OpenRaiser/Intern-Atlas huggingface dataset:
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
Venue: arXiv cs.LG 2023
Year: 2023

The incredible capabilities of generative artificial intelligence models have inevitably led to their application in the domain of drug discovery. Within this domain, the vastness of chemical space motivates the development of more efficient methods for identifying regions with molecules that exhibit desired characteristics. In this work, we present a computationally efficient active learning methodology that requires evaluation of only a subset of the generated data in the constructed sample space to successfully align a generative model with respect to a specified objective. We demonstrate the applicability of this methodology to targeted molecular generation by fine-tuning a GPT-based molecular generator toward a protein with FDA-approved small-molecule inhibitors, c-Abl kinase. Remarkably, the model learns to generate molecules similar to the inhibitors without prior knowledge of their existence, and even reproduces two of them exactly. We also show that the methodology is effective for a protein without any commercially available small-molecule inhibitors, the HNH domain of the CRISPR-associated protein 9 (Cas9) enzyme. We believe that the inherent generality of this method ensures that it will remain applicable as the exciting field of in silico molecular generation evolves. To facilitate implementation and reproducibility, we have made all of our software available through the open-source ChemSpaceAL Python package.
SAGE: Structured Attribute Value Generation for Billion-Scale Product Catalogs
Venue: arXiv cs.IR 2023
Year: 2023

We introduce SAGE; a Generative LLM for inferring attribute values for products across world-wide e-Commerce catalogs. We introduce a novel formulation of the attribute-value prediction problem as a Seq2Seq summarization task, across languages, product types and target attributes. Our novel modeling approach lifts the restriction of predicting attribute values within a pre-specified set of choices, as well as, the requirement that the sought attribute values need to be explicitly mentioned in the text. SAGE can infer attribute values even when such values are mentioned implicitly using periphrastic language, or not-at-all-as is the case for common-sense defaults. Additionally, SAGE is capable of predicting whether an attribute is inapplicable for the product at hand, or non-obtainable from the available information. SAGE is the first method able to tackle all aspects of the attribute-value-prediction task as they arise in practical settings in e-Commerce catalogs. A comprehensive set of experiments demonstrates the effectiveness of the proposed approach, as well as, its superiority against state-of-the-art competing alternatives. Moreover, our experiments highlight SAGE's ability to tackle the task of predicting attribute values in zero-shot setting; thereby, opening up opportunities for significantly reducing the overall number of labeled examples required for training.
On Regularized Sparse Logistic Regression
Venue: arXiv cs.LG 2023
Year: 2023

Sparse logistic regression is for classification and feature selection simultaneously. Although many studies have been done to solve $\ell_1$-regularized logistic regression, there is no equivalently abundant work on solving sparse logistic regression with nonconvex regularization term. In this paper, we propose a unified framework to solve $\ell_1$-regularized logistic regression, which can be naturally extended to nonconvex regularization term, as long as certain requirement is satisfied. In addition, we also utilize a different line search criteria to guarantee monotone convergence for various regularization terms. Empirical experiments on binary classification tasks with real-world datasets demonstrate our proposed algorithms are capable of performing classification and feature selection effectively at a lower computational cost.
Knowledge-Guided Short-Context Action Anticipation in Human-Centric Videos
Venue: arXiv cs.CV 2023
Year: 2023

This work focuses on anticipating long-term human actions, particularly using short video segments, which can speed up editing workflows through improved suggestions while fostering creativity by suggesting narratives. To this end, we imbue a transformer network with a symbolic knowledge graph for action anticipation in video segments by boosting certain aspects of the transformer's attention mechanism at run-time. Demonstrated on two benchmark datasets, Breakfast and 50Salads, our approach outperforms current state-of-the-art methods for long-term action anticipation using short video context by up to 9%.
ChatMPC: Natural Language based MPC Personalization
Venue: arXiv cs.HC 2023
Year: 2023

We address the personalization of control systems, which is an attempt to adjust inherent safety and other essential control performance based on each user's personal preferences. A typical approach to personalization requires a substantial amount of user feedback and data collection, which may result in a burden on users. Moreover, it might be challenging to collect data in real-time. To overcome this drawback, we propose a natural language-based personalization, which places a comparatively lighter burden on users and enables the personalization system to collect data in real-time. In particular, we consider model predictive control (MPC) and introduce an approach that updates the control specification using chat within the MPC framework, namely ChatMPC. In the numerical experiment, we simulated an autonomous robot equipped with ChatMPC. The result shows that the specification in robot control is updated by providing natural language-based chats, which generate different behaviors.
GLAD: Content-aware Dynamic Graphs For Log Anomaly Detection
Venue: arXiv cs.LG 2023
Year: 2023

Logs play a crucial role in system monitoring and debugging by recording valuable system information, including events and states. Although various methods have been proposed to detect anomalies in log sequences, they often overlook the significance of considering relations among system components, such as services and users, which can be identified from log contents. Understanding these relations is vital for detecting anomalies and their underlying causes. To address this issue, we introduce GLAD, a Graph-based Log Anomaly Detection framework designed to detect relational anomalies in system logs. GLAD incorporates log semantics, relational patterns, and sequential patterns into a unified framework for anomaly detection. Specifically, GLAD first introduces a field extraction module that utilizes prompt-based few-shot learning to identify essential fields from log contents. Then GLAD constructs dynamic log graphs for sliding windows by interconnecting extracted fields and log events parsed from the log parser. These graphs represent events and fields as nodes and their relations as edges. Subsequently, GLAD utilizes a temporal-attentive graph edge anomaly detection model for identifying anomalous relations in these dynamic log graphs. This model employs a Graph Neural Network (GNN)-based encoder enhanced with transformers to capture content, structural and temporal features. We evaluate our proposed method on three datasets, and the results demonstrate the effectiveness of GLAD in detecting anomalies indicated by varying relational patterns.
Self-supervised Extraction of Human Motion Structures via Frame-wise Discrete Features
Venue: arXiv cs.CV 2023
Year: 2023

The present paper proposes an encoder-decoder model for extracting the structures of human motions represented by frame-wise discrete features in a self-supervised manner. In the proposed method, features are extracted as codes in a motion codebook without the use of human knowledge, and the relationship between these codes can be visualized on a graph. Since the codes are expected to be temporally sparse compared to the captured frame rate and can be shared by multiple sequences, the proposed network model also addresses the need for training constraints. Specifically, the model consists of self-attention layers and a vector clustering block. The attention layers contribute to finding sparse keyframes and discrete features as motion codes, which are then extracted by vector clustering. The constraints are realized as training losses so that the same motion codes can be as contiguous as possible and can be shared by multiple sequences. In addition, we propose the use of causal self-attention as a method by which to calculate attention for long sequences consisting of numerous frames. In our experiments, the sparse structures of motion codes were used to compile a graph that facilitates visualization of the relationship between the codes and the differences between sequences. We then evaluated the effectiveness of the extracted motion codes by applying them to multiple recognition tasks and found that performance levels comparable to task-optimized methods could be achieved by linear probing.
Interpolation, Approximation and Controllability of Deep Neural Networks
Venue: arXiv cs.LG 2023
Year: 2023

We investigate the expressive power of deep residual neural networks idealized as continuous dynamical systems through control theory. Specifically, we consider two properties that arise from supervised learning, namely universal interpolation - the ability to match arbitrary input and target training samples - and the closely related notion of universal approximation - the ability to approximate input-target functional relationships via flow maps. Under the assumption of affine invariance of the control family, we give a characterisation of universal interpolation, showing that it holds for essentially any architecture with non-linearity. Furthermore, we elucidate the relationship between universal interpolation and universal approximation in the context of general control systems, showing that the two properties cannot be deduced from each other. At the same time, we identify conditions on the control family and the target function that ensures the equivalence of the two notions.
A new meteor detection application robust to camera movements
Venue: arXiv cs.CV 2023
Year: 2023

This article presents a new tool for the automatic detection of meteors. Fast Meteor Detection Toolbox (FMDT) is able to detect meteor sightings by analyzing videos acquired by cameras onboard weather balloons or within airplane with stabilization. The challenge consists in designing a processing chain composed of simple algorithms, that are robust to the high fluctuation of the videos and that satisfy the constraints on power consumption (10 W) and real-time processing (25 frames per second).
BatMan-CLR: Making Few-shots Meta-Learners Resilient Against Label Noise
Venue: arXiv cs.LG 2023
Year: 2023

The negative impact of label noise is well studied in classical supervised learning yet remains an open research question in meta-learning. Meta-learners aim to adapt to unseen learning tasks by learning a good initial model in meta-training and consecutively fine-tuning it according to new tasks during meta-testing. In this paper, we present the first extensive analysis of the impact of varying levels of label noise on the performance of state-of-the-art meta-learners, specifically gradient-based $N$-way $K$-shot learners. We show that the accuracy of Reptile, iMAML, and foMAML drops by up to 42% on the Omniglot and CifarFS datasets when meta-training is affected by label noise. To strengthen the resilience against label noise, we propose two sampling techniques, namely manifold (Man) and batch manifold (BatMan), which transform the noisy supervised learners into semi-supervised ones to increase the utility of noisy labels. We first construct manifold samples of $N$-way $2$-contrastive-shot tasks through augmentation, learning the embedding via a contrastive loss in meta-training, and then perform classification through zeroing on the embedding in meta-testing. We show that our approach can effectively mitigate the impact of meta-training label noise. Even with 60% wrong labels \batman and \man can limit the meta-testing accuracy drop to ${2.5}$, ${9.4}$, ${1.1}$ percent points, respectively, with existing meta-learners across the Omniglot, CifarFS, and MiniImagenet datasets.
HOC-Search: Efficient CAD Model and Pose Retrieval from RGB-D Scans
Venue: arXiv cs.CV 2023
Year: 2023

We present an automated and efficient approach for retrieving high-quality CAD models of objects and their poses in a scene captured by a moving RGB-D camera. We first investigate various objective functions to measure similarity between a candidate CAD object model and the available data, and the best objective function appears to be a "render-and-compare" method comparing depth and mask rendering. We thus introduce a fast-search method that approximates an exhaustive search based on this objective function for simultaneously retrieving the object category, a CAD model, and the pose of an object given an approximate 3D bounding box. This method involves a search tree that organizes the CAD models and object properties including object category and pose for fast retrieval and an algorithm inspired by Monte Carlo Tree Search, that efficiently searches this tree. We show that this method retrieves CAD models that fit the real objects very well, with a speed-up factor of 10x to 120x compared to exhaustive search.
Characterizing Latent Perspectives of Media Houses Towards Public Figures
Venue: arXiv cs.CL 2023
Year: 2023

Media houses reporting on public figures, often come with their own biases stemming from their respective worldviews. A characterization of these underlying patterns helps us in better understanding and interpreting news stories. For this, we need diverse or subjective summarizations, which may not be amenable for classifying into predefined class labels. This work proposes a zero-shot approach for non-extractive or generative characterizations of person entities from a corpus using GPT-2. We use well-articulated articles from several well-known news media houses as a corpus to build a sound argument for this approach. First, we fine-tune a GPT-2 pre-trained language model with a corpus where specific person entities are characterized. Second, we further fine-tune this with demonstrations of person entity characterizations, created from a corpus of programmatically constructed characterizations. This twice fine-tuned model is primed with manual prompts consisting of entity names that were not previously encountered in the second fine-tuning, to generate a simple sentence about the entity. The results were encouraging, when compared against actual characterizations from the corpus.
Online Name-Based Navigation for Software Meta-languages
Venue: arXiv cs.SE 2023
Year: 2023

Software language design and implementation often involve specifications written in various esoteric meta-languages. Language workbenches generally include support for precise name-based navigation when browsing language specifications locally, but such support is lacking when browsing the same specifications online in code repositories. This paper presents a technique to support precise name-based navigation of language specifications in online repositories using ordinary web browsers. The idea is to generate hyperlinked twins: websites where verbatim copies of specification text are enhanced with hyperlinks between name references and declarations. By generating hyperlinks directly from the name binding analysis used internally in a language workbench, online navigation in hyperlinked twins is automatically consistent with local navigation. The presented technique has been implemented for the Spoofax language workbench, and used to generate hyperlinked twin websites from various language specifications in Spoofax meta-languages. However, the applicability of the technique is not limited to Spoofax, and developers of other language workbenches could presumably implement similar tooling, to make their language specifications more accessible to those who do not have the workbench installed.
Measuring vagueness and subjectivity in texts: from symbolic to neural VAGO
Venue: arXiv cs.CL 2023
Year: 2023

We present a hybrid approach to the automated measurement of vagueness and subjectivity in texts. We first introduce the expert system VAGO, we illustrate it on a small benchmark of fact vs. opinion sentences, and then test it on the larger French press corpus FreSaDa to confirm the higher prevalence of subjective markers in satirical vs. regular texts. We then build a neural clone of VAGO, based on a BERT-like architecture, trained on the symbolic VAGO scores obtained on FreSaDa. Using explainability tools (LIME), we show the interest of this neural version for the enrichment of the lexicons of the symbolic version, and for the production of versions in other languages.
Computer Vision Pipeline for Automated Antarctic Krill Analysis
Venue: arXiv cs.CV 2023
Year: 2023

British Antarctic Survey (BAS) researchers launch annual expeditions to the Antarctic in order to estimate Antarctic Krill biomass and assess the change from previous years. These comparisons provide insight into the effects of the current environment on this key component of the marine food chain. In this work we have developed tools for automating the data collection and analysis process, using web-based image annotation tools and deep learning image classification and regression models. We achieve highly accurate krill instance segmentation results with an average 77.28% AP score, as well as separate maturity stage and length estimation of krill specimens with 62.99% accuracy and a 1.98mm length error respectively.
Optimization Guarantees of Unfolded ISTA and ADMM Networks With Smooth Soft-Thresholding
Venue: arXiv cs.LG 2023
Year: 2023

Solving linear inverse problems plays a crucial role in numerous applications. Algorithm unfolding based, model-aware data-driven approaches have gained significant attention for effectively addressing these problems. Learned iterative soft-thresholding algorithm (LISTA) and alternating direction method of multipliers compressive sensing network (ADMM-CSNet) are two widely used such approaches, based on ISTA and ADMM algorithms, respectively. In this work, we study optimization guarantees, i.e., achieving near-zero training loss with the increase in the number of learning epochs, for finite-layer unfolded networks such as LISTA and ADMM-CSNet with smooth soft-thresholding in an over-parameterized (OP) regime. We achieve this by leveraging a modified version of the Polyak-Lojasiewicz, denoted PL$^*$, condition. Satisfying the PL$^*$ condition within a specific region of the loss landscape ensures the existence of a global minimum and exponential convergence from initialization using gradient descent based methods. Hence, we provide conditions, in terms of the network width and the number of training samples, on these unfolded networks for the PL$^*$ condition to hold. We achieve this by deriving the Hessian spectral norm of these networks. Additionally, we show that the threshold on the number of training samples increases with the increase in the network width. Furthermore, we compare the threshold on training samples of unfolded networks with that of a standard fully-connected feed-forward network (FFNN) with smooth soft-thresholding non-linearity. We prove that unfolded networks have a higher threshold value than FFNN. Consequently, one can expect a better expected error for unfolded networks than FFNN.
Petri Net Classes for Collaboration Mining: Assessment and Design Guidelines
Venue: arXiv cs.FL 2023
Year: 2023

Collaboration mining develops discovery, conformance checking, and enhancement techniques for collaboration processes. The collaboration process model is key to represent the discovery result. As for process mining in general, Petri Net classes are candidates for collaboration process models due to their analytical power. However, a standard model class to represent collaboration processes is lacking due to the heterogeneity of collaboration and, thus, of collaboration mining techniques. Collaboration heterogeneity requires to cover, for example, intra-organizational collaborations as well as choreographies that span a process across multiple organizations. A standard collaboration model class would advance collaboration mining by focusing discovery through a common target model, supporting comparison, and enabling flexible mining pipelines. To find a standard model class, we aim at capturing collaboration heterogeneity in a meta model, assess Petri net classes as candidates for collaboration process models through the meta model, and derive design guidelines for the collaboration discovery.
Rethinking Evaluation Metric for Probability Estimation Models Using Esports Data
Venue: arXiv cs.LG 2023
Year: 2023

Probability estimation models play an important role in various fields, such as weather forecasting, recommendation systems, and sports analysis. Among several models estimating probabilities, it is difficult to evaluate which model gives reliable probabilities since the ground-truth probabilities are not available. The win probability estimation model for esports, which calculates the win probability under a certain game state, is also one of the fields being actively studied in probability estimation. However, most of the previous works evaluated their models using accuracy, a metric that only can measure the performance of discrimination. In this work, we firstly investigate the Brier score and the Expected Calibration Error (ECE) as a replacement of accuracy used as a performance evaluation metric for win probability estimation models in esports field. Based on the analysis, we propose a novel metric called Balance score which is a simple yet effective metric in terms of six good properties that probability estimation metric should have. Under the general condition, we also found that the Balance score can be an effective approximation of the true expected calibration error which has been imperfectly approximated by ECE using the binning technique. Extensive evaluations using simulation studies and real game snapshot data demonstrate the promising potential to adopt the proposed metric not only for the win probability estimation model for esports but also for evaluating general probability estimation models.