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Publications
Predicting the Impact of Model Expansion through the Minima Manifold: A Loss Landscape Perspective
The optimal model for a given task is often challenging to determine, requiring training multiple models from scratch which becomes prohibit… (see more)ive as dataset and model sizes grow. A more efficient alternative is to reuse smaller pre-trained models by expanding them, however, this is not widely adopted as how this impacts training dynamics remains poorly understood. While prior works have introduced statistics to measure these effects, they remain flawed. To rectify this, we offer a new approach for understanding and quantifying the impact of expansion through the lens of the loss landscape, which has been shown to contain a manifold of linearly connected minima. Building on this new perspective, we propose a metric to study the impact of expansion by estimating the size of the manifold. Experimental results show a clear relationship between gains in performance and manifold size, enabling the comparison of candidate models and presenting a first step towards expanding models more reliably based on geometric properties of the loss landscape.
Generative modeling over discrete data has recently seen numerous success stories, with applications spanning language modeling, biological … (see more)sequence design, and graph-structured molecular data. The predominant generative modeling paradigm for discrete data is still autoregressive, with more recent alternatives based on diffusion or flow-matching falling short of their impressive performance in continuous data settings, such as image or video generation. In this work, we introduce Fisher-Flow, a novel flow-matching model for discrete data. Fisher-Flow takes a manifestly geometric perspective by considering categorical distributions over discrete data as points residing on a statistical manifold equipped with its natural Riemannian metric: the
Matching objectives underpin the success of modern generative models and rely on constructing conditional paths that transform a source dist… (see more)ribution into a target distribution. Despite being a fundamental building block, conditional paths have been designed principally under the assumption of Euclidean geometry, resulting in straight interpolations. However, this can be particularly restrictive for tasks such as trajectory inference, where straight paths might lie outside the data manifold, thus failing to capture the underlying dynamics giving rise to the observed marginals. In this paper, we propose Metric Flow Matching (MFM), a novel simulation-free framework for conditional flow matching where interpolants are approximate geodesics learned by minimizing the kinetic energy of a data-induced Riemannian metric. This way, the generative model matches vector fields on the data manifold, which corresponds to lower uncertainty and more meaningful interpolations. We prescribe general metrics to instantiate MFM, independent of the task, and test it on a suite of challenging problems including LiDAR navigation, unpaired image translation, and modeling cellular dynamics. We observe that MFM outperforms the Euclidean baselines, particularly achieving SOTA on single-cell trajectory prediction.
The advent of Transformers marked a significant breakthrough in sequence modelling, providing a highly performant architecture capable of le… (see more)veraging GPU parallelism. However, Transformers are computationally expensive at inference time, limiting their applications, particularly in low-resource settings (e.g., mobile and embedded devices). Addressing this, we (1) begin by showing that attention can be viewed as a special Recurrent Neural Network (RNN) with the ability to compute its \textit{many-to-one} RNN output efficiently. We then (2) show that popular attention-based models such as Transformers can be viewed as RNN variants. However, unlike traditional RNNs (e.g., LSTMs), these models cannot be updated efficiently with new tokens, an important property in sequence modelling. Tackling this, we (3) introduce a new efficient method of computing attention's \textit{many-to-many} RNN output based on the parallel prefix scan algorithm. Building on the new attention formulation, we (4) introduce \textbf{Aaren}, an attention-based module that can not only (i) be trained in parallel (like Transformers) but also (ii) be updated efficiently with new tokens, requiring only constant memory for inferences (like traditional RNNs). Empirically, we show Aarens achieve comparable performance to Transformers on
LLM-based assistants, such as GitHub Copilot and ChatGPT, have the potential to generate code that fulfills a programming task described in … (see more)a natural language description, referred to as a prompt. The widespread accessibility of these assistants enables users with diverse backgrounds to generate code and integrate it into software projects. However, studies show that code generated by LLMs is prone to bugs and may miss various corner cases in task specifications. Presenting such buggy code to users can impact their reliability and trust in LLM-based assistants. Moreover, significant efforts are required by the user to detect and repair any bug present in the code, especially if no test cases are available. In this study, we propose a self-refinement method aimed at improving the reliability of code generated by LLMs by minimizing the number of bugs before execution, without human intervention, and in the absence of test cases. Our approach is based on targeted Verification Questions (VQs) to identify potential bugs within the initial code. These VQs target various nodes within the Abstract Syntax Tree (AST) of the initial code, which have the potential to trigger specific types of bug patterns commonly found in LLM-generated code. Finally, our method attempts to repair these potential bugs by re-prompting the LLM with the targeted VQs and the initial code. Our evaluation, based on programming tasks in the CoderEval dataset, demonstrates that our proposed method outperforms state-of-the-art methods by decreasing the number of targeted errors in the code between 21% to 62% and improving the number of executable code instances to 13%.
Defect reduction planning plays a vital role in enhancing software quality and minimizing software maintenance costs. By training a black bo… (see more)x machine learning model and “explaining” its predictions, explainable AI for software engineering aims to identify the code characteristics that impact maintenance risks. However, post-hoc explanations do not always faithfully reflect what the original model computes. In this paper, we introduce CounterACT, a Counterfactual ACTion rule mining approach that can generate defect reduction plans without black-box models. By leveraging action rules, CounterACT provides a course of action that can be considered as a counterfactual explanation for the class (e.g., buggy or not buggy) assigned to a piece of code. We compare the effectiveness of CounterACT with the original action rule mining algorithm and six established defect reduction approaches on 9 software projects. Our evaluation is based on (a) overlap scores between proposed code changes and actual developer modifications; (b) improvement scores in future releases; and (c) the precision, recall, and F1-score of the plans. Our results show that, compared to competing approaches, CounterACT’s explainable plans achieve higher overlap scores at the release level (median 95%) and commit level (median 85.97%), and they offer better trade-off between precision and recall (median F1-score 88.12%). Finally, we venture beyond planning and explore leveraging Large Language models (LLM) for generating code edits from our generated plans. Our results show that suggested LLM code edits supported by our plans are actionable and are more likely to pass relevant test cases than vanilla LLM code recommendations.
Defect reduction planning plays a vital role in enhancing software quality and minimizing software maintenance costs. By training a black bo… (see more)x machine learning model and “explaining” its predictions, explainable AI for software engineering aims to identify the code characteristics that impact maintenance risks. However, post-hoc explanations do not always faithfully reflect what the original model computes. In this paper, we introduce CounterACT, a Counterfactual ACTion rule mining approach that can generate defect reduction plans without black-box models. By leveraging action rules, CounterACT provides a course of action that can be considered as a counterfactual explanation for the class (e.g., buggy or not buggy) assigned to a piece of code. We compare the effectiveness of CounterACT with the original action rule mining algorithm and six established defect reduction approaches on 9 software projects. Our evaluation is based on (a) overlap scores between proposed code changes and actual developer modifications; (b) improvement scores in future releases; and (c) the precision, recall, and F1-score of the plans. Our results show that, compared to competing approaches, CounterACT’s explainable plans achieve higher overlap scores at the release level (median 95%) and commit level (median 85.97%), and they offer better trade-off between precision and recall (median F1-score 88.12%). Finally, we venture beyond planning and explore leveraging Large Language models (LLM) for generating code edits from our generated plans. Our results show that suggested LLM code edits supported by our plans are actionable and are more likely to pass relevant test cases than vanilla LLM code recommendations.
BACKGROUND
In radiotherapy, it is essential to deliver prescribed doses to tumors while minimizing damage to surrounding healthy tissue. Acc… (see more)urate measurements of absorbed dose are required for this purpose. Gafchromic® external beam therapy (EBT) radiochromic films have been widely used in radiotherapy. While the dosimetric characteristics of the EBT3 model film have been extensively studied for photon and charged particle beams (protons, electrons, and carbon ions), little research has been done on α
