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Machine learning classification problems are widespread in bioinformatics, but the technical knowledge required to perform model training, optimization, and inference can prevent researchers from utilizing this technology. This article presents an automated tool for machine learning classification problems to simplify the process of training models and producing results while providing informative visualizations and insights into the data. This tool supports both binary and multiclass classification problems, and it provides access to a variety of models and methods. Synthetic data can be generated within the interface to fill missing values, balance class labels, or generate entirely new datasets. It also provides support for feature evaluation and generates explainability scores to indicate which features influence the output the most. We present CLASSify, an open-source tool for simplifying the user experience of solving classification problems without the need for knowledge of machine learning.

Deep implicit functions (DIFs) have emerged as a powerful paradigm for many computer vision tasks such as 3D shape reconstruction, generation, registration, completion, editing, and understanding. However, given a set of 3D shapes with associated covariates there is at present no shape representation method which allows to precisely represent the shapes while capturing the individual dependencies on each covariate. Such a method would be of high utility to researchers to discover knowledge hidden in a population of shapes. For scientific shape discovery, we propose a 3D Neural Additive Model for Interpretable Shape Representation ($\texttt{NAISR}$) which describes individual shapes by deforming a shape atlas in accordance to the effect of disentangled covariates. Our approach captures shape population trends and allows for patient-specific predictions through shape transfer. $\texttt{NAISR}$ is the first approach to combine the benefits of deep implicit shape representations with an atlas deforming according to specified covariates. We evaluate $\texttt{NAISR}$ with respect to shape reconstruction, shape disentanglement, shape evolution, and shape transfer on three datasets: 1) $\textit{Starman}$, a simulated 2D shape dataset; 2) the ADNI hippocampus 3D shape dataset; and 3) a pediatric airway 3D shape dataset. Our experiments demonstrate that $\textit{Starman}$ achieves excellent shape reconstruction performance while retaining interpretability. Our code is available at $\href{//github.com/uncbiag/NAISR}{//github.com/uncbiag/NAISR}$.

Continual learning allows a model to learn multiple tasks sequentially while retaining the old knowledge without the training data of the preceding tasks. This paper extends the scope of continual learning research to class-incremental learning for \ac{mot}, which is desirable to accommodate the continuously evolving needs of autonomous systems. Previous solutions for continual learning of object detectors do not address the data association stage of appearance-based trackers, leading to catastrophic forgetting of previous classes' re-identification features. We introduce COOLer, a COntrastive- and cOntinual-Learning-based tracker, which incrementally learns to track new categories while preserving past knowledge by training on a combination of currently available ground truth labels and pseudo-labels generated by the past tracker. To further exacerbate the disentanglement of instance representations, we introduce a novel contrastive class-incremental instance representation learning technique. Finally, we propose a practical evaluation protocol for continual learning for MOT and conduct experiments on the \bdd and \shift datasets. Experimental results demonstrate that COOLer continually learns while effectively addressing catastrophic forgetting of both tracking and detection. The code is available at \url{//github.com/BoSmallEar/COOLer}.

Recently, there has been growing interest in extending the context length of large language models (LLMs), aiming to effectively process long inputs of one turn or conversations with more extensive histories. While proprietary models such as GPT-4 and Claude can largely preserve the reasoning ability in an extended context, open-source models are still progressing through the early stages of development. To bridge this gap, we propose L-Eval to institute a more standardized evaluation for long context language models (LCLMs) addressing two key aspects: dataset construction and evaluation metrics. On the one hand, we build a new evaluation suite containing 20 sub-tasks, 508 long documents, and over 2,000 human-labeled query-response pairs encompassing diverse question styles, domains, and input length (3k$\sim$200k tokens). On the other hand, we investigate the effectiveness in evalution metrics for LCLMs. Results show that popular n-gram matching metrics generally can not correlate well with human judgment, and thus we strongly advocate for length-instruction-enhanced (LIE) evaluation and employing LLM judges. We conducted a comprehensive study of 4 popular commercial LLMs and 12 open-source counterparts using the L-Eval benchmark. Our empirical findings offer useful insights into the study of LCLMs and lay the groundwork for the development of more principled evaluation of these models.

Large language models have made significant progress in various language tasks, yet they still struggle with complex mathematics. In this paper, we propose ToRA a series of Tool-integrated Reasoning Agents designed to solve challenging mathematical problems by seamlessly integrating natural language reasoning with the utilization of external tools (e.g., computation libraries and symbolic solvers), thereby amalgamating the analytical prowess of language and the computational efficiency of tools. To train ToRA, we curate interactive tool-use trajectories on mathematical datasets, apply imitation learning on the annotations, and propose output space shaping to further refine models' reasoning behavior. As a result, ToRA models significantly outperform open-source models on 10 mathematical reasoning datasets across all scales with 13%-19% absolute improvements on average. Notably, ToRA-7B reaches 44.6% on the competition-level dataset MATH, surpassing the best open-source model WizardMath-70B by 22% absolute. ToRA-Code-34B is also the first open-source model that achieves an accuracy exceeding 50% on MATH, which significantly outperforms GPT-4's CoT result, and is competitive with GPT-4 solving problems with programs. Additionally, we conduct a comprehensive analysis of the benefits and remaining challenges of tool interaction for mathematical reasoning, providing valuable insights for future research.

The recent advancement of large language models (LLMs) has been achieved through a combo of instruction tuning and human alignment. However, building manually crafted instruction datasets and performing human alignment become the bottleneck for scaling the development of LLMs. In this paper, we exploit the idea of leveraging AI models in lieu of humans as the teacher to train student LLMs. Our method is inspired by how human students refine their writing skills by following the rubrics and learning from the revisions offered by their tutors. Specifically, we employ a teacher LLM to create a curriculum for instruction tuning of the student LLM, namely Curriculum Instruction TunING (CITING). It encompasses two main steps: (1) the teacher LLM crafts the rubrics for evaluating the answers corresponding to various types of questions, and (2) the student LLM learns to follow the rubrics and perform self-correction from the revision made by the teacher. We further iteratively carry out it to embody the procedure of CITING. We compare CITING to a series of state-of-the-art baselines on four datasets. Our method demonstrates strong improvement in terms of articulate, in-depth, and comprehensive by GPT-4 evaluation. Specifically, it achieves an average winning rate of 79.4% over SFT, 73.4% over RLHF, 78.1% over RRHF, and 76.3% over RAFT, respectively.

Generative commonsense reasoning which aims to empower machines to generate sentences with the capacity of reasoning over a set of concepts is a critical bottleneck for text generation. Even the state-of-the-art pre-trained language generation models struggle at this task and often produce implausible and anomalous sentences. One reason is that they rarely consider incorporating the knowledge graph which can provide rich relational information among the commonsense concepts. To promote the ability of commonsense reasoning for text generation, we propose a novel knowledge graph augmented pre-trained language generation model KG-BART, which encompasses the complex relations of concepts through the knowledge graph and produces more logical and natural sentences as output. Moreover, KG-BART can leverage the graph attention to aggregate the rich concept semantics that enhances the model generalization on unseen concept sets. Experiments on benchmark CommonGen dataset verify the effectiveness of our proposed approach by comparing with several strong pre-trained language generation models, particularly KG-BART outperforms BART by 5.80, 4.60, in terms of BLEU-3, 4. Moreover, we also show that the generated context by our model can work as background scenarios to benefit downstream commonsense QA tasks.

Visual dialogue is a challenging task that needs to extract implicit information from both visual (image) and textual (dialogue history) contexts. Classical approaches pay more attention to the integration of the current question, vision knowledge and text knowledge, despising the heterogeneous semantic gaps between the cross-modal information. In the meantime, the concatenation operation has become de-facto standard to the cross-modal information fusion, which has a limited ability in information retrieval. In this paper, we propose a novel Knowledge-Bridge Graph Network (KBGN) model by using graph to bridge the cross-modal semantic relations between vision and text knowledge in fine granularity, as well as retrieving required knowledge via an adaptive information selection mode. Moreover, the reasoning clues for visual dialogue can be clearly drawn from intra-modal entities and inter-modal bridges. Experimental results on VisDial v1.0 and VisDial-Q datasets demonstrate that our model outperforms exiting models with state-of-the-art results.

Transformers have a potential of learning longer-term dependency, but are limited by a fixed-length context in the setting of language modeling. We propose a novel neural architecture Transformer-XL that enables learning dependency beyond a fixed length without disrupting temporal coherence. It consists of a segment-level recurrence mechanism and a novel positional encoding scheme. Our method not only enables capturing longer-term dependency, but also resolves the context fragmentation problem. As a result, Transformer-XL learns dependency that is 80% longer than RNNs and 450% longer than vanilla Transformers, achieves better performance on both short and long sequences, and is up to 1,800+ times faster than vanilla Transformers during evaluation. Notably, we improve the state-of-the-art results of bpc/perplexity to 0.99 on enwiki8, 1.08 on text8, 18.3 on WikiText-103, 21.8 on One Billion Word, and 54.5 on Penn Treebank (without finetuning). When trained only on WikiText-103, Transformer-XL manages to generate reasonably coherent, novel text articles with thousands of tokens. Our code, pretrained models, and hyperparameters are available in both Tensorflow and PyTorch.