Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.

The advantages of forgetting have been investigated in various research fields, including education, philosophy, ecology and linguistics, where forgetting has been found to contribute significantly to the enhancement of humans' decision-making, creativity, and diversity from multiple perspectives. Forgetting, an intrinsic aspect of human memory, does not naturally occur in machines, highlighting a fundamental distinction between humans and artificial systems. In the context of the human brain, overfitting arises when we simply memorise specific examples rather than generalise patterns from them [96]. This narrow focus can cause inflexibility in our thinking and problem-solving abilities, as well as lead to erroneous predictions or assumptions when confronted with unfamiliar situations. Overfitting is also a challenge in machine learning (ML) [50]. By mimicking the human brain, incorporating a forget-and-relearn function into machines has been proposed to be a powerful paradigm for shaping the learning trajectories of artificial neural networks [269], as not all content in the past is equally important for models to remember [203].

Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance in many computer vision tasks. However, high computational and storage demands hinder their deployment into resource-constrained environments, such as embedded devices. Model pruning helps to meet these restrictions by reducing the model size, while maintaining superior performance. Meanwhile, safety-critical applications pose more than just resource and performance constraints. In particular, predictions must not be overly confident, i.e., provide properly calibrated uncertainty estimations (proper uncertainty calibration), and CNNs must be robust against corruptions like naturally occurring input perturbations (natural corruption robustness). This work investigates the important trade-off between uncertainty calibration, natural corruption robustness, and performance for current state-of-research post-hoc CNN pruning techniques in the context of image classification tasks. Our study reveals that post-hoc pruning substantially improves the model's uncertainty calibration, performance, and natural corruption robustness, sparking hope for safe and robust embedded CNNs.Furthermore, uncertainty calibration and natural corruption robustness are not mutually exclusive targets under pruning, as evidenced by the improved safety aspects obtained by post-hoc unstructured pruning with increasing compression.

Predicting the spatiotemporal variation in streamflow along with uncertainty quantification enables decision-making for sustainable management of scarce water resources. Process-based hydrological models (aka physics-based models) are based on physical laws, but using simplifying assumptions which can lead to poor accuracy. Data-driven approaches offer a powerful alternative, but they require large amount of training data and tend to produce predictions that are inconsistent with physical laws. This paper studies a constrained reasoning and learning (CRL) approach where physical laws represented as logical constraints are integrated as a layer in the deep neural network. To address small data setting, we develop a theoretically-grounded training approach to improve the generalization accuracy of deep models. For uncertainty quantification, we combine the synergistic strengths of Gaussian processes (GPs) and deep temporal models (i.e., deep models for time-series forecasting) by passing the learned latent representation as input to a standard distance-based kernel. Experiments on multiple real-world datasets demonstrate the effectiveness of both CRL and GP with deep kernel approaches over strong baseline methods.

Ptychography is a powerful imaging technique that is used in a variety of fields, including materials science, biology, and nanotechnology. However, the accuracy of the reconstructed ptychography image is highly dependent on the accuracy of the recorded probe positions which often contain errors. These errors are typically corrected jointly with phase retrieval through numerical optimization approaches. When the error accumulates along the scan path or when the error magnitude is large, these approaches may not converge with satisfactory result. We propose a fundamentally new approach for ptychography probe position prediction for data with large position errors, where a neural network is used to make single-shot phase retrieval on individual diffraction patterns, yielding the object image at each scan point. The pairwise offsets among these images are then found using a robust image registration method, and the results are combined to yield the complete scan path by constructing and solving a linear equation. We show that our method can achieve good position prediction accuracy for data with large and accumulating errors on the order of $10^2$ pixels, a magnitude that often makes optimization-based algorithms fail to converge. For ptychography instruments without sophisticated position control equipment such as interferometers, our method is of significant practical potential.

Pretrained deep-learning models are the go-to solution for images or text. However, for tabular data the standard is still to train tree-based models. Indeed, transfer learning on tables hits the challenge of data integration: finding correspondences, correspondences in the entries (entity matching) where different words may denote the same entity, correspondences across columns (schema matching), which may come in different orders, names... We propose a neural architecture that does not need such correspondences. As a result, we can pretrain it on background data that has not been matched. The architecture -- CARTE for Context Aware Representation of Table Entries -- uses a graph representation of tabular (or relational) data to process tables with different columns, string embedding of entries and columns names to model an open vocabulary, and a graph-attentional network to contextualize entries with column names and neighboring entries. An extensive benchmark shows that CARTE facilitates learning, outperforming a solid set of baselines including the best tree-based models. CARTE also enables joint learning across tables with unmatched columns, enhancing a small table with bigger ones. CARTE opens the door to large pretrained models for tabular data.

Large language models (LLMs) have shown incredible proficiency in performing tasks that require semantic understanding of natural language instructions. Recently, many works have further expanded this capability to perceive multimodal audio and text inputs, but their capabilities are often limited to specific fine-tuned tasks such as automatic speech recognition and translation. We therefore develop SpeechVerse, a robust multi-task training and curriculum learning framework that combines pre-trained speech and text foundation models via a small set of learnable parameters, while keeping the pre-trained models frozen during training. The models are instruction finetuned using continuous latent representations extracted from the speech foundation model to achieve optimal zero-shot performance on a diverse range of speech processing tasks using natural language instructions. We perform extensive benchmarking that includes comparing our model performance against traditional baselines across several datasets and tasks. Furthermore, we evaluate the model's capability for generalized instruction following by testing on out-of-domain datasets, novel prompts, and unseen tasks. Our empirical experiments reveal that our multi-task SpeechVerse model is even superior to conventional task-specific baselines on 9 out of the 11 tasks.

Evaluating observational estimators of causal effects demands information that is rarely available: unconfounded interventions and outcomes from the population of interest, created either by randomization or adjustment. As a result, it is customary to fall back on simulators when creating benchmark tasks. Simulators offer great control but are often too simplistic to make challenging tasks, either because they are hand-designed and lack the nuances of real-world data, or because they are fit to observational data without structural constraints. In this work, we propose a general, repeatable strategy for turning observational data into sequential structural causal models and challenging estimation tasks by following two simple principles: 1) fitting real-world data where possible, and 2) creating complexity by composing simple, hand-designed mechanisms. We implement these ideas in a highly configurable software package and apply it to the well-known Adult income data set to construct the \tt IncomeSCM simulator. From this, we devise multiple estimation tasks and sample data sets to compare established estimators of causal effects. The tasks present a suitable challenge, with effect estimates varying greatly in quality between methods, despite similar performance in the modeling of factual outcomes, highlighting the need for dedicated causal estimators and model selection criteria.

This survey paper presents a comprehensive and conceptual overview of anomaly detection using dynamic graphs. We focus on existing graph-based anomaly detection (AD) techniques and their applications to dynamic networks. The contributions of this survey paper include the following: i) a comparative study of existing surveys on anomaly detection; ii) a Dynamic Graph-based Anomaly Detection (DGAD) review framework in which approaches for detecting anomalies in dynamic graphs are grouped based on traditional machine-learning models, matrix transformations, probabilistic approaches, and deep-learning approaches; iii) a discussion of graphically representing both discrete and dynamic networks; and iv) a discussion of the advantages of graph-based techniques for capturing the relational structure and complex interactions in dynamic graph data. Finally, this work identifies the potential challenges and future directions for detecting anomalies in dynamic networks. This DGAD survey approach aims to provide a valuable resource for researchers and practitioners by summarizing the strengths and limitations of each approach, highlighting current research trends, and identifying open challenges. In doing so, it can guide future research efforts and promote advancements in anomaly detection in dynamic graphs. Keywords: Graphs, Anomaly Detection, dynamic networks,Graph Neural Networks (GNN), Node anomaly, Graph mining.

The environments in which the collaboration of a robot would be the most helpful to a person are frequently uncontrolled and cluttered with many objects present. Legible robot arm motion is crucial in tasks like these in order to avoid possible collisions, improve the workflow and help ensure the safety of the person. Prior work in this area, however, focuses on solutions that are tested only in uncluttered environments and there are not many results taken from cluttered environments. In this research we present a measure for clutteredness based on an entropic measure of the environment, and a novel motion planner based on potential fields. Both our measures and the planner were tested in a cluttered environment meant to represent a more typical tool sorting task for which the person would collaborate with a robot. The in-person validation study with Baxter robots shows a significant improvement in legibility of our proposed legible motion planner compared to the current state-of-the-art legible motion planner in cluttered environments. Further, the results show a significant difference in the performance of the planners in cluttered and uncluttered environments, and the need to further explore legible motion in cluttered environments. We argue that the inconsistency of our results in cluttered environments with those obtained from uncluttered environments points out several important issues with the current research performed in the area of legible motion planners.