we present a $2$-stable $O(d)$-approximation algorithm for the Independent Set Problem, in the setting where the average degree of the graph is upper bounded by some constant $d$ at all times. We extend this latter algorithm to the fully dynamic model where vertices can also be deleted, achieving a $6$-stable $O(d)$-approximation algorithm.
Despite their remarkable success, large language models (LLMs) have shown limited ability on applied tasks such as vulnerability detection. We investigate various prompting strategies for vulnerability detection and, as part of this exploration, propose a prompting strategy that integrates natural language descriptions of vulnerabilities with a contrastive chain-of-thought reasoning approach, augmented using contrastive samples from a synthetic dataset. Our study highlights the potential of LLMs to detect vulnerabilities by integrating natural language descriptions, contrastive reasoning, and synthetic examples into a comprehensive prompting framework. Our results show that this approach can enhance LLM understanding of vulnerabilities. On a high-quality vulnerability detection dataset such as SVEN, our prompting strategies can improve accuracies, F1-scores, and pairwise accuracies by 23%, 11%, and 14%, respectively.
Adversarial text attack research is useful for testing the robustness of NLP models, however, the rise of transformers has greatly increased the time required to test attacks. Especially when researchers do not have access to adequate resources (e.g. GPUs). This can hinder attack research, as modifying one example for an attack can require hundreds of queries to a model, especially for black-box attacks. Often these attacks remove one token at a time to find the ideal one to change, requiring $n$ queries (the length of the text) right away. We propose a more efficient selection method called BinarySelect which combines binary search and attack selection methods to greatly reduce the number of queries needed to find a token. We find that BinarySelect only needs $\text{log}_2(n) * 2$ queries to find the first token compared to $n$ queries. We also test BinarySelect in an attack setting against 5 classifiers across 3 datasets and find a viable tradeoff between number of queries saved and attack effectiveness. For example, on the Yelp dataset, the number of queries is reduced by 32% (72 less) with a drop in attack effectiveness of only 5 points. We believe that BinarySelect can help future researchers study adversarial attacks and black-box problems more efficiently and opens the door for researchers with access to less resources.
The success of AI models relies on the availability of large, diverse, and high-quality datasets, which can be challenging to obtain due to data scarcity, privacy concerns, and high costs. Synthetic data has emerged as a promising solution by generating artificial data that mimics real-world patterns. This paper provides an overview of synthetic data research, discussing its applications, challenges, and future directions. We present empirical evidence from prior art to demonstrate its effectiveness and highlight the importance of ensuring its factuality, fidelity, and unbiasedness. We emphasize the need for responsible use of synthetic data to build more powerful, inclusive, and trustworthy language models.
Answering questions that require reading texts in an image is challenging for current models. One key difficulty of this task is that rare, polysemous, and ambiguous words frequently appear in images, e.g., names of places, products, and sports teams. To overcome this difficulty, only resorting to pre-trained word embedding models is far from enough. A desired model should utilize the rich information in multiple modalities of the image to help understand the meaning of scene texts, e.g., the prominent text on a bottle is most likely to be the brand. Following this idea, we propose a novel VQA approach, Multi-Modal Graph Neural Network (MM-GNN). It first represents an image as a graph consisting of three sub-graphs, depicting visual, semantic, and numeric modalities respectively. Then, we introduce three aggregators which guide the message passing from one graph to another to utilize the contexts in various modalities, so as to refine the features of nodes. The updated nodes have better features for the downstream question answering module. Experimental evaluations show that our MM-GNN represents the scene texts better and obviously facilitates the performances on two VQA tasks that require reading scene texts.
Knowledge graph completion aims to predict missing relations between entities in a knowledge graph. While many different methods have been proposed, there is a lack of a unifying framework that would lead to state-of-the-art results. Here we develop PathCon, a knowledge graph completion method that harnesses four novel insights to outperform existing methods. PathCon predicts relations between a pair of entities by: (1) Considering the Relational Context of each entity by capturing the relation types adjacent to the entity and modeled through a novel edge-based message passing scheme; (2) Considering the Relational Paths capturing all paths between the two entities; And, (3) adaptively integrating the Relational Context and Relational Path through a learnable attention mechanism. Importantly, (4) in contrast to conventional node-based representations, PathCon represents context and path only using the relation types, which makes it applicable in an inductive setting. Experimental results on knowledge graph benchmarks as well as our newly proposed dataset show that PathCon outperforms state-of-the-art knowledge graph completion methods by a large margin. Finally, PathCon is able to provide interpretable explanations by identifying relations that provide the context and paths that are important for a given predicted relation.
Dynamic programming (DP) solves a variety of structured combinatorial problems by iteratively breaking them down into smaller subproblems. In spite of their versatility, DP algorithms are usually non-differentiable, which hampers their use as a layer in neural networks trained by backpropagation. To address this issue, we propose to smooth the max operator in the dynamic programming recursion, using a strongly convex regularizer. This allows to relax both the optimal value and solution of the original combinatorial problem, and turns a broad class of DP algorithms into differentiable operators. Theoretically, we provide a new probabilistic perspective on backpropagating through these DP operators, and relate them to inference in graphical models. We derive two particular instantiations of our framework, a smoothed Viterbi algorithm for sequence prediction and a smoothed DTW algorithm for time-series alignment. We showcase these instantiations on two structured prediction tasks and on structured and sparse attention for neural machine translation.