Vijay S. Pande

72 papers A* 3A 5B 1Misc 6Journal 56Unranked 1
YearRankTypeTitle / Venue / Authors
2023 J jnl
CoRR
Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio, Anton Gorenko, Michael M. Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João P. G. L. M. Rodrigues, Jaime Rodríguez-Guerra, Andrew C. Simmonett, Jason M. Swails, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, Thomas E. Markland
2020 J jnl
PLoS Comput. Biol.
Keri A. McKiernan, Anna K. Koster, Merritt Maduke, Vijay S. Pande
2020 A* conf
ICLR
Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay S. Pande, Jure Leskovec
2019 J jnl
CoRR
Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay S. Pande, Jure Leskovec
2019 J jnl
CoRR
Evan N. Feinberg, Robert P. Sheridan, Elizabeth Joshi, Vijay S. Pande, Alan C. Cheng
2018 J jnl
CoRR
Mohammad M. Sultan, Vijay S. Pande
2018 J jnl
CoRR
Amir Barati Farimani, Joseph Gomes, Rishi Sharma, Franklin L. Lee, Vijay S. Pande
2018 A* conf
NeurIPS
Jiaxuan You, Bowen Liu, Zhitao Ying, Vijay S. Pande, Jure Leskovec
2018 J jnl
CoRR
Jiaxuan You, Bowen Liu, Rex Ying, Vijay S. Pande, Jure Leskovec
2018 J jnl
CoRR
Rishi Sharma, Shane T. Barratt, Stefano Ermon, Vijay S. Pande
2018 J jnl
CoRR
Hannah K. Wayment-Steele, Vijay S. Pande
2018 J jnl
CoRR
Jade Shi, Rhiju Das, Vijay S. Pande
2018 J jnl
PLoS Comput. Biol.
Peter K. Eastman, Jade Shi, Bharath Ramsundar, Vijay S. Pande
2018 J jnl
CoRR
Evan N. Feinberg, Debnil Sur, Brooke E. Husic, Doris Mai, Yang Li, Jianyi Yang, Bharath Ramsundar, Vijay S. Pande
2018 J jnl
CoRR
Carlos X. Hernández, Mohammad M. Sultan, Vijay S. Pande
2018 J jnl
CoRR
Rishi Sharma, Amir Barati Farimani, Joe Gomes, Peter K. Eastman, Vijay S. Pande
2017 J jnl
CoRR
Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande
2017 J jnl
CoRR
Amir Barati Farimani, Joseph Gomes, Vijay S. Pande
2017 J jnl
J. Comput. Chem.
Baofeng Zhang, Denise Kilburg, Peter K. Eastman, Vijay S. Pande, Emilio Gallicchio
2017 J jnl
J. Chem. Inf. Model.
Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P. Sheridan, Vijay S. Pande
2017 J jnl
J. Open Source Softw.
Carlos X. Hernández, Vijay S. Pande
2017 J jnl
J. Open Source Softw.
Carlos X. Hernández, Matthew P. Harrigan, Mohammad M. Sultan, Vijay S. Pande
2017 J jnl
CoRR
Zhenqin Wu, Bharath Ramsundar, Evan N. Feinberg, Joseph Gomes, Caleb Geniesse, Aneesh S. Pappu, Karl Leswing, Vijay S. Pande
2017 J jnl
PLoS Comput. Biol.
Peter K. Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande
2017 J jnl
CoRR
Bowen Liu, Bharath Ramsundar, Prasad Kawthekar, Jade Shi, Joseph Gomes, Quang Luu Nguyen, Stephen Ho, Jack Sloane, Paul Wender, Vijay S. Pande
2016 J jnl
J. Chem. Inf. Model.
Govindan Subramanian, Bharath Ramsundar, Vijay S. Pande, Rajiah Aldrin Denny
2016 J jnl
CoRR
Bharath Ramsundar, Vijay S. Pande
2016 J jnl
CoRR
Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay S. Pande
2016 J jnl
CoRR
Steven Kearnes, Kevin McCloskey, Marc Berndl, Vijay S. Pande, Patrick Riley
2016 J jnl
J. Comput. Aided Mol. Des.
Steven Kearnes, Kevin McCloskey, Marc Berndl, Vijay S. Pande, Patrick Riley
2016 J jnl
J. Open Source Softw.
Robert T. McGibbon, Carlos X. Hernández, Matthew P. Harrigan, Steven Kearnes, Mohammad M. Sultan, Stanislaw Jastrzebski, Brooke E. Husic, Vijay S. Pande
2016 J jnl
J. Comput. Aided Mol. Des.
Steven Kearnes, Vijay S. Pande
2015 J jnl
CoRR
Bharath Ramsundar, Steven Kearnes, Patrick Riley, Dale Webster, David E. Konerding, Vijay S. Pande
2014 J jnl
J. Chem. Inf. Model.
Steven M. Kearnes, Imran S. Haque, Vijay S. Pande
2014 A* conf
ICML
Robert McGibbon, Bharath Ramsundar, Mohammad Sultan, Gert Kiss, Vijay S. Pande
2013 J jnl
BMC Bioinform.
Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S. Pande, Gunnar E. Carlsson, Leonidas J. Guibas
2013 J jnl
IEEE Trans. Parallel Distributed Syst.
Kai J. Kohlhoff, Vijay S. Pande, Russ B. Altman
2012 J jnl
J. Am. Medical Informatics Assoc.
Scott L. Delp, Joy P. Ku, Vijay S. Pande, Michael A. Sherman, Russ B. Altman
2011 J jnl
J. Chem. Inf. Model.
Imran S. Haque, Vijay S. Pande, W. Patrick Walters
2011 J jnl
Bioinform.
Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman
2011 A conf
SC
Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl
2011 J jnl
J. Chem. Inf. Model.
Imran S. Haque, Vijay S. Pande
2010 J jnl
PLoS Comput. Biol.
Peter M. Kasson, Erik Lindahl, Vijay S. Pande
2010 Misc conf
Pacific Symposium on Biocomputing
Xuhui Huang, Yuan Yao, Gregory R. Bowman, Jian Sun, Leonidas J. Guibas, Gunnar E. Carlsson, Vijay S. Pande
2010 Misc conf
Pacific Symposium on Biocomputing
Peter M. Kasson, Vijay S. Pande
2010 J jnl
J. Comput. Chem.
Peter K. Eastman, Vijay S. Pande
2010 B conf
CCGRID
Imran S. Haque, Vijay S. Pande
2010 Misc conf
Pacific Symposium on Biocomputing
Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande
2010 J jnl
PLoS Comput. Biol.
Del Lucent, Christopher D. Snow, Colin Echeverría Aitken, Vijay S. Pande
2010 J jnl
Comput. Sci. Eng.
Peter K. Eastman, Vijay S. Pande
2010 J jnl
J. Comput. Chem.
Imran S. Haque, Vijay S. Pande
2010 J jnl
J. Chem. Inf. Model.
Imran S. Haque, Vijay S. Pande
2010 J jnl
J. Chem. Inf. Model.
Imran S. Haque, Vijay S. Pande, W. Patrick Walters
2009 Misc conf
Pacific Symposium on Biocomputing
Vincent A. Voelz, Paula Petrone, Vijay S. Pande
2009 J jnl
J. Comput. Chem.
Mark S. Friedrichs, Peter K. Eastman, Vaidyanathan Vishal, Mike Houston, Scott LeGrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande
2009 J jnl
J. Comput. Chem.
Edgar Luttmann, Daniel L. Ensign, Vaidyanathan Vishal, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark S. Friedrichs, Vijay S. Pande
2009 Misc conf
Pacific Symposium on Biocomputing
Peter M. Kasson, Vijay S. Pande
2009 A conf
IPDPS
Adam L. Beberg, Daniel L. Ensign, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande
2009 J jnl
CoRR
Imran S. Haque, Vijay S. Pande
2009 A conf
IPDPS
Adam L. Beberg, Vijay S. Pande
2008 J jnl
J. Comput. Chem.
Alex Robertson, Edgar Luttmann, Vijay S. Pande
2008 J jnl
J. Comput. Chem.
Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo
2008 J jnl
Proc. IEEE
Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor, Vijay S. Pande, Russ B. Altman
2007 J jnl
PLoS Comput. Biol.
Peter M. Kasson, Vijay S. Pande
2007 J jnl
CoRR
Erich Elsen, Vaidyanathan Vishal, Mike Houston, Vijay S. Pande, Pat Hanrahan, Eric Darve
2007 J jnl
Bioinform.
Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, Vijay S. Pande
2007 Misc conf
Pacific Symposium on Biocomputing
Peter M. Kasson, Vijay S. Pande
2007 A conf
IPDPS
Adam L. Beberg, Vijay S. Pande
2006 A conf
SC
Erich Elsen, Mike Houston, Vaidyanathan Vishal, Eric Darve, Pat Hanrahan, Vijay S. Pande
2005 J jnl
J. Comput. Chem.
Sanghyun Park, Randall J. Radmer, Teri E. Klein, Vijay S. Pande
2005 J jnl
J. Comput. Chem.
Eric J. Sorin, Vijay S. Pande
2003 conf
CSB
Peter M. Kasson, Vijay S. Pande
redb/extractors/elf_extractors/elf_notes.py
← Index redb/extractors/elf_extractors/elf_notes.py python
import inspect
import binascii
from datetime import datetime, timezone
from typing import Any, List, Dict

from elftools.elf.elffile import ELFFile
from elftools.common.exceptions import ELFError

from redb.extractors.enum import Tag
from redb.extractors.elf_extractor import ELFExtractor
from redb.models.dataclasses import ELFNote


class ELFNotesExtractor(ELFExtractor):

    def __init__(
        self,
        filepath,
        log,
        exporters=None,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
        elf=None,
    ):
        super().__init__(
            filepath,
            log,
            exporters,
            index_prefix,
            elastic_index,
            known_benign,
            known_malicious,
            elf,
        )
        self.elf_notes = []
        self.elastic_index = self.index_prefix + "-elf_notes"
        self.log.debug(inspect.currentframe().f_code.co_name)

    def _get_note_type_string(self, note_type: int, note_name: str) -> str:
        """Convert note type number to human-readable string."""

        # GNU-specific note types
        if note_name == "GNU":
            gnu_types = {
                1: "NT_GNU_ABI_TAG",
                2: "NT_GNU_HWCAP",
                3: "NT_GNU_BUILD_ID",
                4: "NT_GNU_GOLD_VERSION",
                5: "NT_GNU_PROPERTY_TYPE_0"
            }
            return gnu_types.get(note_type, f"NT_GNU_UNKNOWN_{note_type}")

        # Generic note types
        generic_types = {
            1: "NT_PRSTATUS",
            2: "NT_FPREGSET",
            3: "NT_PRPSINFO",
            4: "NT_TASKSTRUCT",
            5: "NT_AUXV",
            6: "NT_PSTATUS",
            7: "NT_FPREGS",
            8: "NT_PSINFO",
            9: "NT_PRCRED",
            10: "NT_UTSNAME",
            11: "NT_LWPSTATUS",
            12: "NT_LWPSINFO",
            13: "NT_PRFPXREG"
        }

        return generic_types.get(note_type, f"NT_UNKNOWN_{note_type}")

    def _format_note_description(self, note_desc, note_type: int, note_name: str) -> str:
        """Format note description based on type for human readability."""
        try:
            if not note_desc:
                return ""

            # Handle build ID specifically (common case)
            if note_name == "GNU" and note_type == 3:  # NT_GNU_BUILD_ID
                if isinstance(note_desc, bytes):
                    return binascii.hexlify(note_desc).decode('ascii')
                return str(note_desc)

            # Handle ABI tag
            if note_name == "GNU" and note_type == 1:  # NT_GNU_ABI_TAG
                if isinstance(note_desc, bytes) and len(note_desc) >= 16:
                    # ABI tag contains OS, major, minor, subminor
                    import struct
                    try:
                        os_val, major, minor, subminor = struct.unpack('<IIII', note_desc[:16])
                        os_names = {0: "Linux", 1: "GNU", 2: "Solaris", 3: "FreeBSD"}
                        os_name = os_names.get(os_val, f"OS_{os_val}")
                        return f"{os_name} {major}.{minor}.{subminor}"
                    except:
                        pass

            # For binary data, convert to hex
            if isinstance(note_desc, bytes):
                # Limit size for very large descriptions
                if len(note_desc) > 256:
                    return binascii.hexlify(note_desc[:256]).decode('ascii') + "..."
                return binascii.hexlify(note_desc).decode('ascii')

            # For string data
            if isinstance(note_desc, str):
                return note_desc

            # Fallback
            return str(note_desc)

        except Exception as e:
            self.log.error(f"Error formatting note description: {e}")
            return str(note_desc) if note_desc else ""

    def _extract_note_data(self, note, section_name: str) -> ELFNote:
        """Extract data from a single note entry."""
        try:
            # Get note properties
            note_name = note.get('n_name', '').rstrip('\x00') if note.get('n_name') else ""
            note_type_raw = note.get('n_type', 0)
            note_desc_raw = note.get('n_desc', b'')

            # Handle note_type - pyelftools may return string or int
            if isinstance(note_type_raw, str):
                # pyelftools returned the type as a string like 'NT_GNU_BUILD_ID'
                note_type_str = note_type_raw
                # Map known string types to integers
                note_type_map = {
                    'NT_GNU_ABI_TAG': 1,
                    'NT_GNU_HWCAP': 2,
                    'NT_GNU_BUILD_ID': 3,
                    'NT_GNU_GOLD_VERSION': 4,
                    'NT_GNU_PROPERTY_TYPE_0': 5,
                    'NT_PRSTATUS': 1,
                    'NT_FPREGSET': 2,
                    'NT_PRPSINFO': 3,
                    'NT_TASKSTRUCT': 4,
                    'NT_AUXV': 5,
                    'NT_PSTATUS': 6,
                    'NT_FPREGS': 7,
                    'NT_PSINFO': 8,
                    'NT_PRCRED': 9,
                    'NT_UTSNAME': 10,
                    'NT_LWPSTATUS': 11,
                    'NT_LWPSINFO': 12,
                    'NT_PRFPXREG': 13,
                }
                note_type = note_type_map.get(note_type_raw, 0)
            else:
                note_type = note_type_raw
                # Get human-readable type string
                note_type_str = self._get_note_type_string(note_type, note_name)

            # Format description
            note_desc = self._format_note_description(note_desc_raw, note_type, note_name)

            return ELFNote(
                note_name=note_name,
                note_type=note_type,
                note_type_str=note_type_str,
                note_desc=note_desc,
                note_section=section_name
            )

        except Exception as e:
            self.log.error(f"Error extracting note data: {e}")
            return None

    def _extract_notes_from_sections(self, elf) -> List[Dict]:
        """Extract notes from note sections."""
        notes = []

        try:
            # Look for note sections
            for section in elf.iter_sections():
                if (section.name and
                    section.name.startswith('.note') and
                    hasattr(section, 'iter_notes')):

                    section_name = section.name
                    try:
                        for note in section.iter_notes():
                            note_data = self._extract_note_data(note, section_name)
                            if note_data:
                                notes.append(note_data)
                    except Exception as e:
                        self.log.debug(f"Could not process notes in section {section_name}: {e}")

        except Exception as e:
            self.log.error(f"Error extracting notes from sections: {e}")

        return notes

    def _extract_notes_from_segments(self, elf) -> List[Dict]:
        """Extract notes from PT_NOTE segments."""
        notes = []

        try:
            # Look for PT_NOTE segments
            for segment in elf.iter_segments():
                if segment.header.get('p_type') == 'PT_NOTE':
                    segment_name = f"PT_NOTE_segment_{segment.header.get('p_offset', 0)}"

                    try:
                        if hasattr(segment, 'iter_notes'):
                            for note in segment.iter_notes():
                                note_data = self._extract_note_data(note, segment_name)
                                if note_data:
                                    notes.append(note_data)
                    except Exception as e:
                        self.log.debug(f"Could not process notes in segment: {e}")

        except Exception as e:
            self.log.error(f"Error extracting notes from segments: {e}")

        return notes

    def tag(self):
        return Tag.ELF_NOTES.value if hasattr(Tag, 'ELF_NOTES') else "elf_notes"

    def extract(self):
        try:
            self.log.debug(inspect.currentframe().f_code.co_name)

            def extract_data(elf):
                all_notes = []

                # Extract notes from note sections
                section_notes = self._extract_notes_from_sections(elf)
                all_notes.extend(section_notes)

                # Extract notes from PT_NOTE segments
                segment_notes = self._extract_notes_from_segments(elf)
                all_notes.extend(segment_notes)

                # Remove duplicates (same note might appear in section and segment)
                unique_notes = []
                seen_notes = set()
                for note in all_notes:
                    note_key = (note.note_name, note.note_type, note.note_desc)
                    if note_key not in seen_notes:
                        seen_notes.add(note_key)
                        unique_notes.append(note)

                return unique_notes

            if not self._is_elf_file():
                return None

            result = self._with_elf_file(extract_data)
            if result is None:
                return None

            self.elf_notes = result
            return self.elf_notes

        except Exception as e:
            self.log.error(f"Error extracting ELF notes {self.hash.sha256}: {e}")
            return None

    def prepare_export_data(self, exporter_type: str) -> Any:
        self.log.debug(inspect.currentframe().f_code.co_name)

        if exporter_type == "ElasticsearchExporter":
            return self.elf_notes
        elif exporter_type == "ClickHouseExporter":
            try:
                # Return valid empty structure if no notes found
                # None is reserved for actual errors

                # Prepare data arrays for all notes
                data = []
                current_time = datetime.now(timezone.utc)
                for note in self.elf_notes:
                    row = [
                        self.sha256,
                        self.md5,
                        self.sha1,
                        note.note_name,
                        note.note_type,
                        note.note_type_str,
                        note.note_desc,
                        note.note_section,
                        current_time
                    ]
                    data.append(row)

                column_names = [
                    'sha256', 'md5', 'sha1',
                    'note_name', 'note_type', 'note_type_str',
                    'note_desc', 'note_section',
                    'analysis_date'
                ]

                if not data:
                    return None

                column_type_names = [
                    'FixedString(64)', 'FixedString(32)', 'FixedString(40)',
                    'LowCardinality(String)', 'UInt32', 'LowCardinality(String)',
                    'String CODEC(ZSTD(3))', 'LowCardinality(String)',
                    'DateTime64(3, \'UTC\')'
                ]

                return (data, column_names, column_type_names)

            except Exception as e:
                self.log.error(f"Error preparing export data: {e}")
                raise

    def get_clickhouse_table(self) -> str:
        return "redb_elf_notes"