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Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

相關內容

 3D是英文“Three Dimensions”的簡稱,中文是指三維、三個維度、三個坐標,即有長、有寬、有高,換句話說,就是立體的,是相對于只有長和寬的平面(2D)而言。

We revisit and slightly modify the proof of the Gaussian Hanson-Wright inequality where we keep track of the absolute constant in its formulation.

Conventional Unsupervised Domain Adaptation (UDA) strives to minimize distribution discrepancy between domains, which neglects to harness rich semantics from data and struggles to handle complex domain shifts. A promising technique is to leverage the knowledge of large-scale pre-trained vision-language models for more guided adaptation. Despite some endeavors, current methods often learn textual prompts to embed domain semantics for source and target domains separately and perform classification within each domain, limiting cross-domain knowledge transfer. Moreover, prompting only the language branch lacks flexibility to adapt both modalities dynamically. To bridge this gap, we propose Domain-Agnostic Mutual Prompting (DAMP) to exploit domain-invariant semantics by mutually aligning visual and textual embeddings. Specifically, the image contextual information is utilized to prompt the language branch in a domain-agnostic and instance-conditioned way. Meanwhile, visual prompts are imposed based on the domain-agnostic textual prompt to elicit domain-invariant visual embeddings. These two branches of prompts are learned mutually with a cross-attention module and regularized with a semantic-consistency loss and an instance-discrimination contrastive loss. Experiments on three UDA benchmarks demonstrate the superiority of DAMP over state-of-the-art approaches.

Community Question Answering (CQA) in different domains is growing at a large scale because of the availability of several platforms and huge shareable information among users. With the rapid growth of such online platforms, a massive amount of archived data makes it difficult for moderators to retrieve possible duplicates for a new question and identify and confirm existing question pairs as duplicates at the right time. This problem is even more critical in CQAs corresponding to large software systems like askubuntu where moderators need to be experts to comprehend something as a duplicate. Note that the prime challenge in such CQA platforms is that the moderators are themselves experts and are therefore usually extremely busy with their time being extraordinarily expensive. To facilitate the task of the moderators, in this work, we have tackled two significant issues for the askubuntu CQA platform: (1) retrieval of duplicate questions given a new question and (2) duplicate question confirmation time prediction. In the first task, we focus on retrieving duplicate questions from a question pool for a particular newly posted question. In the second task, we solve a regression problem to rank a pair of questions that could potentially take a long time to get confirmed as duplicates. For duplicate question retrieval, we propose a Siamese neural network based approach by exploiting both text and network-based features, which outperforms several state-of-the-art baseline techniques. Our method outperforms DupPredictor and DUPE by 5% and 7% respectively. For duplicate confirmation time prediction, we have used both the standard machine learning models and neural network along with the text and graph-based features. We obtain Spearman's rank correlation of 0.20 and 0.213 (statistically significant) for text and graph based features respectively.

Nowadays, Internet of Things platforms are being deployed in a wide range of application domains. Some of these include use cases with security requirements, where the data generated by an IoT node is the basis for making safety-critical or liability-critical decisions at system level. The challenge is to develop a solution for data exchange while proving and verifying the authenticity of the data from end-to-end. In line with this objective, this paper proposes a novel solution with the proper protocols to provide Trust in Data, making use of two Roots of Trust that are the IOTA Distributed Ledger Technology and the Trusted Platform Module. The paper presents the design of the proposed solution and discusses the key design aspects and relevant trade-offs. The paper concludes with a Proof-of-Concept implementation and an experimental evaluation to confirm its feasibility and to assess the achievable performance.

We consider the fundamental problem of decomposing a large-scale approximate nearest neighbor search (ANNS) problem into smaller sub-problems. The goal is to partition the input points into neighborhood-preserving shards, so that the nearest neighbors of any point are contained in only a few shards. When a query arrives, a routing algorithm is used to identify the shards which should be searched for its nearest neighbors. This approach forms the backbone of distributed ANNS, where the dataset is so large that it must be split across multiple machines. In this paper, we design simple and highly efficient routing methods, and prove strong theoretical guarantees on their performance. A crucial characteristic of our routing algorithms is that they are inherently modular, and can be used with any partitioning method. This addresses a key drawback of prior approaches, where the routing algorithms are inextricably linked to their associated partitioning method. In particular, our new routing methods enable the use of balanced graph partitioning, which is a high-quality partitioning method without a naturally associated routing algorithm. Thus, we provide the first methods for routing using balanced graph partitioning that are extremely fast to train, admit low latency, and achieve high recall. We provide a comprehensive evaluation of our full partitioning and routing pipeline on billion-scale datasets, where it outperforms existing scalable partitioning methods by significant margins, achieving up to 2.14x higher QPS at 90% recall$@10$ than the best competitor.

Many of the world's workers rely on digital platforms for their income. In Venezuela, a nation grappling with extreme inflation and where most of the workforce is self-employed, data production platforms for machine learning have emerged as a viable opportunity for many to earn a flexible income in US dollars. Platform workers are deeply interconnected within a vast network of firms and entities that act as intermediaries for wage payments in digital currencies and its subsequent conversion to the national currency, the bolivar. Past research on embeddedness has noted that being intertwined in multi-tiered socioeconomic networks of companies and individuals can offer significant rewards to social participants, while also connoting a particular set of limitations. This paper furnishes qualitative evidence regarding how this deep embeddedness impacts platform workers in Venezuela. Given the backdrop of a national crisis and rampant hyperinflation, the perks of receiving wages through various financial platforms include access to a more stable currency and the ability to save and invest outside the national financial system. However, relying on numerous digital and local intermediaries often diminishes income due to transaction fees. Moreover, this introduces heightened financial risks, particularly due to the unpredictable nature of cryptocurrencies as an investment. The over-reliance on external financial platforms erodes worker autonomy through power dynamics that lean in favor of the platforms that set the transaction rules and prices. These findings present a multifaceted perspective on deep embeddedness in platform labor, highlighting how the rewards of financial intermediation often come at a substantial cost for the workers in unstable situations, who are saddled with escalating financial risks.

While Reinforcement Learning (RL) achieves tremendous success in sequential decision-making problems of many domains, it still faces key challenges of data inefficiency and the lack of interpretability. Interestingly, many researchers have leveraged insights from the causality literature recently, bringing forth flourishing works to unify the merits of causality and address well the challenges from RL. As such, it is of great necessity and significance to collate these Causal Reinforcement Learning (CRL) works, offer a review of CRL methods, and investigate the potential functionality from causality toward RL. In particular, we divide existing CRL approaches into two categories according to whether their causality-based information is given in advance or not. We further analyze each category in terms of the formalization of different models, ranging from the Markov Decision Process (MDP), Partially Observed Markov Decision Process (POMDP), Multi-Arm Bandits (MAB), and Dynamic Treatment Regime (DTR). Moreover, we summarize the evaluation matrices and open sources while we discuss emerging applications, along with promising prospects for the future development of CRL.

Invariant risk minimization (IRM) has recently emerged as a promising alternative for domain generalization. Nevertheless, the loss function is difficult to optimize for nonlinear classifiers and the original optimization objective could fail when pseudo-invariant features and geometric skews exist. Inspired by IRM, in this paper we propose a novel formulation for domain generalization, dubbed invariant information bottleneck (IIB). IIB aims at minimizing invariant risks for nonlinear classifiers and simultaneously mitigating the impact of pseudo-invariant features and geometric skews. Specifically, we first present a novel formulation for invariant causal prediction via mutual information. Then we adopt the variational formulation of the mutual information to develop a tractable loss function for nonlinear classifiers. To overcome the failure modes of IRM, we propose to minimize the mutual information between the inputs and the corresponding representations. IIB significantly outperforms IRM on synthetic datasets, where the pseudo-invariant features and geometric skews occur, showing the effectiveness of proposed formulation in overcoming failure modes of IRM. Furthermore, experiments on DomainBed show that IIB outperforms $13$ baselines by $0.9\%$ on average across $7$ real datasets.

The military is investigating methods to improve communication and agility in its multi-domain operations (MDO). Nascent popularity of Internet of Things (IoT) has gained traction in public and government domains. Its usage in MDO may revolutionize future battlefields and may enable strategic advantage. While this technology offers leverage to military capabilities, it comes with challenges where one is the uncertainty and associated risk. A key question is how can these uncertainties be addressed. Recently published studies proposed information camouflage to transform information from one data domain to another. As this is comparatively a new approach, we investigate challenges of such transformations and how these associated uncertainties can be detected and addressed, specifically unknown-unknowns to improve decision-making.

Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.

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