Supervised fine-tuning enhances the problem-solving abilities of language models across various mathematical reasoning tasks. To maximize such benefits, existing research focuses on broadening the training set with various data augmentation techniques, which is effective for standard single-round question-answering settings. Our work introduces a novel technique aimed at cultivating a deeper understanding of the training problems at hand, enhancing performance not only in standard settings but also in more complex scenarios that require reflective thinking. Specifically, we propose reflective augmentation, a method that embeds problem reflection into each training instance. It trains the model to consider alternative perspectives and engage with abstractions and analogies, thereby fostering a thorough comprehension through reflective reasoning. Extensive experiments validate the achievement of our aim, underscoring the unique advantages of our method and its complementary nature relative to existing augmentation techniques.

Time Series Representation Learning (TSRL) focuses on generating informative representations for various Time Series (TS) modeling tasks. Traditional Self-Supervised Learning (SSL) methods in TSRL fall into four main categories: reconstructive, adversarial, contrastive, and predictive, each with a common challenge of sensitivity to noise and intricate data nuances. Recently, diffusion-based methods have shown advanced generative capabilities. However, they primarily target specific application scenarios like imputation and forecasting, leaving a gap in leveraging diffusion models for generic TSRL. Our work, Time Series Diffusion Embedding (TSDE), bridges this gap as the first diffusion-based SSL TSRL approach. TSDE segments TS data into observed and masked parts using an Imputation-Interpolation-Forecasting (IIF) mask. It applies a trainable embedding function, featuring dual-orthogonal Transformer encoders with a crossover mechanism, to the observed part. We train a reverse diffusion process conditioned on the embeddings, designed to predict noise added to the masked part. Extensive experiments demonstrate TSDE's superiority in imputation, interpolation, forecasting, anomaly detection, classification, and clustering. We also conduct an ablation study, present embedding visualizations, and compare inference speed, further substantiating TSDE's efficiency and validity in learning representations of TS data.

Parameter-efficient fine-tuning (PEFT) techniques such as low-rank adaptation (LoRA) can effectively adapt large pre-trained foundation models to downstream tasks using only a small fraction (0.1%-10%) of the original trainable weights. An under-explored question of PEFT is in extending the pre-training phase without supervised labels; that is, can we adapt a pre-trained foundation model to a new domain via efficient self-supervised pre-training on this new domain? In this work, we introduce ExPLoRA, a highly effective technique to improve transfer learning of pre-trained vision transformers (ViTs) under domain shifts. Initializing a ViT with pre-trained weights on large, natural-image datasets such as from DinoV2 or MAE, ExPLoRA continues the unsupervised pre-training objective on a new domain. In this extended pre-training phase, ExPLoRA only unfreezes 1-2 pre-trained ViT blocks and all normalization layers, and then tunes all other layers with LoRA. Finally, we fine-tune the resulting model only with LoRA on this new domain for supervised learning. Our experiments demonstrate state-of-the-art results on satellite imagery, even outperforming fully pre-training and fine-tuning ViTs. Using the DinoV2 training objective, we demonstrate up to 7% improvement in linear probing top-1 accuracy on downstream tasks while using <10% of the number of parameters that are used in prior fully-tuned state-of-the art approaches. Our ablation studies confirm the efficacy of our approach over other baselines, including PEFT and simply unfreezing more transformer blocks.

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative heterogeneous graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements various cutting-edge methods. Secondly, a single task on \textit{de novo} molecule generation can hardly reflect their capabilities. To broaden the scope, we have adapted these models to a range of tasks essential in drug design, which are considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of \textit{de novo} molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide the pre-trained versions of the state-of-the-art models and deep insights with analysis from empirical studies. The codebase for CBGBench is publicly accessible at \url{https://github.com/Edapinenut/CBGBench}.

Given a task in the form of a basic description and its training examples, prompt optimization is the problem of synthesizing the given information into a text prompt for a large language model (LLM). Humans solve this problem by also considering the different facets that define a task (e.g., counter-examples, explanations, analogies) and including them in the prompt. However, it is unclear whether existing algorithmic approaches, based on iteratively editing a given prompt or automatically selecting a few in-context examples, can cover the multiple facets required to solve a complex task. In this work, we view prompt optimization as that of learning multiple facets of a task from a set of training examples. We identify and exploit structure in the prompt optimization problem -- first, we find that prompts can be broken down into loosely coupled semantic sections that have a relatively independent effect on the prompt's performance; second, we cluster the input space and use clustered batches so that the optimization procedure can learn the different facets of a task across batches. The resulting algorithm, UniPrompt, consists of a generative model to generate initial candidates for each prompt section; and a feedback mechanism that aggregates suggested edits from multiple mini-batches into a conceptual description for the section. Empirical evaluation on multiple datasets and a real-world task shows that prompts generated using UniPrompt obtain higher accuracy than human-tuned prompts and those from state-of-the-art methods. In particular, our algorithm can generate long, complex prompts that existing methods are unable to generate. Code for UniPrompt will be available at \url{https://aka.ms/uniprompt}.

We present a suite of experiments that allow us to understand the underlying challenges of language model adaptation to nonstandard text. We do so by designing interventions that approximate several types of linguistic variation and their interactions with existing biases of language models. Applying our interventions during language model adaptation with varying size and nature of training data, we gain important insights into when knowledge transfer can be successful, as well as the aspects of linguistic variation that are particularly difficult for language models to deal with. For instance, on text with character-level variation, performance improves with even a few training examples but approaches a plateau, suggesting that more data is not the solution. In contrast, on text with variation involving new words or meanings, far more data is needed, but it leads to a massive breakthrough in performance. Our findings reveal that existing models lack the necessary infrastructure to handle diverse forms of nonstandard text and linguistic variation, guiding the development of more resilient language modeling techniques for the future. We make the code for our interventions, which can be applied to any English text data, publicly available.

Dietary Restriction (DR) is one of the most popular anti-ageing interventions, prompting exhaustive research into genes associated with its mechanisms. Recently, Machine Learning (ML) has been explored to identify potential DR-related genes among ageing-related genes, aiming to minimize costly wet lab experiments needed to expand our knowledge on DR. However, to train a model from positive (DR-related) and negative (non-DR-related) examples, existing ML methods naively label genes without known DR relation as negative examples, assuming that lack of DR-related annotation for a gene represents evidence of absence of DR-relatedness, rather than absence of evidence; this hinders the reliability of the negative examples (non-DR-related genes) and the method's ability to identify novel DR-related genes. This work introduces a novel gene prioritization method based on the two-step Positive-Unlabelled (PU) Learning paradigm: using a similarity-based, KNN-inspired approach, our method first selects reliable negative examples among the genes without known DR associations. Then, these reliable negatives and all known positives are used to train a classifier that effectively differentiates DR-related and non-DR-related genes, which is finally employed to generate a more reliable ranking of promising genes for novel DR-relatedness. Our method significantly outperforms the existing state-of-the-art non-PU approach for DR-relatedness prediction in three relevant performance metrics. In addition, curation of existing literature finds support for the top-ranked candidate DR-related genes identified by our model.

Severe data imbalance naturally exists among web-scale vision-language datasets. Despite this, we find CLIP pre-trained thereupon exhibits notable robustness to the data imbalance compared to supervised learning, and demonstrates significant effectiveness in learning generalizable representations. With an aim to investigate the reasons behind this finding, we conduct controlled experiments to study various underlying factors, and reveal that CLIP's pretext task forms a dynamic classification problem wherein only a subset of classes is present in training. This isolates the bias from dominant classes and implicitly balances the learning signal. Furthermore, the robustness and discriminability of CLIP improve with more descriptive language supervision, larger data scale, and broader open-world concepts, which are inaccessible to supervised learning. Our study not only uncovers the mechanisms behind CLIP's generalizability beyond data imbalance but also provides transferable insights for the research community. The findings are validated in both supervised and self-supervised learning, enabling models trained on imbalanced data to achieve CLIP-level performance on diverse recognition tasks.

We consider the problem of \textit{true} open-world semi-supervised node classification, in which nodes in a graph either belong to known or new classes, with the latter not present during training. Existing methods detect and reject new classes but fail to distinguish between different new classes. We adapt existing methods and show they do not solve the problem sufficiently. We introduce a novel end-to-end approach for classification into known classes and new classes based on class prototypes, which we call Prototypical Open-World Learning for Node Classification (POWN). Our method combines graph semi-supervised learning, self-supervised learning, and pseudo-labeling to learn prototype representations of new classes in a zero-shot way. In contrast to existing solutions from the vision domain, POWN does not require data augmentation techniques for node classification. Experiments on benchmark datasets demonstrate the effectiveness of POWN, where it outperforms baselines by up to $20\%$ accuracy on the small and up to $30\%$ on the large datasets. Source code is available at https://github.com/Bobowner/POWN.

Learning a parametric model from a given dataset indeed enables to capture intrinsic dependencies between random variables via a parametric conditional probability distribution and in turn predict the value of a label variable given observed variables. In this paper, we undertake a comparative analysis of generative and discriminative approaches which differ in their construction and the structure of the underlying inference problem. Our objective is to compare the ability of both approaches to leverage information from various sources in an epistemic uncertainty aware inference via the posterior predictive distribution. We assess the role of a prior distribution, explicit in the generative case and implicit in the discriminative case, leading to a discussion about discriminative models suffering from imbalanced dataset. We next examine the double role played by the observed variables in the generative case, and discuss the compatibility of both approaches with semi-supervised learning. We also provide with practical insights and we examine how the modeling choice impacts the sampling from the posterior predictive distribution. With regard to this, we propose a general sampling scheme enabling supervised learning for both approaches, as well as semi-supervised learning when compatible with the considered modeling approach. Throughout this paper, we illustrate our arguments and conclusions using the example of affine regression, and validate our comparative analysis through classification simulations using neural network based models.