Kazi Sajeed Mehrab

M. Maruf, Arka Daw, Kazi Sajeed Mehrab et al. · microsoft-research

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Kazi Sajeed Mehrab, M. Maruf, Arka Daw et al.

We introduce Fish-Visual Trait Analysis (Fish-Vista), the first organismal image dataset designed for the analysis of visual traits of aquatic species directly from images using problem formulations in computer vision. Fish-Vista contains 69,126 annotated images spanning 4,154 fish species, curated and organized to serve three downstream tasks of species classification, trait identification, and trait segmentation. Our work makes two key contributions. First, we perform a fully reproducible data processing pipeline to process images sourced from various museum collections. We annotate these images with carefully curated labels from biological databases and manual annotations to create an AI-ready dataset of visual traits, contributing to the advancement of AI in biodiversity science. Second, our proposed downstream tasks offer fertile grounds for novel computer vision research in addressing a variety of challenges such as long-tailed distributions, out-of-distribution generalization, learning with weak labels, explainable AI, and segmenting small objects. We benchmark the performance of several existing methods for our proposed tasks to expose future research opportunities in AI for biodiversity science problems involving visual traits.

Harish Babu Manogaran, M. Maruf, Arka Daw et al.

A grand challenge in biology is to discover evolutionary traits - features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of image repositories in biology, there is a tremendous opportunity to discover evolutionary traits directly from images in the form of a hierarchy of prototypes. However, current prototype-based methods are mostly designed to operate over a flat structure of classes and face several challenges in discovering hierarchical prototypes, including the issue of learning over-specific prototypes at internal nodes. To overcome these challenges, we introduce the framework of Hierarchy aligned Commonality through Prototypical Networks (HComP-Net). The key novelties in HComP-Net include a novel over-specificity loss to avoid learning over-specific prototypes, a novel discriminative loss to ensure prototypes at an internal node are absent in the contrasting set of species with different ancestry, and a novel masking module to allow for the exclusion of over-specific prototypes at higher levels of the tree without hampering classification performance. We empirically show that HComP-Net learns prototypes that are accurate, semantically consistent, and generalizable to unseen species in comparison to baselines.

Arpita Chowdhury, Dipanjyoti Paul, Zheda Mai et al. · microsoft-research

We present a simple approach to make pre-trained Vision Transformers (ViTs) interpretable for fine-grained analysis, aiming to identify and localize the traits that distinguish visually similar categories, such as bird species. Pre-trained ViTs, such as DINO, have demonstrated remarkable capabilities in extracting localized, discriminative features. However, saliency maps like Grad-CAM often fail to identify these traits, producing blurred, coarse heatmaps that highlight entire objects instead. We propose a novel approach, Prompt Class Attention Map (Prompt-CAM), to address this limitation. Prompt-CAM learns class-specific prompts for a pre-trained ViT and uses the corresponding outputs for classification. To correctly classify an image, the true-class prompt must attend to unique image patches not present in other classes' images (i.e., traits). As a result, the true class's multi-head attention maps reveal traits and their locations. Implementation-wise, Prompt-CAM is almost a ``free lunch,'' requiring only a modification to the prediction head of Visual Prompt Tuning (VPT). This makes Prompt-CAM easy to train and apply, in stark contrast to other interpretable methods that require designing specific models and training processes. Extensive empirical studies on a dozen datasets from various domains (e.g., birds, fishes, insects, fungi, flowers, food, and cars) validate the superior interpretation capability of Prompt-CAM. The source code and demo are available at https://github.com/Imageomics/Prompt_CAM.

Masum Hasan, Tanveer Muttaqueen, Abdullah Al Ishtiaq et al.

Translation between natural language and source code can help software development by enabling developers to comprehend, ideate, search, and write computer programs in natural language. Despite growing interest from the industry and the research community, this task is often difficult due to the lack of large standard datasets suitable for training deep neural models, standard noise removal methods, and evaluation benchmarks. This leaves researchers to collect new small-scale datasets, resulting in inconsistencies across published works. In this study, we present CoDesc -- a large parallel dataset composed of 4.2 million Java methods and natural language descriptions. With extensive analysis, we identify and remove prevailing noise patterns from the dataset. We demonstrate the proficiency of CoDesc in two complementary tasks for code-description pairs: code summarization and code search. We show that the dataset helps improve code search by up to 22\% and achieves the new state-of-the-art in code summarization. Furthermore, we show CoDesc's effectiveness in pre-training--fine-tuning setup, opening possibilities in building pretrained language models for Java. To facilitate future research, we release the dataset, a data processing tool, and a benchmark at \url{https://github.com/csebuetnlp/CoDesc}.

Masum Hasan, Kazi Sajeed Mehrab, Wasi Uddin Ahmad et al.

We present Text2App -- a framework that allows users to create functional Android applications from natural language specifications. The conventional method of source code generation tries to generate source code directly, which is impractical for creating complex software. We overcome this limitation by transforming natural language into an abstract intermediate formal language representing an application with a substantially smaller number of tokens. The intermediate formal representation is then compiled into target source codes. This abstraction of programming details allows seq2seq networks to learn complex application structures with less overhead. In order to train sequence models, we introduce a data synthesis method grounded in a human survey. We demonstrate that Text2App generalizes well to unseen combination of app components and it is capable of handling noisy natural language instructions. We explore the possibility of creating applications from highly abstract instructions by coupling our system with GPT-3 -- a large pretrained language model. We perform an extensive human evaluation and identify the capabilities and limitations of our system. The source code, a ready-to-run demo notebook, and a demo video are publicly available at \url{https://github.com/text2app/Text2App}.

Amartya Dutta, Kazi Sajeed Mehrab, Medha Sawhney et al.

Scene-Graph Generation (SGG) seeks to recognize objects in an image and distill their salient pairwise relationships. Most methods depend on dataset-specific supervision to learn the variety of interactions, restricting their usefulness in open-world settings, involving novel objects and/or relations. Even methods that leverage large Vision Language Models (VLMs) typically require benchmark-specific fine-tuning. We introduce Open-World SGG, a training-free, efficient, model-agnostic framework that taps directly into the pretrained knowledge of VLMs to produce scene graphs with zero additional learning. Casting SGG as a zero-shot structured-reasoning problem, our method combines multimodal prompting, embedding alignment, and a lightweight pair-refinement strategy, enabling inference over unseen object vocabularies and relation sets. To assess this setting, we formalize an Open-World evaluation protocol that measures performance when no SGG-specific data have been observed either in terms of objects and relations. Experiments on Visual Genome, Open Images V6, and the Panoptic Scene Graph (PSG) dataset demonstrate the capacity of pretrained VLMs to perform relational understanding without task-level training.

Jie Bu, Kazi Sajeed Mehrab, Anuj Karpatne

Conditional graph generation tasks involve training a model to generate a graph given a set of input conditions. Many previous studies employ autoregressive models to incrementally generate graph components such as nodes and edges. However, as graphs typically lack a natural ordering among their components, converting a graph into a sequence of tokens is not straightforward. While prior works mostly rely on conventional heuristics or graph traversal methods like breadth-first search (BFS) or depth-first search (DFS) to convert graphs to sequences, the impact of ordering on graph generation has largely been unexplored. This paper contributes to this problem by: (1) highlighting the crucial role of ordering in autoregressive graph generation models, (2) proposing a novel theoretical framework that perceives ordering as a dimensionality reduction problem, thereby facilitating a deeper understanding of the relationship between orderings and generated graph accuracy, and (3) introducing "latent sort," a learning-based ordering scheme to perform dimensionality reduction of graph tokens. Our experimental results showcase the effectiveness of latent sort across a wide range of graph generation tasks, encouraging future works to further explore and develop learning-based ordering schemes for autoregressive graph generation.

Abdullah Al Ishtiaq, Masum Hasan, Md. Mahim Anjum Haque et al.

Millions of repetitive code snippets are submitted to code repositories every day. To search from these large codebases using simple natural language queries would allow programmers to ideate, prototype, and develop easier and faster. Although the existing methods have shown good performance in searching codes when the natural language description contains keywords from the code, they are still far behind in searching codes based on the semantic meaning of the natural language query and semantic structure of the code. In recent years, both natural language and programming language research communities have created techniques to embed them in vector spaces. In this work, we leverage the efficacy of these embedding models using a simple, lightweight 2-layer neural network in the task of semantic code search. We show that our model learns the inherent relationship between the embedding spaces and further probes into the scope of improvement by empirically analyzing the embedding methods. In this analysis, we show that the quality of the code embedding model is the bottleneck for our model's performance, and discuss future directions of study in this area.